revert

Merge latest upstream changes

.github/dependabot.yml

@@ -12,7 +12,7 @@ updates:
   - package-ecosystem: "maven"
     directory: "/jvm-packages/xgboost4j"
     schedule:
-      interval: "monthly"
+      interval: "daily"
   - package-ecosystem: "maven"
     directory: "/jvm-packages/xgboost4j-gpu"
     schedule:
@@ -24,12 +24,8 @@ updates:
   - package-ecosystem: "maven"
     directory: "/jvm-packages/xgboost4j-spark"
     schedule:
-      interval: "monthly"
+      interval: "daily"
   - package-ecosystem: "maven"
     directory: "/jvm-packages/xgboost4j-spark-gpu"
     schedule:
       interval: "monthly"
-  - package-ecosystem: "github-actions"
-    directory: /
-    schedule:
-      interval: "monthly"

.github/workflows/freebsd.yml

@@ -1,34 +0,0 @@
-name: FreeBSD
-
-on: [push, pull_request]
-
-permissions:
-  contents: read # to fetch code (actions/checkout)
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    timeout-minutes: 20
-    name: A job to run test in FreeBSD
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        submodules: 'true'
-    - name: Test in FreeBSD
-      id: test
-      uses: vmactions/freebsd-vm@v1
-      with:
-        usesh: true
-        prepare: |
-          pkg install -y cmake git ninja googletest
-
-        run: |
-          mkdir build
-          cd build
-          cmake .. -GNinja -DGOOGLE_TEST=ON
-          ninja -v
-          ./testxgboost

.github/workflows/i386.yml

@@ -19,15 +19,15 @@ jobs:
         ports:
           - 5000:5000
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@v2.5.0
       with:
         submodules: 'true'
     - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v3.6.1
+      uses: docker/setup-buildx-action@v3
       with:
         driver-opts: network=host
     - name: Build and push container
-      uses: docker/build-push-action@v6
+      uses: docker/build-push-action@v5
       with:
         context: .
         file: tests/ci_build/Dockerfile.i386

.github/workflows/jvm_tests.yml

@@ -12,50 +12,48 @@ concurrency:
 jobs:
   test-with-jvm:
     name: Test JVM on OS ${{ matrix.os }}
-    timeout-minutes: 30
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [windows-latest, ubuntu-latest, macos-13]
+        os: [windows-latest, ubuntu-latest, macos-11]
 
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
       with:
         submodules: 'true'
 
-    - uses: actions/setup-java@6a0805fcefea3d4657a47ac4c165951e33482018  # v4.2.2
+    - uses: mamba-org/setup-micromamba@422500192359a097648154e8db4e39bdb6c6eed7  # v1.8.1
       with:
-        distribution: 'temurin'
-        java-version: '8'
-
-    - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca  # v3.0.4
-      with:
-        miniforge-variant: Mambaforge
-        miniforge-version: latest
-        activate-environment: jvm_tests
-        environment-file: tests/ci_build/conda_env/jvm_tests.yml
-        use-mamba: true
+        micromamba-version: '1.5.6-0'
+        environment-name: jvm_tests
+        create-args: >-
+          python=3.10
+          awscli
+        cache-downloads: true
+        cache-environment: true
+        init-shell: bash powershell
 
     - name: Cache Maven packages
-      uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
+      uses: actions/cache@13aacd865c20de90d75de3b17ebe84f7a17d57d2  # v4.0.0
       with:
         path: ~/.m2
         key: ${{ runner.os }}-m2-${{ hashFiles('./jvm-packages/pom.xml') }}
         restore-keys: ${{ runner.os }}-m2-${{ hashFiles('./jvm-packages/pom.xml') }}
 
+    - name: Build xgboost4j.dll
+      run: |
+        mkdir build
+        cd build
+        cmake .. -G"Visual Studio 17 2022" -A x64 -DJVM_BINDINGS=ON
+        cmake --build . --config Release
+      if: matrix.os == 'windows-latest'
+
     - name: Test XGBoost4J (Core)
       run: |
         cd jvm-packages
         mvn test -B -pl :xgboost4j_2.12
 
-    - name: Test XGBoost4J (Core, Spark, Examples)
-      run: |
-        rm -rfv build/
-        cd jvm-packages
-        mvn -B test
-      if: matrix.os == 'ubuntu-latest'  # Distributed training doesn't work on Windows
-
     - name: Extract branch name
       shell: bash
       run: |
@@ -63,7 +61,7 @@ jobs:
       id: extract_branch
       if: |
         (github.ref == 'refs/heads/master' || contains(github.ref, 'refs/heads/release_')) &&
-        (matrix.os == 'windows-latest' || matrix.os == 'macos-13')
+        (matrix.os == 'windows-latest' || matrix.os == 'macos-11')
 
     - name: Publish artifact xgboost4j.dll to S3
       run: |
@@ -87,14 +85,27 @@ jobs:
         python -m awscli s3 cp libxgboost4j_${{ github.sha }}.dylib s3://xgboost-nightly-builds/${{ steps.extract_branch.outputs.branch }}/libxgboost4j/ --acl public-read --region us-west-2
       if: |
         (github.ref == 'refs/heads/master' || contains(github.ref, 'refs/heads/release_')) &&
-        matrix.os == 'macos-13'
+        matrix.os == 'macos-11'
       env:
         AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID_IAM_S3_UPLOADER }}
         AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY_IAM_S3_UPLOADER }}
 
+
+    - name: Test XGBoost4J (Core, Spark, Examples)
+      run: |
+        rm -rfv build/
+        cd jvm-packages
+        mvn -B test
+      if: matrix.os == 'ubuntu-latest'  # Distributed training doesn't work on Windows
+      env:
+        RABIT_MOCK: ON
+
+
     - name: Build and Test XGBoost4J with scala 2.13
       run: |
         rm -rfv build/
         cd jvm-packages
         mvn -B clean install test -Pdefault,scala-2.13
       if: matrix.os == 'ubuntu-latest'  # Distributed training doesn't work on Windows
+      env:
+        RABIT_MOCK: ON

.github/workflows/main.yml

@@ -21,9 +21,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macos-12]
+        os: [macos-11]
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
     - name: Install system packages
@@ -33,7 +33,7 @@ jobs:
       run: |
         mkdir build
         cd build
-        cmake .. -DGOOGLE_TEST=ON -DUSE_OPENMP=ON -DUSE_DMLC_GTEST=ON -GNinja -DBUILD_DEPRECATED_CLI=ON -DUSE_SANITIZER=ON -DENABLED_SANITIZERS=address -DCMAKE_BUILD_TYPE=RelWithDebInfo
+        cmake .. -DGOOGLE_TEST=ON -DUSE_OPENMP=ON -DUSE_DMLC_GTEST=ON -GNinja -DBUILD_DEPRECATED_CLI=ON
         ninja -v
     - name: Run gtest binary
       run: |
@@ -49,7 +49,7 @@ jobs:
       matrix:
         os: [ubuntu-latest]
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
     - name: Install system packages
@@ -74,18 +74,18 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.10"]
+        python-version: ["3.8"]
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
-    - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca  # v3.0.4
+    - uses: mamba-org/provision-with-micromamba@f347426e5745fe3dfc13ec5baf20496990d0281f # v14
       with:
-        miniforge-variant: Mambaforge
-        miniforge-version: latest
-        activate-environment: linux_sycl_test
+        cache-downloads: true
+        cache-env: true
+        environment-name: linux_sycl_test
         environment-file: tests/ci_build/conda_env/linux_sycl_test.yml
-        use-mamba: true
+
     - name: Display Conda env
       run: |
         conda info
@@ -95,7 +95,7 @@ jobs:
       run: |
         mkdir build
         cd build
-        cmake .. -DGOOGLE_TEST=ON -DUSE_DMLC_GTEST=ON -DPLUGIN_SYCL=ON -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX
+        cmake .. -DGOOGLE_TEST=ON -DUSE_DMLC_GTEST=ON -DPLUGIN_SYCL=ON -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX
         make -j$(nproc)
     - name: Run gtest binary for SYCL
       run: |
@@ -116,18 +116,17 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.10"]
+        python-version: ["3.8"]
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
-    - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca  # v3.0.4
+    - uses: mamba-org/provision-with-micromamba@f347426e5745fe3dfc13ec5baf20496990d0281f # v14
       with:
-        miniforge-variant: Mambaforge
-        miniforge-version: latest
-        activate-environment: cpp_test
+        cache-downloads: true
+        cache-env: true
+        environment-name: cpp_test
         environment-file: tests/ci_build/conda_env/cpp_test.yml
-        use-mamba: true
     - name: Display Conda env
       run: |
         conda info
@@ -156,9 +155,8 @@ jobs:
     - name: Build and install XGBoost shared library
       run: |
         cd build
-        cmake .. -DBUILD_STATIC_LIB=OFF -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX -GNinja -DPLUGIN_FEDERATED=ON -DGOOGLE_TEST=ON
+        cmake .. -DBUILD_STATIC_LIB=OFF -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX -GNinja
         ninja -v install
-        ./testxgboost
         cd -
     - name: Build and run C API demo with shared
       run: |
@@ -177,12 +175,12 @@ jobs:
     runs-on: ubuntu-latest
     name: Code linting for C++
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
-    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
       with:
-        python-version: "3.10"
+        python-version: "3.8"
         architecture: 'x64'
     - name: Install Python packages
       run: |

.github/workflows/python_tests.yml

@@ -21,16 +21,15 @@ jobs:
       matrix:
         os: [ubuntu-latest]
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
-    - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca  # v3.0.4
+    - uses: mamba-org/provision-with-micromamba@f347426e5745fe3dfc13ec5baf20496990d0281f # v14
       with:
-        miniforge-variant: Mambaforge
-        miniforge-version: latest
-        activate-environment: python_lint
+        cache-downloads: true
+        cache-env: true
+        environment-name: python_lint
         environment-file: tests/ci_build/conda_env/python_lint.yml
-        use-mamba: true
     - name: Display Conda env
       run: |
         conda info
@@ -53,16 +52,15 @@ jobs:
       matrix:
         os: [ubuntu-latest]
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
-    - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca  # v3.0.4
+    - uses: mamba-org/provision-with-micromamba@f347426e5745fe3dfc13ec5baf20496990d0281f # v14
       with:
-        miniforge-variant: Mambaforge
-        miniforge-version: latest
-        activate-environment: sdist_test
+        cache-downloads: true
+        cache-env: true
+        environment-name: sdist_test
         environment-file: tests/ci_build/conda_env/sdist_test.yml
-        use-mamba: true
     - name: Display Conda env
       run: |
         conda info
@@ -83,17 +81,17 @@ jobs:
     name: Test installing XGBoost Python source package on ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-13, windows-latest]
-        python-version: ["3.10"]
+        os: [macos-11, windows-latest]
+        python-version: ["3.8"]
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
     - name: Install osx system dependencies
-      if: matrix.os == 'macos-13'
+      if: matrix.os == 'macos-11'
       run: |
         brew install ninja libomp
-    - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3.0.4
+    - uses: conda-incubator/setup-miniconda@35d1405e78aa3f784fe3ce9a2eb378d5eeb62169 # v2.1.1
       with:
         auto-update-conda: true
         python-version: ${{ matrix.python-version }}
@@ -121,20 +119,19 @@ jobs:
     strategy:
       matrix:
         config:
-          - {os: macos-13}
+          - {os: macos-11}
 
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
 
-    - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca  # v3.0.4
+    - uses: mamba-org/provision-with-micromamba@f347426e5745fe3dfc13ec5baf20496990d0281f # v14
       with:
-        miniforge-variant: Mambaforge
-        miniforge-version: latest
-        activate-environment: macos_cpu_test
+        cache-downloads: true
+        cache-env: true
+        environment-name: macos_test
         environment-file: tests/ci_build/conda_env/macos_cpu_test.yml
-        use-mamba: true
 
     - name: Display Conda env
       run: |
@@ -174,14 +171,14 @@ jobs:
     strategy:
       matrix:
         config:
-          - {os: windows-latest, python-version: '3.10'}
+          - {os: windows-latest, python-version: '3.8'}
 
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
 
-    - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3.0.4
+    - uses: conda-incubator/setup-miniconda@35d1405e78aa3f784fe3ce9a2eb378d5eeb62169 # v2.1.1
       with:
         auto-update-conda: true
         python-version: ${{ matrix.config.python-version }}
@@ -218,20 +215,19 @@ jobs:
     strategy:
       matrix:
         config:
-          - {os: ubuntu-latest, python-version: "3.10"}
+          - {os: ubuntu-latest, python-version: "3.8"}
 
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@v2
       with:
         submodules: 'true'
 
-    - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca  # v3.0.4
+    - uses: mamba-org/provision-with-micromamba@f347426e5745fe3dfc13ec5baf20496990d0281f # v14
       with:
-        miniforge-variant: Mambaforge
-        miniforge-version: latest
-        activate-environment: linux_cpu_test
+        cache-downloads: true
+        cache-env: true
+        environment-name: linux_cpu_test
         environment-file: tests/ci_build/conda_env/linux_cpu_test.yml
-        use-mamba: true
 
     - name: Display Conda env
       run: |
@@ -271,20 +267,19 @@ jobs:
     strategy:
       matrix:
         config:
-          - {os: ubuntu-latest, python-version: "3.10"}
+          - {os: ubuntu-latest, python-version: "3.8"}
 
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@v2
       with:
         submodules: 'true'
 
-    - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca  # v3.0.4
+    - uses: mamba-org/provision-with-micromamba@f347426e5745fe3dfc13ec5baf20496990d0281f # v14
       with:
-        miniforge-variant: Mambaforge
-        miniforge-version: latest
-        activate-environment: linux_sycl_test
+        cache-downloads: true
+        cache-env: true
+        environment-name: linux_sycl_test
         environment-file: tests/ci_build/conda_env/linux_sycl_test.yml
-        use-mamba: true
 
     - name: Display Conda env
       run: |
@@ -294,7 +289,7 @@ jobs:
       run: |
         mkdir build
         cd build
-        cmake .. -DPLUGIN_SYCL=ON -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
+        cmake .. -DPLUGIN_SYCL=ON -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
         make -j$(nproc)
     - name: Install Python package
       run: |
@@ -314,14 +309,14 @@ jobs:
         os: [ubuntu-latest]
 
     steps:
-      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      - uses: actions/checkout@v2
         with:
           submodules: 'true'
 
-      - name: Set up Python 3.10
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
+      - name: Set up Python 3.8
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
         with:
-          python-version: "3.10"
+          python-version: 3.8
 
       - name: Install ninja
         run: |

.github/workflows/python_wheels.yml

@@ -5,10 +5,6 @@ on: [push, pull_request]
 permissions:
   contents: read # to fetch code (actions/checkout)
 
-defaults:
-  run:
-    shell: bash -l {0}
-
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
@@ -20,36 +16,30 @@ jobs:
     strategy:
       matrix:
         include:
-        - os: macos-13
+        - os: macos-latest
           platform_id: macosx_x86_64
-        - os: macos-14
+        - os: macos-latest
           platform_id: macosx_arm64
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # v3.0.0
       with:
         submodules: 'true'
-    - name: Set up homebrew
-      uses: Homebrew/actions/setup-homebrew@68fa6aeb1ccb0596d311f2b34ec74ec21ee68e54
-    - name: Install libomp
-      run: brew install libomp
-    - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca  # v3.0.4
+    - name: Setup Python
+      uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
       with:
-        miniforge-variant: Mambaforge
-        miniforge-version: latest
-        python-version: "3.10"
-        use-mamba: true
+        python-version: "3.8"
     - name: Build wheels
       run: bash tests/ci_build/build_python_wheels.sh ${{ matrix.platform_id }} ${{ github.sha }}
     - name: Extract branch name
-      run: |
-        echo "branch=${GITHUB_REF#refs/heads/}" >> "$GITHUB_OUTPUT"
+      shell: bash
+      run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
       id: extract_branch
       if: github.ref == 'refs/heads/master' || contains(github.ref, 'refs/heads/release_')
     - name: Upload Python wheel
       if: github.ref == 'refs/heads/master' || contains(github.ref, 'refs/heads/release_')
       run: |
         python -m pip install awscli
-        python -m awscli s3 cp wheelhouse/*.whl s3://xgboost-nightly-builds/${{ steps.extract_branch.outputs.branch }}/ --acl public-read --region us-west-2
+        python -m awscli s3 cp wheelhouse/*.whl s3://xgboost-nightly-builds/${{ steps.extract_branch.outputs.branch }}/ --acl public-read
       env:
         AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID_IAM_S3_UPLOADER }}
         AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY_IAM_S3_UPLOADER }}

.github/workflows/r_nold.yml

@@ -27,7 +27,7 @@ jobs:
       run: |
         apt update && apt install libcurl4-openssl-dev libssl-dev libssh2-1-dev libgit2-dev libglpk-dev libxml2-dev libharfbuzz-dev libfribidi-dev git -y
 
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
 

.github/workflows/r_tests.yml

@@ -25,20 +25,20 @@ jobs:
       RSPM: ${{ matrix.config.rspm }}
 
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
 
-    - uses: r-lib/actions/setup-r@929c772977a3a13c8733b363bf5a2f685c25dd91 # v2.9.0
+    - uses: r-lib/actions/setup-r@e40ad904310fc92e96951c1b0d64f3de6cbe9e14 # v2.6.5
       with:
         r-version: ${{ matrix.config.r }}
 
     - name: Cache R packages
-      uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
+      uses: actions/cache@937d24475381cd9c75ae6db12cb4e79714b926ed # v3.0.11
       with:
         path: ${{ env.R_LIBS_USER }}
-        key: ${{ runner.os }}-r-${{ matrix.config.r }}-7-${{ hashFiles('R-package/DESCRIPTION') }}
-        restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-7-${{ hashFiles('R-package/DESCRIPTION') }}
+        key: ${{ runner.os }}-r-${{ matrix.config.r }}-6-${{ hashFiles('R-package/DESCRIPTION') }}
+        restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-6-${{ hashFiles('R-package/DESCRIPTION') }}
 
     - name: Install dependencies
       shell: Rscript {0}
@@ -69,24 +69,24 @@ jobs:
         sudo apt update
         sudo apt install libcurl4-openssl-dev libssl-dev libssh2-1-dev libgit2-dev libglpk-dev libxml2-dev libharfbuzz-dev libfribidi-dev
       if: matrix.config.os == 'ubuntu-latest'
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
 
-    - uses: r-lib/actions/setup-r@929c772977a3a13c8733b363bf5a2f685c25dd91 # v2.9.0
+    - uses: r-lib/actions/setup-r@e40ad904310fc92e96951c1b0d64f3de6cbe9e14 # v2.6.5
       with:
         r-version: ${{ matrix.config.r }}
 
     - name: Cache R packages
-      uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
+      uses: actions/cache@937d24475381cd9c75ae6db12cb4e79714b926ed # v3.0.11
       with:
         path: ${{ env.R_LIBS_USER }}
-        key: ${{ runner.os }}-r-${{ matrix.config.r }}-7-${{ hashFiles('R-package/DESCRIPTION') }}
-        restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-7-${{ hashFiles('R-package/DESCRIPTION') }}
+        key: ${{ runner.os }}-r-${{ matrix.config.r }}-6-${{ hashFiles('R-package/DESCRIPTION') }}
+        restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-6-${{ hashFiles('R-package/DESCRIPTION') }}
 
-    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
       with:
-        python-version: "3.10"
+        python-version: "3.8"
         architecture: 'x64'
 
     - uses: r-lib/actions/setup-tinytex@v2
@@ -123,7 +123,7 @@ jobs:
       run: |
         git config --global --add safe.directory "${GITHUB_WORKSPACE}"
 
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@e2f20e631ae6d7dd3b768f56a5d2af784dd54791 # v2.5.0
       with:
         submodules: 'true'
 
@@ -137,7 +137,7 @@ jobs:
       run: |
         python3 tests/ci_build/test_r_package.py --r=/usr/bin/R --build-tool=autotools --task=check
 
-    - uses: dorny/paths-filter@v3
+    - uses: dorny/paths-filter@v2
       id: changes
       with:
         filters: |

.github/workflows/scorecards.yml

@@ -22,12 +22,12 @@ jobs:
 
     steps:
       - name: "Checkout code"
-        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+        uses: actions/checkout@a12a3943b4bdde767164f792f33f40b04645d846 # v3.0.0
         with:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@62b2cac7ed8198b15735ed49ab1e5cf35480ba46 # v2.4.0
+        uses: ossf/scorecard-action@0864cf19026789058feabb7e87baa5f140aac736 # v2.3.1
         with:
           results_file: results.sarif
           results_format: sarif
@@ -41,7 +41,7 @@ jobs:
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
       - name: "Upload artifact"
-        uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4.3.1
         with:
           name: SARIF file
           path: results.sarif

.github/workflows/update_rapids.yml

@@ -25,7 +25,7 @@ jobs:
     name: Check latest RAPIDS
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+    - uses: actions/checkout@v2
       with:
         submodules: 'true'
     - name: Check latest RAPIDS and update conftest.sh

.gitignore

@@ -27,13 +27,12 @@
 *vali
 *sdf
 Release
-*exe
+*exe*
 *exp
 ipch
 *.filters
 *.user
 *log
-rmm_log.txt
 Debug
 *suo
 .Rhistory
@@ -64,7 +63,6 @@ java/xgboost4j-demo/data/
 java/xgboost4j-demo/tmp/
 java/xgboost4j-demo/model/
 nb-configuration*
-
 # Eclipse
 .project
 .cproject
@@ -86,7 +84,6 @@ target
 *.gcov
 *.gcda
 *.gcno
-*.ubj
 build_tests
 /tests/cpp/xgboost_test
 
@@ -100,7 +97,6 @@ metastore_db
 
 # files from R-package source install
 **/config.status
-R-package/config.h
 R-package/src/Makevars
 *.lib
 
@@ -156,6 +152,3 @@ model*.json
 *.rds
 Rplots.pdf
 *.zip
-
-# nsys
-*.nsys-rep

.gitmodules

@@ -5,3 +5,6 @@
 [submodule "gputreeshap"]
 	path = gputreeshap
 	url = https://github.com/rapidsai/gputreeshap.git
+[submodule "rocgputreeshap"]
+	path = rocgputreeshap
+	url = https://github.com/ROCmSoftwarePlatform/rocgputreeshap

.readthedocs.yaml

@@ -12,7 +12,7 @@ submodules:
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.8"
   apt_packages:
     - graphviz
     - cmake

CMakeLists.txt

@@ -1,10 +1,12 @@
 cmake_minimum_required(VERSION 3.18 FATAL_ERROR)
 
 if(PLUGIN_SYCL)
+  set(CMAKE_CXX_COMPILER  "g++")
+  set(CMAKE_C_COMPILER  "gcc")
   string(REPLACE " -isystem ${CONDA_PREFIX}/include" "" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
 endif()
 
-project(xgboost LANGUAGES CXX C VERSION 2.2.0)
+project(xgboost LANGUAGES CXX C VERSION 2.1.0)
 include(cmake/Utils.cmake)
 list(APPEND CMAKE_MODULE_PATH "${xgboost_SOURCE_DIR}/cmake/modules")
 
@@ -64,13 +66,15 @@ option(ENABLE_ALL_WARNINGS "Enable all compiler warnings. Only effective for GCC
 option(LOG_CAPI_INVOCATION "Log all C API invocations for debugging" OFF)
 option(GOOGLE_TEST "Build google tests" OFF)
 option(USE_DMLC_GTEST "Use google tests bundled with dmlc-core submodule" OFF)
-option(USE_DEVICE_DEBUG "Generate CUDA device debug info." OFF)
+option(USE_DEVICE_DEBUG "Generate CUDA/HIP device debug info." OFF)
 option(USE_NVTX "Build with cuda profiling annotations. Developers only." OFF)
 set(NVTX_HEADER_DIR "" CACHE PATH "Path to the stand-alone nvtx header")
+option(RABIT_MOCK "Build rabit with mock" OFF)
 option(HIDE_CXX_SYMBOLS "Build shared library and hide all C++ symbols" OFF)
 option(KEEP_BUILD_ARTIFACTS_IN_BINARY_DIR "Output build artifacts in CMake binary dir" OFF)
 ## CUDA
 option(USE_CUDA  "Build with GPU acceleration" OFF)
+option(USE_PER_THREAD_DEFAULT_STREAM "Build with per-thread default stream" ON)
 option(USE_NCCL  "Build with NCCL to enable distributed GPU support." OFF)
 # This is specifically designed for PyPI binary release and should be disabled for most of the cases.
 option(USE_DLOPEN_NCCL "Whether to load nccl dynamically." OFF)
@@ -95,6 +99,12 @@ cmake_dependent_option(USE_CUDA_LTO
   "${CMAKE_INTERPROCEDURAL_OPTIMIZATION}"
   "CMAKE_VERSION VERSION_GREATER_EQUAL 3.25;USE_CUDA;CMAKE_INTERPROCEDURAL_OPTIMIZATION"
   OFF)
+## HIP
+option(USE_HIP  "Build with GPU acceleration" OFF)
+option(USE_RCCL "Build with RCCL to enable distributed GPU support." OFF)
+# This is specifically designed for PyPI binary release and should be disabled for most of the cases.
+option(USE_DLOPEN_RCCL "Whether to load nccl dynamically." OFF)
+option(BUILD_WITH_SHARED_RCCL "Build with shared RCCL library." OFF)
 ## Sanitizers
 option(USE_SANITIZER "Use santizer flags" OFF)
 option(SANITIZER_PATH "Path to sanitizes.")
@@ -127,6 +137,18 @@ endif()
 if(USE_DLOPEN_NCCL AND (NOT (CMAKE_SYSTEM_NAME STREQUAL "Linux")))
   message(SEND_ERROR "`USE_DLOPEN_NCCL` supports only Linux at the moment.")
 endif()
+if(USE_RCCL AND NOT (USE_HIP))
+    message(SEND_ERROR "`USE_RCCL` must be enabled with `USE_HIP` flag.")
+endif()
+if(BUILD_WITH_SHARED_RCCL AND (NOT USE_RCCL))
+  message(SEND_ERROR "Build XGBoost with -DUSE_RCCL=ON to enable BUILD_WITH_SHARED_RCCL.")
+endif()
+if(USE_DLOPEN_RCCL AND (NOT USE_RCCL))
+  message(SEND_ERROR "Build XGBoost with -DUSE_RCCL=ON to enable USE_DLOPEN_RCCL.")
+endif()
+if(USE_DLOPEN_RCCL AND (NOT (CMAKE_SYSTEM_NAME STREQUAL "Linux")))
+  message(SEND_ERROR "`USE_DLOPEN_RCCL` supports only Linux at the moment.")
+endif()
 if(JVM_BINDINGS AND R_LIB)
   message(SEND_ERROR "`R_LIB' is not compatible with `JVM_BINDINGS' as they both have customized configurations.")
 endif()
@@ -218,28 +240,30 @@ if(USE_CUDA)
   if(DEFINED GPU_COMPUTE_VER)
     compute_cmake_cuda_archs("${GPU_COMPUTE_VER}")
   endif()
+  add_subdirectory(${PROJECT_SOURCE_DIR}/gputreeshap)
 
   find_package(CUDAToolkit REQUIRED)
-  find_package(CCCL CONFIG)
-  if(NOT CCCL_FOUND)
-    message(STATUS "Standalone CCCL not found. Attempting to use CCCL from CUDA Toolkit...")
-    find_package(CCCL CONFIG
-      HINTS ${CUDAToolkit_LIBRARY_DIR}/cmake)
-    if(NOT CCCL_FOUND)
-      message(STATUS "Could not locate CCCL from CUDA Toolkit. Using Thrust and CUB from CUDA Toolkit...")
-      find_package(libcudacxx CONFIG REQUIRED
-        HINTS ${CUDAToolkit_LIBRARY_DIR}/cmake)
-      find_package(CUB CONFIG REQUIRED
-        HINTS ${CUDAToolkit_LIBRARY_DIR}/cmake)
-      find_package(Thrust CONFIG REQUIRED
-        HINTS ${CUDAToolkit_LIBRARY_DIR}/cmake)
-      thrust_create_target(Thrust HOST CPP DEVICE CUDA)
-      add_library(CCCL::CCCL INTERFACE IMPORTED GLOBAL)
-      target_link_libraries(CCCL::CCCL INTERFACE libcudacxx::libcudacxx CUB::CUB Thrust)
-    endif()
-  endif()
 endif()
 
+if (USE_HIP)
+  set(USE_OPENMP ON CACHE BOOL "HIP requires OpenMP" FORCE)
+  # `export CXX=' is ignored by CMake HIP.
+  set(CMAKE_HIP_HOST_COMPILER ${CMAKE_CXX_COMPILER})
+  message(STATUS "Configured HIP host compiler: ${CMAKE_HIP_HOST_COMPILER}")
+
+  enable_language(HIP)
+  find_package(hip REQUIRED)
+  find_package(rocthrust REQUIRED)
+  find_package(hipcub REQUIRED)
+
+  set(CMAKE_HIP_FLAGS "${CMAKE_HIP_FLAGS} -I${HIP_INCLUDE_DIRS}")
+  set(CMAKE_HIP_FLAGS "${CMAKE_HIP_FLAGS} -Wunused-result -w")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D__HIP_PLATFORM_AMD__")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -I${HIP_INCLUDE_DIRS}")
+  #set(CMAKE_HIP_SEPARABLE_COMPILATION ON)
+  add_subdirectory(${PROJECT_SOURCE_DIR}/rocgputreeshap)
+endif (USE_HIP)
+
 if(FORCE_COLORED_OUTPUT AND (CMAKE_GENERATOR STREQUAL "Ninja") AND
     ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") OR
       (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
@@ -248,17 +272,28 @@ endif()
 
 find_package(Threads REQUIRED)
 
-# -- OpenMP
-include(cmake/FindOpenMPMacOS.cmake)
 if(USE_OPENMP)
   if(APPLE)
-    find_openmp_macos()
+    find_package(OpenMP)
+    if(NOT OpenMP_FOUND)
+      # Try again with extra path info; required for libomp 15+ from Homebrew
+      execute_process(COMMAND brew --prefix libomp
+                      OUTPUT_VARIABLE HOMEBREW_LIBOMP_PREFIX
+                      OUTPUT_STRIP_TRAILING_WHITESPACE)
+      set(OpenMP_C_FLAGS
+        "-Xpreprocessor -fopenmp -I${HOMEBREW_LIBOMP_PREFIX}/include")
+      set(OpenMP_CXX_FLAGS
+        "-Xpreprocessor -fopenmp -I${HOMEBREW_LIBOMP_PREFIX}/include")
+      set(OpenMP_C_LIB_NAMES omp)
+      set(OpenMP_CXX_LIB_NAMES omp)
+      set(OpenMP_omp_LIBRARY ${HOMEBREW_LIBOMP_PREFIX}/lib/libomp.dylib)
+      find_package(OpenMP REQUIRED)
+    endif()
   else()
     find_package(OpenMP REQUIRED)
   endif()
 endif()
-
-# Add for IBM i
+#Add for IBM i
 if(${CMAKE_SYSTEM_NAME} MATCHES "OS400")
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
   set(CMAKE_CXX_ARCHIVE_CREATE "<CMAKE_AR> -X64 qc <TARGET> <OBJECTS>")
@@ -268,18 +303,15 @@ if(USE_NCCL)
   find_package(Nccl REQUIRED)
 endif()
 
-if(MSVC)
-  if(FORCE_SHARED_CRT)
-    message(STATUS "XGBoost: Using dynamically linked MSVC runtime...")
-    set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>DLL")
-  else()
-    message(STATUS "XGBoost: Using statically linked MSVC runtime...")
-    set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
-  endif()
-endif()
+if (USE_RCCL)
+  find_package(rccl REQUIRED)
+endif (USE_RCCL)
 
 # dmlc-core
-set(DMLC_FORCE_SHARED_CRT ${FORCE_SHARED_CRT})
+msvc_use_static_runtime()
+if(FORCE_SHARED_CRT)
+  set(DMLC_FORCE_SHARED_CRT ON)
+endif()
 add_subdirectory(${xgboost_SOURCE_DIR}/dmlc-core)
 
 if(MSVC)
@@ -291,6 +323,9 @@ if(MSVC)
   endif()
 endif()
 
+# rabit
+add_subdirectory(rabit)
+
 # core xgboost
 add_subdirectory(${xgboost_SOURCE_DIR}/src)
 target_link_libraries(objxgboost PUBLIC dmlc)
@@ -356,6 +391,7 @@ if(BUILD_DEPRECATED_CLI)
     PRIVATE
     ${xgboost_SOURCE_DIR}/include
     ${xgboost_SOURCE_DIR}/dmlc-core/include
+    ${xgboost_SOURCE_DIR}/rabit/include
   )
   set_target_properties(runxgboost PROPERTIES OUTPUT_NAME xgboost)
   xgboost_target_properties(runxgboost)
@@ -383,10 +419,6 @@ if(JVM_BINDINGS)
   xgboost_target_defs(xgboost4j)
 endif()
 
-if(USE_OPENMP AND APPLE)
-  patch_openmp_path_macos(xgboost libxgboost)
-endif()
-
 if(KEEP_BUILD_ARTIFACTS_IN_BINARY_DIR)
   set_output_directory(xgboost ${xgboost_BINARY_DIR}/lib)
 else()
@@ -503,6 +535,11 @@ if(GOOGLE_TEST)
   endif()
 endif()
 
+# For MSVC: Call msvc_use_static_runtime() once again to completely
+# replace /MD with /MT. See https://github.com/dmlc/xgboost/issues/4462
+# for issues caused by mixing of /MD and /MT flags
+msvc_use_static_runtime()
+
 # Add xgboost.pc
 if(ADD_PKGCONFIG)
   configure_file(${xgboost_SOURCE_DIR}/cmake/xgboost.pc.in ${xgboost_BINARY_DIR}/xgboost.pc @ONLY)

NEWS.md

@@ -1,8 +1,6 @@
 XGBoost Change Log
 ==================
 
-**Starting from 2.1.0, release note is recorded in the documentation.**
-
 This file records the changes in xgboost library in reverse chronological order.
 
 ## 2.0.0 (2023 Aug 16)

R-package/CMakeLists.txt

@@ -29,6 +29,7 @@ target_compile_definitions(
   -DDMLC_LOG_BEFORE_THROW=0
   -DDMLC_DISABLE_STDIN=1
   -DDMLC_LOG_CUSTOMIZE=1
+  -DRABIT_STRICT_CXX98_
 )
 
 target_include_directories(
@@ -36,6 +37,7 @@ target_include_directories(
   ${LIBR_INCLUDE_DIRS}
   ${PROJECT_SOURCE_DIR}/include
   ${PROJECT_SOURCE_DIR}/dmlc-core/include
+  ${PROJECT_SOURCE_DIR}/rabit/include
 )
 
 target_link_libraries(xgboost-r PUBLIC ${LIBR_CORE_LIBRARY})

R-package/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: xgboost
 Type: Package
 Title: Extreme Gradient Boosting
-Version: 2.2.0.0
-Date: 2024-06-03
+Version: 2.1.0.0
+Date: 2023-08-19
 Authors@R: c(
   person("Tianqi", "Chen", role = c("aut"),
          email = "tianqi.tchen@gmail.com"),
@@ -57,8 +57,7 @@ Suggests:
     igraph (>= 1.0.1),
     float,
     titanic,
-    RhpcBLASctl,
-    survival
+    RhpcBLASctl
 Depends:
     R (>= 4.3.0)
 Imports:
@@ -67,6 +66,6 @@ Imports:
     data.table (>= 1.9.6),
     jsonlite (>= 1.0)
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 SystemRequirements: GNU make, C++17

R-package/NAMESPACE

@@ -13,7 +13,6 @@ S3method(predict,xgb.Booster)
 S3method(print,xgb.Booster)
 S3method(print,xgb.DMatrix)
 S3method(print,xgb.cv.synchronous)
-S3method(print,xgboost)
 S3method(setinfo,xgb.Booster)
 S3method(setinfo,xgb.DMatrix)
 S3method(variable.names,xgb.Booster)
@@ -29,7 +28,7 @@ export(xgb.DMatrix.hasinfo)
 export(xgb.DMatrix.save)
 export(xgb.DataBatch)
 export(xgb.DataIter)
-export(xgb.ExtMemDMatrix)
+export(xgb.ExternalDMatrix)
 export(xgb.QuantileDMatrix)
 export(xgb.QuantileDMatrix.from_iterator)
 export(xgb.attr)

R-package/R/callbacks.R

@@ -1,166 +1,172 @@
 .reserved_cb_names <- c("names", "class", "call", "params", "niter", "nfeatures", "folds")
 
-#' XGBoost Callback Constructor
-#'
-#' Constructor for defining the structure of callback functions that can be executed
+#' @title XGBoost Callback Constructor
+#' @description Constructor for defining the structure of callback functions that can be executed
 #' at different stages of model training (before / after training, before / after each boosting
 #' iteration).
+#' @param cb_name Name for the callback.
 #'
-#' @details
-#' Arguments that will be passed to the supplied functions are as follows:
-#' - env The same environment that is passed under argument `env`.
+#' If the callback produces some non-NULL result (from executing the function passed under
+#' `f_after_training`), that result will be added as an R attribute to the resulting booster
+#' (or as a named element in the result of CV), with the attribute name specified here.
 #'
-#'   It may be modified by the functions in order to e.g. keep tracking of what happens
-#'   across iterations or similar.
+#' Names of callbacks must be unique - i.e. there cannot be two callbacks with the same name.
+#' @param env An environment object that will be passed to the different functions in the callback.
+#' Note that this environment will not be shared with other callbacks.
+#' @param f_before_training A function that will be executed before the training has started.
 #'
-#'   This environment is only used by the functions supplied to the callback, and will
-#'   not be kept after the model fitting function terminates (see parameter `f_after_training`).
+#' If passing `NULL` for this or for the other function inputs, then no function will be executed.
 #'
-#' - model The booster object when using [xgb.train()], or the folds when using [xgb.cv()].
+#' If passing a function, it will be called with parameters supplied as non-named arguments
+#' matching the function signatures that are shown in the default value for each function argument.
+#' @param f_before_iter A function that will be executed before each boosting round.
 #'
-#'   For [xgb.cv()], folds are a list with a structure as follows:
-#'     - `dtrain`: The training data for the fold (as an `xgb.DMatrix` object).
-#'     - `bst`: Rhe `xgb.Booster` object for the fold.
-#'     - `evals`: A list containing two DMatrices, with names `train` and `test`
-#'       (`test` is the held-out data for the fold).
-#'     - `index`: The indices of the hold-out data for that fold (base-1 indexing),
-#'       from which the `test` entry in `evals` was obtained.
+#' This function can signal whether the training should be finalized or not, by outputting
+#' a value that evaluates to `TRUE` - i.e. if the output from the function provided here at
+#' a given round is `TRUE`, then training will be stopped before the current iteration happens.
 #'
-#'   This object should **not** be in-place modified in ways that conflict with the
-#'   training (e.g. resetting the parameters for a training update in a way that resets
-#'   the number of rounds to zero in order to overwrite rounds).
+#' Return values of `NULL` will be interpreted as `FALSE`.
+#' @param f_after_iter A function that will be executed after each boosting round.
 #'
-#'   Note that any R attributes that are assigned to the booster during the callback functions,
-#'   will not be kept thereafter as the booster object variable is not re-assigned during
-#'   training. It is however possible to set C-level attributes of the booster through
-#'   [xgb.attr()] or [xgb.attributes()], which should remain available for the rest
-#'   of the iterations and after the training is done.
+#' This function can signal whether the training should be finalized or not, by outputting
+#' a value that evaluates to `TRUE` - i.e. if the output from the function provided here at
+#' a given round is `TRUE`, then training will be stopped at that round.
 #'
-#'   For keeping variables across iterations, it's recommended to use `env` instead.
-#' - data The data to which the model is being fit, as an `xgb.DMatrix` object.
+#' Return values of `NULL` will be interpreted as `FALSE`.
+#' @param f_after_training A function that will be executed after training is finished.
 #'
-#'   Note that, for [xgb.cv()], this will be the full data, while data for the specific
-#'   folds can be found in the `model` object.
-#' - evals The evaluation data, as passed under argument `evals` to [xgb.train()].
+#' This function can optionally output something non-NULL, which will become part of the R
+#' attributes of the booster (assuming one passes `keep_extra_attributes=TRUE` to \link{xgb.train})
+#' under the name supplied for parameter `cb_name` imn the case of \link{xgb.train}; or a part
+#' of the named elements in the result of \link{xgb.cv}.
+#' @return An `xgb.Callback` object, which can be passed to \link{xgb.train} or \link{xgb.cv}.
+#' @details Arguments that will be passed to the supplied functions are as follows:\itemize{
 #'
-#'   For [xgb.cv()], this will always be `NULL`.
-#' - begin_iteration Index of the first boosting iteration that will be executed (base-1 indexing).
+#' \item env The same environment that is passed under argument `env`.
 #'
-#'   This will typically be '1', but when using training continuation, depending on the
-#'   parameters for updates, boosting rounds will be continued from where the previous
-#'   model ended, in which case this will be larger than 1.
+#' It may be modified by the functions in order to e.g. keep tracking of what happens
+#' across iterations or similar.
 #'
-#' - end_iteration Index of the last boostign iteration that will be executed
-#'   (base-1 indexing, inclusive of this end).
+#' This environment is only used by the functions supplied to the callback, and will
+#' not be kept after the model fitting function terminates (see parameter `f_after_training`).
 #'
-#'   It should match with argument `nrounds` passed to [xgb.train()] or [xgb.cv()].
+#' \item model The booster object when using \link{xgb.train}, or the folds when using
+#' \link{xgb.cv}.
 #'
-#'   Note that boosting might be interrupted before reaching this last iteration, for
-#'   example by using the early stopping callback [xgb.cb.early.stop()].
-#' - iteration Index of the iteration number that is being executed (first iteration
-#'   will be the same as parameter `begin_iteration`, then next one will add +1, and so on).
+#' For \link{xgb.cv}, folds are a list with a structure as follows:\itemize{
+#' \item `dtrain`: The training data for the fold (as an `xgb.DMatrix` object).
+#' \item `bst`: Rhe `xgb.Booster` object for the fold.
+#' \item `evals`: A list containing two DMatrices, with names `train` and `test`
+#' (`test` is the held-out data for the fold).
+#' \item `index`: The indices of the hold-out data for that fold (base-1 indexing),
+#' from which the `test` entry in `evals` was obtained.
+#' }
 #'
-#' - iter_feval Evaluation metrics for `evals` that were supplied, either
-#'   determined by the objective, or by parameter `feval`.
+#' This object should \bold{not} be in-place modified in ways that conflict with the
+#' training (e.g. resetting the parameters for a training update in a way that resets
+#' the number of rounds to zero in order to overwrite rounds).
 #'
-#'   For [xgb.train()], this will be a named vector with one entry per element in
-#'   `evals`, where the names are determined as 'evals name' + '-' + 'metric name' - for
-#'   example, if `evals` contains an entry named "tr" and the metric is "rmse",
-#'   this will be a one-element vector with name "tr-rmse".
+#' Note that any R attributes that are assigned to the booster during the callback functions,
+#' will not be kept thereafter as the booster object variable is not re-assigned during
+#' training. It is however possible to set C-level attributes of the booster through
+#' \link{xgb.attr} or \link{xgb.attributes}, which should remain available for the rest
+#' of the iterations and after the training is done.
 #'
-#'   For [xgb.cv()], this will be a 2d matrix with dimensions `[length(evals), nfolds]`,
-#'   where the row names will follow the same naming logic as the one-dimensional vector
-#'   that is passed in [xgb.train()].
+#' For keeping variables across iterations, it's recommended to use `env` instead.
+#' \item data The data to which the model is being fit, as an `xgb.DMatrix` object.
 #'
-#'   Note that, internally, the built-in callbacks such as [xgb.cb.print.evaluation] summarize
-#'   this table by calculating the row-wise means and standard deviations.
+#' Note that, for \link{xgb.cv}, this will be the full data, while data for the specific
+#' folds can be found in the `model` object.
 #'
-#' - final_feval The evaluation results after the last boosting round is executed
-#'   (same format as `iter_feval`, and will be the exact same input as passed under
-#'   `iter_feval` to the last round that is executed during model fitting).
+#' \item evals The evaluation data, as passed under argument `evals` to
+#' \link{xgb.train}.
 #'
-#' - prev_cb_res Result from a previous run of a callback sharing the same name
-#'   (as given by parameter `cb_name`) when conducting training continuation, if there
-#'   was any in the booster R attributes.
+#' For \link{xgb.cv}, this will always be `NULL`.
 #'
-#'   Sometimes, one might want to append the new results to the previous one, and this will
-#'   be done automatically by the built-in callbacks such as [xgb.cb.evaluation.log],
-#'   which will append the new rows to the previous table.
+#' \item begin_iteration Index of the first boosting iteration that will be executed
+#' (base-1 indexing).
 #'
-#'   If no such previous callback result is available (which it never will when fitting
-#'   a model from start instead of updating an existing model), this will be `NULL`.
+#' This will typically be '1', but when using training continuation, depending on the
+#' parameters for updates, boosting rounds will be continued from where the previous
+#' model ended, in which case this will be larger than 1.
 #'
-#'   For [xgb.cv()], which doesn't support training continuation, this will always be `NULL`.
+#' \item end_iteration Index of the last boostign iteration that will be executed
+#' (base-1 indexing, inclusive of this end).
 #'
-#' The following names (`cb_name` values) are reserved for internal callbacks:
-#' - print_evaluation
-#' - evaluation_log
-#' - reset_parameters
-#' - early_stop
-#' - save_model
-#' - cv_predict
-#' - gblinear_history
+#' It should match with argument `nrounds` passed to \link{xgb.train} or \link{xgb.cv}.
 #'
-#' The following names are reserved for other non-callback attributes:
-#' - names
-#' - class
-#' - call
-#' - params
-#' - niter
-#' - nfeatures
-#' - folds
+#' Note that boosting might be interrupted before reaching this last iteration, for
+#' example by using the early stopping callback \link{xgb.cb.early.stop}.
 #'
-#' When using the built-in early stopping callback ([xgb.cb.early.stop]), said callback
+#' \item iteration Index of the iteration number that is being executed (first iteration
+#' will be the same as parameter `begin_iteration`, then next one will add +1, and so on).
+#'
+#' \item iter_feval Evaluation metrics for `evals` that were supplied, either
+#' determined by the objective, or by parameter `feval`.
+#'
+#' For \link{xgb.train}, this will be a named vector with one entry per element in
+#' `evals`, where the names are determined as 'evals name' + '-' + 'metric name' - for
+#' example, if `evals` contains an entry named "tr" and the metric is "rmse",
+#' this will be a one-element vector with name "tr-rmse".
+#'
+#' For \link{xgb.cv}, this will be a 2d matrix with dimensions `[length(evals), nfolds]`,
+#' where the row names will follow the same naming logic as the one-dimensional vector
+#' that is passed in \link{xgb.train}.
+#'
+#' Note that, internally, the built-in callbacks such as \link{xgb.cb.print.evaluation} summarize
+#' this table by calculating the row-wise means and standard deviations.
+#'
+#' \item final_feval The evaluation results after the last boosting round is executed
+#' (same format as `iter_feval`, and will be the exact same input as passed under
+#' `iter_feval` to the last round that is executed during model fitting).
+#'
+#' \item prev_cb_res Result from a previous run of a callback sharing the same name
+#' (as given by parameter `cb_name`) when conducting training continuation, if there
+#' was any in the booster R attributes.
+#'
+#' Some times, one might want to append the new results to the previous one, and this will
+#' be done automatically by the built-in callbacks such as \link{xgb.cb.evaluation.log},
+#' which will append the new rows to the previous table.
+#'
+#' If no such previous callback result is available (which it never will when fitting
+#' a model from start instead of updating an existing model), this will be `NULL`.
+#'
+#' For \link{xgb.cv}, which doesn't support training continuation, this will always be `NULL`.
+#' }
+#'
+#' The following names (`cb_name` values) are reserved for internal callbacks:\itemize{
+#' \item print_evaluation
+#' \item evaluation_log
+#' \item reset_parameters
+#' \item early_stop
+#' \item save_model
+#' \item cv_predict
+#' \item gblinear_history
+#' }
+#'
+#' The following names are reserved for other non-callback attributes:\itemize{
+#' \item names
+#' \item class
+#' \item call
+#' \item params
+#' \item niter
+#' \item nfeatures
+#' \item folds
+#' }
+#'
+#' When using the built-in early stopping callback (\link{xgb.cb.early.stop}), said callback
 #' will always be executed before the others, as it sets some booster C-level attributes
 #' that other callbacks might also use. Otherwise, the order of execution will match with
 #' the order in which the callbacks are passed to the model fitting function.
-#'
-#' @param cb_name Name for the callback.
-#'
-#'   If the callback produces some non-NULL result (from executing the function passed under
-#'   `f_after_training`), that result will be added as an R attribute to the resulting booster
-#'   (or as a named element in the result of CV), with the attribute name specified here.
-#'
-#'   Names of callbacks must be unique - i.e. there cannot be two callbacks with the same name.
-#' @param env An environment object that will be passed to the different functions in the callback.
-#'   Note that this environment will not be shared with other callbacks.
-#' @param f_before_training A function that will be executed before the training has started.
-#'
-#'   If passing `NULL` for this or for the other function inputs, then no function will be executed.
-#'
-#'   If passing a function, it will be called with parameters supplied as non-named arguments
-#'   matching the function signatures that are shown in the default value for each function argument.
-#' @param f_before_iter A function that will be executed before each boosting round.
-#'
-#'   This function can signal whether the training should be finalized or not, by outputting
-#'   a value that evaluates to `TRUE` - i.e. if the output from the function provided here at
-#'   a given round is `TRUE`, then training will be stopped before the current iteration happens.
-#'
-#'   Return values of `NULL` will be interpreted as `FALSE`.
-#' @param f_after_iter A function that will be executed after each boosting round.
-#'
-#'   This function can signal whether the training should be finalized or not, by outputting
-#'   a value that evaluates to `TRUE` - i.e. if the output from the function provided here at
-#'   a given round is `TRUE`, then training will be stopped at that round.
-#'
-#'   Return values of `NULL` will be interpreted as `FALSE`.
-#' @param f_after_training A function that will be executed after training is finished.
-#'
-#'   This function can optionally output something non-NULL, which will become part of the R
-#'   attributes of the booster (assuming one passes `keep_extra_attributes=TRUE` to [xgb.train()])
-#'   under the name supplied for parameter `cb_name` imn the case of [xgb.train()]; or a part
-#'   of the named elements in the result of [xgb.cv()].
-#' @return An `xgb.Callback` object, which can be passed to [xgb.train()] or [xgb.cv()].
-#'
-#' @seealso Built-in callbacks:
-#' - [xgb.cb.print.evaluation]
-#' - [xgb.cb.evaluation.log]
-#' - [xgb.cb.reset.parameters]
-#' - [xgb.cb.early.stop]
-#' - [xgb.cb.save.model]
-#' - [xgb.cb.cv.predict]
-#' - [xgb.cb.gblinear.history]
-#
+#' @seealso Built-in callbacks:\itemize{
+#' \item \link{xgb.cb.print.evaluation}
+#' \item \link{xgb.cb.evaluation.log}
+#' \item \link{xgb.cb.reset.parameters}
+#' \item \link{xgb.cb.early.stop}
+#' \item \link{xgb.cb.save.model}
+#' \item \link{xgb.cb.cv.predict}
+#' \item \link{xgb.cb.gblinear.history}
+#' }
 #' @examples
 #' # Example constructing a custom callback that calculates
 #' # squared error on the training data (no separate test set),
@@ -197,10 +203,8 @@
 #' )
 #'
 #' data(mtcars)
-#'
 #' y <- mtcars$mpg
 #' x <- as.matrix(mtcars[, -1])
-#'
 #' dm <- xgb.DMatrix(x, label = y, nthread = 1)
 #' model <- xgb.train(
 #'   data = dm,
@@ -403,18 +407,16 @@ xgb.Callback <- function(
   return(paste0(iter, res))
 }
 
-#' Callback for printing the result of evaluation
-#'
+#' @title Callback for printing the result of evaluation
+#' @param period results would be printed every number of periods
+#' @param showsd whether standard deviations should be printed (when available)
+#' @return An `xgb.Callback` object, which can be passed to \link{xgb.train} or \link{xgb.cv}.
 #' @description
-#' The callback function prints the result of evaluation at every `period` iterations.
+#' The callback function prints the result of evaluation at every \code{period} iterations.
 #' The initial and the last iteration's evaluations are always printed.
 #'
-#' Does not leave any attribute in the booster (see [xgb.cb.evaluation.log] for that).
-#'
-#' @param period Results would be printed every number of periods.
-#' @param showsd Whether standard deviations should be printed (when available).
-#' @return An `xgb.Callback` object, which can be passed to [xgb.train()] or [xgb.cv()].
-#' @seealso [xgb.Callback]
+#' Does not leave any attribute in the booster (see \link{xgb.cb.evaluation.log} for that).
+#' @seealso \link{xgb.Callback}
 #' @export
 xgb.cb.print.evaluation <- function(period = 1, showsd = TRUE) {
   if (length(period) != 1 || period != floor(period) || period < 1) {
@@ -448,16 +450,14 @@ xgb.cb.print.evaluation <- function(period = 1, showsd = TRUE) {
   )
 }
 
-#' Callback for logging the evaluation history
-#'
+#' @title Callback for logging the evaluation history
+#' @return An `xgb.Callback` object, which can be passed to \link{xgb.train} or \link{xgb.cv}.
 #' @details This callback creates a table with per-iteration evaluation metrics (see parameters
-#' `evals` and `feval` in [xgb.train()]).
-#'
+#' `evals` and `feval` in \link{xgb.train}).
+#' @details
 #' Note: in the column names of the final data.table, the dash '-' character is replaced with
 #' the underscore '_' in order to make the column names more like regular R identifiers.
-#'
-#' @return An `xgb.Callback` object, which can be passed to [xgb.train()] or [xgb.cv()].
-#' @seealso [xgb.cb.print.evaluation]
+#' @seealso \link{xgb.cb.print.evaluation}
 #' @export
 xgb.cb.evaluation.log <- function() {
   xgb.Callback(
@@ -517,22 +517,20 @@ xgb.cb.evaluation.log <- function() {
   )
 }
 
-#' Callback for resetting booster parameters at each iteration
-#'
+#' @title Callback for resetting the booster's parameters at each iteration.
+#' @param new_params a list where each element corresponds to a parameter that needs to be reset.
+#'        Each element's value must be either a vector of values of length \code{nrounds}
+#'        to be set at each iteration,
+#'        or a function of two parameters \code{learning_rates(iteration, nrounds)}
+#'        which returns a new parameter value by using the current iteration number
+#'        and the total number of boosting rounds.
+#' @return An `xgb.Callback` object, which can be passed to \link{xgb.train} or \link{xgb.cv}.
 #' @details
 #' Note that when training is resumed from some previous model, and a function is used to
-#' reset a parameter value, the `nrounds` argument in this function would be the
+#' reset a parameter value, the \code{nrounds} argument in this function would be the
 #' the number of boosting rounds in the current training.
 #'
 #' Does not leave any attribute in the booster.
-#'
-#' @param new_params List of parameters needed to be reset.
-#'   Each element's value must be either a vector of values of length `nrounds`
-#'   to be set at each iteration,
-#'   or a function of two parameters `learning_rates(iteration, nrounds)`
-#'   which returns a new parameter value by using the current iteration number
-#'   and the total number of boosting rounds.
-#' @return An `xgb.Callback` object, which can be passed to [xgb.train()] or [xgb.cv()].
 #' @export
 xgb.cb.reset.parameters <- function(new_params) {
   stopifnot(is.list(new_params))
@@ -585,39 +583,39 @@ xgb.cb.reset.parameters <- function(new_params) {
   )
 }
 
-#' Callback to activate early stopping
-#'
+#' @title Callback to activate early stopping
+#' @param stopping_rounds The number of rounds with no improvement in
+#'        the evaluation metric in order to stop the training.
+#' @param maximize Whether to maximize the evaluation metric.
+#' @param metric_name The name of an evaluation column to use as a criteria for early
+#'        stopping. If not set, the last column would be used.
+#'        Let's say the test data in \code{evals} was labelled as \code{dtest},
+#'        and one wants to use the AUC in test data for early stopping regardless of where
+#'        it is in the \code{evals}, then one of the following would need to be set:
+#'        \code{metric_name='dtest-auc'} or \code{metric_name='dtest_auc'}.
+#'        All dash '-' characters in metric names are considered equivalent to '_'.
+#' @param verbose Whether to print the early stopping information.
+#' @param keep_all_iter Whether to keep all of the boosting rounds that were produced
+#'        in the resulting object. If passing `FALSE`, will only keep the boosting rounds
+#'        up to the detected best iteration, discarding the ones that come after.
+#' @return An `xgb.Callback` object, which can be passed to \link{xgb.train} or \link{xgb.cv}.
 #' @description
 #' This callback function determines the condition for early stopping.
 #'
 #' The following attributes are assigned to the booster's object:
-#' - `best_score` the evaluation score at the best iteration
-#' - `best_iteration` at which boosting iteration the best score has occurred
+#' \itemize{
+#' \item \code{best_score} the evaluation score at the best iteration
+#' \item \code{best_iteration} at which boosting iteration the best score has occurred
 #' (0-based index for interoperability of binary models)
+#' }
 #'
 #' The same values are also stored as R attributes as a result of the callback, plus an additional
 #' attribute `stopped_by_max_rounds` which indicates whether an early stopping by the `stopping_rounds`
 #' condition occurred. Note that the `best_iteration` that is stored under R attributes will follow
 #' base-1 indexing, so it will be larger by '1' than the C-level 'best_iteration' that is accessed
-#' through [xgb.attr()] or  [xgb.attributes()].
+#' through \link{xgb.attr} or \link{xgb.attributes}.
 #'
 #' At least one dataset is required in `evals` for early stopping to work.
-#'
-#' @param stopping_rounds The number of rounds with no improvement in
-#'   the evaluation metric in order to stop the training.
-#' @param maximize Whether to maximize the evaluation metric.
-#' @param metric_name The name of an evaluation column to use as a criteria for early
-#'   stopping. If not set, the last column would be used.
-#'   Let's say the test data in `evals` was labelled as `dtest`,
-#'   and one wants to use the AUC in test data for early stopping regardless of where
-#'   it is in the `evals`, then one of the following would need to be set:
-#'   `metric_name = 'dtest-auc'` or `metric_name = 'dtest_auc'`.
-#'   All dash '-' characters in metric names are considered equivalent to '_'.
-#' @param verbose Whether to print the early stopping information.
-#' @param keep_all_iter Whether to keep all of the boosting rounds that were produced
-#'   in the resulting object. If passing `FALSE`, will only keep the boosting rounds
-#'   up to the detected best iteration, discarding the ones that come after.
-#' @return An `xgb.Callback` object, which can be passed to [xgb.train()] or [xgb.cv()].
 #' @export
 xgb.cb.early.stop <- function(
   stopping_rounds,
@@ -773,22 +771,21 @@ xgb.cb.early.stop <- function(
   xgb.save(model, save_name)
 }
 
-#' Callback for saving a model file
-#'
+#' @title Callback for saving a model file.
+#' @param save_period Save the model to disk after every
+#'        \code{save_period} iterations; 0 means save the model at the end.
+#' @param save_name The name or path for the saved model file.
+#'        It can contain a \code{\link[base]{sprintf}} formatting specifier
+#'        to include the integer iteration number in the file name.
+#'        E.g., with \code{save_name} = 'xgboost_%04d.model',
+#'        the file saved at iteration 50 would be named "xgboost_0050.model".
+#' @return An `xgb.Callback` object, which can be passed to \link{xgb.train},
+#'         but \bold{not} to \link{xgb.cv}.
 #' @description
 #' This callback function allows to save an xgb-model file, either periodically
-#' after each `save_period`'s or at the end.
+#' after each \code{save_period}'s or at the end.
 #'
 #' Does not leave any attribute in the booster.
-#'
-#' @param save_period Save the model to disk after every `save_period` iterations;
-#'   0 means save the model at the end.
-#' @param save_name The name or path for the saved model file.
-#'   It can contain a [sprintf()] formatting specifier to include the integer
-#'   iteration number in the file name. E.g., with `save_name = 'xgboost_%04d.model'`,
-#'   the file saved at iteration 50 would be named "xgboost_0050.model".
-#' @return An `xgb.Callback` object, which can be passed to [xgb.train()],
-#'   but **not** to [xgb.cv()].
 #' @export
 xgb.cb.save.model <- function(save_period = 0, save_name = "xgboost.ubj") {
   if (save_period < 0) {
@@ -820,26 +817,24 @@ xgb.cb.save.model <- function(save_period = 0, save_name = "xgboost.ubj") {
   )
 }
 
-#' Callback for returning cross-validation based predictions
-#'
-#' This callback function saves predictions for all of the test folds,
-#' and also allows to save the folds' models.
-#'
-#' @details
-#' Predictions are saved inside of the `pred` element, which is either a vector or a matrix,
-#' depending on the number of prediction outputs per data row. The order of predictions corresponds
-#' to the order of rows in the original dataset. Note that when a custom `folds` list is
-#' provided in [xgb.cv()], the predictions would only be returned properly when this list is a
-#' non-overlapping list of k sets of indices, as in a standard k-fold CV. The predictions would not be
-#' meaningful when user-provided folds have overlapping indices as in, e.g., random sampling splits.
-#' When some of the indices in the training dataset are not included into user-provided `folds`,
-#' their prediction value would be `NA`.
-#'
+#' @title Callback for returning cross-validation based predictions.
 #' @param save_models A flag for whether to save the folds' models.
 #' @param outputmargin Whether to save margin predictions (same effect as passing this
-#'   parameter to [predict.xgb.Booster]).
-#' @return An `xgb.Callback` object, which can be passed to [xgb.cv()],
-#'   but **not** to [xgb.train()].
+#' parameter to \link{predict.xgb.Booster}).
+#' @return An `xgb.Callback` object, which can be passed to \link{xgb.cv},
+#'         but \bold{not} to \link{xgb.train}.
+#' @description
+#' This callback function saves predictions for all of the test folds,
+#' and also allows to save the folds' models.
+#' @details
+#' Predictions are saved inside of the \code{pred} element, which is either a vector or a matrix,
+#' depending on the number of prediction outputs per data row. The order of predictions corresponds
+#' to the order of rows in the original dataset. Note that when a custom \code{folds} list is
+#' provided in \code{xgb.cv}, the predictions would only be returned properly when this list is a
+#' non-overlapping list of k sets of indices, as in a standard k-fold CV. The predictions would not be
+#' meaningful when user-provided folds have overlapping indices as in, e.g., random sampling splits.
+#' When some of the indices in the training dataset are not included into user-provided \code{folds},
+#' their prediction value would be \code{NA}.
 #' @export
 xgb.cb.cv.predict <- function(save_models = FALSE, outputmargin = FALSE) {
   xgb.Callback(
@@ -858,7 +853,8 @@ xgb.cb.cv.predict <- function(save_models = FALSE, outputmargin = FALSE) {
         pr <- predict(
           fd$bst,
           fd$evals[[2L]],
-          outputmargin = env$outputmargin
+          outputmargin = env$outputmargin,
+          reshape = TRUE
         )
         if (is.null(pred)) {
           if (NCOL(pr) > 1L) {
@@ -908,15 +904,19 @@ xgb.cb.cv.predict <- function(save_models = FALSE, outputmargin = FALSE) {
   return(coefs)
 }
 
-#' Callback for collecting coefficients history of a gblinear booster
-#'
+#' @title Callback for collecting coefficients history of a gblinear booster
+#' @param sparse when set to `FALSE`/`TRUE`, a dense/sparse matrix is used to store the result.
+#'       Sparse format is useful when one expects only a subset of coefficients to be non-zero,
+#'       when using the "thrifty" feature selector with fairly small number of top features
+#'       selected per iteration.
+#' @return An `xgb.Callback` object, which can be passed to \link{xgb.train} or \link{xgb.cv}.
 #' @details
 #' To keep things fast and simple, gblinear booster does not internally store the history of linear
 #' model coefficients at each boosting iteration. This callback provides a workaround for storing
 #' the coefficients' path, by extracting them after each training iteration.
 #'
 #' This callback will construct a matrix where rows are boosting iterations and columns are
-#' feature coefficients (same order as when calling [coef.xgb.Booster], with the intercept
+#' feature coefficients (same order as when calling \link{coef.xgb.Booster}, with the intercept
 #' corresponding to the first column).
 #'
 #' When there is more than one coefficient per feature (e.g. multi-class classification),
@@ -929,18 +929,13 @@ xgb.cb.cv.predict <- function(save_models = FALSE, outputmargin = FALSE) {
 #' one coefficient per feature) the names will be composed as 'column name' + ':' + 'class index'
 #' (so e.g. column 'c1' for class '0' will be named 'c1:0').
 #'
-#' With [xgb.train()], the output is either a dense or a sparse matrix.
-#' With with [xgb.cv()], it is a list (one element per each fold) of such matrices.
+#' With \code{xgb.train}, the output is either a dense or a sparse matrix.
+#' With with \code{xgb.cv}, it is a list (one element per each fold) of such
+#' matrices.
 #'
-#' Function [xgb.gblinear.history] provides an easy way to retrieve the
+#' Function \link{xgb.gblinear.history} function provides an easy way to retrieve the
 #' outputs from this callback.
-#'
-#' @param sparse When set to `FALSE`/`TRUE`, a dense/sparse matrix is used to store the result.
-#'   Sparse format is useful when one expects only a subset of coefficients to be non-zero,
-#'   when using the "thrifty" feature selector with fairly small number of top features
-#'   selected per iteration.
-#' @return An `xgb.Callback` object, which can be passed to [xgb.train()] or [xgb.cv()].
-#' @seealso [xgb.gblinear.history], [coef.xgb.Booster].
+#' @seealso \link{xgb.gblinear.history}, \link{coef.xgb.Booster}.
 #' @examples
 #' #### Binary classification:
 #'
@@ -950,109 +945,57 @@ xgb.cb.cv.predict <- function(save_models = FALSE, outputmargin = FALSE) {
 #'
 #' # In the iris dataset, it is hard to linearly separate Versicolor class from the rest
 #' # without considering the 2nd order interactions:
-#' x <- model.matrix(Species ~ .^2, iris)[, -1]
+#' x <- model.matrix(Species ~ .^2, iris)[,-1]
 #' colnames(x)
-#' dtrain <- xgb.DMatrix(
-#'   scale(x),
-#'   label = 1 * (iris$Species == "versicolor"),
-#'   nthread = nthread
-#' )
-#' param <- list(
-#'   booster = "gblinear",
-#'   objective = "reg:logistic",
-#'   eval_metric = "auc",
-#'   lambda = 0.0003,
-#'   alpha = 0.0003,
-#'   nthread = nthread
-#' )
-#'
+#' dtrain <- xgb.DMatrix(scale(x), label = 1*(iris$Species == "versicolor"), nthread = nthread)
+#' param <- list(booster = "gblinear", objective = "reg:logistic", eval_metric = "auc",
+#'               lambda = 0.0003, alpha = 0.0003, nthread = nthread)
 #' # For 'shotgun', which is a default linear updater, using high eta values may result in
 #' # unstable behaviour in some datasets. With this simple dataset, however, the high learning
 #' # rate does not break the convergence, but allows us to illustrate the typical pattern of
 #' # "stochastic explosion" behaviour of this lock-free algorithm at early boosting iterations.
-#' bst <- xgb.train(
-#'   param,
-#'   dtrain,
-#'   list(tr = dtrain),
-#'   nrounds = 200,
-#'   eta = 1.,
-#'   callbacks = list(xgb.cb.gblinear.history())
-#' )
-#'
+#' bst <- xgb.train(param, dtrain, list(tr=dtrain), nrounds = 200, eta = 1.,
+#'                  callbacks = list(xgb.cb.gblinear.history()))
 #' # Extract the coefficients' path and plot them vs boosting iteration number:
 #' coef_path <- xgb.gblinear.history(bst)
-#' matplot(coef_path, type = "l")
+#' matplot(coef_path, type = 'l')
 #'
 #' # With the deterministic coordinate descent updater, it is safer to use higher learning rates.
 #' # Will try the classical componentwise boosting which selects a single best feature per round:
-#' bst <- xgb.train(
-#'   param,
-#'   dtrain,
-#'   list(tr = dtrain),
-#'   nrounds = 200,
-#'   eta = 0.8,
-#'   updater = "coord_descent",
-#'   feature_selector = "thrifty",
-#'   top_k = 1,
-#'   callbacks = list(xgb.cb.gblinear.history())
-#' )
-#' matplot(xgb.gblinear.history(bst), type = "l")
+#' bst <- xgb.train(param, dtrain, list(tr=dtrain), nrounds = 200, eta = 0.8,
+#'                  updater = 'coord_descent', feature_selector = 'thrifty', top_k = 1,
+#'                  callbacks = list(xgb.cb.gblinear.history()))
+#' matplot(xgb.gblinear.history(bst), type = 'l')
 #' #  Componentwise boosting is known to have similar effect to Lasso regularization.
 #' # Try experimenting with various values of top_k, eta, nrounds,
 #' # as well as different feature_selectors.
 #'
 #' # For xgb.cv:
-#' bst <- xgb.cv(
-#'   param,
-#'   dtrain,
-#'   nfold = 5,
-#'   nrounds = 100,
-#'   eta = 0.8,
-#'   callbacks = list(xgb.cb.gblinear.history())
-#' )
+#' bst <- xgb.cv(param, dtrain, nfold = 5, nrounds = 100, eta = 0.8,
+#'               callbacks = list(xgb.cb.gblinear.history()))
 #' # coefficients in the CV fold #3
-#' matplot(xgb.gblinear.history(bst)[[3]], type = "l")
+#' matplot(xgb.gblinear.history(bst)[[3]], type = 'l')
 #'
 #'
 #' #### Multiclass classification:
+#' #
 #' dtrain <- xgb.DMatrix(scale(x), label = as.numeric(iris$Species) - 1, nthread = nthread)
-#'
-#' param <- list(
-#'   booster = "gblinear",
-#'   objective = "multi:softprob",
-#'   num_class = 3,
-#'   lambda = 0.0003,
-#'   alpha = 0.0003,
-#'   nthread = nthread
-#' )
-#'
+#' param <- list(booster = "gblinear", objective = "multi:softprob", num_class = 3,
+#'               lambda = 0.0003, alpha = 0.0003, nthread = nthread)
 #' # For the default linear updater 'shotgun' it sometimes is helpful
 #' # to use smaller eta to reduce instability
-#' bst <- xgb.train(
-#'   param,
-#'   dtrain,
-#'   list(tr = dtrain),
-#'   nrounds = 50,
-#'   eta = 0.5,
-#'   callbacks = list(xgb.cb.gblinear.history())
-#' )
-#'
+#' bst <- xgb.train(param, dtrain, list(tr=dtrain), nrounds = 50, eta = 0.5,
+#'                  callbacks = list(xgb.cb.gblinear.history()))
 #' # Will plot the coefficient paths separately for each class:
-#' matplot(xgb.gblinear.history(bst, class_index = 0), type = "l")
-#' matplot(xgb.gblinear.history(bst, class_index = 1), type = "l")
-#' matplot(xgb.gblinear.history(bst, class_index = 2), type = "l")
+#' matplot(xgb.gblinear.history(bst, class_index = 0), type = 'l')
+#' matplot(xgb.gblinear.history(bst, class_index = 1), type = 'l')
+#' matplot(xgb.gblinear.history(bst, class_index = 2), type = 'l')
 #'
 #' # CV:
-#' bst <- xgb.cv(
-#'   param,
-#'   dtrain,
-#'   nfold = 5,
-#'   nrounds = 70,
-#'   eta = 0.5,
-#'   callbacks = list(xgb.cb.gblinear.history(FALSE))
-#' )
+#' bst <- xgb.cv(param, dtrain, nfold = 5, nrounds = 70, eta = 0.5,
+#'               callbacks = list(xgb.cb.gblinear.history(FALSE)))
 #' # 1st fold of 1st class
-#' matplot(xgb.gblinear.history(bst, class_index = 0)[[1]], type = "l")
+#' matplot(xgb.gblinear.history(bst, class_index = 0)[[1]], type = 'l')
 #'
 #' @export
 xgb.cb.gblinear.history <- function(sparse = FALSE) {
@@ -1155,31 +1098,28 @@ xgb.cb.gblinear.history <- function(sparse = FALSE) {
   )
 }
 
-#' Extract gblinear coefficients history
-#'
-#' A helper function to extract the matrix of linear coefficients' history
-#' from a gblinear model created while using the [xgb.cb.gblinear.history]
-#' callback (which must be added manually as by default it is not used).
-#'
-#' @details
-#' Note that this is an R-specific function that relies on R attributes that
-#' are not saved when using XGBoost's own serialization functions like [xgb.load()]
-#' or [xgb.load.raw()].
+#' @title Extract gblinear coefficients history.
+#' @description A helper function to extract the matrix of linear coefficients' history
+#' from a gblinear model created while using the \link{xgb.cb.gblinear.history}
+#' callback (which must be added manually as by default it's not used).
+#' @details Note that this is an R-specific function that relies on R attributes that
+#' are not saved when using xgboost's own serialization functions like \link{xgb.load}
+#' or \link{xgb.load.raw}.
 #'
 #' In order for a serialized model to be accepted by this function, one must use R
-#' serializers such as [saveRDS()].
-#' @param model Either an `xgb.Booster` or a result of [xgb.cv()], trained
-#'   using the [xgb.cb.gblinear.history] callback, but **not** a booster
-#'   loaded from [xgb.load()] or [xgb.load.raw()].
+#' serializers such as \link{saveRDS}.
+#' @param model either an \code{xgb.Booster} or a result of \code{xgb.cv()}, trained
+#'        using the \link{xgb.cb.gblinear.history} callback, but \bold{not} a booster
+#'        loaded from \link{xgb.load} or \link{xgb.load.raw}.
 #' @param class_index zero-based class index to extract the coefficients for only that
-#'   specific class in a multinomial multiclass model. When it is `NULL`, all the
-#'   coefficients are returned. Has no effect in non-multiclass models.
+#'        specific class in a multinomial multiclass model. When it is NULL, all the
+#'        coefficients are returned. Has no effect in non-multiclass models.
 #'
 #' @return
-#' For an [xgb.train()] result, a matrix (either dense or sparse) with the columns
+#' For an \link{xgb.train} result, a matrix (either dense or sparse) with the columns
 #' corresponding to iteration's coefficients and the rows corresponding to boosting iterations.
 #'
-#' For an [xgb.cv()] result, a list of such matrices is returned with the elements
+#' For an \link{xgb.cv} result, a list of such matrices is returned with the elements
 #' corresponding to CV folds.
 #'
 #' When there is more than one coefficient per feature (e.g. multi-class classification)
@@ -1187,7 +1127,7 @@ xgb.cb.gblinear.history <- function(sparse = FALSE) {
 #' the result will be reshaped into a vector where coefficients are arranged first by features and
 #' then by class (e.g. first 1 through N coefficients will be for the first class, then
 #' coefficients N+1 through 2N for the second class, and so on).
-#' @seealso [xgb.cb.gblinear.history], [coef.xgb.Booster].
+#' @seealso \link{xgb.cb.gblinear.history}, \link{coef.xgb.Booster}.
 #' @export
 xgb.gblinear.history <- function(model, class_index = NULL) {
 

R-package/R/utils.R

@@ -27,41 +27,8 @@ NVL <- function(x, val) {
 }
 
 .RANKING_OBJECTIVES <- function() {
-  return(c('rank:pairwise', 'rank:ndcg', 'rank:map'))
-}
-
-.OBJECTIVES_NON_DEFAULT_MODE <- function() {
-  return(c("reg:logistic", "binary:logitraw", "multi:softmax"))
-}
-
-.BINARY_CLASSIF_OBJECTIVES <- function() {
-  return(c("binary:logistic", "binary:hinge"))
-}
-
-.MULTICLASS_CLASSIF_OBJECTIVES <- function() {
-  return("multi:softprob")
-}
-
-.SURVIVAL_RIGHT_CENSORING_OBJECTIVES <- function() { # nolint
-  return(c("survival:cox", "survival:aft"))
-}
-
-.SURVIVAL_ALL_CENSORING_OBJECTIVES <- function() { # nolint
-  return("survival:aft")
-}
-
-.REGRESSION_OBJECTIVES <- function() {
-  return(c(
-    "reg:squarederror", "reg:squaredlogerror", "reg:logistic", "reg:pseudohubererror",
-    "reg:absoluteerror", "reg:quantileerror", "count:poisson", "reg:gamma", "reg:tweedie"
-  ))
-}
-
-.MULTI_TARGET_OBJECTIVES <- function() {
-  return(c(
-    "reg:squarederror", "reg:squaredlogerror", "reg:logistic", "reg:pseudohubererror",
-    "reg:quantileerror", "reg:gamma"
-  ))
+  return(c('binary:logistic', 'binary:logitraw', 'binary:hinge', 'multi:softmax',
+           'multi:softprob'))
 }
 
 
@@ -104,7 +71,7 @@ check.booster.params <- function(params, ...) {
 
   # for multiclass, expect num_class to be set
   if (typeof(params[['objective']]) == "character" &&
-      startsWith(NVL(params[['objective']], 'x'), 'multi:') &&
+      substr(NVL(params[['objective']], 'x'), 1, 6) == 'multi:' &&
       as.numeric(NVL(params[['num_class']], 0)) < 2) {
         stop("'num_class' > 1 parameter must be set for multiclass classification")
   }
@@ -199,7 +166,8 @@ xgb.iter.update <- function(bst, dtrain, iter, obj) {
       bst,
       dtrain,
       outputmargin = TRUE,
-      training = TRUE
+      training = TRUE,
+      reshape = TRUE
     )
     gpair <- obj(pred, dtrain)
     n_samples <- dim(dtrain)[1]
@@ -410,7 +378,7 @@ xgb.createFolds <- function(y, k) {
 #' At this time, some of the parameter names were changed in order to make the code style more uniform.
 #' The deprecated parameters would be removed in the next release.
 #'
-#' To see all the current deprecated and new parameters, check the `xgboost:::depr_par_lut` table.
+#' To see all the current deprecated and new parameters, check the \code{xgboost:::depr_par_lut} table.
 #'
 #' A deprecation warning is shown when any of the deprecated parameters is used in a call.
 #' An additional warning is shown when there was a partial match to a deprecated parameter
@@ -419,90 +387,70 @@ xgb.createFolds <- function(y, k) {
 #' @name xgboost-deprecated
 NULL
 
-#' Model Serialization and Compatibility
-#'
+#' @title Model Serialization and Compatibility
 #' @description
+#'
 #' When it comes to serializing XGBoost models, it's possible to use R serializers such as
-#' [save()] or [saveRDS()] to serialize an XGBoost R model, but XGBoost also provides
+#' \link{save} or \link{saveRDS} to serialize an XGBoost R model, but XGBoost also provides
 #' its own serializers with better compatibility guarantees, which allow loading
 #' said models in other language bindings of XGBoost.
 #'
-#' Note that an `xgb.Booster` object (**as produced by [xgb.train()]**, see rest of the doc
-#' for objects produced by [xgboost()]), outside of its core components, might also keep:
-#' - Additional model configuration (accessible through [xgb.config()]), which includes
-#'   model fitting parameters like `max_depth` and runtime parameters like `nthread`.
-#'   These are not necessarily useful for prediction/importance/plotting.
-#' - Additional R specific attributes  - e.g. results of callbacks, such as evaluation logs,
-#'   which are kept as a `data.table` object, accessible through
-#'   `attributes(model)$evaluation_log` if present.
+#' Note that an `xgb.Booster` object, outside of its core components, might also keep:\itemize{
+#' \item Additional model configuration (accessible through \link{xgb.config}),
+#' which includes model fitting parameters like `max_depth` and runtime parameters like `nthread`.
+#' These are not necessarily useful for prediction/importance/plotting.
+#' \item Additional R-specific attributes  - e.g. results of callbacks, such as evaluation logs,
+#' which are kept as a `data.table` object, accessible through `attributes(model)$evaluation_log`
+#' if present.
+#' }
 #'
 #' The first one (configurations) does not have the same compatibility guarantees as
-#' the model itself, including attributes that are set and accessed through
-#' [xgb.attributes()] - that is, such configuration might be lost after loading the
-#' booster in a different XGBoost version, regardless of the serializer that was used.
-#' These are saved when using [saveRDS()], but will be discarded if loaded into an
-#' incompatible XGBoost version. They are not saved when using XGBoost's
-#' serializers from its public interface including [xgb.save()] and [xgb.save.raw()].
+#' the model itself, including attributes that are set and accessed through \link{xgb.attributes} - that is, such configuration
+#' might be lost after loading the booster in a different XGBoost version, regardless of the
+#' serializer that was used. These are saved when using \link{saveRDS}, but will be discarded
+#' if loaded into an incompatible XGBoost version. They are not saved when using XGBoost's
+#' serializers from its public interface including \link{xgb.save} and \link{xgb.save.raw}.
 #'
-#' The second ones (R attributes) are not part of the standard XGBoost model structure,
-#' and thus are not saved when using XGBoost's own serializers. These attributes are
-#' only used for informational purposes, such as keeping track of evaluation metrics as
-#' the model was fit, or saving the R call that produced the model, but are otherwise
-#' not used for prediction / importance / plotting / etc.
+#' The second ones (R attributes) are not part of the standard XGBoost model structure, and thus are
+#' not saved when using XGBoost's own serializers. These attributes are only used for informational
+#' purposes, such as keeping track of evaluation metrics as the model was fit, or saving the R
+#' call that produced the model, but are otherwise not used for prediction / importance / plotting / etc.
 #' These R attributes are only preserved when using R's serializers.
 #'
-#' In addition to the regular `xgb.Booster` objects producted by [xgb.train()], the
-#' function [xgboost()] produces a different subclass `xgboost`, which keeps other
-#' additional metadata as R attributes such as class names in classification problems,
-#' and which has a dedicated `predict` method that uses different defaults. XGBoost's
-#' own serializers can work with this `xgboost` class, but as they do not keep R
-#' attributes, the resulting object, when deserialized, is downcasted to the regular
-#' `xgb.Booster` class (i.e. it loses the metadata, and the resulting object will use
-#' `predict.xgb.Booster` instead of `predict.xgboost`) - for these `xgboost` objects,
-#' `saveRDS` might thus be a better option if the extra functionalities are needed.
-#'
-#' Note that XGBoost models in R starting from version `2.1.0` and onwards, and
-#' XGBoost models before version `2.1.0`; have a very different R object structure and
-#' are incompatible with each other. Hence, models that were saved with R serializers
-#' like [saveRDS()] or [save()] before version `2.1.0` will not work with latter
-#' `xgboost` versions and vice versa. Be aware that the structure of R model objects
-#' could in theory change again in the future, so XGBoost's serializers
+#' Note that XGBoost models in R starting from version `2.1.0` and onwards, and XGBoost models
+#' before version `2.1.0`; have a very different R object structure and are incompatible with
+#' each other. Hence, models that were saved with R serializers live `saveRDS` or `save` before
+#' version `2.1.0` will not work with latter `xgboost` versions and vice versa. Be aware that
+#' the structure of R model objects could in theory change again in the future, so XGBoost's serializers
 #' should be preferred for long-term storage.
 #'
-#' Furthermore, note that using the package `qs` for serialization will require
-#' version 0.26 or higher of said package, and will have the same compatibility
-#' restrictions as R serializers.
+#' Furthermore, note that using the package `qs` for serialization will require version 0.26 or
+#' higher of said package, and will have the same compatibility restrictions as R serializers.
 #'
 #' @details
-#' Use [xgb.save()] to save the XGBoost model as a stand-alone file. You may opt into
+#' Use \code{\link{xgb.save}} to save the XGBoost model as a stand-alone file. You may opt into
 #' the JSON format by specifying the JSON extension. To read the model back, use
-#' [xgb.load()].
+#' \code{\link{xgb.load}}.
 #'
-#' Use [xgb.save.raw()] to save the XGBoost model as a sequence (vector) of raw bytes
+#' Use \code{\link{xgb.save.raw}} to save the XGBoost model as a sequence (vector) of raw bytes
 #' in a future-proof manner. Future releases of XGBoost will be able to read the raw bytes and
-#' re-construct the corresponding model. To read the model back, use [xgb.load.raw()].
-#' The [xgb.save.raw()] function is useful if you would like to persist the XGBoost model
+#' re-construct the corresponding model. To read the model back, use \code{\link{xgb.load.raw}}.
+#' The \code{\link{xgb.save.raw}} function is useful if you'd like to persist the XGBoost model
 #' as part of another R object.
 #'
-#' Use [saveRDS()] if you require the R-specific attributes that a booster might have, such
-#' as evaluation logs or the model class `xgboost` instead of `xgb.Booster`, but note that
-#' future compatibility of such objects is outside XGBoost's control as it relies on R's
-#' serialization format (see e.g. the details section in [serialize] and [save()] from base R).
+#' Use \link{saveRDS} if you require the R-specific attributes that a booster might have, such
+#' as evaluation logs, but note that future compatibility of such objects is outside XGBoost's
+#' control as it relies on R's serialization format (see e.g. the details section in
+#' \link{serialize} and \link{save} from base R).
 #'
 #' For more details and explanation about model persistence and archival, consult the page
 #' \url{https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html}.
 #'
 #' @examples
-#' data(agaricus.train, package = "xgboost")
-#'
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
-#'   max_depth = 2,
-#'   eta = 1,
-#'   nthread = 2,
-#'   nrounds = 2,
-#'   objective = "binary:logistic"
-#' )
+#' data(agaricus.train, package='xgboost')
+#' bst <- xgb.train(data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
+#'                  max_depth = 2, eta = 1, nthread = 2, nrounds = 2,
+#'                  objective = "binary:logistic")
 #'
 #' # Save as a stand-alone file; load it with xgb.load()
 #' fname <- file.path(tempdir(), "xgb_model.ubj")

R-package/R/xgb.Booster.R

@@ -1,4 +1,4 @@
-# Construct an internal XGBoost Booster and get its current number of rounds.
+# Construct an internal xgboost Booster and get its current number of rounds.
 # internal utility function
 # Note: the number of rounds in the C booster gets reset to zero when changing
 # key booster parameters like 'process_type=update', but in some cases, when
@@ -64,7 +64,7 @@ xgb.get.handle <- function(object) {
   if (inherits(object, "xgb.Booster")) {
     handle <- object$ptr
     if (is.null(handle) || !inherits(handle, "externalptr")) {
-      stop("'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.")
+      stop("'xgb.Booster' object is corrupted or is from an incompatible xgboost version.")
     }
   } else {
     stop("argument must be an 'xgb.Booster' object.")
@@ -77,96 +77,84 @@ xgb.get.handle <- function(object) {
 
 #' Predict method for XGBoost model
 #'
-#' Predict values on data based on XGBoost model.
+#' Predict values on data based on xgboost model.
 #'
 #' @param object Object of class `xgb.Booster`.
 #' @param newdata Takes `data.frame`, `matrix`, `dgCMatrix`, `dgRMatrix`, `dsparseVector`,
-#'   local data file, or `xgb.DMatrix`.
+#'        local data file, or `xgb.DMatrix`.
 #'
-#'   For single-row predictions on sparse data, it is recommended to use CSR format. If passing
-#'   a sparse vector, it will take it as a row vector.
+#'        For single-row predictions on sparse data, it's recommended to use CSR format. If passing
+#'        a sparse vector, it will take it as a row vector.
 #'
-#'   Note that, for repeated predictions on the same data, one might want to create a DMatrix to
-#'   pass here instead of passing R types like matrices or data frames, as predictions will be
-#'   faster on DMatrix.
+#'        Note that, for repeated predictions on the same data, one might want to create a DMatrix to
+#'        pass here instead of passing R types like matrices or data frames, as predictions will be
+#'        faster on DMatrix.
 #'
-#'   If `newdata` is a `data.frame`, be aware that:
-#'   - Columns will be converted to numeric if they aren't already, which could potentially make
-#'     the operation slower than in an equivalent `matrix` object.
-#'   - The order of the columns must match with that of the data from which the model was fitted
-#'     (i.e. columns will not be referenced by their names, just by their order in the data).
-#'   - If the model was fitted to data with categorical columns, these columns must be of
-#'     `factor` type here, and must use the same encoding (i.e. have the same levels).
-#'   - If `newdata` contains any `factor` columns, they will be converted to base-0
-#'     encoding (same as during DMatrix creation) - hence, one should not pass a `factor`
-#'     under a column which during training had a different type.
-#' @param missing Float value that represents missing values in data
-#'   (e.g., 0 or some other extreme value).
+#'        If `newdata` is a `data.frame`, be aware that:\itemize{
+#'        \item Columns will be converted to numeric if they aren't already, which could potentially make
+#'              the operation slower than in an equivalent `matrix` object.
+#'        \item The order of the columns must match with that of the data from which the model was fitted
+#'              (i.e. columns will not be referenced by their names, just by their order in the data).
+#'        \item If the model was fitted to data with categorical columns, these columns must be of
+#'              `factor` type here, and must use the same encoding (i.e. have the same levels).
+#'        \item If `newdata` contains any `factor` columns, they will be converted to base-0
+#'              encoding (same as during DMatrix creation) - hence, one should not pass a `factor`
+#'              under a column which during training had a different type.
+#'        }
+#' @param missing Float value that represents missing values in data (e.g., 0 or some other extreme value).
 #'
-#'   This parameter is not used when `newdata` is an `xgb.DMatrix` - in such cases,
-#'   should pass this as an argument to the DMatrix constructor instead.
-#' @param outputmargin Whether the prediction should be returned in the form of
-#'   original untransformed sum of predictions from boosting iterations' results.
-#'   E.g., setting `outputmargin = TRUE` for logistic regression would return log-odds
-#'   instead of probabilities.
+#'        This parameter is not used when `newdata` is an `xgb.DMatrix` - in such cases, should pass
+#'        this as an argument to the DMatrix constructor instead.
+#' @param outputmargin Whether the prediction should be returned in the form of original untransformed
+#'        sum of predictions from boosting iterations' results. E.g., setting `outputmargin=TRUE` for
+#'        logistic regression would return log-odds instead of probabilities.
 #' @param predleaf Whether to predict per-tree leaf indices.
 #' @param predcontrib Whether to return feature contributions to individual predictions (see Details).
 #' @param approxcontrib Whether to use a fast approximation for feature contributions (see Details).
 #' @param predinteraction Whether to return contributions of feature interactions to individual predictions (see Details).
+#' @param reshape Whether to reshape the vector of predictions to matrix form when there are several
+#'        prediction outputs per case. No effect if `predleaf`, `predcontrib`,
+#'        or `predinteraction` is `TRUE`.
 #' @param training Whether the prediction result is used for training. For dart booster,
-#'   training predicting will perform dropout.
+#'        training predicting will perform dropout.
 #' @param iterationrange Sequence of rounds/iterations from the model to use for prediction, specified by passing
-#'   a two-dimensional vector with the start and end numbers in the sequence (same format as R's `seq` - i.e.
-#'   base-1 indexing, and inclusive of both ends).
+#'        a two-dimensional vector with the start and end numbers in the sequence (same format as R's `seq` - i.e.
+#'        base-1 indexing, and inclusive of both ends).
 #'
-#'   For example, passing `c(1,20)` will predict using the first twenty iterations, while passing `c(1,1)` will
-#'   predict using only the first one.
+#'        For example, passing `c(1,20)` will predict using the first twenty iterations, while passing `c(1,1)` will
+#'        predict using only the first one.
 #'
-#'   If passing `NULL`, will either stop at the best iteration if the model used early stopping, or use all
-#'   of the iterations (rounds) otherwise.
+#'        If passing `NULL`, will either stop at the best iteration if the model used early stopping, or use all
+#'        of the iterations (rounds) otherwise.
 #'
-#'   If passing "all", will use all of the rounds regardless of whether the model had early stopping or not.
-#' @param strict_shape Whether to always return an array with the same dimensions for the given prediction mode
-#'   regardless of the model type - meaning that, for example, both a multi-class and a binary classification
-#'   model would generate output arrays with the same number of dimensions, with the 'class' dimension having
-#'   size equal to '1' for the binary model.
-#'
-#'   If passing `FALSE` (the default), dimensions will be simplified according to the model type, so that a
-#'   binary classification model for example would not have a redundant dimension for 'class'.
-#'
-#'   See documentation for the return type for the exact shape of the output arrays for each prediction mode.
-#' @param avoid_transpose Whether to output the resulting predictions in the same memory layout in which they
-#'   are generated by the core XGBoost library, without transposing them to match the expected output shape.
-#'
-#'   Internally, XGBoost uses row-major order for the predictions it generates, while R arrays use column-major
-#'   order, hence the result needs to be transposed in order to have the expected shape when represented as
-#'   an R array or matrix, which might be a slow operation.
-#'
-#'   If passing `TRUE`, then the result will have dimensions in reverse order - for example, rows
-#'   will be the last dimensions instead of the first dimension.
+#'        If passing "all", will use all of the rounds regardless of whether the model had early stopping or not.
+#' @param strict_shape Default is `FALSE`. When set to `TRUE`, the output
+#'        type and shape of predictions are invariant to the model type.
 #' @param base_margin Base margin used for boosting from existing model.
 #'
-#'   Note that, if `newdata` is an `xgb.DMatrix` object, this argument will
-#'   be ignored as it needs to be added to the DMatrix instead (e.g. by passing it as
-#'   an argument in its constructor, or by calling [setinfo.xgb.DMatrix()].
-#' @param validate_features When `TRUE`, validate that the Booster's and newdata's
-#'   feature_names match (only applicable when both `object` and `newdata` have feature names).
+#'        Note that, if `newdata` is an `xgb.DMatrix` object, this argument will
+#'        be ignored as it needs to be added to the DMatrix instead (e.g. by passing it as
+#'        an argument in its constructor, or by calling \link{setinfo.xgb.DMatrix}).
 #'
-#'   If the column names differ and `newdata` is not an `xgb.DMatrix`, will try to reorder
-#'   the columns in `newdata` to match with the booster's.
+#' @param validate_features When `TRUE`, validate that the Booster's and newdata's feature_names
+#'        match (only applicable when both `object` and `newdata` have feature names).
 #'
-#'   If the booster has feature types and `newdata` is either an `xgb.DMatrix` or
-#'   `data.frame`, will additionally verify that categorical columns are of the
-#'   correct type in `newdata`, throwing an error if they do not match.
+#'        If the column names differ and `newdata` is not an `xgb.DMatrix`, will try to reorder
+#'        the columns in `newdata` to match with the booster's.
 #'
-#'   If passing `FALSE`, it is assumed that the feature names and types are the same,
-#'   and come in the same order as in the training data.
+#'        If the booster has feature types and `newdata` is either an `xgb.DMatrix` or `data.frame`,
+#'        will additionally verify that categorical columns are of the correct type in `newdata`,
+#'        throwing an error if they do not match.
 #'
-#'   Note that this check might add some sizable latency to the predictions, so it's
-#'   recommended to disable it for performance-sensitive applications.
+#'        If passing `FALSE`, it is assumed that the feature names and types are the same,
+#'        and come in the same order as in the training data.
+#'
+#'        Note that this check might add some sizable latency to the predictions, so it's
+#'        recommended to disable it for performance-sensitive applications.
 #' @param ... Not used.
 #'
 #' @details
+#'
 #' Note that `iterationrange` would currently do nothing for predictions from "gblinear",
 #' since "gblinear" doesn't keep its boosting history.
 #'
@@ -192,45 +180,28 @@ xgb.get.handle <- function(object) {
 #' Note that converting a matrix to [xgb.DMatrix()] uses multiple threads too.
 #'
 #' @return
-#' A numeric vector or array, with corresponding dimensions depending on the prediction mode and on
-#' parameter `strict_shape` as follows:
+#' The return type depends on `strict_shape`. If `FALSE` (default):
+#' - For regression or binary classification: A vector of length `nrows(newdata)`.
+#' - For multiclass classification: A vector of length `num_class * nrows(newdata)` or
+#'   a `(nrows(newdata), num_class)` matrix, depending on the `reshape` value.
+#' - When `predleaf = TRUE`: A matrix with one column per tree.
+#' - When `predcontrib = TRUE`: When not multiclass, a matrix with
+#' ` num_features + 1` columns. The last "+ 1" column corresponds to the baseline value.
+#'   In the multiclass case, a list of `num_class` such matrices.
+#'   The contribution values are on the scale of untransformed margin
+#'   (e.g., for binary classification, the values are log-odds deviations from the baseline).
+#' - When `predinteraction = TRUE`: When not multiclass, the output is a 3d array of
+#'   dimension `c(nrow, num_features + 1, num_features + 1)`. The off-diagonal (in the last two dimensions)
+#'   elements represent different feature interaction contributions. The array is symmetric WRT the last
+#'   two dimensions. The "+ 1" columns corresponds to the baselines. Summing this array along the last dimension should
+#'   produce practically the same result as `predcontrib = TRUE`.
+#'   In the multiclass case, a list of `num_class` such arrays.
 #'
-#' If passing `strict_shape=FALSE`:\itemize{
-#' \item For regression or binary classification: a vector of length `nrows`.
-#' \item For multi-class and multi-target objectives: a matrix of dimensions `[nrows, ngroups]`.
-#'
-#' Note that objective variant `multi:softmax` defaults towards predicting most likely class (a vector
-#' `nrows`) instead of per-class probabilities.
-#' \item For `predleaf`: a matrix with one column per tree.
-#'
-#' For multi-class / multi-target, they will be arranged so that columns in the output will have
-#' the leafs from one group followed by leafs of the other group (e.g. order will be `group1:feat1`,
-#' `group1:feat2`, ..., `group2:feat1`, `group2:feat2`, ...).
-#' \item For `predcontrib`: when not multi-class / multi-target, a matrix with dimensions
-#' `[nrows, nfeats+1]`. The last "+ 1" column corresponds to the baseline value.
-#'
-#' For multi-class and multi-target objectives, will be an array with dimensions `[nrows, ngroups, nfeats+1]`.
-#'
-#' The contribution values are on the scale of untransformed margin (e.g., for binary classification,
-#' the values are log-odds deviations from the baseline).
-#' \item For `predinteraction`: when not multi-class / multi-target, the output is a 3D array of
-#' dimensions `[nrows, nfeats+1, nfeats+1]`. The off-diagonal (in the last two dimensions)
-#' elements represent different feature interaction contributions. The array is symmetric w.r.t. the last
-#' two dimensions. The "+ 1" columns corresponds to the baselines. Summing this array along the last
-#' dimension should produce practically the same result as `predcontrib = TRUE`.
-#'
-#' For multi-class and multi-target, will be a 4D array with dimensions `[nrows, ngroups, nfeats+1, nfeats+1]`
-#' }
-#'
-#' If passing `strict_shape=FALSE`, the result is always an array:
-#' - For normal predictions, the dimension is `[nrows, ngroups]`.
-#' - For `predcontrib=TRUE`, the dimension is `[nrows, ngroups, nfeats+1]`.
-#' - For `predinteraction=TRUE`, the dimension is `[nrows, ngroups, nfeats+1, nfeats+1]`.
-#' - For `predleaf=TRUE`, the dimension is `[nrows, niter, ngroups, num_parallel_tree]`.
-#'
-#' If passing `avoid_transpose=TRUE`, then the dimensions in all cases will be in reverse order - for
-#' example, for `predinteraction`, they will be `[nfeats+1, nfeats+1, ngroups, nrows]`
-#' instead of `[nrows, ngroups, nfeats+1, nfeats+1]`.
+#' When `strict_shape = TRUE`, the output is always an array:
+#' - For normal predictions, the output has dimension `(num_class, nrow(newdata))`.
+#' - For `predcontrib = TRUE`, the dimension is `(ncol(newdata) + 1, num_class, nrow(newdata))`.
+#' - For `predinteraction = TRUE`, the dimension is `(ncol(newdata) + 1, ncol(newdata) + 1, num_class, nrow(newdata))`.
+#' - For `predleaf = TRUE`, the dimension is `(n_trees_in_forest, num_class, n_iterations, nrow(newdata))`.
 #' @seealso [xgb.train()]
 #' @references
 #' 1. Scott M. Lundberg, Su-In Lee, "A Unified Approach to Interpreting Model Predictions",
@@ -278,7 +249,7 @@ xgb.get.handle <- function(object) {
 #' summary(rowSums(pred_contr) - qlogis(pred))
 #' # for the 1st record, let's inspect its features that had non-zero contribution to prediction:
 #' contr1 <- pred_contr[1,]
-#' contr1 <- contr1[-length(contr1)]    # drop intercept
+#' contr1 <- contr1[-length(contr1)]    # drop BIAS
 #' contr1 <- contr1[contr1 != 0]        # drop non-contributing features
 #' contr1 <- contr1[order(abs(contr1))] # order by contribution magnitude
 #' old_mar <- par("mar")
@@ -308,6 +279,8 @@ xgb.get.handle <- function(object) {
 #' # predict for softmax returns num_class probability numbers per case:
 #' pred <- predict(bst, as.matrix(iris[, -5]))
 #' str(pred)
+#' # reshape it to a num_class-columns matrix
+#' pred <- matrix(pred, ncol = num_class, byrow = TRUE)
 #' # convert the probabilities to softmax labels
 #' pred_labels <- max.col(pred) - 1
 #' # the following should result in the same error as seen in the last iteration
@@ -338,11 +311,8 @@ xgb.get.handle <- function(object) {
 #' @export
 predict.xgb.Booster <- function(object, newdata, missing = NA, outputmargin = FALSE,
                                 predleaf = FALSE, predcontrib = FALSE, approxcontrib = FALSE, predinteraction = FALSE,
-                                training = FALSE, iterationrange = NULL, strict_shape = FALSE, avoid_transpose = FALSE,
+                                reshape = FALSE, training = FALSE, iterationrange = NULL, strict_shape = FALSE,
                                 validate_features = FALSE, base_margin = NULL, ...) {
-  if (NROW(list(...))) {
-    warning("Passed unused prediction arguments: ", paste(names(list(...)), collapse = ", "), ".")
-  }
   if (validate_features) {
     newdata <- validate.features(object, newdata)
   }
@@ -353,11 +323,6 @@ predict.xgb.Booster <- function(object, newdata, missing = NA, outputmargin = FA
       " Should be passed as argument to 'xgb.DMatrix' constructor."
     )
   }
-  if (is_dmatrix) {
-    rnames <- NULL
-  } else {
-    rnames <- row.names(newdata)
-  }
 
   use_as_df <- FALSE
   use_as_dense_matrix <- FALSE
@@ -450,9 +415,10 @@ predict.xgb.Booster <- function(object, newdata, missing = NA, outputmargin = FA
     return(val)
   }
 
+  ## We set strict_shape to TRUE then drop the dimensions conditionally
   args <- list(
     training = box(training),
-    strict_shape = as.logical(strict_shape),
+    strict_shape = box(TRUE),
     iteration_begin = box(as.integer(iterationrange[1])),
     iteration_end = box(as.integer(iterationrange[2])),
     type = box(as.integer(0))
@@ -479,49 +445,96 @@ predict.xgb.Booster <- function(object, newdata, missing = NA, outputmargin = FA
 
   json_conf <- jsonlite::toJSON(args, auto_unbox = TRUE)
   if (is_dmatrix) {
-    arr <- .Call(
+    predts <- .Call(
       XGBoosterPredictFromDMatrix_R, xgb.get.handle(object), newdata, json_conf
     )
   } else if (use_as_dense_matrix) {
-    arr <- .Call(
+    predts <- .Call(
       XGBoosterPredictFromDense_R, xgb.get.handle(object), newdata, missing, json_conf, base_margin
     )
   } else if (use_as_csr_matrix) {
-    arr <- .Call(
+    predts <- .Call(
       XGBoosterPredictFromCSR_R, xgb.get.handle(object), csr_data, missing, json_conf, base_margin
     )
   } else if (use_as_df) {
-    arr <- .Call(
+    predts <- .Call(
       XGBoosterPredictFromColumnar_R, xgb.get.handle(object), newdata, missing, json_conf, base_margin
     )
   }
 
-  ## Needed regardless of whether strict shape is being used.
-  if ((predcontrib || predinteraction) && !is.null(colnames(newdata))) {
-    cnames <- c(colnames(newdata), "(Intercept)")
-    dim_names <- vector(mode = "list", length = length(dim(arr)))
-    dim_names[[1L]] <- cnames
-    if (predinteraction) dim_names[[2L]] <- cnames
-    .Call(XGSetArrayDimNamesInplace_R, arr, dim_names)
+  names(predts) <- c("shape", "results")
+  shape <- predts$shape
+  arr <- predts$results
+
+  n_ret <- length(arr)
+  if (n_row != shape[1]) {
+    stop("Incorrect predict shape.")
   }
 
-  if (NROW(rnames)) {
-    if (is.null(dim(arr))) {
-      .Call(XGSetVectorNamesInplace_R, arr, rnames)
+  .Call(XGSetArrayDimInplace_R, arr, rev(shape))
+
+  cnames <- if (!is.null(colnames(newdata))) c(colnames(newdata), "BIAS") else NULL
+  n_groups <- shape[2]
+
+  ## Needed regardless of whether strict shape is being used.
+  if (predcontrib) {
+    .Call(XGSetArrayDimNamesInplace_R, arr, list(cnames, NULL, NULL))
+  } else if (predinteraction) {
+    .Call(XGSetArrayDimNamesInplace_R, arr, list(cnames, cnames, NULL, NULL))
+  }
+  if (strict_shape) {
+    return(arr) # strict shape is calculated by libxgboost uniformly.
+  }
+
+  if (predleaf) {
+    ## Predict leaf
+    if (n_ret == n_row) {
+      .Call(XGSetArrayDimInplace_R, arr, c(n_row, 1L))
     } else {
-      dim_names <- dimnames(arr)
-      if (is.null(dim_names)) {
-        dim_names <- vector(mode = "list", length = length(dim(arr)))
-      }
-      dim_names[[length(dim_names)]] <- rnames
-      .Call(XGSetArrayDimNamesInplace_R, arr, dim_names)
+      arr <- matrix(arr, nrow = n_row, byrow = TRUE)
+    }
+  } else if (predcontrib) {
+    ## Predict contribution
+    arr <- aperm(a = arr, perm = c(2, 3, 1)) # [group, row, col]
+    if (n_ret == n_row) {
+      .Call(XGSetArrayDimInplace_R, arr, c(n_row, 1L))
+      .Call(XGSetArrayDimNamesInplace_R, arr, list(NULL, cnames))
+    } else if (n_groups != 1) {
+      ## turns array into list of matrices
+      arr <- lapply(seq_len(n_groups), function(g) arr[g, , ])
+    } else {
+      ## remove the first axis (group)
+      newdim <- dim(arr)[2:3]
+      newdn <- dimnames(arr)[2:3]
+      arr <- arr[1, , ]
+      .Call(XGSetArrayDimInplace_R, arr, newdim)
+      .Call(XGSetArrayDimNamesInplace_R, arr, newdn)
+    }
+  } else if (predinteraction) {
+    ## Predict interaction
+    arr <- aperm(a = arr, perm = c(3, 4, 1, 2)) # [group, row, col, col]
+    if (n_ret == n_row) {
+      .Call(XGSetArrayDimInplace_R, arr, c(n_row, 1L))
+      .Call(XGSetArrayDimNamesInplace_R, arr, list(NULL, cnames))
+    } else if (n_groups != 1) {
+      ## turns array into list of matrices
+      arr <- lapply(seq_len(n_groups), function(g) arr[g, , , ])
+    } else {
+      ## remove the first axis (group)
+      arr <- arr[1, , , , drop = FALSE]
+      newdim <- dim(arr)[2:4]
+      newdn <- dimnames(arr)[2:4]
+      .Call(XGSetArrayDimInplace_R, arr, newdim)
+      .Call(XGSetArrayDimNamesInplace_R, arr, newdn)
+    }
+  } else {
+    ## Normal prediction
+    if (reshape && n_groups != 1) {
+      arr <- matrix(arr, ncol = n_groups, byrow = TRUE)
+    } else {
+      .Call(XGSetArrayDimInplace_R, arr, NULL)
     }
   }
-
-  if (!avoid_transpose && is.array(arr)) {
-    arr <- aperm(arr)
-  }
-
   return(arr)
 }
 
@@ -605,20 +618,29 @@ validate.features <- function(bst, newdata) {
 }
 
 
-#' Accessors for serializable attributes of a model
+#' @title Accessors for serializable attributes of a model
 #'
-#' These methods allow to manipulate the key-value attribute strings of an XGBoost model.
+#' @description These methods allow to manipulate the key-value attribute strings of an xgboost model.
+#'
+#' @param object Object of class `xgb.Booster`. \bold{Will be modified in-place} when assigning to it.
+#' @param name A non-empty character string specifying which attribute is to be accessed.
+#' @param value For `xgb.attr<-`, a value of an attribute; for `xgb.attributes<-`,
+#'        it is a list (or an object coercible to a list) with the names of attributes to set
+#'        and the elements corresponding to attribute values.
+#'        Non-character values are converted to character.
+#'        When an attribute value is not a scalar, only the first index is used.
+#'        Use `NULL` to remove an attribute.
 #'
 #' @details
-#' The primary purpose of XGBoost model attributes is to store some meta data about the model.
+#' The primary purpose of xgboost model attributes is to store some meta data about the model.
 #' Note that they are a separate concept from the object attributes in R.
-#' Specifically, they refer to key-value strings that can be attached to an XGBoost model,
+#' Specifically, they refer to key-value strings that can be attached to an xgboost model,
 #' stored together with the model's binary representation, and accessed later
 #' (from R or any other interface).
 #' In contrast, any R attribute assigned to an R object of `xgb.Booster` class
-#' would not be saved by [xgb.save()] because an XGBoost model is an external memory object
+#' would not be saved by [xgb.save()] because an xgboost model is an external memory object
 #' and its serialization is handled externally.
-#' Also, setting an attribute that has the same name as one of XGBoost's parameters wouldn't
+#' Also, setting an attribute that has the same name as one of xgboost's parameters wouldn't
 #' change the value of that parameter for a model.
 #' Use [xgb.parameters<-()] to set or change model parameters.
 #'
@@ -628,17 +650,9 @@ validate.features <- function(bst, newdata) {
 #' Important: since this modifies the booster's C object, semantics for assignment here
 #' will differ from R's, as any object reference to the same booster will be modified
 #' too, while assignment of R attributes through `attributes(model)$<attr> <- <value>`
-#' will follow the usual copy-on-write R semantics (see [xgb.copy.Booster()] for an
+#' will follow the usual copy-on-write R semantics (see \link{xgb.copy.Booster} for an
 #' example of these behaviors).
 #'
-#' @param object Object of class `xgb.Booster`. **Will be modified in-place** when assigning to it.
-#' @param name A non-empty character string specifying which attribute is to be accessed.
-#' @param value For `xgb.attr<-`, a value of an attribute; for `xgb.attributes<-`,
-#'   it is a list (or an object coercible to a list) with the names of attributes to set
-#'   and the elements corresponding to attribute values.
-#'   Non-character values are converted to character.
-#'   When an attribute value is not a scalar, only the first index is used.
-#'   Use `NULL` to remove an attribute.
 #' @return
 #' - `xgb.attr()` returns either a string value of an attribute
 #'   or `NULL` if an attribute wasn't stored in a model.
@@ -649,8 +663,9 @@ validate.features <- function(bst, newdata) {
 #' data(agaricus.train, package = "xgboost")
 #' train <- agaricus.train
 #'
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(train$data, label = train$label),
+#' bst <- xgboost(
+#'   data = train$data,
+#'   label = train$label,
 #'   max_depth = 2,
 #'   eta = 1,
 #'   nthread = 2,
@@ -735,18 +750,15 @@ xgb.attributes <- function(object) {
   return(object)
 }
 
-#' Accessors for model parameters as JSON string
-#'
-#' @details
-#' Note that assignment is performed in-place on the booster C object, which unlike assignment
+#' @title Accessors for model parameters as JSON string
+#' @details Note that assignment is performed in-place on the booster C object, which unlike assignment
 #' of R attributes, doesn't follow typical copy-on-write semantics for assignment - i.e. all references
 #' to the same booster will also get updated.
 #'
-#' See [xgb.copy.Booster()] for an example of this behavior.
-#'
-#' @param object Object of class `xgb.Booster`.**Will be modified in-place** when assigning to it.
-#' @param value A list.
-#' @return Parameters as a list.
+#' See \link{xgb.copy.Booster} for an example of this behavior.
+#' @param object Object of class `xgb.Booster`. \bold{Will be modified in-place} when assigning to it.
+#' @param value An R list.
+#' @return `xgb.config` will return the parameters as an R list.
 #' @examples
 #' data(agaricus.train, package = "xgboost")
 #'
@@ -755,8 +767,9 @@ xgb.attributes <- function(object) {
 #' data.table::setDTthreads(nthread)
 #' train <- agaricus.train
 #'
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(train$data, label = train$label),
+#' bst <- xgboost(
+#'   data = train$data,
+#'   label = train$label,
 #'   max_depth = 2,
 #'   eta = 1,
 #'   nthread = nthread,
@@ -785,31 +798,28 @@ xgb.config <- function(object) {
   return(object)
 }
 
-#' Accessors for model parameters
-#'
-#' Only the setter for XGBoost parameters is currently implemented.
-#'
-#' @details
-#' Just like [xgb.attr()], this function will make in-place modifications
+#' @title Accessors for model parameters
+#' @description Only the setter for xgboost parameters is currently implemented.
+#' @details Just like \link{xgb.attr}, this function will make in-place modifications
 #' on the booster object which do not follow typical R assignment semantics - that is,
 #' all references to the same booster will also be updated, unlike assingment of R
 #' attributes which follow copy-on-write semantics.
 #'
-#' See [xgb.copy.Booster()] for an example of this behavior.
+#' See \link{xgb.copy.Booster} for an example of this behavior.
 #'
 #' Be aware that setting parameters of a fitted booster related to training continuation / updates
 #' will reset its number of rounds indicator to zero.
-#' @param object Object of class `xgb.Booster`. **Will be modified in-place**.
+#' @param object Object of class `xgb.Booster`. \bold{Will be modified in-place}.
 #' @param value A list (or an object coercible to a list) with the names of parameters to set
 #'        and the elements corresponding to parameter values.
 #' @return The same booster `object`, which gets modified in-place.
 #' @examples
 #' data(agaricus.train, package = "xgboost")
-#'
 #' train <- agaricus.train
 #'
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(train$data, label = train$label),
+#' bst <- xgboost(
+#'   data = train$data,
+#'   label = train$label,
 #'   max_depth = 2,
 #'   eta = 1,
 #'   nthread = 2,
@@ -881,12 +891,11 @@ setinfo.xgb.Booster <- function(object, name, info) {
   return(TRUE)
 }
 
-#' Get number of boosting in a fitted booster
-#'
+#' @title Get number of boosting in a fitted booster
 #' @param model,x A fitted `xgb.Booster` model.
-#' @return The number of rounds saved in the model as an integer.
+#' @return The number of rounds saved in the model, as an integer.
 #' @details Note that setting booster parameters related to training
-#' continuation / updates through [xgb.parameters<-()] will reset the
+#' continuation / updates through \link{xgb.parameters<-} will reset the
 #' number of rounds to zero.
 #' @export
 #' @rdname xgb.get.num.boosted.rounds
@@ -900,19 +909,16 @@ length.xgb.Booster <- function(x) {
   return(xgb.get.num.boosted.rounds(x))
 }
 
-#' Slice Booster by Rounds
-#'
-#' Creates a new booster including only a selected range of rounds / iterations
+#' @title Slice Booster by Rounds
+#' @description Creates a new booster including only a selected range of rounds / iterations
 #' from an existing booster, as given by the sequence `seq(start, end, step)`.
-#'
-#' @details
-#' Note that any R attributes that the booster might have, will not be copied into
+#' @details Note that any R attributes that the booster might have, will not be copied into
 #' the resulting object.
-#'
 #' @param model,x A fitted `xgb.Booster` object, which is to be sliced by taking only a subset
 #' of its rounds / iterations.
-#' @param start Start of the slice (base-1 and inclusive, like R's [seq()]).
-#' @param end End of the slice (base-1 and inclusive, like R's [seq()]).
+#' @param start Start of the slice (base-1 and inclusive, like R's \link{seq}).
+#' @param end End of the slice (base-1 and inclusive, like R's \link{seq}).
+#'
 #' Passing a value of zero here is equivalent to passing the full number of rounds in the
 #' booster object.
 #' @param step Step size of the slice. Passing '1' will take every round in the sequence defined by
@@ -920,10 +926,8 @@ length.xgb.Booster <- function(x) {
 #' @return A sliced booster object containing only the requested rounds.
 #' @examples
 #' data(mtcars)
-#'
 #' y <- mtcars$mpg
 #' x <- as.matrix(mtcars[, -1])
-#'
 #' dm <- xgb.DMatrix(x, label = y, nthread = 1)
 #' model <- xgb.train(data = dm, params = list(nthread = 1), nrounds = 5)
 #' model_slice <- xgb.slice.Booster(model, 1, 3)
@@ -976,12 +980,10 @@ xgb.slice.Booster <- function(model, start, end = xgb.get.num.boosted.rounds(mod
   return(xgb.slice.Booster(x, i[1L], i[length(i)], steps[1L]))
 }
 
-#' Get Features Names from Booster
-#'
-#' @description
-#' Returns the feature / variable / column names from a fitted
-#' booster object, which are set automatically during the call to [xgb.train()]
-#' from the DMatrix names, or which can be set manually through [setinfo()].
+#' @title Get Features Names from Booster
+#' @description Returns the feature / variable / column names from a fitted
+#' booster object, which are set automatically during the call to \link{xgb.train}
+#' from the DMatrix names, or which can be set manually through \link{setinfo}.
 #'
 #' If the object doesn't have feature names, will return `NULL`.
 #'
@@ -1032,25 +1034,23 @@ xgb.best_iteration <- function(bst) {
   return(out)
 }
 
-#' Extract coefficients from linear booster
-#'
-#' @description
-#' Extracts the coefficients from a 'gblinear' booster object,
-#' as produced by [xgb.train()] when using parameter `booster="gblinear"`.
+#' @title Extract coefficients from linear booster
+#' @description Extracts the coefficients from a 'gblinear' booster object,
+#' as produced by \code{xgb.train} when using parameter `booster="gblinear"`.
 #'
 #' Note: this function will error out if passing a booster model
 #' which is not of "gblinear" type.
-#'
 #' @param object A fitted booster of 'gblinear' type.
 #' @param ... Not used.
-#' @return The extracted coefficients:
-#'   - If there is only one coefficient per column in the data, will be returned as a
-#'     vector, potentially containing the feature names if available, with the intercept
-#'     as first column.
-#'   - If there is more than one coefficient per column in the data (e.g. when using
-#'     `objective="multi:softmax"`), will be returned as a matrix with dimensions equal
-#'     to `[num_features, num_cols]`, with the intercepts as first row. Note that the column
-#'     (classes in multi-class classification) dimension will not be named.
+#' @return The extracted coefficients:\itemize{
+#' \item If there's only one coefficient per column in the data, will be returned as a
+#' vector, potentially containing the feature names if available, with the intercept
+#' as first column.
+#' \item If there's more than one coefficient per column in the data (e.g. when using
+#' `objective="multi:softmax"`), will be returned as a matrix with dimensions equal
+#' to `[num_features, num_cols]`, with the intercepts as first row. Note that the column
+#' (classes in multi-class classification) dimension will not be named.
+#' }
 #'
 #' The intercept returned here will include the 'base_score' parameter (unlike the 'bias'
 #' or the last coefficient in the model dump, which doesn't have 'base_score' added to it),
@@ -1059,15 +1059,12 @@ xgb.best_iteration <- function(bst) {
 #'
 #' Be aware that the coefficients are obtained by first converting them to strings and
 #' back, so there will always be some very small lose of precision compared to the actual
-#' coefficients as used by [predict.xgb.Booster].
+#' coefficients as used by \link{predict.xgb.Booster}.
 #' @examples
 #' library(xgboost)
-#'
 #' data(mtcars)
-#'
 #' y <- mtcars[, 1]
 #' x <- as.matrix(mtcars[, -1])
-#'
 #' dm <- xgb.DMatrix(data = x, label = y, nthread = 1)
 #' params <- list(booster = "gblinear", nthread = 1)
 #' model <- xgb.train(data = dm, params = params, nrounds = 2)
@@ -1108,48 +1105,34 @@ coef.xgb.Booster <- function(object, ...) {
   if (n_cols == 1L) {
     out <- c(intercepts, coefs)
     if (add_names) {
-      .Call(XGSetVectorNamesInplace_R, out, feature_names)
+      names(out) <- feature_names
     }
   } else {
     coefs <- matrix(coefs, nrow = num_feature, byrow = TRUE)
     dim(intercepts) <- c(1L, n_cols)
     out <- rbind(intercepts, coefs)
-    out_names <- vector(mode = "list", length = 2)
     if (add_names) {
-      out_names[[1L]] <- feature_names
+      row.names(out) <- feature_names
     }
-    if (inherits(object, "xgboost")) {
-      metadata <- attributes(object)$metadata
-      if (NROW(metadata$y_levels)) {
-        out_names[[2L]] <- metadata$y_levels
-      } else if (NROW(metadata$y_names)) {
-        out_names[[2L]] <- metadata$y_names
-      }
-    }
-    .Call(XGSetArrayDimNamesInplace_R, out, out_names)
+    # TODO: if a class names attributes is added,
+    # should use those names here.
   }
   return(out)
 }
 
-#' Deep-copies a Booster Object
-#'
-#' Creates a deep copy of an 'xgb.Booster' object, such that the
+#' @title Deep-copies a Booster Object
+#' @description Creates a deep copy of an 'xgb.Booster' object, such that the
 #' C object pointer contained will be a different object, and hence functions
-#' like [xgb.attr()] will not affect the object from which it was copied.
-#'
+#' like \link{xgb.attr} will not affect the object from which it was copied.
 #' @param model An 'xgb.Booster' object.
 #' @return A deep copy of `model` - it will be identical in every way, but C-level
-#'   functions called on that copy will not affect the `model` variable.
+#' functions called on that copy will not affect the `model` variable.
 #' @examples
 #' library(xgboost)
-#'
 #' data(mtcars)
-#'
 #' y <- mtcars$mpg
 #' x <- mtcars[, -1]
-#'
 #' dm <- xgb.DMatrix(x, label = y, nthread = 1)
-#'
 #' model <- xgb.train(
 #'   data = dm,
 #'   params = list(nthread = 1),
@@ -1184,35 +1167,29 @@ xgb.copy.Booster <- function(model) {
   return(.Call(XGDuplicate_R, model))
 }
 
-#' Check if two boosters share the same C object
-#'
-#' Checks whether two booster objects refer to the same underlying C object.
-#'
-#' @details
-#' As booster objects (as returned by e.g. [xgb.train()]) contain an R 'externalptr'
+#' @title Check if two boosters share the same C object
+#' @description Checks whether two booster objects refer to the same underlying C object.
+#' @details As booster objects (as returned by e.g. \link{xgb.train}) contain an R 'externalptr'
 #' object, they don't follow typical copy-on-write semantics of other R objects - that is, if
 #' one assigns a booster to a different variable and modifies that new variable through in-place
-#' methods like [xgb.attr<-()], the modification will be applied to both the old and the new
+#' methods like \link{xgb.attr<-}, the modification will be applied to both the old and the new
 #' variable, unlike typical R assignments which would only modify the latter.
 #'
 #' This function allows checking whether two booster objects share the same 'externalptr',
 #' regardless of the R attributes that they might have.
 #'
 #' In order to duplicate a booster in such a way that the copy wouldn't share the same
-#' 'externalptr', one can use function [xgb.copy.Booster()].
+#' 'externalptr', one can use function \link{xgb.copy.Booster}.
 #' @param obj1 Booster model to compare with `obj2`.
 #' @param obj2 Booster model to compare with `obj1`.
-#' @return Either `TRUE` or `FALSE` according to whether the two boosters share the
-#'   underlying C object.
-#' @seealso [xgb.copy.Booster()]
+#' @return Either `TRUE` or `FALSE` according to whether the two boosters share
+#' the underlying C object.
+#' @seealso \link{xgb.copy.Booster}
 #' @examples
 #' library(xgboost)
-#'
 #' data(mtcars)
-#'
 #' y <- mtcars$mpg
 #' x <- as.matrix(mtcars[, -1])
-#'
 #' model <- xgb.train(
 #'   params = list(nthread = 1),
 #'   data = xgb.DMatrix(x, label = y, nthread = 1),
@@ -1253,8 +1230,9 @@ xgb.is.same.Booster <- function(obj1, obj2) {
 #' data(agaricus.train, package = "xgboost")
 #' train <- agaricus.train
 #'
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(train$data, label = train$label),
+#' bst <- xgboost(
+#'   data = train$data,
+#'   label = train$label,
 #'   max_depth = 2,
 #'   eta = 1,
 #'   nthread = 2,
@@ -1265,10 +1243,10 @@ xgb.is.same.Booster <- function(obj1, obj2) {
 #' attr(bst, "myattr") <- "memo"
 #'
 #' print(bst)
-#' @method print xgb.Booster
+#'
 #' @export
 print.xgb.Booster <- function(x, ...) {
-  # this lets it error out when the object comes from an earlier R XGBoost version
+  # this lets it error out when the object comes from an earlier R xgboost version
   handle <- xgb.get.handle(x)
   cat('##### xgb.Booster\n')
 

R-package/R/xgb.DMatrix.R

@@ -1,9 +1,9 @@
 #' Construct xgb.DMatrix object
 #'
 #' Construct an 'xgb.DMatrix' object from a given data source, which can then be passed to functions
-#' such as [xgb.train()] or [predict()].
+#' such as \link{xgb.train} or \link{predict.xgb.Booster}.
 #'
-#' Function `xgb.QuantileDMatrix()` will construct a DMatrix with quantization for the histogram
+#' Function 'xgb.QuantileDMatrix' will construct a DMatrix with quantization for the histogram
 #' method already applied to it, which can be used to reduce memory usage (compared to using a
 #' a regular DMatrix first and then creating a quantization out of it) when using the histogram
 #' method (`tree_method = "hist"`, which is the default algorithm), but is not usable for the
@@ -24,20 +24,20 @@
 #'
 #' Other column types are not supported.
 #' \item CSR matrices, as class `dgRMatrix` from package `Matrix`.
-#' \item CSC matrices, as class `dgCMatrix` from package `Matrix`. These are **not** supported for
+#' \item CSC matrices, as class `dgCMatrix` from package `Matrix`. These are \bold{not} supported for
 #' 'xgb.QuantileDMatrix'.
 #' \item Single-row CSR matrices, as class `dsparseVector` from package `Matrix`, which is interpreted
 #' as a single row (only when making predictions from a fitted model).
 #' \item Text files in a supported format, passed as a `character` variable containing the URI path to
 #' the file, with an optional format specifier.
 #'
-#' These are **not** supported for `xgb.QuantileDMatrix`. Supported formats are:\itemize{
-#'   \item XGBoost's own binary format for DMatrices, as produced by [xgb.DMatrix.save()].
+#' These are \bold{not} supported for `xgb.QuantileDMatrix`. Supported formats are:\itemize{
+#'   \item XGBoost's own binary format for DMatrices, as produced by \link{xgb.DMatrix.save}.
 #'   \item SVMLight (a.k.a. LibSVM) format for CSR matrices. This format can be signaled by suffix
-#'     `?format=libsvm` at the end of the file path. It will be the default format if not
-#'     otherwise specified.
+#'         `?format=libsvm` at the end of the file path. It will be the default format if not
+#'         otherwise specified.
 #'   \item CSV files (comma-separated values). This format can be specified by adding suffix
-#'     `?format=csv` at the end ofthe file path. It will **not** be auto-deduced from file extensions.
+#'         `?format=csv` at the end ofthe file path. It will \bold{not} be auto-deduced from file extensions.
 #'   }
 #'
 #' Be aware that the format of the file will not be auto-deduced - for example, if a file is named 'file.csv',
@@ -54,41 +54,44 @@
 #' integers with numeration starting at zero.
 #' @param weight Weight for each instance.
 #'
-#'   Note that, for ranking task, weights are per-group.  In ranking task, one weight
-#'   is assigned to each group (not each data point). This is because we
-#'   only care about the relative ordering of data points within each group,
-#'   so it doesn't make sense to assign weights to individual data points.
+#' Note that, for ranking task, weights are per-group.  In ranking task, one weight
+#' is assigned to each group (not each data point). This is because we
+#' only care about the relative ordering of data points within each group,
+#' so it doesn't make sense to assign weights to individual data points.
 #' @param base_margin Base margin used for boosting from existing model.
 #'
-#'   In the case of multi-output models, one can also pass multi-dimensional base_margin.
+#'        In the case of multi-output models, one can also pass multi-dimensional base_margin.
 #' @param missing A float value to represents missing values in data (not used when creating DMatrix
-#'   from text files). It is useful to change when a zero, infinite, or some other
-#'   extreme value represents missing values in data.
+#'        from text files).
+#'        It is useful to change when a zero, infinite, or some other extreme value represents missing
+#'        values in data.
 #' @param silent whether to suppress printing an informational message after loading from a file.
-#' @param feature_names Set names for features. Overrides column names in data frame and matrix.
+#' @param feature_names Set names for features. Overrides column names in data
+#'        frame and matrix.
 #'
-#'   Note: columns are not referenced by name when calling `predict`, so the column order there
-#'   must be the same as in the DMatrix construction, regardless of the column names.
+#'        Note: columns are not referenced by name when calling `predict`, so the column order there
+#'        must be the same as in the DMatrix construction, regardless of the column names.
 #' @param feature_types Set types for features.
 #'
-#'   If `data` is a `data.frame` and passing `feature_types` is not supplied,
-#'   feature types will be deduced automatically from the column types.
+#' If `data` is a `data.frame` and passing `feature_types` is not supplied, feature types will be deduced
+#' automatically from the column types.
 #'
-#'   Otherwise, one can pass a character vector with the same length as number of columns in `data`,
-#'   with the following possible values:
-#'   - "c", which represents categorical columns.
-#'   - "q", which represents numeric columns.
-#'   - "int", which represents integer columns.
-#'   - "i", which represents logical (boolean) columns.
+#' Otherwise, one can pass a character vector with the same length as number of columns in `data`,
+#' with the following possible values:\itemize{
+#' \item "c", which represents categorical columns.
+#' \item "q", which represents numeric columns.
+#' \item "int", which represents integer columns.
+#' \item "i", which represents logical (boolean) columns.
+#' }
 #'
-#'   Note that, while categorical types are treated differently from the rest for model fitting
-#'   purposes, the other types do not influence the generated model, but have effects in other
-#'   functionalities such as feature importances.
+#' Note that, while categorical types are treated differently from the rest for model fitting
+#' purposes, the other types do not influence the generated model, but have effects in other
+#' functionalities such as feature importances.
 #'
-#'   **Important**: Categorical features, if specified manually through `feature_types`, must
-#'   be encoded as integers with numeration starting at zero, and the same encoding needs to be
-#'   applied when passing data to [predict()]. Even if passing `factor` types, the encoding will
-#'   not be saved, so make sure that `factor` columns passed to `predict` have the same `levels`.
+#' \bold{Important}: categorical features, if specified manually through `feature_types`, must
+#' be encoded as integers with numeration starting at zero, and the same encoding needs to be
+#' applied when passing data to `predict`. Even if passing `factor` types, the encoding will
+#' not be saved, so make sure that `factor` columns passed to `predict` have the same `levels`.
 #' @param nthread Number of threads used for creating DMatrix.
 #' @param group Group size for all ranking group.
 #' @param qid Query ID for data samples, used for ranking.
@@ -96,24 +99,23 @@
 #' @param label_upper_bound Upper bound for survival training.
 #' @param feature_weights Set feature weights for column sampling.
 #' @param data_split_mode When passing a URI (as R `character`) as input, this signals
-#'   whether to split by row or column. Allowed values are `"row"` and `"col"`.
+#' whether to split by row or column. Allowed values are `"row"` and `"col"`.
 #'
-#'   In distributed mode, the file is split accordingly; otherwise this is only an indicator on
-#'   how the file was split beforehand. Default to row.
+#' In distributed mode, the file is split accordingly; otherwise this is only an indicator on
+#' how the file was split beforehand. Default to row.
 #'
-#'   This is not used when `data` is not a URI.
+#' This is not used when `data` is not a URI.
 #' @return An 'xgb.DMatrix' object. If calling 'xgb.QuantileDMatrix', it will have additional
 #' subclass 'xgb.QuantileDMatrix'.
 #'
 #' @details
-#' Note that DMatrix objects are not serializable through R functions such as [saveRDS()] or [save()].
+#' Note that DMatrix objects are not serializable through R functions such as \code{saveRDS} or \code{save}.
 #' If a DMatrix gets serialized and then de-serialized (for example, when saving data in an R session or caching
 #' chunks in an Rmd file), the resulting object will not be usable anymore and will need to be reconstructed
 #' from the original source of data.
 #'
 #' @examples
-#' data(agaricus.train, package = "xgboost")
-#'
+#' data(agaricus.train, package='xgboost')
 #' ## Keep the number of threads to 1 for examples
 #' nthread <- 1
 #' data.table::setDTthreads(nthread)
@@ -316,13 +318,13 @@ xgb.DMatrix <- function(
 }
 
 #' @param ref The training dataset that provides quantile information, needed when creating
-#' validation/test dataset with [xgb.QuantileDMatrix()]. Supplying the training DMatrix
+#' validation/test dataset with `xgb.QuantileDMatrix`. Supplying the training DMatrix
 #' as a reference means that the same quantisation applied to the training data is
 #' applied to the validation/test data
 #' @param max_bin The number of histogram bin, should be consistent with the training parameter
-#'   `max_bin`.
+#' `max_bin`.
 #'
-#'   This is only supported when constructing a QuantileDMatrix.
+#' This is only supported when constructing a QuantileDMatrix.
 #' @export
 #' @rdname xgb.DMatrix
 xgb.QuantileDMatrix <- function(
@@ -409,42 +411,40 @@ xgb.QuantileDMatrix <- function(
   return(dmat)
 }
 
-#' XGBoost Data Iterator
-#'
-#' @description
-#' Interface to create a custom data iterator in order to construct a DMatrix
+#' @title XGBoost Data Iterator
+#' @description Interface to create a custom data iterator in order to construct a DMatrix
 #' from external memory.
 #'
 #' This function is responsible for generating an R object structure containing callback
 #' functions and an environment shared with them.
 #'
-#' The output structure from this function is then meant to be passed to [xgb.ExtMemDMatrix()],
+#' The output structure from this function is then meant to be passed to \link{xgb.ExternalDMatrix},
 #' which will consume the data and create a DMatrix from it by executing the callback functions.
 #'
-#' For more information, and for a usage example, see the documentation for [xgb.ExtMemDMatrix()].
-#'
+#' For more information, and for a usage example, see the documentation for \link{xgb.ExternalDMatrix}.
 #' @param env An R environment to pass to the callback functions supplied here, which can be
-#'   used to keep track of variables to determine how to handle the batches.
+#' used to keep track of variables to determine how to handle the batches.
 #'
-#'   For example, one might want to keep track of an iteration number in this environment in order
-#'   to know which part of the data to pass next.
-#' @param f_next `function(env)` which is responsible for:
-#'   - Accessing or retrieving the next batch of data in the iterator.
-#'   - Supplying this data by calling function [xgb.DataBatch()] on it and returning the result.
-#'   - Keeping track of where in the iterator batch it is or will go next, which can for example
-#'     be done by modifiying variables in the `env` variable that is passed here.
-#'   - Signaling whether there are more batches to be consumed or not, by returning `NULL`
-#'     when the stream of data ends (all batches in the iterator have been consumed), or the result from
-#'     calling [xgb.DataBatch()] when there are more batches in the line to be consumed.
+#' For example, one might want to keep track of an iteration number in this environment in order
+#' to know which part of the data to pass next.
+#' @param f_next `function(env)` which is responsible for:\itemize{
+#' \item Accessing or retrieving the next batch of data in the iterator.
+#' \item Supplying this data by calling function \link{xgb.DataBatch} on it and returning the result.
+#' \item Keeping track of where in the iterator batch it is or will go next, which can for example
+#' be done by modifiying variables in the `env` variable that is passed here.
+#' \item Signaling whether there are more batches to be consumed or not, by returning `NULL`
+#' when the stream of data ends (all batches in the iterator have been consumed), or the result from
+#' calling \link{xgb.DataBatch} when there are more batches in the line to be consumed.
+#' }
 #' @param f_reset `function(env)` which is responsible for reseting the data iterator
-#'   (i.e. taking it back to the first batch, called before and after the sequence of batches
-#'   has been consumed).
+#' (i.e. taking it back to the first batch, called before and after the sequence of batches
+#' has been consumed).
 #'
-#'   Note that, after resetting the iterator, the batches will be accessed again, so the same data
-#'   (and in the same order) must be passed in subsequent iterations.
+#' Note that, after resetting the iterator, the batches will be accessed again, so the same data
+#' (and in the same order) must be passed in subsequent iterations.
 #' @return An `xgb.DataIter` object, containing the same inputs supplied here, which can then
-#'   be passed to [xgb.ExtMemDMatrix()].
-#' @seealso [xgb.ExtMemDMatrix()], [xgb.DataBatch()].
+#' be passed to \link{xgb.ExternalDMatrix}.
+#' @seealso \link{xgb.ExternalDMatrix}, \link{xgb.DataBatch}.
 #' @export
 xgb.DataIter <- function(env = new.env(), f_next, f_reset) {
   if (!is.function(f_next)) {
@@ -508,39 +508,38 @@ xgb.DataIter <- function(env = new.env(), f_next, f_reset) {
   return(out)
 }
 
-#' Structure for Data Batches
+#' @title Structure for Data Batches
+#' @description Helper function to supply data in batches of a data iterator when
+#' constructing a DMatrix from external memory through \link{xgb.ExternalDMatrix}
+#' or through \link{xgb.QuantileDMatrix.from_iterator}.
 #'
-#' @description
-#' Helper function to supply data in batches of a data iterator when
-#' constructing a DMatrix from external memory through [xgb.ExtMemDMatrix()]
-#' or through [xgb.QuantileDMatrix.from_iterator()].
-#'
-#' This function is **only** meant to be called inside of a callback function (which
-#' is passed as argument to function [xgb.DataIter()] to construct a data iterator)
+#' This function is \bold{only} meant to be called inside of a callback function (which
+#' is passed as argument to function \link{xgb.DataIter} to construct a data iterator)
 #' when constructing a DMatrix through external memory - otherwise, one should call
-#' [xgb.DMatrix()] or [xgb.QuantileDMatrix()].
+#' \link{xgb.DMatrix} or \link{xgb.QuantileDMatrix}.
 #'
-#' The object that results from calling this function directly is **not** like
+#' The object that results from calling this function directly is \bold{not} like
 #' an `xgb.DMatrix` - i.e. cannot be used to train a model, nor to get predictions - only
 #' possible usage is to supply data to an iterator, from which a DMatrix is then constructed.
 #'
-#' For more information and for example usage, see the documentation for [xgb.ExtMemDMatrix()].
+#' For more information and for example usage, see the documentation for \link{xgb.ExternalDMatrix}.
 #' @inheritParams xgb.DMatrix
 #' @param data Batch of data belonging to this batch.
 #'
-#'   Note that not all of the input types supported by [xgb.DMatrix()] are possible
-#'   to pass here. Supported types are:
-#'   - `matrix`, with types `numeric`, `integer`, and `logical`. Note that for types
-#'     `integer` and `logical`, missing values might not be automatically recognized as
-#'     as such - see the documentation for parameter `missing` in [xgb.ExtMemDMatrix()]
-#'     for details on this.
-#'   - `data.frame`, with the same types as supported by 'xgb.DMatrix' and same
-#'     conversions applied to it. See the documentation for parameter `data` in
-#'     [xgb.DMatrix()] for details on it.
-#'   - CSR matrices, as class `dgRMatrix` from package "Matrix".
+#' Note that not all of the input types supported by \link{xgb.DMatrix} are possible
+#' to pass here. Supported types are:\itemize{
+#' \item `matrix`, with types `numeric`, `integer`, and `logical`. Note that for types
+#' `integer` and `logical`, missing values might not be automatically recognized as
+#' as such - see the documentation for parameter `missing` in \link{xgb.ExternalDMatrix}
+#' for details on this.
+#' \item `data.frame`, with the same types as supported by 'xgb.DMatrix' and same
+#' conversions applied to it. See the documentation for parameter `data` in
+#' \link{xgb.DMatrix} for details on it.
+#' \item CSR matrices, as class `dgRMatrix` from package `Matrix`.
+#' }
 #' @return An object of class `xgb.DataBatch`, which is just a list containing the
-#'   data and parameters passed here. It does **not** inherit from `xgb.DMatrix`.
-#' @seealso [xgb.DataIter()], [xgb.ExtMemDMatrix()].
+#' data and parameters passed here. It does \bold{not} inherit from `xgb.DMatrix`.
+#' @seealso \link{xgb.DataIter}, \link{xgb.ExternalDMatrix}.
 #' @export
 xgb.DataBatch <- function(
   data,
@@ -617,43 +616,42 @@ xgb.ProxyDMatrix <- function(proxy_handle, data_iterator) {
   return(1L)
 }
 
-#' DMatrix from External Data
-#'
-#' @description
-#' Create a special type of XGBoost 'DMatrix' object from external data
-#' supplied by an [xgb.DataIter()] object, potentially passed in batches from a
+#' @title DMatrix from External Data
+#' @description Create a special type of xgboost 'DMatrix' object from external data
+#' supplied by an \link{xgb.DataIter} object, potentially passed in batches from a
 #' bigger set that might not fit entirely in memory.
 #'
 #' The data supplied by the iterator is accessed on-demand as needed, multiple times,
-#' without being concatenated, but note that fields like 'label' **will** be
+#' without being concatenated, but note that fields like 'label' \bold{will} be
 #' concatenated from multiple calls to the data iterator.
 #'
 #' For more information, see the guide 'Using XGBoost External Memory Version':
 #' \url{https://xgboost.readthedocs.io/en/stable/tutorials/external_memory.html}
 #' @inheritParams xgb.DMatrix
-#' @param data_iterator A data iterator structure as returned by [xgb.DataIter()],
-#'   which includes an environment shared between function calls, and functions to access
-#'   the data in batches on-demand.
+#' @param data_iterator A data iterator structure as returned by \link{xgb.DataIter},
+#' which includes an environment shared between function calls, and functions to access
+#' the data in batches on-demand.
 #' @param cache_prefix The path of cache file, caller must initialize all the directories in this path.
 #' @param missing A float value to represents missing values in data.
 #'
-#'   Note that, while functions like [xgb.DMatrix()] can take a generic `NA` and interpret it
-#'   correctly for different types like `numeric` and `integer`, if an `NA` value is passed here,
-#'   it will not be adapted for different input types.
+#' Note that, while functions like \link{xgb.DMatrix} can take a generic `NA` and interpret it
+#' correctly for different types like `numeric` and `integer`, if an `NA` value is passed here,
+#' it will not be adapted for different input types.
 #'
-#'   For example, in R `integer` types, missing values are represented by integer number `-2147483648`
-#'   (since machine 'integer' types do not have an inherent 'NA' value) - hence, if one passes `NA`,
-#'   which is interpreted as a floating-point NaN by [xgb.ExtMemDMatrix()] and by
-#'   [xgb.QuantileDMatrix.from_iterator()], these integer missing values will not be treated as missing.
-#'   This should not pose any problem for `numeric` types, since they do have an inheret NaN value.
-#' @return An 'xgb.DMatrix' object, with subclass 'xgb.ExtMemDMatrix', in which the data is not
-#'   held internally but accessed through the iterator when needed.
-#' @seealso [xgb.DataIter()], [xgb.DataBatch()], [xgb.QuantileDMatrix.from_iterator()]
+#' For example, in R `integer` types, missing values are represented by integer number `-2147483648`
+#' (since machine 'integer' types do not have an inherent 'NA' value) - hence, if one passes `NA`,
+#' which is interpreted as a floating-point NaN by 'xgb.ExternalDMatrix' and by
+#' 'xgb.QuantileDMatrix.from_iterator', these integer missing values will not be treated as missing.
+#' This should not pose any problem for `numeric` types, since they do have an inheret NaN value.
+#' @return An 'xgb.DMatrix' object, with subclass 'xgb.ExternalDMatrix', in which the data is not
+#' held internally but accessed through the iterator when needed.
+#' @seealso \link{xgb.DataIter}, \link{xgb.DataBatch}, \link{xgb.QuantileDMatrix.from_iterator}
 #' @examples
+#' library(xgboost)
 #' data(mtcars)
 #'
-#' # This custom environment will be passed to the iterator
-#' # functions at each call. It is up to the user to keep
+#' # this custom environment will be passed to the iterator
+#' # functions at each call. It's up to the user to keep
 #' # track of the iteration number in this environment.
 #' iterator_env <- as.environment(
 #'   list(
@@ -706,7 +704,7 @@ xgb.ProxyDMatrix <- function(proxy_handle, data_iterator) {
 #' cache_prefix <- tempdir()
 #'
 #' # DMatrix will be constructed from the iterator's batches
-#' dm <- xgb.ExtMemDMatrix(data_iterator, cache_prefix, nthread = 1)
+#' dm <- xgb.ExternalDMatrix(data_iterator, cache_prefix, nthread = 1)
 #'
 #' # After construction, can be used as a regular DMatrix
 #' params <- list(nthread = 1, objective = "reg:squarederror")
@@ -717,7 +715,7 @@ xgb.ProxyDMatrix <- function(proxy_handle, data_iterator) {
 #' pred_dm <- predict(model, dm)
 #' pred_mat <- predict(model, as.matrix(mtcars[, -1]))
 #' @export
-xgb.ExtMemDMatrix <- function(
+xgb.ExternalDMatrix <- function(
   data_iterator,
   cache_prefix = tempdir(),
   missing = NA,
@@ -753,34 +751,32 @@ xgb.ExtMemDMatrix <- function(
   )
 
   attributes(dmat) <- list(
-    class = c("xgb.DMatrix", "xgb.ExtMemDMatrix"),
+    class = c("xgb.DMatrix", "xgb.ExternalDMatrix"),
     fields = attributes(proxy_handle)$fields
   )
   return(dmat)
 }
 
 
-#' QuantileDMatrix from External Data
-#'
-#' @description
-#' Create an `xgb.QuantileDMatrix` object (exact same class as would be returned by
-#' calling function [xgb.QuantileDMatrix()], with the same advantages and limitations) from
-#' external data supplied by [xgb.DataIter()], potentially passed in batches from
-#' a bigger set that might not fit entirely in memory, same way as [xgb.ExtMemDMatrix()].
+#' @title QuantileDMatrix from External Data
+#' @description Create an `xgb.QuantileDMatrix` object (exact same class as would be returned by
+#' calling function \link{xgb.QuantileDMatrix}, with the same advantages and limitations) from
+#' external data supplied by an \link{xgb.DataIter} object, potentially passed in batches from
+#' a bigger set that might not fit entirely in memory, same way as \link{xgb.ExternalDMatrix}.
 #'
 #' Note that, while external data will only be loaded through the iterator (thus the full data
 #' might not be held entirely in-memory), the quantized representation of the data will get
 #' created in-memory, being concatenated from multiple calls to the data iterator. The quantized
 #' version is typically lighter than the original data, so there might be cases in which this
-#' representation could potentially fit in memory even if the full data does not.
+#' representation could potentially fit in memory even if the full data doesn't.
 #'
 #' For more information, see the guide 'Using XGBoost External Memory Version':
 #' \url{https://xgboost.readthedocs.io/en/stable/tutorials/external_memory.html}
-#' @inheritParams xgb.ExtMemDMatrix
+#' @inheritParams xgb.ExternalDMatrix
 #' @inheritParams xgb.QuantileDMatrix
 #' @return An 'xgb.DMatrix' object, with subclass 'xgb.QuantileDMatrix'.
-#' @seealso [xgb.DataIter()], [xgb.DataBatch()], [xgb.ExtMemDMatrix()],
-#' [xgb.QuantileDMatrix()]
+#' @seealso \link{xgb.DataIter}, \link{xgb.DataBatch}, \link{xgb.ExternalDMatrix},
+#' \link{xgb.QuantileDMatrix}
 #' @export
 xgb.QuantileDMatrix.from_iterator <- function( # nolint
   data_iterator,
@@ -827,18 +823,18 @@ xgb.QuantileDMatrix.from_iterator <- function( # nolint
   return(dmat)
 }
 
-#' Check whether DMatrix object has a field
-#'
-#' Checks whether an xgb.DMatrix object has a given field assigned to
+#' @title Check whether DMatrix object has a field
+#' @description Checks whether an xgb.DMatrix object has a given field assigned to
 #' it, such as weights, labels, etc.
-#' @param object The DMatrix object to check for the given `info` field.
-#' @param info The field to check for presence or absence in `object`.
-#' @seealso [xgb.DMatrix()], [getinfo.xgb.DMatrix()], [setinfo.xgb.DMatrix()]
+#' @param object The DMatrix object to check for the given \code{info} field.
+#' @param info The field to check for presence or absence in \code{object}.
+#' @seealso \link{xgb.DMatrix}, \link{getinfo.xgb.DMatrix}, \link{setinfo.xgb.DMatrix}
 #' @examples
+#' library(xgboost)
 #' x <- matrix(1:10, nrow = 5)
 #' dm <- xgb.DMatrix(x, nthread = 1)
 #'
-#' # 'dm' so far does not have any fields set
+#' # 'dm' so far doesn't have any fields set
 #' xgb.DMatrix.hasinfo(dm, "label")
 #'
 #' # Fields can be added after construction
@@ -857,21 +853,49 @@ xgb.DMatrix.hasinfo <- function(object, info) {
 }
 
 
+# get dmatrix from data, label
+# internal helper method
+xgb.get.DMatrix <- function(data, label, missing, weight, nthread) {
+  if (inherits(data, "dgCMatrix") || is.matrix(data)) {
+    if (is.null(label)) {
+      stop("label must be provided when data is a matrix")
+    }
+    dtrain <- xgb.DMatrix(data, label = label, missing = missing, nthread = nthread)
+    if (!is.null(weight)) {
+      setinfo(dtrain, "weight", weight)
+    }
+  } else {
+    if (!is.null(label)) {
+      warning("xgboost: label will be ignored.")
+    }
+    if (is.character(data)) {
+      data <- path.expand(data)
+      dtrain <- xgb.DMatrix(data[1])
+    } else if (inherits(data, "xgb.DMatrix")) {
+      dtrain <- data
+    } else if (inherits(data, "data.frame")) {
+      stop("xgboost doesn't support data.frame as input. Convert it to matrix first.")
+    } else {
+      stop("xgboost: invalid input data")
+    }
+  }
+  return(dtrain)
+}
+
+
 #' Dimensions of xgb.DMatrix
 #'
-#' Returns a vector of numbers of rows and of columns in an `xgb.DMatrix`.
-#'
-#' @param x Object of class `xgb.DMatrix`
+#' Returns a vector of numbers of rows and of columns in an \code{xgb.DMatrix}.
+#' @param x Object of class \code{xgb.DMatrix}
 #'
 #' @details
-#' Note: since [nrow()] and [ncol()] internally use [dim()], they can also
-#' be directly used with an `xgb.DMatrix` object.
+#' Note: since \code{nrow} and \code{ncol} internally use \code{dim}, they can also
+#' be directly used with an \code{xgb.DMatrix} object.
 #'
 #' @examples
-#' data(agaricus.train, package = "xgboost")
-#'
+#' data(agaricus.train, package='xgboost')
 #' train <- agaricus.train
-#' dtrain <- xgb.DMatrix(train$data, label = train$label, nthread = 2)
+#' dtrain <- xgb.DMatrix(train$data, label=train$label, nthread = 2)
 #'
 #' stopifnot(nrow(dtrain) == nrow(train$data))
 #' stopifnot(ncol(dtrain) == ncol(train$data))
@@ -883,28 +907,27 @@ dim.xgb.DMatrix <- function(x) {
 }
 
 
-#' Handling of column names of `xgb.DMatrix`
+#' Handling of column names of \code{xgb.DMatrix}
 #'
-#' Only column names are supported for `xgb.DMatrix`, thus setting of
-#' row names would have no effect and returned row names would be `NULL`.
+#' Only column names are supported for \code{xgb.DMatrix}, thus setting of
+#' row names would have no effect and returned row names would be NULL.
 #'
-#' @param x Object of class `xgb.DMatrix`.
-#' @param value A list of two elements: the first one is ignored
-#'   and the second one is column names
+#' @param x object of class \code{xgb.DMatrix}
+#' @param value a list of two elements: the first one is ignored
+#'        and the second one is column names
 #'
 #' @details
-#' Generic [dimnames()] methods are used by [colnames()].
-#' Since row names are irrelevant, it is recommended to use [colnames()] directly.
+#' Generic \code{dimnames} methods are used by \code{colnames}.
+#' Since row names are irrelevant, it is recommended to use \code{colnames} directly.
 #'
 #' @examples
-#' data(agaricus.train, package = "xgboost")
-#'
+#' data(agaricus.train, package='xgboost')
 #' train <- agaricus.train
-#' dtrain <- xgb.DMatrix(train$data, label = train$label, nthread = 2)
+#' dtrain <- xgb.DMatrix(train$data, label=train$label, nthread = 2)
 #' dimnames(dtrain)
 #' colnames(dtrain)
 #' colnames(dtrain) <- make.names(1:ncol(train$data))
-#' print(dtrain, verbose = TRUE)
+#' print(dtrain, verbose=TRUE)
 #'
 #' @rdname dimnames.xgb.DMatrix
 #' @export
@@ -933,45 +956,47 @@ dimnames.xgb.DMatrix <- function(x) {
 }
 
 
-#' Get or set information of xgb.DMatrix and xgb.Booster objects
-#'
-#' @param object Object of class `xgb.DMatrix` or `xgb.Booster`.
-#' @param name The name of the information field to get (see details).
-#' @return For `getinfo()`, will return the requested field. For `setinfo()`,
-#'   will always return value `TRUE` if it succeeds.
+#' @title Get or set information of xgb.DMatrix and xgb.Booster objects
+#' @param object Object of class \code{xgb.DMatrix} of `xgb.Booster`.
+#' @param name the name of the information field to get (see details)
+#' @return For `getinfo`, will return the requested field. For `setinfo`, will always return value `TRUE`
+#' if it succeeds.
 #' @details
-#' The `name` field can be one of the following for `xgb.DMatrix`:
-#' - label
-#' - weight
-#' - base_margin
-#' - label_lower_bound
-#' - label_upper_bound
-#' - group
-#' - feature_type
-#' - feature_name
-#' - nrow
+#' The \code{name} field can be one of the following for `xgb.DMatrix`:
 #'
-#' See the documentation for [xgb.DMatrix()] for more information about these fields.
+#' \itemize{
+#'     \item \code{label}
+#'     \item \code{weight}
+#'     \item \code{base_margin}
+#'     \item \code{label_lower_bound}
+#'     \item \code{label_upper_bound}
+#'     \item \code{group}
+#'     \item \code{feature_type}
+#'     \item \code{feature_name}
+#'     \item \code{nrow}
+#' }
+#' See the documentation for \link{xgb.DMatrix} for more information about these fields.
 #'
 #' For `xgb.Booster`, can be one of the following:
-#' - `feature_type`
-#' - `feature_name`
+#' \itemize{
+#'     \item \code{feature_type}
+#'     \item \code{feature_name}
+#' }
 #'
-#' Note that, while 'qid' cannot be retrieved, it is possible to get the equivalent 'group'
+#' Note that, while 'qid' cannot be retrieved, it's possible to get the equivalent 'group'
 #' for a DMatrix that had 'qid' assigned.
 #'
-#' **Important**: when calling [setinfo()], the objects are modified in-place. See
-#' [xgb.copy.Booster()] for an idea of this in-place assignment works.
+#' \bold{Important}: when calling `setinfo`, the objects are modified in-place. See
+#' \link{xgb.copy.Booster} for an idea of this in-place assignment works.
 #' @examples
-#' data(agaricus.train, package = "xgboost")
-#'
+#' data(agaricus.train, package='xgboost')
 #' dtrain <- with(agaricus.train, xgb.DMatrix(data, label = label, nthread = 2))
 #'
-#' labels <- getinfo(dtrain, "label")
-#' setinfo(dtrain, "label", 1 - labels)
+#' labels <- getinfo(dtrain, 'label')
+#' setinfo(dtrain, 'label', 1-labels)
 #'
-#' labels2 <- getinfo(dtrain, "label")
-#' stopifnot(all(labels2 == 1 - labels))
+#' labels2 <- getinfo(dtrain, 'label')
+#' stopifnot(all(labels2 == 1-labels))
 #' @rdname getinfo
 #' @export
 getinfo <- function(object, name) UseMethod("getinfo")
@@ -1016,29 +1041,28 @@ getinfo.xgb.DMatrix <- function(object, name) {
 }
 
 #' @rdname getinfo
-#' @param info The specific field of information to set.
+#' @param info the specific field of information to set
 #'
 #' @details
-#' See the documentation for [xgb.DMatrix()] for possible fields that can be set
+#' See the documentation for \link{xgb.DMatrix} for possible fields that can be set
 #' (which correspond to arguments in that function).
 #'
-#' Note that the following fields are allowed in the construction of an `xgb.DMatrix`
-#' but **are not** allowed here:
-#' - data
-#' - missing
-#' - silent
-#' - nthread
+#' Note that the following fields are allowed in the construction of an \code{xgb.DMatrix}
+#' but \bold{aren't} allowed here:\itemize{
+#' \item data
+#' \item missing
+#' \item silent
+#' \item nthread
+#' }
 #'
 #' @examples
-#' data(agaricus.train, package = "xgboost")
-#'
+#' data(agaricus.train, package='xgboost')
 #' dtrain <- with(agaricus.train, xgb.DMatrix(data, label = label, nthread = 2))
 #'
-#' labels <- getinfo(dtrain, "label")
-#' setinfo(dtrain, "label", 1 - labels)
-#'
-#' labels2 <- getinfo(dtrain, "label")
-#' stopifnot(all.equal(labels2, 1 - labels))
+#' labels <- getinfo(dtrain, 'label')
+#' setinfo(dtrain, 'label', 1-labels)
+#' labels2 <- getinfo(dtrain, 'label')
+#' stopifnot(all.equal(labels2, 1-labels))
 #' @export
 setinfo <- function(object, name, info) UseMethod("setinfo")
 
@@ -1123,11 +1147,9 @@ setinfo.xgb.DMatrix <- function(object, name, info) {
   stop("setinfo: unknown info name ", name)
 }
 
-#' Get Quantile Cuts from DMatrix
-#'
-#' @description
-#' Get the quantile cuts (a.k.a. borders) from an `xgb.DMatrix`
-#' that has been quantized for the histogram method (`tree_method = "hist"`).
+#' @title Get Quantile Cuts from DMatrix
+#' @description Get the quantile cuts (a.k.a. borders) from an `xgb.DMatrix`
+#' that has been quantized for the histogram method (`tree_method="hist"`).
 #'
 #' These cuts are used in order to assign observations to bins - i.e. these are ordered
 #' boundaries which are used to determine assignment condition `border_low < x < border_high`.
@@ -1138,18 +1160,19 @@ setinfo.xgb.DMatrix <- function(object, name, info) {
 #' which will be output in sorted order from lowest to highest.
 #'
 #' Different columns can have different numbers of bins according to their range.
-#' @param dmat An `xgb.DMatrix` object, as returned by [xgb.DMatrix()].
-#' @param output Output format for the quantile cuts. Possible options are:
-#'   - "list"` will return the output as a list with one entry per column, where
-#'     each column will have a numeric vector with the cuts. The list will be named if
-#'     `dmat` has column names assigned to it.
-#'   - `"arrays"` will return a list with entries `indptr` (base-0 indexing) and
-#'     `data`. Here, the cuts for column 'i' are obtained by slicing 'data' from entries
-#' `   indptr[i]+1` to `indptr[i+1]`.
+#' @param dmat An `xgb.DMatrix` object, as returned by \link{xgb.DMatrix}.
+#' @param output Output format for the quantile cuts. Possible options are:\itemize{
+#' \item `"list"` will return the output as a list with one entry per column, where
+#' each column will have a numeric vector with the cuts. The list will be named if
+#' `dmat` has column names assigned to it.
+#' \item `"arrays"` will return a list with entries `indptr` (base-0 indexing) and
+#' `data`. Here, the cuts for column 'i' are obtained by slicing 'data' from entries
+#' `indptr[i]+1` to `indptr[i+1]`.
+#' }
 #' @return The quantile cuts, in the format specified by parameter `output`.
 #' @examples
+#' library(xgboost)
 #' data(mtcars)
-#'
 #' y <- mtcars$mpg
 #' x <- as.matrix(mtcars[, -1])
 #' dm <- xgb.DMatrix(x, label = y, nthread = 1)
@@ -1157,7 +1180,11 @@ setinfo.xgb.DMatrix <- function(object, name, info) {
 #' # DMatrix is not quantized right away, but will be once a hist model is generated
 #' model <- xgb.train(
 #'   data = dm,
-#'   params = list(tree_method = "hist", max_bin = 8, nthread = 1),
+#'   params = list(
+#'     tree_method = "hist",
+#'     max_bin = 8,
+#'     nthread = 1
+#'   ),
 #'   nrounds = 3
 #' )
 #'
@@ -1192,19 +1219,17 @@ xgb.get.DMatrix.qcut <- function(dmat, output = c("list", "arrays")) { # nolint
   }
 }
 
-#' Get Number of Non-Missing Entries in DMatrix
-#'
-#' @param dmat An `xgb.DMatrix` object, as returned by [xgb.DMatrix()].
-#' @return The number of non-missing entries in the DMatrix.
+#' @title Get Number of Non-Missing Entries in DMatrix
+#' @param dmat An `xgb.DMatrix` object, as returned by \link{xgb.DMatrix}.
+#' @return The number of non-missing entries in the DMatrix
 #' @export
 xgb.get.DMatrix.num.non.missing <- function(dmat) { # nolint
   stopifnot(inherits(dmat, "xgb.DMatrix"))
   return(.Call(XGDMatrixNumNonMissing_R, dmat))
 }
 
-#' Get DMatrix Data
-#'
-#' @param dmat An `xgb.DMatrix` object, as returned by [xgb.DMatrix()].
+#' @title Get DMatrix Data
+#' @param dmat An `xgb.DMatrix` object, as returned by \link{xgb.DMatrix}.
 #' @return The data held in the DMatrix, as a sparse CSR matrix (class `dgRMatrix`
 #' from package `Matrix`). If it had feature names, these will be added as column names
 #' in the output.
@@ -1228,27 +1253,27 @@ xgb.get.DMatrix.data <- function(dmat) {
   return(out)
 }
 
-#' Slice DMatrix
+#' Get a new DMatrix containing the specified rows of
+#' original xgb.DMatrix object
 #'
-#' Get a new DMatrix containing the specified rows of original xgb.DMatrix object.
+#' Get a new DMatrix containing the specified rows of
+#' original xgb.DMatrix object
 #'
-#' @param object Object of class `xgb.DMatrix`.
+#' @param object Object of class "xgb.DMatrix".
 #' @param idxset An integer vector of indices of rows needed (base-1 indexing).
 #' @param allow_groups Whether to allow slicing an `xgb.DMatrix` with `group` (or
-#'   equivalently `qid`) field. Note that in such case, the result will not have
-#'   the groups anymore - they need to be set manually through [setinfo()].
-#' @param colset Currently not used (columns subsetting is not available).
+#'        equivalently `qid`) field. Note that in such case, the result will not have
+#'        the groups anymore - they need to be set manually through `setinfo`.
+#' @param colset currently not used (columns subsetting is not available)
 #'
 #' @examples
-#' data(agaricus.train, package = "xgboost")
-#'
+#' data(agaricus.train, package='xgboost')
 #' dtrain <- with(agaricus.train, xgb.DMatrix(data, label = label, nthread = 2))
 #'
 #' dsub <- xgb.slice.DMatrix(dtrain, 1:42)
-#' labels1 <- getinfo(dsub, "label")
-#'
+#' labels1 <- getinfo(dsub, 'label')
 #' dsub <- dtrain[1:42, ]
-#' labels2 <- getinfo(dsub, "label")
+#' labels2 <- getinfo(dsub, 'label')
 #' all.equal(labels1, labels2)
 #'
 #' @rdname xgb.slice.DMatrix
@@ -1297,17 +1322,16 @@ xgb.slice.DMatrix <- function(object, idxset, allow_groups = FALSE) {
 #' Print information about xgb.DMatrix.
 #' Currently it displays dimensions and presence of info-fields and colnames.
 #'
-#' @param x An xgb.DMatrix object.
-#' @param verbose Whether to print colnames (when present).
-#' @param ... Not currently used.
+#' @param x an xgb.DMatrix object
+#' @param verbose whether to print colnames (when present)
+#' @param ... not currently used
 #'
 #' @examples
-#' data(agaricus.train, package = "xgboost")
-#'
+#' data(agaricus.train, package='xgboost')
 #' dtrain <- with(agaricus.train, xgb.DMatrix(data, label = label, nthread = 2))
-#' dtrain
 #'
-#' print(dtrain, verbose = TRUE)
+#' dtrain
+#' print(dtrain, verbose=TRUE)
 #'
 #' @method print xgb.DMatrix
 #' @export
@@ -1318,8 +1342,8 @@ print.xgb.DMatrix <- function(x, verbose = FALSE, ...) {
   }
   class_print <- if (inherits(x, "xgb.QuantileDMatrix")) {
     "xgb.QuantileDMatrix"
-  } else if (inherits(x, "xgb.ExtMemDMatrix")) {
-    "xgb.ExtMemDMatrix"
+  } else if (inherits(x, "xgb.ExternalDMatrix")) {
+    "xgb.ExternalDMatrix"
   } else if (inherits(x, "xgb.ProxyDMatrix")) {
     "xgb.ProxyDMatrix"
   } else {

R-package/R/xgb.DMatrix.save.R

@@ -2,13 +2,12 @@
 #'
 #' Save xgb.DMatrix object to binary file
 #'
-#' @param dmatrix the `xgb.DMatrix` object
+#' @param dmatrix the \code{xgb.DMatrix} object
 #' @param fname the name of the file to write.
 #'
 #' @examples
 #' \dontshow{RhpcBLASctl::omp_set_num_threads(1)}
-#' data(agaricus.train, package = "xgboost")
-#'
+#' data(agaricus.train, package='xgboost')
 #' dtrain <- with(agaricus.train, xgb.DMatrix(data, label = label, nthread = 2))
 #' fname <- file.path(tempdir(), "xgb.DMatrix.data")
 #' xgb.DMatrix.save(dtrain, fname)

R-package/R/xgb.config.R

@@ -1,26 +1,24 @@
-#' Set and get global configuration
-#'
 #' Global configuration consists of a collection of parameters that can be applied in the global
 #' scope. See \url{https://xgboost.readthedocs.io/en/stable/parameter.html} for the full list of
-#' parameters supported in the global configuration. Use `xgb.set.config()` to update the
-#' values of one or more global-scope parameters. Use `xgb.get.config()` to fetch the current
+#' parameters supported in the global configuration. Use \code{xgb.set.config} to update the
+#' values of one or more global-scope parameters. Use \code{xgb.get.config} to fetch the current
 #' values of all global-scope parameters (listed in
 #' \url{https://xgboost.readthedocs.io/en/stable/parameter.html}).
-#'
 #' @details
 #' Note that serialization-related functions might use a globally-configured number of threads,
 #' which is managed by the system's OpenMP (OMP) configuration instead. Typically, XGBoost methods
-#' accept an `nthreads` parameter, but some methods like [readRDS()] might get executed before such
+#' accept an `nthreads` parameter, but some methods like `readRDS` might get executed before such
 #' parameter can be supplied.
 #'
 #' The number of OMP threads can in turn be configured for example through an environment variable
 #' `OMP_NUM_THREADS` (needs to be set before R is started), or through `RhpcBLASctl::omp_set_num_threads`.
 #' @rdname xgbConfig
+#' @title Set and get global configuration
 #' @name xgb.set.config, xgb.get.config
 #' @export xgb.set.config xgb.get.config
 #' @param ... List of parameters to be set, as keyword arguments
 #' @return
-#' `xgb.set.config()` returns `TRUE` to signal success. `xgb.get.config()` returns
+#' \code{xgb.set.config} returns \code{TRUE} to signal success. \code{xgb.get.config} returns
 #' a list containing all global-scope parameters and their values.
 #'
 #' @examples

R-package/R/xgb.create.features.R

@@ -1,15 +1,20 @@
 #' Create new features from a previously learned model
 #'
-#' May improve the learning by adding new features to the training data based on the
-#' decision trees from a previously learned model.
+#' May improve the learning by adding new features to the training data based on the decision trees from a previously learned model.
+#'
+#' @param model decision tree boosting model learned on the original data
+#' @param data original data (usually provided as a \code{dgCMatrix} matrix)
+#' @param ... currently not used
+#'
+#' @return \code{dgCMatrix} matrix including both the original data and the new features.
 #'
 #' @details
 #' This is the function inspired from the paragraph 3.1 of the paper:
 #'
-#' **Practical Lessons from Predicting Clicks on Ads at Facebook**
+#' \strong{Practical Lessons from Predicting Clicks on Ads at Facebook}
 #'
-#' *(Xinran He, Junfeng Pan, Ou Jin, Tianbing Xu, Bo Liu, Tao Xu, Yan, xin Shi, Antoine Atallah, Ralf Herbrich, Stuart Bowers,
-#' Joaquin Quinonero Candela)*
+#' \emph{(Xinran He, Junfeng Pan, Ou Jin, Tianbing Xu, Bo Liu, Tao Xu, Yan, xin Shi, Antoine Atallah, Ralf Herbrich, Stuart Bowers,
+#' Joaquin Quinonero Candela)}
 #'
 #' International Workshop on Data Mining for Online Advertising (ADKDD) - August 24, 2014
 #'
@@ -28,11 +33,11 @@
 #' where the first subtree has 3 leafs and the second 2 leafs. If an
 #' instance ends up in leaf 2 in the first subtree and leaf 1 in
 #' second subtree, the overall input to the linear classifier will
-#' be the binary vector `[0, 1, 0, 1, 0]`, where the first 3 entries
+#' be the binary vector \code{[0, 1, 0, 1, 0]}, where the first 3 entries
 #' correspond to the leaves of the first subtree and last 2 to
 #' those of the second subtree.
 #'
-#' ...
+#' [...]
 #'
 #' We can understand boosted decision tree
 #' based transformation as a supervised feature encoding that
@@ -40,23 +45,16 @@
 #' vector. A traversal from root node to a leaf node represents
 #' a rule on certain features."
 #'
-#' @param model Decision tree boosting model learned on the original data.
-#' @param data Original data (usually provided as a `dgCMatrix` matrix).
-#' @param ... Currently not used.
-#'
-#' @return A `dgCMatrix` matrix including both the original data and the new features.
-#'
 #' @examples
-#' data(agaricus.train, package = "xgboost")
-#' data(agaricus.test, package = "xgboost")
-#'
+#' data(agaricus.train, package='xgboost')
+#' data(agaricus.test, package='xgboost')
 #' dtrain <- with(agaricus.train, xgb.DMatrix(data, label = label, nthread = 2))
 #' dtest <- with(agaricus.test, xgb.DMatrix(data, label = label, nthread = 2))
 #'
-#' param <- list(max_depth = 2, eta = 1, objective = 'binary:logistic')
+#' param <- list(max_depth=2, eta=1, objective='binary:logistic')
 #' nrounds = 4
 #'
-#' bst <- xgb.train(params = param, data = dtrain, nrounds = nrounds, nthread = 2)
+#' bst = xgb.train(params = param, data = dtrain, nrounds = nrounds, nthread = 2)
 #'
 #' # Model accuracy without new features
 #' accuracy.before <- sum((predict(bst, agaricus.test$data) >= 0.5) == agaricus.test$label) /

R-package/R/xgb.cv.R

@@ -2,141 +2,141 @@
 #'
 #' The cross validation function of xgboost.
 #'
-#' @param params The list of parameters. The complete list of parameters is available in the
-#'   [online documentation](http://xgboost.readthedocs.io/en/latest/parameter.html).
-#'   Below is a shorter summary:
-#'   - `objective`: Objective function, common ones are
-#'      - `reg:squarederror`: Regression with squared loss.
-#'      - `binary:logistic`: Logistic regression for classification.
+#' @param params the list of parameters. The complete list of parameters is
+#'   available in the \href{http://xgboost.readthedocs.io/en/latest/parameter.html}{online documentation}. Below
+#'   is a shorter summary:
+#' \itemize{
+#'   \item \code{objective} objective function, common ones are
+#'   \itemize{
+#'     \item \code{reg:squarederror} Regression with squared loss.
+#'     \item \code{binary:logistic} logistic regression for classification.
+#'     \item See \code{\link[=xgb.train]{xgb.train}()} for complete list of objectives.
+#'   }
+#'   \item \code{eta} step size of each boosting step
+#'   \item \code{max_depth} maximum depth of the tree
+#'   \item \code{nthread} number of thread used in training, if not set, all threads are used
+#' }
 #'
-#'     See [xgb.train()] for complete list of objectives.
-#'   - `eta`: Step size of each boosting step
-#'   - `max_depth`: Maximum depth of the tree
-#'   - `nthread`: Number of threads used in training. If not set, all threads are used
+#'   See \code{\link{xgb.train}} for further details.
+#'   See also demo/ for walkthrough example in R.
 #'
-#'   See [xgb.train()] for further details.
-#'   See also demo for walkthrough example in R.
-#'
-#'   Note that, while `params` accepts a `seed` entry and will use such parameter for model training if
-#'   supplied, this seed is not used for creation of train-test splits, which instead rely on R's own RNG
-#'   system - thus, for reproducible results, one needs to call the [set.seed()] function beforehand.
+#' Note that, while `params` accepts a `seed` entry and will use such parameter for model training if
+#' supplied, this seed is not used for creation of train-test splits, which instead rely on R's own RNG
+#' system - thus, for reproducible results, one needs to call the `set.seed` function beforehand.
 #' @param data An `xgb.DMatrix` object, with corresponding fields like `label` or bounds as required
-#'   for model training by the objective.
+#'        for model training by the objective.
 #'
-#'   Note that only the basic `xgb.DMatrix` class is supported - variants such as `xgb.QuantileDMatrix`
-#'   or `xgb.ExtMemDMatrix` are not supported here.
-#' @param nrounds The max number of iterations.
-#' @param nfold The original dataset is randomly partitioned into `nfold` equal size subsamples.
+#'        Note that only the basic `xgb.DMatrix` class is supported - variants such as `xgb.QuantileDMatrix`
+#'        or `xgb.ExternalDMatrix` are not supported here.
+#' @param nrounds the max number of iterations
+#' @param nfold the original dataset is randomly partitioned into \code{nfold} equal size subsamples.
 #' @param prediction A logical value indicating whether to return the test fold predictions
-#'   from each CV model. This parameter engages the [xgb.cb.cv.predict()] callback.
-#' @param showsd Logical value whether to show standard deviation of cross validation.
-#' @param metrics List of evaluation metrics to be used in cross validation,
+#'        from each CV model. This parameter engages the \code{\link{xgb.cb.cv.predict}} callback.
+#' @param showsd \code{boolean}, whether to show standard deviation of cross validation
+#' @param metrics, list of evaluation metrics to be used in cross validation,
 #'   when it is not specified, the evaluation metric is chosen according to objective function.
 #'   Possible options are:
-#'   - `error`: Binary classification error rate
-#'   - `rmse`: Root mean square error
-#'   - `logloss`: Negative log-likelihood function
-#'   - `mae`: Mean absolute error
-#'   - `mape`: Mean absolute percentage error
-#'   - `auc`: Area under curve
-#'   - `aucpr`: Area under PR curve
-#'   - `merror`: Exact matching error used to evaluate multi-class classification
-#' @param obj Customized objective function. Returns gradient and second order
-#'   gradient with given prediction and dtrain.
-#' @param feval Customized evaluation function. Returns
-#'   `list(metric='metric-name', value='metric-value')` with given prediction and dtrain.
-#' @param stratified Logical flag indicating whether sampling of folds should be stratified
-#'   by the values of outcome labels. For real-valued labels in regression objectives,
-#'   stratification will be done by discretizing the labels into up to 5 buckets beforehand.
+#' \itemize{
+#'   \item \code{error} binary classification error rate
+#'   \item \code{rmse} Rooted mean square error
+#'   \item \code{logloss} negative log-likelihood function
+#'   \item \code{mae} Mean absolute error
+#'   \item \code{mape} Mean absolute percentage error
+#'   \item \code{auc} Area under curve
+#'   \item \code{aucpr} Area under PR curve
+#'   \item \code{merror} Exact matching error, used to evaluate multi-class classification
+#' }
+#' @param obj customized objective function. Returns gradient and second order
+#'        gradient with given prediction and dtrain.
+#' @param feval customized evaluation function. Returns
+#'        \code{list(metric='metric-name', value='metric-value')} with given
+#'        prediction and dtrain.
+#' @param stratified A \code{boolean} indicating whether sampling of folds should be stratified
+#'        by the values of outcome labels. For real-valued labels in regression objectives,
+#'        stratification will be done by discretizing the labels into up to 5 buckets beforehand.
 #'
-#'   If passing "auto", will be set to `TRUE` if the objective in `params` is a classification
-#'   objective (from XGBoost's built-in objectives, doesn't apply to custom ones), and to
-#'   `FALSE` otherwise.
+#'        If passing "auto", will be set to `TRUE` if the objective in `params` is a classification
+#'        objective (from XGBoost's built-in objectives, doesn't apply to custom ones), and to
+#'        `FALSE` otherwise.
 #'
-#'   This parameter is ignored when `data` has a `group` field - in such case, the splitting
-#'   will be based on whole groups (note that this might make the folds have different sizes).
+#'        This parameter is ignored when `data` has a `group` field - in such case, the splitting
+#'        will be based on whole groups (note that this might make the folds have different sizes).
 #'
-#'   Value `TRUE` here is **not** supported for custom objectives.
-#' @param folds List with pre-defined CV folds (each element must be a vector of test fold's indices).
-#'   When folds are supplied, the `nfold` and `stratified` parameters are ignored.
+#'        Value `TRUE` here is \bold{not} supported for custom objectives.
+#' @param folds \code{list} provides a possibility to use a list of pre-defined CV folds
+#'        (each element must be a vector of test fold's indices). When folds are supplied,
+#'        the \code{nfold} and \code{stratified} parameters are ignored.
 #'
-#'   If `data` has a `group` field and the objective requires this field, each fold (list element)
-#'   must additionally have two attributes (retrievable through `attributes`) named `group_test`
-#'   and `group_train`, which should hold the `group` to assign through [setinfo.xgb.DMatrix()] to
-#'   the resulting DMatrices.
-#' @param train_folds List specifying which indices to use for training. If `NULL`
-#'   (the default) all indices not specified in `folds` will be used for training.
+#'        If `data` has a `group` field and the objective requires this field, each fold (list element)
+#'        must additionally have two attributes (retrievable through \link{attributes}) named `group_test`
+#'        and `group_train`, which should hold the `group` to assign through \link{setinfo.xgb.DMatrix} to
+#'        the resulting DMatrices.
+#' @param train_folds \code{list} list specifying which indicies to use for training. If \code{NULL}
+#'        (the default) all indices not specified in \code{folds} will be used for training.
 #'
-#'   This is not supported when `data` has `group` field.
-#' @param verbose Logical flag. Should statistics be printed during the process?
-#' @param print_every_n Print each nth iteration evaluation messages when `verbose > 0`.
-#'   Default is 1 which means all messages are printed. This parameter is passed to the
-#'   [xgb.cb.print.evaluation()] callback.
-#' @param early_stopping_rounds If `NULL`, the early stopping function is not triggered.
-#'   If set to an integer `k`, training with a validation set will stop if the performance
-#'   doesn't improve for `k` rounds.
-#'   Setting this parameter engages the [xgb.cb.early.stop()] callback.
-#' @param maximize If `feval` and `early_stopping_rounds` are set,
-#'   then this parameter must be set as well.
-#'   When it is `TRUE`, it means the larger the evaluation score the better.
-#'   This parameter is passed to the [xgb.cb.early.stop()] callback.
-#' @param callbacks A list of callback functions to perform various task during boosting.
-#'   See [xgb.Callback()]. Some of the callbacks are automatically created depending on the
-#'   parameters' values. User can provide either existing or their own callback methods in order
-#'   to customize the training process.
-#' @param ... Other parameters to pass to `params`.
+#'        This is not supported when `data` has `group` field.
+#' @param verbose \code{boolean}, print the statistics during the process
+#' @param print_every_n Print each n-th iteration evaluation messages when \code{verbose>0}.
+#'        Default is 1 which means all messages are printed. This parameter is passed to the
+#'        \code{\link{xgb.cb.print.evaluation}} callback.
+#' @param early_stopping_rounds If \code{NULL}, the early stopping function is not triggered.
+#'        If set to an integer \code{k}, training with a validation set will stop if the performance
+#'        doesn't improve for \code{k} rounds.
+#'        Setting this parameter engages the \code{\link{xgb.cb.early.stop}} callback.
+#' @param maximize If \code{feval} and \code{early_stopping_rounds} are set,
+#'        then this parameter must be set as well.
+#'        When it is \code{TRUE}, it means the larger the evaluation score the better.
+#'        This parameter is passed to the \code{\link{xgb.cb.early.stop}} callback.
+#' @param callbacks a list of callback functions to perform various task during boosting.
+#'        See \code{\link{xgb.Callback}}. Some of the callbacks are automatically created depending on the
+#'        parameters' values. User can provide either existing or their own callback methods in order
+#'        to customize the training process.
+#' @param ... other parameters to pass to \code{params}.
 #'
 #' @details
-#' The original sample is randomly partitioned into `nfold` equal size subsamples.
+#' The original sample is randomly partitioned into \code{nfold} equal size subsamples.
 #'
-#' Of the `nfold` subsamples, a single subsample is retained as the validation data for testing the model,
-#' and the remaining `nfold - 1` subsamples are used as training data.
+#' Of the \code{nfold} subsamples, a single subsample is retained as the validation data for testing the model,
+#' and the remaining \code{nfold - 1} subsamples are used as training data.
 #'
-#' The cross-validation process is then repeated `nrounds` times, with each of the
-#' `nfold` subsamples used exactly once as the validation data.
+#' The cross-validation process is then repeated \code{nrounds} times, with each of the
+#' \code{nfold} subsamples used exactly once as the validation data.
 #'
 #' All observations are used for both training and validation.
 #'
 #' Adapted from \url{https://en.wikipedia.org/wiki/Cross-validation_\%28statistics\%29}
 #'
 #' @return
-#'   An object of class 'xgb.cv.synchronous' with the following elements:
-#'   - `call`: Function call.
-#'   - `params`: Parameters that were passed to the xgboost library. Note that it does not
-#'     capture parameters changed by the [xgb.cb.reset.parameters()] callback.
-#'   - `evaluation_log`: Evaluation history stored as a `data.table` with the
-#'     first column corresponding to iteration number and the rest corresponding to the
-#'     CV-based evaluation means and standard deviations for the training and test CV-sets.
-#'     It is created by the [xgb.cb.evaluation.log()] callback.
-#'   - `niter`: Number of boosting iterations.
-#'   - `nfeatures`: Number of features in training data.
-#'   - `folds`: The list of CV folds' indices - either those passed through the `folds`
-#'      parameter or randomly generated.
-#'   - `best_iteration`: Iteration number with the best evaluation metric value
-#'      (only available with early stopping).
+#' An object of class \code{xgb.cv.synchronous} with the following elements:
+#' \itemize{
+#'   \item \code{call} a function call.
+#'   \item \code{params} parameters that were passed to the xgboost library. Note that it does not
+#'         capture parameters changed by the \code{\link{xgb.cb.reset.parameters}} callback.
+#'   \item \code{evaluation_log} evaluation history stored as a \code{data.table} with the
+#'         first column corresponding to iteration number and the rest corresponding to the
+#'         CV-based evaluation means and standard deviations for the training and test CV-sets.
+#'         It is created by the \code{\link{xgb.cb.evaluation.log}} callback.
+#'   \item \code{niter} number of boosting iterations.
+#'   \item \code{nfeatures} number of features in training data.
+#'   \item \code{folds} the list of CV folds' indices - either those passed through the \code{folds}
+#'         parameter or randomly generated.
+#'   \item \code{best_iteration} iteration number with the best evaluation metric value
+#'         (only available with early stopping).
+#' }
 #'
-#'   Plus other potential elements that are the result of callbacks, such as a list `cv_predict` with
-#'   a sub-element `pred` when passing `prediction = TRUE`, which is added by the [xgb.cb.cv.predict()]
-#'   callback (note that one can also pass it manually under `callbacks` with different settings,
-#'   such as saving also the models created during cross validation); or a list `early_stop` which
-#'   will contain elements such as `best_iteration` when using the early stopping callback ([xgb.cb.early.stop()]).
+#' Plus other potential elements that are the result of callbacks, such as a list `cv_predict` with
+#' a sub-element `pred` when passing `prediction = TRUE`, which is added by the \link{xgb.cb.cv.predict}
+#' callback (note that one can also pass it manually under `callbacks` with different settings,
+#' such as saving also the models created during cross validation); or a list `early_stop` which
+#' will contain elements such as `best_iteration` when using the early stopping callback (\link{xgb.cb.early.stop}).
 #'
 #' @examples
-#' data(agaricus.train, package = "xgboost")
-#'
+#' data(agaricus.train, package='xgboost')
 #' dtrain <- with(agaricus.train, xgb.DMatrix(data, label = label, nthread = 2))
-#'
-#' cv <- xgb.cv(
-#'   data = dtrain,
-#'   nrounds = 3,
-#'   nthread = 2,
-#'   nfold = 5,
-#'   metrics = list("rmse","auc"),
-#'   max_depth = 3,
-#'   eta = 1,objective = "binary:logistic"
-#' )
+#' cv <- xgb.cv(data = dtrain, nrounds = 3, nthread = 2, nfold = 5, metrics = list("rmse","auc"),
+#'              max_depth = 3, eta = 1, objective = "binary:logistic")
 #' print(cv)
-#' print(cv, verbose = TRUE)
+#' print(cv, verbose=TRUE)
 #'
 #' @export
 xgb.cv <- function(params = list(), data, nrounds, nfold,
@@ -325,31 +325,23 @@ xgb.cv <- function(params = list(), data, nrounds, nfold,
 
 #' Print xgb.cv result
 #'
-#' Prints formatted results of [xgb.cv()].
+#' Prints formatted results of \code{xgb.cv}.
 #'
-#' @param x An `xgb.cv.synchronous` object.
-#' @param verbose Whether to print detailed data.
-#' @param ... Passed to `data.table.print()`.
+#' @param x an \code{xgb.cv.synchronous} object
+#' @param verbose whether to print detailed data
+#' @param ... passed to \code{data.table.print}
 #'
 #' @details
 #' When not verbose, it would only print the evaluation results,
 #' including the best iteration (when available).
 #'
 #' @examples
-#' data(agaricus.train, package = "xgboost")
-#'
+#' data(agaricus.train, package='xgboost')
 #' train <- agaricus.train
-#' cv <- xgb.cv(
-#'   data = xgb.DMatrix(train$data, label = train$label),
-#'   nfold = 5,
-#'   max_depth = 2,
-#'   eta = 1,
-#'   nthread = 2,
-#'   nrounds = 2,
-#'   objective = "binary:logistic"
-#' )
+#' cv <- xgb.cv(data = xgb.DMatrix(train$data, label = train$label), nfold = 5, max_depth = 2,
+#'              eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic")
 #' print(cv)
-#' print(cv, verbose = TRUE)
+#' print(cv, verbose=TRUE)
 #'
 #' @rdname print.xgb.cv
 #' @method print xgb.cv.synchronous

R-package/R/xgb.dump.R

@@ -1,44 +1,36 @@
-#' Dump an XGBoost model in text format.
+#' Dump an xgboost model in text format.
 #'
-#' Dump an XGBoost model in text format.
+#' Dump an xgboost model in text format.
 #'
-#' @param model The model object.
-#' @param fname The name of the text file where to save the model text dump.
-#'   If not provided or set to `NULL`, the model is returned as a character vector.
-#' @param fmap Feature map file representing feature types. See demo/ for a walkthrough
-#'   example in R, and \url{https://github.com/dmlc/xgboost/blob/master/demo/data/featmap.txt}
-#'   to see an example of the value.
-#' @param with_stats Whether to dump some additional statistics about the splits.
-#'   When this option is on, the model dump contains two additional values:
-#'   gain is the approximate loss function gain we get in each split;
-#'   cover is the sum of second order gradient in each node.
-#' @param dump_format Either 'text', 'json', or 'dot' (graphviz) format could be specified.
+#' @param model the model object.
+#' @param fname the name of the text file where to save the model text dump.
+#'        If not provided or set to \code{NULL}, the model is returned as a \code{character} vector.
+#' @param fmap feature map file representing feature types.
+#'        See demo/ for walkthrough example in R, and
+#'        \url{https://github.com/dmlc/xgboost/blob/master/demo/data/featmap.txt}
+#'        for example Format.
+#' @param with_stats whether to dump some additional statistics about the splits.
+#'        When this option is on, the model dump contains two additional values:
+#'        gain is the approximate loss function gain we get in each split;
+#'        cover is the sum of second order gradient in each node.
+#' @param dump_format either 'text', 'json', or 'dot' (graphviz) format could be specified.
 #'
-#'   Format 'dot' for a single tree can be passed directly to packages that consume this format
-#'   for graph visualization, such as function `DiagrammeR::grViz()`
-#' @param ... Currently not used
+#' Format 'dot' for a single tree can be passed directly to packages that consume this format
+#' for graph visualization, such as function [DiagrammeR::grViz()]
+#' @param ... currently not used
 #'
 #' @return
-#' If fname is not provided or set to `NULL` the function will return the model
-#' as a character vector. Otherwise it will return `TRUE`.
+#' If fname is not provided or set to \code{NULL} the function will return the model
+#' as a \code{character} vector. Otherwise it will return \code{TRUE}.
 #'
 #' @examples
 #' \dontshow{RhpcBLASctl::omp_set_num_threads(1)}
-#' data(agaricus.train, package = "xgboost")
-#' data(agaricus.test, package = "xgboost")
-#'
+#' data(agaricus.train, package='xgboost')
+#' data(agaricus.test, package='xgboost')
 #' train <- agaricus.train
 #' test <- agaricus.test
-#'
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(train$data, label = train$label),
-#'   max_depth = 2,
-#'   eta = 1,
-#'   nthread = 2,
-#'   nrounds = 2,
-#'   objective = "binary:logistic"
-#' )
-#'
+#' bst <- xgboost(data = train$data, label = train$label, max_depth = 2,
+#'                eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic")
 #' # save the model in file 'xgb.model.dump'
 #' dump_path = file.path(tempdir(), 'model.dump')
 #' xgb.dump(bst, dump_path, with_stats = TRUE)
@@ -47,7 +39,7 @@
 #' print(xgb.dump(bst, with_stats = TRUE))
 #'
 #' # print in JSON format:
-#' cat(xgb.dump(bst, with_stats = TRUE, dump_format = "json"))
+#' cat(xgb.dump(bst, with_stats = TRUE, dump_format='json'))
 #'
 #' # plot first tree leveraging the 'dot' format
 #' if (requireNamespace('DiagrammeR', quietly = TRUE)) {

R-package/R/xgb.ggplot.R

@@ -1,5 +1,6 @@
 # ggplot backend for the xgboost plotting facilities
 
+
 #' @rdname xgb.plot.importance
 #' @export
 xgb.ggplot.importance <- function(importance_matrix = NULL, top_n = NULL, measure = NULL,
@@ -102,27 +103,6 @@ xgb.ggplot.deepness <- function(model = NULL, which = c("2x1", "max.depth", "med
 #' @export
 xgb.ggplot.shap.summary <- function(data, shap_contrib = NULL, features = NULL, top_n = 10, model = NULL,
                                     trees = NULL, target_class = NULL, approxcontrib = FALSE, subsample = NULL) {
-  if (inherits(data, "xgb.DMatrix")) {
-    stop(
-      "'xgb.ggplot.shap.summary' is not compatible with 'xgb.DMatrix' objects. Try passing a matrix or data.frame."
-    )
-  }
-  cols_categ <- NULL
-  if (!is.null(model)) {
-    ftypes <- getinfo(model, "feature_type")
-    if (NROW(ftypes)) {
-      if (length(ftypes) != ncol(data)) {
-        stop(sprintf("'data' has incorrect number of columns (expected: %d, got: %d).", length(ftypes), ncol(data)))
-      }
-      cols_categ <- colnames(data)[ftypes == "c"]
-    }
-  } else if (inherits(data, "data.frame")) {
-    cols_categ <- names(data)[sapply(data, function(x) is.factor(x) || is.character(x))]
-  }
-  if (NROW(cols_categ)) {
-    warning("Categorical features are ignored in 'xgb.ggplot.shap.summary'.")
-  }
-
   data_list <- xgb.shap.data(
     data = data,
     shap_contrib = shap_contrib,
@@ -135,10 +115,6 @@ xgb.ggplot.shap.summary <- function(data, shap_contrib = NULL, features = NULL,
     subsample = subsample,
     max_observations = 10000  # 10,000 samples per feature.
   )
-  if (NROW(cols_categ)) {
-    data_list <- lapply(data_list, function(x) x[, !(colnames(x) %in% cols_categ), drop = FALSE])
-  }
-
   p_data <- prepare.ggplot.shap.data(data_list, normalize = TRUE)
   # Reverse factor levels so that the first level is at the top of the plot
   p_data[, "feature" := factor(feature, rev(levels(feature)))]
@@ -159,8 +135,8 @@ xgb.ggplot.shap.summary <- function(data, shap_contrib = NULL, features = NULL,
 #' @param data_list The result of `xgb.shap.data()`.
 #' @param normalize Whether to standardize feature values to mean 0 and
 #'   standard deviation 1. This is useful for comparing multiple features on the same
-#'   plot. Default is `FALSE`. Note that it cannot be used when the data contains
-#'   categorical features.
+#'   plot. Default is \code{FALSE}.
+#'
 #' @return A `data.table` containing the observation ID, the feature name, the
 #'   feature value (normalized if specified), and the SHAP contribution value.
 #' @noRd
@@ -191,6 +167,7 @@ prepare.ggplot.shap.data <- function(data_list, normalize = FALSE) {
 #' Useful to compare multiple features on the same plot.
 #'
 #' @param x Numeric vector.
+#'
 #' @return Numeric vector with mean 0 and standard deviation 1.
 #' @noRd
 #' @keywords internal

R-package/R/xgb.importance.R

@@ -2,25 +2,27 @@
 #'
 #' Creates a `data.table` of feature importances.
 #'
+#' @param feature_names Character vector used to overwrite the feature names
+#'        of the model. The default is `NULL` (use original feature names).
+#' @param model Object of class `xgb.Booster`.
+#' @param trees An integer vector of tree indices that should be included
+#'        into the importance calculation (only for the "gbtree" booster).
+#'        The default (`NULL`) parses all trees.
+#'        It could be useful, e.g., in multiclass classification to get feature importances
+#'        for each class separately. *Important*: the tree index in XGBoost models
+#'        is zero-based (e.g., use `trees = 0:4` for the first five trees).
+#' @param data Deprecated.
+#' @param label Deprecated.
+#' @param target Deprecated.
+#'
 #' @details
+#'
 #' This function works for both linear and tree models.
 #'
 #' For linear models, the importance is the absolute magnitude of linear coefficients.
 #' To obtain a meaningful ranking by importance for linear models, the features need to
 #' be on the same scale (which is also recommended when using L1 or L2 regularization).
 #'
-#' @param feature_names Character vector used to overwrite the feature names
-#'   of the model. The default is `NULL` (use original feature names).
-#' @param model Object of class `xgb.Booster`.
-#' @param trees An integer vector of tree indices that should be included
-#'   into the importance calculation (only for the "gbtree" booster).
-#'   The default (`NULL`) parses all trees.
-#'   It could be useful, e.g., in multiclass classification to get feature importances
-#'   for each class separately. *Important*: the tree index in XGBoost models
-#'   is zero-based (e.g., use `trees = 0:4` for the first five trees).
-#' @param data Deprecated.
-#' @param label Deprecated.
-#' @param target Deprecated.
 #' @return A `data.table` with the following columns:
 #'
 #' For a tree model:
@@ -44,8 +46,9 @@
 #' # binomial classification using "gbtree":
 #' data(agaricus.train, package = "xgboost")
 #'
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
+#' bst <- xgboost(
+#'   data = agaricus.train$data,
+#'   label = agaricus.train$label,
 #'   max_depth = 2,
 #'   eta = 1,
 #'   nthread = 2,
@@ -56,8 +59,9 @@
 #' xgb.importance(model = bst)
 #'
 #' # binomial classification using "gblinear":
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
+#' bst <- xgboost(
+#'   data = agaricus.train$data,
+#'   label = agaricus.train$label,
 #'   booster = "gblinear",
 #'   eta = 0.3,
 #'   nthread = 1,
@@ -69,11 +73,9 @@
 #' # multiclass classification using "gbtree":
 #' nclass <- 3
 #' nrounds <- 10
-#' mbst <- xgb.train(
-#'   data = xgb.DMatrix(
-#'     as.matrix(iris[, -5]),
-#'     label = as.numeric(iris$Species) - 1
-#'   ),
+#' mbst <- xgboost(
+#'   data = as.matrix(iris[, -5]),
+#'   label = as.numeric(iris$Species) - 1,
 #'   max_depth = 3,
 #'   eta = 0.2,
 #'   nthread = 2,
@@ -97,11 +99,9 @@
 #' )
 #'
 #' # multiclass classification using "gblinear":
-#' mbst <- xgb.train(
-#'   data = xgb.DMatrix(
-#'     scale(as.matrix(iris[, -5])),
-#'     label = as.numeric(iris$Species) - 1
-#'   ),
+#' mbst <- xgboost(
+#'   data = scale(as.matrix(iris[, -5])),
+#'   label = as.numeric(iris$Species) - 1,
 #'   booster = "gblinear",
 #'   eta = 0.2,
 #'   nthread = 1,

R-package/R/xgb.load.R

@@ -1,27 +1,28 @@
-#' Load XGBoost model from binary file
+#' Load xgboost model from binary file
 #'
-#' Load XGBoost model from binary model file.
+#' Load xgboost model from the binary model file.
 #'
-#' @param modelfile The name of the binary input file.
+#' @param modelfile the name of the binary input file.
 #'
 #' @details
-#' The input file is expected to contain a model saved in an XGBoost model format
-#' using either [xgb.save()] in R, or using some
-#' appropriate methods from other XGBoost interfaces. E.g., a model trained in Python and
-#' saved from there in XGBoost format, could be loaded from R.
+#' The input file is expected to contain a model saved in an xgboost model format
+#' using either \code{\link{xgb.save}} or \code{\link{xgb.cb.save.model}} in R, or using some
+#' appropriate methods from other xgboost interfaces. E.g., a model trained in Python and
+#' saved from there in xgboost format, could be loaded from R.
 #'
-#' Note: a model saved as an R object has to be loaded using corresponding R-methods,
-#' not by [xgb.load()].
+#' Note: a model saved as an R-object, has to be loaded using corresponding R-methods,
+#' not \code{xgb.load}.
 #'
 #' @return
-#' An object of `xgb.Booster` class.
+#' An object of \code{xgb.Booster} class.
 #'
-#' @seealso [xgb.save()]
+#' @seealso
+#' \code{\link{xgb.save}}
 #'
 #' @examples
 #' \dontshow{RhpcBLASctl::omp_set_num_threads(1)}
-#' data(agaricus.train, package = "xgboost")
-#' data(agaricus.test, package = "xgboost")
+#' data(agaricus.train, package='xgboost')
+#' data(agaricus.test, package='xgboost')
 #'
 #' ## Keep the number of threads to 1 for examples
 #' nthread <- 1
@@ -29,7 +30,6 @@
 #'
 #' train <- agaricus.train
 #' test <- agaricus.test
-#'
 #' bst <- xgb.train(
 #'   data = xgb.DMatrix(train$data, label = train$label),
 #'   max_depth = 2,

R-package/R/xgb.load.raw.R

@@ -1,8 +1,8 @@
-#' Load serialised XGBoost model from R's raw vector
+#' Load serialised xgboost model from R's raw vector
 #'
-#' User can generate raw memory buffer by calling [xgb.save.raw()].
+#' User can generate raw memory buffer by calling xgb.save.raw
 #'
-#' @param buffer The buffer returned by [xgb.save.raw()].
+#' @param buffer the buffer returned by xgb.save.raw
 #' @export
 xgb.load.raw <- function(buffer) {
   cachelist <- list()

R-package/R/xgb.model.dt.tree.R

@@ -2,17 +2,18 @@
 #'
 #' Parse a boosted tree model text dump into a `data.table` structure.
 #'
-#' @param model Object of class `xgb.Booster`. If it contains feature names (they can
-#'   be set through [setinfo()]), they will be used in the output from this function.
+#' @param model Object of class `xgb.Booster`. If it contains feature names (they can be set through
+#'        \link{setinfo}), they will be used in the output from this function.
 #' @param text Character vector previously generated by the function [xgb.dump()]
-#'   (called with parameter `with_stats = TRUE`). `text` takes precedence over `model`.
-#' @param trees An integer vector of tree indices that should be used. The default
-#'   (`NULL`) uses all trees. Useful, e.g., in multiclass classification to get only
-#'   the trees of one class. *Important*: the tree index in XGBoost models
-#'   is zero-based (e.g., use `trees = 0:4` for the first five trees).
+#'        (called with parameter `with_stats = TRUE`). `text` takes precedence over `model`.
+#' @param trees An integer vector of tree indices that should be used.
+#'        The default (`NULL`) uses all trees.
+#'        Useful, e.g., in multiclass classification to get only
+#'        the trees of one class. *Important*: the tree index in XGBoost models
+#'        is zero-based (e.g., use `trees = 0:4` for the first five trees).
 #' @param use_int_id A logical flag indicating whether nodes in columns "Yes", "No", and
-#'   "Missing" should be represented as integers (when `TRUE`) or as "Tree-Node"
-#'   character strings (when `FALSE`, default).
+#'        "Missing" should be represented as integers (when `TRUE`) or as "Tree-Node"
+#'        character strings (when `FALSE`, default).
 #' @param ... Currently not used.
 #'
 #' @return
@@ -42,8 +43,9 @@
 #' nthread <- 1
 #' data.table::setDTthreads(nthread)
 #'
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
+#' bst <- xgboost(
+#'   data = agaricus.train$data,
+#'   label = agaricus.train$label,
 #'   max_depth = 2,
 #'   eta = 1,
 #'   nthread = nthread,
@@ -89,7 +91,7 @@ xgb.model.dt.tree <- function(model = NULL, text = NULL,
     from_text <- FALSE
   }
 
-  if (length(text) < 2 || !any(grepl('leaf=(-?\\d+)', text))) {
+  if (length(text) < 2 || !any(grepl('leaf=(\\d+)', text))) {
     stop("Non-tree model detected! This function can only be used with tree models.")
   }
 
@@ -108,7 +110,7 @@ xgb.model.dt.tree <- function(model = NULL, text = NULL,
   } else {
     trees <- trees[trees >= 0 & trees <= max(td$Tree)]
   }
-  td <- td[Tree %in% trees & !is.na(t) & !startsWith(t, 'booster')]
+  td <- td[Tree %in% trees & !grepl('^booster', t)]
 
   td[, Node := as.integer(sub("^([0-9]+):.*", "\\1", t))]
   if (!use_int_id) td[, ID := add.tree.id(Node, Tree)]
@@ -194,7 +196,7 @@ xgb.model.dt.tree <- function(model = NULL, text = NULL,
   td[order(Tree, Node)]
 }
 
-# Avoid notes during CRAN check.
+# Avoid error messages during CRAN check.
 # The reason is that these variables are never declared
 # They are mainly column names inferred by Data.table...
 globalVariables(c("Tree", "Node", "ID", "Feature", "t", "isLeaf", ".SD", ".SDcols"))

R-package/R/xgb.plot.deepness.R

@@ -4,8 +4,7 @@
 #' - `xgb.plot.deepness()` uses base R graphics, while
 #' - `xgb.ggplot.deepness()` uses "ggplot2".
 #'
-#' @param model Either an `xgb.Booster` model, or the "data.table" returned
-#'   by [xgb.model.dt.tree()].
+#' @param model Either an `xgb.Booster` model, or the "data.table" returned by [xgb.model.dt.tree()].
 #' @param which Which distribution to plot (see details).
 #' @param plot Should the plot be shown? Default is `TRUE`.
 #' @param ... Other parameters passed to [graphics::barplot()] or [graphics::plot()].
@@ -49,8 +48,9 @@
 #' data.table::setDTthreads(nthread)
 #'
 #' ## Change max_depth to a higher number to get a more significant result
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
+#' bst <- xgboost(
+#'   data = agaricus.train$data,
+#'   label = agaricus.train$label,
 #'   max_depth = 6,
 #'   nthread = nthread,
 #'   nrounds = 50,

R-package/R/xgb.plot.importance.R

@@ -4,9 +4,25 @@
 #' - `xgb.plot.importance()` uses base R graphics, while
 #' - `xgb.ggplot.importance()` uses "ggplot".
 #'
+#' @param importance_matrix A `data.table` as returned by [xgb.importance()].
+#' @param top_n Maximal number of top features to include into the plot.
+#' @param measure The name of importance measure to plot.
+#'        When `NULL`, 'Gain' would be used for trees and 'Weight' would be used for gblinear.
+#' @param rel_to_first Whether importance values should be represented as relative to
+#'        the highest ranked feature, see Details.
+#' @param left_margin Adjust the left margin size to fit feature names.
+#'        When `NULL`, the existing `par("mar")` is used.
+#' @param cex Passed as `cex.names` parameter to [graphics::barplot()].
+#' @param plot Should the barplot be shown? Default is `TRUE`.
+#' @param n_clusters A numeric vector containing the min and the max range
+#'        of the possible number of clusters of bars.
+#' @param ... Other parameters passed to [graphics::barplot()]
+#'        (except `horiz`, `border`, `cex.names`, `names.arg`, and `las`).
+#'        Only used in `xgb.plot.importance()`.
+#'
 #' @details
-#' The graph represents each feature as a horizontal bar of length proportional to the
-#' importance of a feature. Features are sorted by decreasing importance.
+#' The graph represents each feature as a horizontal bar of length proportional to the importance of a feature.
+#' Features are sorted by decreasing importance.
 #' It works for both "gblinear" and "gbtree" models.
 #'
 #' When `rel_to_first = FALSE`, the values would be plotted as in `importance_matrix`.
@@ -19,21 +35,6 @@
 #' The "ggplot" backend performs 1-D clustering of the importance values,
 #' with bar colors corresponding to different clusters having similar importance values.
 #'
-#' @param importance_matrix A `data.table` as returned by [xgb.importance()].
-#' @param top_n Maximal number of top features to include into the plot.
-#' @param measure The name of importance measure to plot.
-#'   When `NULL`, 'Gain' would be used for trees and 'Weight' would be used for gblinear.
-#' @param rel_to_first Whether importance values should be represented as relative to
-#'   the highest ranked feature, see Details.
-#' @param left_margin Adjust the left margin size to fit feature names.
-#'   When `NULL`, the existing `par("mar")` is used.
-#' @param cex Passed as `cex.names` parameter to [graphics::barplot()].
-#' @param plot Should the barplot be shown? Default is `TRUE`.
-#' @param n_clusters A numeric vector containing the min and the max range
-#'   of the possible number of clusters of bars.
-#' @param ... Other parameters passed to [graphics::barplot()]
-#'   (except `horiz`, `border`, `cex.names`, `names.arg`, and `las`).
-#'   Only used in `xgb.plot.importance()`.
 #' @return
 #' The return value depends on the function:
 #' - `xgb.plot.importance()`: Invisibly, a "data.table" with `n_top` features sorted
@@ -50,8 +51,9 @@
 #' nthread <- 2
 #' data.table::setDTthreads(nthread)
 #'
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
+#' bst <- xgboost(
+#'   data = agaricus.train$data,
+#'   label = agaricus.train$label,
 #'   max_depth = 3,
 #'   eta = 1,
 #'   nthread = nthread,

R-package/R/xgb.plot.multi.trees.R

@@ -2,7 +2,12 @@
 #'
 #' Visualization of the ensemble of trees as a single collective unit.
 #'
+#' @inheritParams xgb.plot.tree
+#' @param features_keep Number of features to keep in each position of the multi trees,
+#'        by default 5.
+#'
 #' @details
+#'
 #' This function tries to capture the complexity of a gradient boosted tree model
 #' in a cohesive way by compressing an ensemble of trees into a single tree-graph representation.
 #' The goal is to improve the interpretability of a model generally seen as black box.
@@ -20,9 +25,6 @@
 #' This function is inspired by this blog post:
 #' <https://wellecks.wordpress.com/2015/02/21/peering-into-the-black-box-visualizing-lambdamart/>
 #'
-#' @inheritParams xgb.plot.tree
-#' @param features_keep Number of features to keep in each position of the multi trees,
-#'   by default 5.
 #' @inherit xgb.plot.tree return
 #'
 #' @examples
@@ -33,8 +35,9 @@
 #' nthread <- 2
 #' data.table::setDTthreads(nthread)
 #'
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
+#' bst <- xgboost(
+#'   data = agaricus.train$data,
+#'   label = agaricus.train$label,
 #'   max_depth = 15,
 #'   eta = 1,
 #'   nthread = nthread,
@@ -109,10 +112,11 @@ xgb.plot.multi.trees <- function(model, features_keep = 5, plot_width = NULL, pl
 
   edges.dt <- data.table::rbindlist(
     l = list(
-      tree.matrix[Feature != "Leaf", .(From = abs.node.position, To = Yes)],
-      tree.matrix[Feature != "Leaf", .(From = abs.node.position, To = No)]
+      tree.matrix[Feature != "Leaf", .(abs.node.position, Yes)],
+      tree.matrix[Feature != "Leaf", .(abs.node.position, No)]
     )
   )
+  data.table::setnames(edges.dt, c("From", "To"))
   edges.dt <- edges.dt[, .N, .(From, To)]
   edges.dt[, N := NULL]
 

R-package/R/xgb.plot.shap.R

@@ -2,43 +2,44 @@
 #'
 #' Visualizes SHAP values against feature values to gain an impression of feature effects.
 #'
-#' @param data The data to explain as a `matrix`, `dgCMatrix`, or `data.frame`.
+#' @param data The data to explain as a `matrix` or `dgCMatrix`.
 #' @param shap_contrib Matrix of SHAP contributions of `data`.
-#'   The default (`NULL`) computes it from `model` and `data`.
-#' @param features Vector of column indices or feature names to plot. When `NULL`
-#'   (default), the `top_n` most important features are selected by [xgb.importance()].
+#'        The default (`NULL`) computes it from `model` and `data`.
+#' @param features Vector of column indices or feature names to plot.
+#'        When `NULL` (default), the `top_n` most important features are selected
+#'        by [xgb.importance()].
 #' @param top_n How many of the most important features (<= 100) should be selected?
-#'   By default 1 for SHAP dependence and 10 for SHAP summary.
-#'   Only used when `features = NULL`.
+#'        By default 1 for SHAP dependence and 10 for SHAP summary).
+#'        Only used when `features = NULL`.
 #' @param model An `xgb.Booster` model. Only required when `shap_contrib = NULL` or
-#'   `features = NULL`.
+#'        `features = NULL`.
 #' @param trees Passed to [xgb.importance()] when `features = NULL`.
 #' @param target_class Only relevant for multiclass models. The default (`NULL`)
-#'   averages the SHAP values over all classes. Pass a (0-based) class index
-#'   to show only SHAP values of that class.
+#'        averages the SHAP values over all classes. Pass a (0-based) class index
+#'        to show only SHAP values of that class.
 #' @param approxcontrib Passed to `predict()` when `shap_contrib = NULL`.
 #' @param subsample Fraction of data points randomly picked for plotting.
-#'   The default (`NULL`) will use up to 100k data points.
+#'        The default (`NULL`) will use up to 100k data points.
 #' @param n_col Number of columns in a grid of plots.
 #' @param col Color of the scatterplot markers.
 #' @param pch Scatterplot marker.
 #' @param discrete_n_uniq Maximal number of unique feature values to consider the
-#'   feature as discrete.
+#'        feature as discrete.
 #' @param discrete_jitter Jitter amount added to the values of discrete features.
 #' @param ylab The y-axis label in 1D plots.
 #' @param plot_NA Should contributions of cases with missing values be plotted?
-#'   Default is `TRUE`.
+#'        Default is `TRUE`.
 #' @param col_NA Color of marker for missing value contributions.
 #' @param pch_NA Marker type for `NA` values.
 #' @param pos_NA Relative position of the x-location where `NA` values are shown:
-#'   `min(x) + (max(x) - min(x)) * pos_NA`.
+#'        `min(x) + (max(x) - min(x)) * pos_NA`.
 #' @param plot_loess Should loess-smoothed curves be plotted? (Default is `TRUE`).
-#'   The smoothing is only done for features with more than 5 distinct values.
+#'        The smoothing is only done for features with more than 5 distinct values.
 #' @param col_loess Color of loess curves.
 #' @param span_loess The `span` parameter of [stats::loess()].
 #' @param which Whether to do univariate or bivariate plotting. Currently, only "1d" is implemented.
 #' @param plot Should the plot be drawn? (Default is `TRUE`).
-#'   If `FALSE`, only a list of matrices is returned.
+#'        If `FALSE`, only a list of matrices is returned.
 #' @param ... Other parameters passed to [graphics::plot()].
 #'
 #' @details
@@ -81,8 +82,9 @@
 #' data.table::setDTthreads(nthread)
 #' nrounds <- 20
 #'
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(agaricus.train$data, agaricus.train$label),
+#' bst <- xgboost(
+#'   agaricus.train$data,
+#'   agaricus.train$label,
 #'   nrounds = nrounds,
 #'   eta = 0.1,
 #'   max_depth = 3,
@@ -106,8 +108,9 @@
 #' set.seed(123)
 #' is.na(x[sample(nrow(x) * 4, 30)]) <- TRUE # introduce some missing values
 #'
-#' mbst <- xgb.train(
-#'   data = xgb.DMatrix(x, label = as.numeric(iris$Species) - 1),
+#' mbst <- xgboost(
+#'   data = x,
+#'   label = as.numeric(iris$Species) - 1,
 #'   nrounds = nrounds,
 #'   max_depth = 2,
 #'   eta = 0.3,
@@ -119,7 +122,6 @@
 #' )
 #' trees0 <- seq(from = 0, by = nclass, length.out = nrounds)
 #' col <- rgb(0, 0, 1, 0.5)
-#'
 #' xgb.plot.shap(
 #'   x,
 #'   model = mbst,
@@ -285,11 +287,8 @@ xgb.plot.shap.summary <- function(data, shap_contrib = NULL, features = NULL, to
 xgb.shap.data <- function(data, shap_contrib = NULL, features = NULL, top_n = 1, model = NULL,
                           trees = NULL, target_class = NULL, approxcontrib = FALSE,
                           subsample = NULL, max_observations = 100000) {
-  if (!inherits(data, c("matrix", "dsparseMatrix", "data.frame")))
-    stop("data: must be matrix, sparse matrix, or data.frame.")
-  if (inherits(data, "data.frame") && length(class(data)) > 1L) {
-    data <- as.data.frame(data)
-  }
+  if (!is.matrix(data) && !inherits(data, "dgCMatrix"))
+    stop("data: must be either matrix or dgCMatrix")
 
   if (is.null(shap_contrib) && (is.null(model) || !inherits(model, "xgb.Booster")))
     stop("when shap_contrib is not provided, one must provide an xgb.Booster model")
@@ -297,10 +296,8 @@ xgb.shap.data <- function(data, shap_contrib = NULL, features = NULL, top_n = 1,
   if (is.null(features) && (is.null(model) || !inherits(model, "xgb.Booster")))
     stop("when features are not provided, one must provide an xgb.Booster model to rank the features")
 
-  last_dim <- function(v) dim(v)[length(dim(v))]
-
   if (!is.null(shap_contrib) &&
-      (!is.array(shap_contrib) || nrow(shap_contrib) != nrow(data) || last_dim(shap_contrib) != ncol(data) + 1))
+      (!is.matrix(shap_contrib) || nrow(shap_contrib) != nrow(data) || ncol(shap_contrib) != ncol(data) + 1))
     stop("shap_contrib is not compatible with the provided data")
 
   if (is.character(features) && is.null(colnames(data)))
@@ -314,14 +311,7 @@ xgb.shap.data <- function(data, shap_contrib = NULL, features = NULL, top_n = 1,
     stop("if model has no feature_names, columns in `data` must match features in model")
 
   if (!is.null(subsample)) {
-    if (subsample <= 0 || subsample >= 1) {
-      stop("'subsample' must be a number between zero and one (non-inclusive).")
-    }
-    sample_size <- as.integer(subsample * nrow(data))
-    if (sample_size < 2) {
-      stop("Sampling fraction involves less than 2 rows.")
-    }
-    idx <- sample(x = seq_len(nrow(data)), size = sample_size, replace = FALSE)
+    idx <- sample(x = seq_len(nrow(data)), size = as.integer(subsample * nrow(data)), replace = FALSE)
   } else {
     idx <- seq_len(min(nrow(data), max_observations))
   }
@@ -330,39 +320,19 @@ xgb.shap.data <- function(data, shap_contrib = NULL, features = NULL, top_n = 1,
     colnames(data) <- paste0("X", seq_len(ncol(data)))
   }
 
-  reshape_3d_shap_contrib <- function(shap_contrib, target_class) {
-    # multiclass: either choose a class or merge
-    if (is.list(shap_contrib)) {
-      if (!is.null(target_class)) {
-        shap_contrib <- shap_contrib[[target_class + 1]]
-      } else {
-        shap_contrib <- Reduce("+", lapply(shap_contrib, abs))
-      }
-    } else if (length(dim(shap_contrib)) > 2) {
-      if (!is.null(target_class)) {
-        orig_shape <- dim(shap_contrib)
-        shap_contrib <- shap_contrib[, target_class + 1, , drop = TRUE]
-        if (!is.matrix(shap_contrib)) {
-          shap_contrib <- matrix(shap_contrib, orig_shape[c(1L, 3L)])
-        }
-      } else {
-        shap_contrib <- apply(abs(shap_contrib), c(1L, 3L), sum)
-      }
+  if (!is.null(shap_contrib)) {
+    if (is.list(shap_contrib)) { # multiclass: either choose a class or merge
+      shap_contrib <- if (!is.null(target_class)) shap_contrib[[target_class + 1]] else Reduce("+", lapply(shap_contrib, abs))
+    }
+    shap_contrib <- shap_contrib[idx, ]
+    if (is.null(colnames(shap_contrib))) {
+      colnames(shap_contrib) <- paste0("X", seq_len(ncol(data)))
+    }
+  } else {
+    shap_contrib <- predict(model, newdata = data, predcontrib = TRUE, approxcontrib = approxcontrib)
+    if (is.list(shap_contrib)) { # multiclass: either choose a class or merge
+      shap_contrib <- if (!is.null(target_class)) shap_contrib[[target_class + 1]] else Reduce("+", lapply(shap_contrib, abs))
     }
-    return(shap_contrib)
-  }
-
-  if (is.null(shap_contrib)) {
-    shap_contrib <- predict(
-      model,
-      newdata = data,
-      predcontrib = TRUE,
-      approxcontrib = approxcontrib
-    )
-  }
-  shap_contrib <- reshape_3d_shap_contrib(shap_contrib, target_class)
-  if (is.null(colnames(shap_contrib))) {
-    colnames(shap_contrib) <- paste0("X", seq_len(ncol(data)))
   }
 
   if (is.null(features)) {

R-package/R/xgb.plot.tree.R

@@ -2,7 +2,36 @@
 #'
 #' Read a tree model text dump and plot the model.
 #'
+#' @param model Object of class `xgb.Booster`. If it contains feature names (they can be set through
+#'        \link{setinfo}), they will be used in the output from this function.
+#' @param trees An integer vector of tree indices that should be used.
+#'        The default (`NULL`) uses all trees.
+#'        Useful, e.g., in multiclass classification to get only
+#'        the trees of one class. *Important*: the tree index in XGBoost models
+#'        is zero-based (e.g., use `trees = 0:2` for the first three trees).
+#' @param plot_width,plot_height Width and height of the graph in pixels.
+#'        The values are passed to [DiagrammeR::render_graph()].
+#' @param render Should the graph be rendered or not? The default is `TRUE`.
+#' @param show_node_id a logical flag for whether to show node id's in the graph.
+#' @param style Style to use for the plot. Options are:\itemize{
+#' \item `"xgboost"`: will use the plot style defined in the core XGBoost library,
+#' which is shared between different interfaces through the 'dot' format. This
+#' style was not available before version 2.1.0 in R. It always plots the trees
+#' vertically (from top to bottom).
+#' \item `"R"`: will use the style defined from XGBoost's R interface, which predates
+#' the introducition of the standardized style from the core library. It might plot
+#' the trees horizontally (from left to right).
+#' }
+#'
+#' Note that `style="xgboost"` is only supported when all of the following conditions are met:\itemize{
+#' \item Only a single tree is being plotted.
+#' \item Node IDs are not added to the graph.
+#' \item The graph is being returned as `htmlwidget` (`render=TRUE`).
+#' }
+#' @param ... currently not used.
+#'
 #' @details
+#'
 #' When using `style="xgboost"`, the content of each node is visualized as follows:
 #' - For non-terminal nodes, it will display the split condition (number or name if
 #'   available, and the condition that would decide to which node to go next).
@@ -27,31 +56,6 @@
 #'
 #' This function uses [GraphViz](https://www.graphviz.org/) as DiagrammeR backend.
 #'
-#' @param model Object of class `xgb.Booster`. If it contains feature names (they can be set through
-#'   [setinfo()], they will be used in the output from this function.
-#' @param trees An integer vector of tree indices that should be used.
-#'   The default (`NULL`) uses all trees.
-#'   Useful, e.g., in multiclass classification to get only
-#'   the trees of one class. *Important*: the tree index in XGBoost models
-#'   is zero-based (e.g., use `trees = 0:2` for the first three trees).
-#' @param plot_width,plot_height Width and height of the graph in pixels.
-#'   The values are passed to `DiagrammeR::render_graph()`.
-#' @param render Should the graph be rendered or not? The default is `TRUE`.
-#' @param show_node_id a logical flag for whether to show node id's in the graph.
-#' @param style Style to use for the plot:
-#'   - `"xgboost"`: will use the plot style defined in the core XGBoost library,
-#'     which is shared between different interfaces through the 'dot' format. This
-#'     style was not available before version 2.1.0 in R. It always plots the trees
-#'     vertically (from top to bottom).
-#'   - `"R"`: will use the style defined from XGBoost's R interface, which predates
-#'     the introducition of the standardized style from the core library. It might plot
-#'     the trees horizontally (from left to right).
-#'
-#'   Note that `style="xgboost"` is only supported when all of the following conditions are met:
-#'   - Only a single tree is being plotted.
-#'   - Node IDs are not added to the graph.
-#'   - The graph is being returned as `htmlwidget` (`render=TRUE`).
-#' @param ... Currently not used.
 #' @return
 #' The value depends on the `render` parameter:
 #' - If `render = TRUE` (default): Rendered graph object which is an htmlwidget of
@@ -59,13 +63,14 @@
 #'   running from the command line.
 #' - If `render = FALSE`: Graph object which is of DiagrammeR's class `dgr_graph`.
 #'   This could be useful if one wants to modify some of the graph attributes
-#'   before rendering the graph with `DiagrammeR::render_graph()`.
+#'   before rendering the graph with [DiagrammeR::render_graph()].
 #'
 #' @examples
 #' data(agaricus.train, package = "xgboost")
 #'
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(agaricus.train$data, agaricus.train$label),
+#' bst <- xgboost(
+#'   data = agaricus.train$data,
+#'   label = agaricus.train$label,
 #'   max_depth = 3,
 #'   eta = 1,
 #'   nthread = 2,

R-package/R/xgb.save.R

@@ -1,39 +1,43 @@
-#' Save XGBoost model to binary file
+#' Save xgboost model to binary file
 #'
-#' Save XGBoost model to a file in binary or JSON format.
+#' Save xgboost model to a file in binary or JSON format.
 #'
-#' @param model Model object of `xgb.Booster` class.
-#' @param fname Name of the file to write. Its extension determines the serialization format:
-#'   - ".ubj": Use the universal binary JSON format (recommended).
-#'     This format uses binary types for e.g. floating point numbers, thereby preventing any loss
-#'     of precision when converting to a human-readable JSON text or similar.
-#'   - ".json": Use plain JSON, which is a human-readable format.
-#'   - ".deprecated": Use **deprecated** binary format. This format will
-#'     not be able to save attributes introduced after v1 of XGBoost, such as the "best_iteration"
-#'     attribute that boosters might keep, nor feature names or user-specifiec attributes.
-#'   - If the format is not specified by passing one of the file extensions above, will
-#'     default to UBJ.
+#' @param model Model object of \code{xgb.Booster} class.
+#' @param fname Name of the file to write.
+#'
+#' Note that the extension of this file name determined the serialization format to use:\itemize{
+#' \item Extension ".ubj" will use the universal binary JSON format (recommended).
+#' This format uses binary types for e.g. floating point numbers, thereby preventing any loss
+#' of precision when converting to a human-readable JSON text or similar.
+#' \item Extension ".json" will use plain JSON, which is a human-readable format.
+#' \item Extension ".deprecated" will use a \bold{deprecated} binary format. This format will
+#' not be able to save attributes introduced after v1 of XGBoost, such as the "best_iteration"
+#' attribute that boosters might keep, nor feature names or user-specifiec attributes.
+#' \item If the format is not specified by passing one of the file extensions above, will
+#' default to UBJ.
+#' }
 #'
 #' @details
+#' This methods allows to save a model in an xgboost-internal binary or text format which is universal
+#' among the various xgboost interfaces. In R, the saved model file could be read-in later
+#' using either the \code{\link{xgb.load}} function or the \code{xgb_model} parameter
+#' of \code{\link{xgb.train}}.
 #'
-#' This methods allows to save a model in an XGBoost-internal binary or text format which is universal
-#' among the various xgboost interfaces. In R, the saved model file could be read later
-#' using either the [xgb.load()] function or the `xgb_model` parameter of [xgb.train()].
-#'
-#' Note: a model can also be saved as an R object (e.g., by using [readRDS()]
-#' or [save()]). However, it would then only be compatible with R, and
-#' corresponding R methods would need to be used to load it. Moreover, persisting the model with
-#' [readRDS()] or [save()] might cause compatibility problems in
-#' future versions of XGBoost. Consult [a-compatibility-note-for-saveRDS-save] to learn
-#' how to persist models in a future-proof way, i.e., to make the model accessible in future
+#' Note: a model can also be saved as an R-object (e.g., by using \code{\link[base]{readRDS}}
+#' or \code{\link[base]{save}}). However, it would then only be compatible with R, and
+#' corresponding R-methods would need to be used to load it. Moreover, persisting the model with
+#' \code{\link[base]{readRDS}} or \code{\link[base]{save}}) might cause compatibility problems in
+#' future versions of XGBoost. Consult \code{\link{a-compatibility-note-for-saveRDS-save}} to learn
+#' how to persist models in a future-proof way, i.e. to make the model accessible in future
 #' releases of XGBoost.
 #'
-#' @seealso [xgb.load()]
+#' @seealso
+#' \code{\link{xgb.load}}
 #'
 #' @examples
 #' \dontshow{RhpcBLASctl::omp_set_num_threads(1)}
-#' data(agaricus.train, package = "xgboost")
-#' data(agaricus.test, package = "xgboost")
+#' data(agaricus.train, package='xgboost')
+#' data(agaricus.test, package='xgboost')
 #'
 #' ## Keep the number of threads to 1 for examples
 #' nthread <- 1
@@ -41,7 +45,6 @@
 #'
 #' train <- agaricus.train
 #' test <- agaricus.test
-#'
 #' bst <- xgb.train(
 #'   data = xgb.DMatrix(train$data, label = train$label),
 #'   max_depth = 2,
@@ -50,7 +53,6 @@
 #'   nrounds = 2,
 #'   objective = "binary:logistic"
 #' )
-#'
 #' fname <- file.path(tempdir(), "xgb.ubj")
 #' xgb.save(bst, fname)
 #' bst <- xgb.load(fname)

R-package/R/xgb.save.raw.R

@@ -1,34 +1,29 @@
-#' Save XGBoost model to R's raw vector
+#' Save xgboost model to R's raw vector,
+#' user can call xgb.load.raw to load the model back from raw vector
 #'
-#' Save XGBoost model from [xgboost()] or [xgb.train()].
-#' Call [xgb.load.raw()] to load the model back from raw vector.
+#' Save xgboost model from xgboost or xgb.train
 #'
-#' @param model The model object.
-#' @param raw_format The format for encoding the booster:
-#'   - "json": Encode the booster into JSON text document.
-#'   - "ubj":  Encode the booster into Universal Binary JSON.
-#'   - "deprecated": Encode the booster into old customized binary format.
+#' @param model the model object.
+#' @param raw_format The format for encoding the booster.  Available options are
+#' \itemize{
+#'     \item \code{json}: Encode the booster into JSON text document.
+#'     \item \code{ubj}:  Encode the booster into Universal Binary JSON.
+#'     \item \code{deprecated}: Encode the booster into old customized binary format.
+#' }
 #'
 #' @examples
 #' \dontshow{RhpcBLASctl::omp_set_num_threads(1)}
-#' data(agaricus.train, package = "xgboost")
-#' data(agaricus.test, package = "xgboost")
+#' data(agaricus.train, package='xgboost')
+#' data(agaricus.test, package='xgboost')
 #'
-#' ## Keep the number of threads to 1 for examples
-#' nthread <- 1
+#' ## Keep the number of threads to 2 for examples
+#' nthread <- 2
 #' data.table::setDTthreads(nthread)
 #'
 #' train <- agaricus.train
 #' test <- agaricus.test
-#'
-#' bst <- xgb.train(
-#'   data = xgb.DMatrix(train$data, label = train$label),
-#'   max_depth = 2,
-#'   eta = 1,
-#'   nthread = nthread,
-#'   nrounds = 2,
-#'   objective = "binary:logistic"
-#' )
+#' bst <- xgb.train(data = xgb.DMatrix(train$data, label = train$label), max_depth = 2,
+#'                  eta = 1, nthread = nthread, nrounds = 2,objective = "binary:logistic")
 #'
 #' raw <- xgb.save.raw(bst)
 #' bst <- xgb.load.raw(raw)

R-package/R/xgb.train.R

@@ -1,186 +1,183 @@
 #' eXtreme Gradient Boosting Training
 #'
-#' `xgb.train()` is an advanced interface for training an xgboost model.
-#' The [xgboost()] function is a simpler wrapper for `xgb.train()`.
+#' \code{xgb.train} is an advanced interface for training an xgboost model.
+#' The \code{xgboost} function is a simpler wrapper for \code{xgb.train}.
 #'
 #' @param params the list of parameters. The complete list of parameters is
-#'   available in the [online documentation](http://xgboost.readthedocs.io/en/latest/parameter.html).
-#'   Below is a shorter summary:
+#'   available in the \href{http://xgboost.readthedocs.io/en/latest/parameter.html}{online documentation}. Below
+#'   is a shorter summary:
 #'
-#'   **1. General Parameters**
+#' 1. General Parameters
 #'
-#'   - `booster`: Which booster to use, can be `gbtree` or `gblinear`. Default: `gbtree`.
+#' \itemize{
+#'   \item \code{booster} which booster to use, can be \code{gbtree} or \code{gblinear}. Default: \code{gbtree}.
+#' }
 #'
-#'   **2. Booster Parameters**
+#' 2. Booster Parameters
 #'
-#'   **2.1. Parameters for Tree Booster**
-#'   - `eta`: The learning rate: scale the contribution of each tree by a factor of `0 < eta < 1`
-#'     when it is added to the current approximation.
-#'     Used to prevent overfitting by making the boosting process more conservative.
-#'     Lower value for `eta` implies larger value for `nrounds`: low `eta` value means model
-#'     more robust to overfitting but slower to compute. Default: 0.3.
-#'   - `gamma`: Minimum loss reduction required to make a further partition on a leaf node of the tree.
-#'     the larger, the more conservative the algorithm will be.
-#'   - `max_depth`: Maximum depth of a tree. Default: 6.
-#'   - `min_child_weight`: Minimum sum of instance weight (hessian) needed in a child.
-#'     If the tree partition step results in a leaf node with the sum of instance weight less than min_child_weight,
-#'     then the building process will give up further partitioning.
-#'     In linear regression mode, this simply corresponds to minimum number of instances needed to be in each node.
-#'     The larger, the more conservative the algorithm will be. Default: 1.
-#'   - `subsample`: Subsample ratio of the training instance.
-#'     Setting it to 0.5 means that xgboost randomly collected half of the data instances to grow trees
-#'     and this will prevent overfitting. It makes computation shorter (because less data to analyse).
-#'     It is advised to use this parameter with `eta` and increase `nrounds`. Default: 1.
-#'   - `colsample_bytree`: Subsample ratio of columns when constructing each tree. Default: 1.
-#'   - `lambda`: L2 regularization term on weights. Default: 1.
-#'   - `alpha`: L1 regularization term on weights. (there is no L1 reg on bias because it is not important). Default: 0.
-#'   - `num_parallel_tree`: Experimental parameter. number of trees to grow per round.
-#'     Useful to test Random Forest through XGBoost.
-#'     (set `colsample_bytree < 1`, `subsample  < 1` and `round = 1`) accordingly.
-#'     Default: 1.
-#'   - `monotone_constraints`: A numerical vector consists of `1`, `0` and `-1` with its length
-#'     equals to the number of features in the training data.
-#'     `1` is increasing, `-1` is decreasing and `0` is no constraint.
-#'   - `interaction_constraints`: A list of vectors specifying feature indices of permitted interactions.
-#'     Each item of the list represents one permitted interaction where specified features are allowed to interact with each other.
-#'     Feature index values should start from `0` (`0` references the first column).
-#'     Leave argument unspecified for no interaction constraints.
+#' 2.1. Parameters for Tree Booster
 #'
-#'   **2.2. Parameters for Linear Booster**
+#' \itemize{
+#'   \item{ \code{eta} control the learning rate: scale the contribution of each tree by a factor of \code{0 < eta < 1}
+#'          when it is added to the current approximation.
+#'          Used to prevent overfitting by making the boosting process more conservative.
+#'          Lower value for \code{eta} implies larger value for \code{nrounds}: low \code{eta} value means model
+#'          more robust to overfitting but slower to compute. Default: 0.3}
+#'   \item{ \code{gamma} minimum loss reduction required to make a further partition on a leaf node of the tree.
+#'          the larger, the more conservative the algorithm will be.}
+#'   \item \code{max_depth} maximum depth of a tree. Default: 6
+#'   \item{\code{min_child_weight} minimum sum of instance weight (hessian) needed in a child.
+#'         If the tree partition step results in a leaf node with the sum of instance weight less than min_child_weight,
+#'         then the building process will give up further partitioning.
+#'         In linear regression mode, this simply corresponds to minimum number of instances needed to be in each node.
+#'         The larger, the more conservative the algorithm will be. Default: 1}
+#'   \item{ \code{subsample} subsample ratio of the training instance.
+#'         Setting it to 0.5 means that xgboost randomly collected half of the data instances to grow trees
+#'         and this will prevent overfitting. It makes computation shorter (because less data to analyse).
+#'         It is advised to use this parameter with \code{eta} and increase \code{nrounds}. Default: 1}
+#'   \item \code{colsample_bytree} subsample ratio of columns when constructing each tree. Default: 1
+#'   \item \code{lambda} L2 regularization term on weights. Default: 1
+#'   \item \code{alpha} L1 regularization term on weights. (there is no L1 reg on bias because it is not important). Default: 0
+#'   \item{ \code{num_parallel_tree} Experimental parameter. number of trees to grow per round.
+#'          Useful to test Random Forest through XGBoost
+#'          (set \code{colsample_bytree < 1}, \code{subsample  < 1}  and \code{round = 1}) accordingly.
+#'          Default: 1}
+#'   \item{ \code{monotone_constraints} A numerical vector consists of \code{1}, \code{0} and \code{-1} with its length
+#'          equals to the number of features in the training data.
+#'          \code{1} is increasing, \code{-1} is decreasing and \code{0} is no constraint.}
+#'   \item{ \code{interaction_constraints} A list of vectors specifying feature indices of permitted interactions.
+#'        Each item of the list represents one permitted interaction where specified features are allowed to interact with each other.
+#'        Feature index values should start from \code{0} (\code{0} references the first column).
+#'        Leave argument unspecified for no interaction constraints.}
+#' }
 #'
-#'   - `lambda`: L2 regularization term on weights. Default: 0.
-#'   - `lambda_bias`: L2 regularization term on bias. Default: 0.
-#'   - `alpha`: L1 regularization term on weights. (there is no L1 reg on bias because it is not important). Default: 0.
+#' 2.2. Parameters for Linear Booster
 #'
-#'   **3. Task Parameters**
+#' \itemize{
+#'   \item \code{lambda} L2 regularization term on weights. Default: 0
+#'   \item \code{lambda_bias} L2 regularization term on bias. Default: 0
+#'   \item \code{alpha} L1 regularization term on weights. (there is no L1 reg on bias because it is not important). Default: 0
+#' }
 #'
-#'   - `objective`: Specifies the learning task and the corresponding learning objective.
-#'     users can pass a self-defined function to it. The default objective options are below:
-#'     - `reg:squarederror`: Regression with squared loss (default).
-#'     - `reg:squaredlogerror`: Regression with squared log loss \eqn{1/2 \cdot (\log(pred + 1) - \log(label + 1))^2}.
-#'       All inputs are required to be greater than -1.
-#'       Also, see metric rmsle for possible issue with this objective.
-#'     - `reg:logistic`: Logistic regression.
-#'     - `reg:pseudohubererror`: Regression with Pseudo Huber loss, a twice differentiable alternative to absolute loss.
-#'     - `binary:logistic`: Logistic regression for binary classification. Output probability.
-#'     - `binary:logitraw`: Logistic regression for binary classification, output score before logistic transformation.
-#'     - `binary:hinge`: Hinge loss for binary classification. This makes predictions of 0 or 1, rather than producing probabilities.
-#'     - `count:poisson`: Poisson regression for count data, output mean of Poisson distribution.
-#'       The parameter `max_delta_step` is set to 0.7 by default in poisson regression
-#'       (used to safeguard optimization).
-#'     - `survival:cox`: Cox regression for right censored survival time data (negative values are considered right censored).
-#'       Note that predictions are returned on the hazard ratio scale (i.e., as HR = exp(marginal_prediction) in the proportional
-#'       hazard function \eqn{h(t) = h_0(t) \cdot HR}.
-#'     - `survival:aft`: Accelerated failure time model for censored survival time data. See
-#'       [Survival Analysis with Accelerated Failure Time](https://xgboost.readthedocs.io/en/latest/tutorials/aft_survival_analysis.html)
-#'       for details.
-#'       The parameter `aft_loss_distribution` specifies the Probability Density Function
-#'       used by `survival:aft` and the `aft-nloglik` metric.
-#'     - `multi:softmax`: Set xgboost to do multiclass classification using the softmax objective.
-#'       Class is represented by a number and should be from 0 to `num_class - 1`.
-#'     - `multi:softprob`: Same as softmax, but prediction outputs a vector of ndata * nclass elements, which can be
-#'       further reshaped to ndata, nclass matrix. The result contains predicted probabilities of each data point belonging
-#'       to each class.
-#'     - `rank:pairwise`: Set XGBoost to do ranking task by minimizing the pairwise loss.
-#'     - `rank:ndcg`: Use LambdaMART to perform list-wise ranking where
-#'       [Normalized Discounted Cumulative Gain (NDCG)](https://en.wikipedia.org/wiki/Discounted_cumulative_gain) is maximized.
-#'     - `rank:map`: Use LambdaMART to perform list-wise ranking where
-#'       [Mean Average Precision (MAP)](https://en.wikipedia.org/wiki/Evaluation_measures_(information_retrieval)#Mean_average_precision)
-#'       is maximized.
-#'     - `reg:gamma`: Gamma regression with log-link. Output is a mean of gamma distribution.
-#'       It might be useful, e.g., for modeling insurance claims severity, or for any outcome that might be
-#'       [gamma-distributed](https://en.wikipedia.org/wiki/Gamma_distribution#Applications).
-#'     - `reg:tweedie`: Tweedie regression with log-link.
-#'       It might be useful, e.g., for modeling total loss in insurance, or for any outcome that might be
-#'       [Tweedie-distributed](https://en.wikipedia.org/wiki/Tweedie_distribution#Applications).
+#' 3. Task Parameters
 #'
-#'      For custom objectives, one should pass a function taking as input the current predictions (as a numeric
-#'      vector or matrix) and the training data (as an `xgb.DMatrix` object) that will return a list with elements
-#'      `grad` and `hess`, which should be numeric vectors or matrices with number of rows matching to the numbers
-#'      of rows in the training data (same shape as the predictions that are passed as input to the function).
-#'      For multi-valued custom objectives, should have shape `[nrows, ntargets]`. Note that negative values of
-#'      the Hessian will be clipped, so one might consider using the expected Hessian (Fisher information) if the
-#'      objective is non-convex.
+#' \itemize{
+#' \item{ \code{objective} specify the learning task and the corresponding learning objective, users can pass a self-defined function to it.
+#'        The default objective options are below:
+#'   \itemize{
+#'     \item \code{reg:squarederror} Regression with squared loss (Default).
+#'     \item{ \code{reg:squaredlogerror}: regression with squared log loss \eqn{1/2 * (log(pred + 1) - log(label + 1))^2}.
+#'            All inputs are required to be greater than -1.
+#'            Also, see metric rmsle for possible issue with this objective.}
+#'     \item \code{reg:logistic} logistic regression.
+#'     \item \code{reg:pseudohubererror}: regression with Pseudo Huber loss, a twice differentiable alternative to absolute loss.
+#'     \item \code{binary:logistic} logistic regression for binary classification. Output probability.
+#'     \item \code{binary:logitraw} logistic regression for binary classification, output score before logistic transformation.
+#'     \item \code{binary:hinge}: hinge loss for binary classification. This makes predictions of 0 or 1, rather than producing probabilities.
+#'     \item{ \code{count:poisson}: Poisson regression for count data, output mean of Poisson distribution.
+#'            \code{max_delta_step} is set to 0.7 by default in poisson regression (used to safeguard optimization).}
+#'     \item{ \code{survival:cox}: Cox regression for right censored survival time data (negative values are considered right censored).
+#'            Note that predictions are returned on the hazard ratio scale (i.e., as HR = exp(marginal_prediction) in the proportional
+#'            hazard function \code{h(t) = h0(t) * HR)}.}
+#'     \item{ \code{survival:aft}: Accelerated failure time model for censored survival time data. See
+#'            \href{https://xgboost.readthedocs.io/en/latest/tutorials/aft_survival_analysis.html}{Survival Analysis with Accelerated Failure Time}
+#'            for details.}
+#'     \item \code{aft_loss_distribution}: Probability Density Function used by \code{survival:aft} and \code{aft-nloglik} metric.
+#'     \item{ \code{multi:softmax} set xgboost to do multiclass classification using the softmax objective.
+#'            Class is represented by a number and should be from 0 to \code{num_class - 1}.}
+#'     \item{ \code{multi:softprob} same as softmax, but prediction outputs a vector of ndata * nclass elements, which can be
+#'            further reshaped to ndata, nclass matrix. The result contains predicted probabilities of each data point belonging
+#'            to each class.}
+#'     \item \code{rank:pairwise} set xgboost to do ranking task by minimizing the pairwise loss.
+#'     \item{ \code{rank:ndcg}: Use LambdaMART to perform list-wise ranking where
+#'            \href{https://en.wikipedia.org/wiki/Discounted_cumulative_gain}{Normalized Discounted Cumulative Gain (NDCG)} is maximized.}
+#'     \item{ \code{rank:map}: Use LambdaMART to perform list-wise ranking where
+#'            \href{https://en.wikipedia.org/wiki/Evaluation_measures_(information_retrieval)#Mean_average_precision}{Mean Average Precision (MAP)}
+#'            is maximized.}
+#'     \item{ \code{reg:gamma}: gamma regression with log-link.
+#'            Output is a mean of gamma distribution.
+#'            It might be useful, e.g., for modeling insurance claims severity, or for any outcome that might be
+#'            \href{https://en.wikipedia.org/wiki/Gamma_distribution#Applications}{gamma-distributed}.}
+#'     \item{ \code{reg:tweedie}: Tweedie regression with log-link.
+#'            It might be useful, e.g., for modeling total loss in insurance, or for any outcome that might be
+#'            \href{https://en.wikipedia.org/wiki/Tweedie_distribution#Applications}{Tweedie-distributed}.}
+#'   }
+#'  }
+#'   \item \code{base_score} the initial prediction score of all instances, global bias. Default: 0.5
+#'   \item{ \code{eval_metric} evaluation metrics for validation data.
+#'          Users can pass a self-defined function to it.
+#'          Default: metric will be assigned according to objective
+#'          (rmse for regression, and error for classification, mean average precision for ranking).
+#'          List is provided in detail section.}
+#' }
 #'
-#'      See the tutorials [Custom Objective and Evaluation Metric](https://xgboost.readthedocs.io/en/stable/tutorials/custom_metric_obj.html)
-#'      and [Advanced Usage of Custom Objectives](https://xgboost.readthedocs.io/en/stable/tutorials/advanced_custom_obj)
-#'      for more information about custom objectives.
-#'
-#'   - `base_score`: The initial prediction score of all instances, global bias. Default: 0.5.
-#'   - `eval_metric`: Evaluation metrics for validation data.
-#'     Users can pass a self-defined function to it.
-#'     Default: metric will be assigned according to objective
-#'     (rmse for regression, and error for classification, mean average precision for ranking).
-#'     List is provided in detail section.
-#' @param data Training dataset. `xgb.train()` accepts only an `xgb.DMatrix` as the input.
-#'   [xgboost()], in addition, also accepts `matrix`, `dgCMatrix`, or name of a local data file.
-#' @param nrounds Max number of boosting iterations.
+#' @param data training dataset. \code{xgb.train} accepts only an \code{xgb.DMatrix} as the input.
+#'        \code{xgboost}, in addition, also accepts \code{matrix}, \code{dgCMatrix}, or name of a local data file.
+#' @param nrounds max number of boosting iterations.
 #' @param evals Named list of `xgb.DMatrix` datasets to use for evaluating model performance.
-#'   Metrics specified in either `eval_metric` or `feval` will be computed for each
-#'   of these datasets during each boosting iteration, and stored in the end as a field named
-#'   `evaluation_log` in the resulting object. When either `verbose>=1` or
-#'   [xgb.cb.print.evaluation()] callback is engaged, the performance results are continuously
-#'   printed out during the training.
-#'   E.g., specifying `evals=list(validation1=mat1, validation2=mat2)` allows to track
-#'   the performance of each round's model on mat1 and mat2.
-#' @param obj Customized objective function. Should take two arguments: the first one will be the
-#'   current predictions (either a numeric vector or matrix depending on the number of targets / classes),
-#'   and the second one will be the `data` DMatrix object that is used for training.
-#'
-#'   It should return a list with two elements `grad` and `hess` (in that order), as either
-#'   numeric vectors or numeric matrices depending on the number of targets / classes (same
-#'   dimension as the predictions that are passed as first argument).
-#' @param feval Customized evaluation function. Just like `obj`, should take two arguments, with
-#'   the first one being the predictions and the second one the `data` DMatrix.
-#'
-#'   Should return a list with two elements `metric` (name that will be displayed for this metric,
-#'   should be a string / character), and `value` (the number that the function calculates, should
-#'   be a numeric scalar).
-#'
-#'   Note that even if passing `feval`, objectives also have an associated default metric that
-#'   will be evaluated in addition to it. In order to disable the built-in metric, one can pass
-#'   parameter `disable_default_eval_metric = TRUE`.
+#'        Metrics specified in either \code{eval_metric} or \code{feval} will be computed for each
+#'        of these datasets during each boosting iteration, and stored in the end as a field named
+#'        \code{evaluation_log} in the resulting object. When either \code{verbose>=1} or
+#'        \code{\link{xgb.cb.print.evaluation}} callback is engaged, the performance results are continuously
+#'        printed out during the training.
+#'        E.g., specifying \code{evals=list(validation1=mat1, validation2=mat2)} allows to track
+#'        the performance of each round's model on mat1 and mat2.
+#' @param obj customized objective function. Returns gradient and second order
+#'        gradient with given prediction and dtrain.
+#' @param feval customized evaluation function. Returns
+#'        \code{list(metric='metric-name', value='metric-value')} with given
+#'        prediction and dtrain.
 #' @param verbose If 0, xgboost will stay silent. If 1, it will print information about performance.
-#'   If 2, some additional information will be printed out.
-#'   Note that setting `verbose > 0` automatically engages the
-#'   `xgb.cb.print.evaluation(period=1)` callback function.
-#' @param print_every_n Print each nth iteration evaluation messages when `verbose>0`.
-#'   Default is 1 which means all messages are printed. This parameter is passed to the
-#'   [xgb.cb.print.evaluation()] callback.
-#' @param early_stopping_rounds If `NULL`, the early stopping function is not triggered.
-#'   If set to an integer `k`, training with a validation set will stop if the performance
-#'   doesn't improve for `k` rounds. Setting this parameter engages the [xgb.cb.early.stop()] callback.
-#' @param maximize If `feval` and `early_stopping_rounds` are set, then this parameter must be set as well.
-#'   When it is `TRUE`, it means the larger the evaluation score the better.
-#'   This parameter is passed to the [xgb.cb.early.stop()] callback.
-#' @param save_period When not `NULL`, model is saved to disk after every `save_period` rounds.
-#'   0 means save at the end. The saving is handled by the [xgb.cb.save.model()] callback.
+#'        If 2, some additional information will be printed out.
+#'        Note that setting \code{verbose > 0} automatically engages the
+#'        \code{xgb.cb.print.evaluation(period=1)} callback function.
+#' @param print_every_n Print each n-th iteration evaluation messages when \code{verbose>0}.
+#'        Default is 1 which means all messages are printed. This parameter is passed to the
+#'        \code{\link{xgb.cb.print.evaluation}} callback.
+#' @param early_stopping_rounds If \code{NULL}, the early stopping function is not triggered.
+#'        If set to an integer \code{k}, training with a validation set will stop if the performance
+#'        doesn't improve for \code{k} rounds.
+#'        Setting this parameter engages the \code{\link{xgb.cb.early.stop}} callback.
+#' @param maximize If \code{feval} and \code{early_stopping_rounds} are set,
+#'        then this parameter must be set as well.
+#'        When it is \code{TRUE}, it means the larger the evaluation score the better.
+#'        This parameter is passed to the \code{\link{xgb.cb.early.stop}} callback.
+#' @param save_period when it is non-NULL, model is saved to disk after every \code{save_period} rounds,
+#'        0 means save at the end. The saving is handled by the \code{\link{xgb.cb.save.model}} callback.
 #' @param save_name the name or path for periodically saved model file.
-#' @param xgb_model A previously built model to continue the training from.
-#'   Could be either an object of class `xgb.Booster`, or its raw data, or the name of a
-#'   file with a previously saved model.
-#' @param callbacks A list of callback functions to perform various task during boosting.
-#'   See [xgb.Callback()]. Some of the callbacks are automatically created depending on the
-#'   parameters' values. User can provide either existing or their own callback methods in order
-#'   to customize the training process.
+#' @param xgb_model a previously built model to continue the training from.
+#'        Could be either an object of class \code{xgb.Booster}, or its raw data, or the name of a
+#'        file with a previously saved model.
+#' @param callbacks a list of callback functions to perform various task during boosting.
+#'        See \code{\link{xgb.Callback}}. Some of the callbacks are automatically created depending on the
+#'        parameters' values. User can provide either existing or their own callback methods in order
+#'        to customize the training process.
 #'
-#'   Note that some callbacks might try to leave attributes in the resulting model object,
-#'   such as an evaluation log (a `data.table` object) - be aware that these objects are kept
-#'   as R attributes, and thus do not get saved when using XGBoost's own serializaters like
-#'   [xgb.save()] (but are kept when using R serializers like [saveRDS()]).
-#' @param ... other parameters to pass to `params`.
+#'        Note that some callbacks might try to leave attributes in the resulting model object,
+#'        such as an evaluation log (a `data.table` object) - be aware that these objects are kept
+#'        as R attributes, and thus do not get saved when using XGBoost's own serializaters like
+#'        \link{xgb.save} (but are kept when using R serializers like \link{saveRDS}).
+#' @param ... other parameters to pass to \code{params}.
+#' @param label vector of response values. Should not be provided when data is
+#'        a local data file name or an \code{xgb.DMatrix}.
+#' @param missing by default is set to NA, which means that NA values should be considered as 'missing'
+#'        by the algorithm. Sometimes, 0 or other extreme value might be used to represent missing values.
+#'        This parameter is only used when input is a dense matrix.
+#' @param weight a vector indicating the weight for each row of the input.
 #'
-#' @return An object of class `xgb.Booster`.
+#' @return
+#' An object of class \code{xgb.Booster}.
 #'
 #' @details
-#' These are the training functions for [xgboost()].
+#' These are the training functions for \code{xgboost}.
 #'
-#' The `xgb.train()` interface supports advanced features such as `evals`,
+#' The \code{xgb.train} interface supports advanced features such as \code{evals},
 #' customized objective and evaluation metric functions, therefore it is more flexible
-#' than the [xgboost()] interface.
+#' than the \code{xgboost} interface.
 #'
-#' Parallelization is automatically enabled if OpenMP is present.
-#' Number of threads can also be manually specified via the `nthread` parameter.
+#' Parallelization is automatically enabled if \code{OpenMP} is present.
+#' Number of threads can also be manually specified via the \code{nthread}
+#' parameter.
 #'
 #' While in other interfaces, the default random seed defaults to zero, in R, if a parameter `seed`
 #' is not manually supplied, it will generate a random seed through R's own random number generator,
@@ -188,56 +185,64 @@
 #' RNG from R.
 #'
 #' The evaluation metric is chosen automatically by XGBoost (according to the objective)
-#' when the `eval_metric` parameter is not provided.
-#' User may set one or several `eval_metric` parameters.
+#' when the \code{eval_metric} parameter is not provided.
+#' User may set one or several \code{eval_metric} parameters.
 #' Note that when using a customized metric, only this single metric can be used.
 #' The following is the list of built-in metrics for which XGBoost provides optimized implementation:
-#' - `rmse`: Root mean square error. \url{https://en.wikipedia.org/wiki/Root_mean_square_error}
-#' - `logloss`: Negative log-likelihood. \url{https://en.wikipedia.org/wiki/Log-likelihood}
-#' - `mlogloss`: Multiclass logloss. \url{https://scikit-learn.org/stable/modules/generated/sklearn.metrics.log_loss.html}
-#' - `error`: Binary classification error rate. It is calculated as `(# wrong cases) / (# all cases)`.
-#'     By default, it uses the 0.5 threshold for predicted values to define negative and positive instances.
-#'     Different threshold (e.g., 0.) could be specified as `error@0`.
-#' - `merror`: Multiclass classification error rate. It is calculated as `(# wrong cases) / (# all cases)`.
-#' - `mae`: Mean absolute error.
-#' - `mape`: Mean absolute percentage error.
-#' - `auc`: Area under the curve.
-#'   \url{https://en.wikipedia.org/wiki/Receiver_operating_characteristic#'Area_under_curve} for ranking evaluation.
-#' - `aucpr`: Area under the PR curve. \url{https://en.wikipedia.org/wiki/Precision_and_recall} for ranking evaluation.
-#' - `ndcg`: Normalized Discounted Cumulative Gain (for ranking task). \url{https://en.wikipedia.org/wiki/NDCG}
+#'   \itemize{
+#'      \item \code{rmse} root mean square error. \url{https://en.wikipedia.org/wiki/Root_mean_square_error}
+#'      \item \code{logloss} negative log-likelihood. \url{https://en.wikipedia.org/wiki/Log-likelihood}
+#'      \item \code{mlogloss} multiclass logloss. \url{https://scikit-learn.org/stable/modules/generated/sklearn.metrics.log_loss.html}
+#'      \item \code{error} Binary classification error rate. It is calculated as \code{(# wrong cases) / (# all cases)}.
+#'            By default, it uses the 0.5 threshold for predicted values to define negative and positive instances.
+#'            Different threshold (e.g., 0.) could be specified as "error@0."
+#'      \item \code{merror} Multiclass classification error rate. It is calculated as \code{(# wrong cases) / (# all cases)}.
+#'      \item \code{mae} Mean absolute error
+#'      \item \code{mape} Mean absolute percentage error
+#'      \item{ \code{auc} Area under the curve.
+#'             \url{https://en.wikipedia.org/wiki/Receiver_operating_characteristic#'Area_under_curve} for ranking evaluation.}
+#'      \item \code{aucpr} Area under the PR curve. \url{https://en.wikipedia.org/wiki/Precision_and_recall} for ranking evaluation.
+#'      \item \code{ndcg} Normalized Discounted Cumulative Gain (for ranking task). \url{https://en.wikipedia.org/wiki/NDCG}
+#'   }
 #'
 #' The following callbacks are automatically created when certain parameters are set:
-#' - [xgb.cb.print.evaluation()] is turned on when `verbose > 0` and the `print_every_n`
-#'   parameter is passed to it.
-#' - [xgb.cb.evaluation.log()] is on when `evals` is present.
-#' - [xgb.cb.early.stop()]: When `early_stopping_rounds` is set.
-#' - [xgb.cb.save.model()]: When `save_period > 0` is set.
+#' \itemize{
+#'   \item \code{xgb.cb.print.evaluation} is turned on when \code{verbose > 0};
+#'         and the \code{print_every_n} parameter is passed to it.
+#'   \item \code{xgb.cb.evaluation.log} is on when \code{evals} is present.
+#'   \item \code{xgb.cb.early.stop}: when \code{early_stopping_rounds} is set.
+#'   \item \code{xgb.cb.save.model}: when \code{save_period > 0} is set.
+#' }
 #'
 #' Note that objects of type `xgb.Booster` as returned by this function behave a bit differently
 #' from typical R objects (it's an 'altrep' list class), and it makes a separation between
-#' internal booster attributes (restricted to jsonifyable data), accessed through [xgb.attr()]
-#' and shared between interfaces through serialization functions like [xgb.save()]; and
-#' R-specific attributes (typically the result from a callback), accessed through [attributes()]
-#' and [attr()], which are otherwise
-#' only used in the R interface, only kept when using R's serializers like [saveRDS()], and
-#' not anyhow used by functions like `predict.xgb.Booster()`.
+#' internal booster attributes (restricted to jsonifyable data), accessed through \link{xgb.attr}
+#' and shared between interfaces through serialization functions like \link{xgb.save}; and
+#' R-specific attributes (typically the result from a callback), accessed through \link{attributes}
+#' and \link{attr}, which are otherwise
+#' only used in the R interface, only kept when using R's serializers like \link{saveRDS}, and
+#' not anyhow used by functions like \link{predict.xgb.Booster}.
 #'
 #' Be aware that one such R attribute that is automatically added is `params` - this attribute
 #' is assigned from the `params` argument to this function, and is only meant to serve as a
 #' reference for what went into the booster, but is not used in other methods that take a booster
 #' object - so for example, changing the booster's configuration requires calling `xgb.config<-`
-#' or `xgb.parameters<-`, while simply modifying `attributes(model)$params$<...>` will have no
+#' or 'xgb.parameters<-', while simply modifying `attributes(model)$params$<...>` will have no
 #' effect elsewhere.
 #'
-#' @seealso [xgb.Callback()], [predict.xgb.Booster()], [xgb.cv()]
+#' @seealso
+#' \code{\link{xgb.Callback}},
+#' \code{\link{predict.xgb.Booster}},
+#' \code{\link{xgb.cv}}
 #'
 #' @references
+#'
 #' Tianqi Chen and Carlos Guestrin, "XGBoost: A Scalable Tree Boosting System",
 #' 22nd SIGKDD Conference on Knowledge Discovery and Data Mining, 2016, \url{https://arxiv.org/abs/1603.02754}
 #'
 #' @examples
-#' data(agaricus.train, package = "xgboost")
-#' data(agaricus.test, package = "xgboost")
+#' data(agaricus.train, package='xgboost')
+#' data(agaricus.test, package='xgboost')
 #'
 #' ## Keep the number of threads to 1 for examples
 #' nthread <- 1
@@ -252,13 +257,8 @@
 #' evals <- list(train = dtrain, eval = dtest)
 #'
 #' ## A simple xgb.train example:
-#' param <- list(
-#'   max_depth = 2,
-#'   eta = 1,
-#'   nthread = nthread,
-#'   objective = "binary:logistic",
-#'   eval_metric = "auc"
-#' )
+#' param <- list(max_depth = 2, eta = 1, nthread = nthread,
+#'               objective = "binary:logistic", eval_metric = "auc")
 #' bst <- xgb.train(param, dtrain, nrounds = 2, evals = evals, verbose = 0)
 #'
 #' ## An xgb.train example where custom objective and evaluation metric are
@@ -278,67 +278,38 @@
 #'
 #' # These functions could be used by passing them either:
 #' #  as 'objective' and 'eval_metric' parameters in the params list:
-#' param <- list(
-#'   max_depth = 2,
-#'   eta = 1,
-#'   nthread = nthread,
-#'   objective = logregobj,
-#'   eval_metric = evalerror
-#' )
+#' param <- list(max_depth = 2, eta = 1, nthread = nthread,
+#'               objective = logregobj, eval_metric = evalerror)
 #' bst <- xgb.train(param, dtrain, nrounds = 2, evals = evals, verbose = 0)
 #'
 #' #  or through the ... arguments:
 #' param <- list(max_depth = 2, eta = 1, nthread = nthread)
-#' bst <- xgb.train(
-#'   param,
-#'   dtrain,
-#'   nrounds = 2,
-#'   evals = evals,
-#'   verbose = 0,
-#'   objective = logregobj,
-#'   eval_metric = evalerror
-#' )
+#' bst <- xgb.train(param, dtrain, nrounds = 2, evals = evals, verbose = 0,
+#'                  objective = logregobj, eval_metric = evalerror)
 #'
 #' #  or as dedicated 'obj' and 'feval' parameters of xgb.train:
-#' bst <- xgb.train(
-#'   param, dtrain, nrounds = 2, evals = evals, obj = logregobj, feval = evalerror
-#' )
+#' bst <- xgb.train(param, dtrain, nrounds = 2, evals = evals,
+#'                  obj = logregobj, feval = evalerror)
 #'
 #'
 #' ## An xgb.train example of using variable learning rates at each iteration:
-#' param <- list(
-#'   max_depth = 2,
-#'   eta = 1,
-#'   nthread = nthread,
-#'   objective = "binary:logistic",
-#'   eval_metric = "auc"
-#' )
+#' param <- list(max_depth = 2, eta = 1, nthread = nthread,
+#'               objective = "binary:logistic", eval_metric = "auc")
 #' my_etas <- list(eta = c(0.5, 0.1))
-#'
-#' bst <- xgb.train(
-#'  param,
-#'  dtrain,
-#'  nrounds = 2,
-#'  evals = evals,
-#'  verbose = 0,
-#'  callbacks = list(xgb.cb.reset.parameters(my_etas))
-#' )
+#' bst <- xgb.train(param, dtrain, nrounds = 2, evals = evals, verbose = 0,
+#'                  callbacks = list(xgb.cb.reset.parameters(my_etas)))
 #'
 #' ## Early stopping:
-#' bst <- xgb.train(
-#'   param, dtrain, nrounds = 25, evals = evals, early_stopping_rounds = 3
-#' )
+#' bst <- xgb.train(param, dtrain, nrounds = 25, evals = evals,
+#'                  early_stopping_rounds = 3)
 #'
 #' ## An 'xgboost' interface example:
-#' bst <- xgboost(
-#'   x = agaricus.train$data,
-#'   y = factor(agaricus.train$label),
-#'   params = list(max_depth = 2, eta = 1),
-#'   nthread = nthread,
-#'   nrounds = 2
-#' )
+#' bst <- xgboost(data = agaricus.train$data, label = agaricus.train$label,
+#'                max_depth = 2, eta = 1, nthread = nthread, nrounds = 2,
+#'                objective = "binary:logistic")
 #' pred <- predict(bst, agaricus.test$data)
 #'
+#' @rdname xgb.train
 #' @export
 xgb.train <- function(params = list(), data, nrounds, evals = list(),
                       obj = NULL, feval = NULL, verbose = 1, print_every_n = 1L,

R-package/config.h.in

@@ -1,66 +0,0 @@
-/* config.h.in.  Generated from configure.ac by autoheader.  */
-
-/* Define if building universal (internal helper macro) */
-#undef AC_APPLE_UNIVERSAL_BUILD
-
-/* Define to 1 if you have the <inttypes.h> header file. */
-#undef HAVE_INTTYPES_H
-
-/* Define to 1 if you have the <stdint.h> header file. */
-#undef HAVE_STDINT_H
-
-/* Define to 1 if you have the <stdio.h> header file. */
-#undef HAVE_STDIO_H
-
-/* Define to 1 if you have the <stdlib.h> header file. */
-#undef HAVE_STDLIB_H
-
-/* Define to 1 if you have the <strings.h> header file. */
-#undef HAVE_STRINGS_H
-
-/* Define to 1 if you have the <string.h> header file. */
-#undef HAVE_STRING_H
-
-/* Define to 1 if you have the <sys/stat.h> header file. */
-#undef HAVE_SYS_STAT_H
-
-/* Define to 1 if you have the <sys/types.h> header file. */
-#undef HAVE_SYS_TYPES_H
-
-/* Define to 1 if you have the <unistd.h> header file. */
-#undef HAVE_UNISTD_H
-
-/* Define to the address where bug reports for this package should be sent. */
-#undef PACKAGE_BUGREPORT
-
-/* Define to the full name of this package. */
-#undef PACKAGE_NAME
-
-/* Define to the full name and version of this package. */
-#undef PACKAGE_STRING
-
-/* Define to the one symbol short name of this package. */
-#undef PACKAGE_TARNAME
-
-/* Define to the home page for this package. */
-#undef PACKAGE_URL
-
-/* Define to the version of this package. */
-#undef PACKAGE_VERSION
-
-/* Define to 1 if all of the C90 standard headers exist (not just the ones
-   required in a freestanding environment). This macro is provided for
-   backward compatibility; new code need not use it. */
-#undef STDC_HEADERS
-
-/* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most
-   significant byte first (like Motorola and SPARC, unlike Intel). */
-#if defined AC_APPLE_UNIVERSAL_BUILD
-# if defined __BIG_ENDIAN__
-#  define WORDS_BIGENDIAN 1
-# endif
-#else
-# ifndef WORDS_BIGENDIAN
-#  undef WORDS_BIGENDIAN
-# endif
-#endif

R-package/configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for xgboost 2.2.0.
+# Generated by GNU Autoconf 2.71 for xgboost 2.1.0.
 #
 #
 # Copyright (C) 1992-1996, 1998-2017, 2020-2021 Free Software Foundation,
@@ -607,50 +607,17 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='xgboost'
 PACKAGE_TARNAME='xgboost'
-PACKAGE_VERSION='2.2.0'
-PACKAGE_STRING='xgboost 2.2.0'
+PACKAGE_VERSION='2.1.0'
+PACKAGE_STRING='xgboost 2.1.0'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
-# Factoring default headers for most tests.
-ac_includes_default="\
-#include <stddef.h>
-#ifdef HAVE_STDIO_H
-# include <stdio.h>
-#endif
-#ifdef HAVE_STDLIB_H
-# include <stdlib.h>
-#endif
-#ifdef HAVE_STRING_H
-# include <string.h>
-#endif
-#ifdef HAVE_INTTYPES_H
-# include <inttypes.h>
-#endif
-#ifdef HAVE_STDINT_H
-# include <stdint.h>
-#endif
-#ifdef HAVE_STRINGS_H
-# include <strings.h>
-#endif
-#ifdef HAVE_SYS_TYPES_H
-# include <sys/types.h>
-#endif
-#ifdef HAVE_SYS_STAT_H
-# include <sys/stat.h>
-#endif
-#ifdef HAVE_UNISTD_H
-# include <unistd.h>
-#endif"
-
-ac_header_cxx_list=
 ac_subst_vars='LTLIBOBJS
 LIBOBJS
 BACKTRACE_LIB
 ENDIAN_FLAG
 OPENMP_LIB
 OPENMP_CXXFLAGS
-USE_LITTLE_ENDIAN
 OBJEXT
 EXEEXT
 ac_ct_CXX
@@ -709,8 +676,7 @@ CXXFLAGS
 LDFLAGS
 LIBS
 CPPFLAGS
-CCC
-USE_LITTLE_ENDIAN'
+CCC'
 
 
 # Initialize some variables set by options.
@@ -1259,7 +1225,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures xgboost 2.2.0 to adapt to many kinds of systems.
+\`configure' configures xgboost 2.1.0 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1321,7 +1287,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of xgboost 2.2.0:";;
+     short | recursive ) echo "Configuration of xgboost 2.1.0:";;
    esac
   cat <<\_ACEOF
 
@@ -1333,9 +1299,6 @@ Some influential environment variables:
   LIBS        libraries to pass to the linker, e.g. -l<library>
   CPPFLAGS    (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
               you have headers in a nonstandard directory <include dir>
-  USE_LITTLE_ENDIAN
-              "Whether to build with little endian (checks at compile time if
-              unset)"
 
 Use these variables to override the choices made by `configure' or to help
 it to find libraries and programs with nonstandard names/locations.
@@ -1404,7 +1367,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-xgboost configure 2.2.0
+xgboost configure 2.1.0
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -1546,39 +1509,6 @@ fi
   as_fn_set_status $ac_retval
 
 } # ac_fn_cxx_try_run
-
-# ac_fn_cxx_check_header_compile LINENO HEADER VAR INCLUDES
-# ---------------------------------------------------------
-# Tests whether HEADER exists and can be compiled using the include files in
-# INCLUDES, setting the cache variable VAR accordingly.
-ac_fn_cxx_check_header_compile ()
-{
-  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
-printf %s "checking for $2... " >&6; }
-if eval test \${$3+y}
-then :
-  printf %s "(cached) " >&6
-else $as_nop
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-$4
-#include <$2>
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"
-then :
-  eval "$3=yes"
-else $as_nop
-  eval "$3=no"
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
-fi
-eval ac_res=\$$3
-	       { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-printf "%s\n" "$ac_res" >&6; }
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
-
-} # ac_fn_cxx_check_header_compile
 ac_configure_args_raw=
 for ac_arg
 do
@@ -1603,7 +1533,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by xgboost $as_me 2.2.0, which was
+It was created by xgboost $as_me 2.1.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -2090,15 +2020,6 @@ main (int argc, char **argv)
 }
 "
 
-as_fn_append ac_header_cxx_list " stdio.h stdio_h HAVE_STDIO_H"
-as_fn_append ac_header_cxx_list " stdlib.h stdlib_h HAVE_STDLIB_H"
-as_fn_append ac_header_cxx_list " string.h string_h HAVE_STRING_H"
-as_fn_append ac_header_cxx_list " inttypes.h inttypes_h HAVE_INTTYPES_H"
-as_fn_append ac_header_cxx_list " stdint.h stdint_h HAVE_STDINT_H"
-as_fn_append ac_header_cxx_list " strings.h strings_h HAVE_STRINGS_H"
-as_fn_append ac_header_cxx_list " sys/stat.h sys_stat_h HAVE_SYS_STAT_H"
-as_fn_append ac_header_cxx_list " sys/types.h sys_types_h HAVE_SYS_TYPES_H"
-as_fn_append ac_header_cxx_list " unistd.h unistd_h HAVE_UNISTD_H"
 # Check that the precious variables saved in the cache have kept the same
 # value.
 ac_cache_corrupted=false
@@ -2871,289 +2792,38 @@ fi
 
 
 ### Endian detection
-
-ac_header= ac_cache=
-for ac_item in $ac_header_cxx_list
-do
-  if test $ac_cache; then
-    ac_fn_cxx_check_header_compile "$LINENO" $ac_header ac_cv_header_$ac_cache "$ac_includes_default"
-    if eval test \"x\$ac_cv_header_$ac_cache\" = xyes; then
-      printf "%s\n" "#define $ac_item 1" >> confdefs.h
-    fi
-    ac_header= ac_cache=
-  elif test $ac_header; then
-    ac_cache=$ac_item
-  else
-    ac_header=$ac_item
-  fi
-done
-
-
-
-
-
-
-
-
-if test $ac_cv_header_stdlib_h = yes && test $ac_cv_header_string_h = yes
+{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking endian" >&5
+printf %s "checking endian... " >&6; }
+{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: " >&5
+printf "%s\n" "" >&6; }
+if test "$cross_compiling" = yes
 then :
-
-printf "%s\n" "#define STDC_HEADERS 1" >>confdefs.h
-
-fi
-if test -z "${USE_LITTLE_ENDIAN+x}"
-then :
-
-  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: Checking system endianness as USE_LITTLE_ENDIAN is unset" >&5
-printf "%s\n" "$as_me: Checking system endianness as USE_LITTLE_ENDIAN is unset" >&6;}
-  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking system endianness" >&5
-printf %s "checking system endianness... " >&6; }
-   { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether byte ordering is bigendian" >&5
-printf %s "checking whether byte ordering is bigendian... " >&6; }
-if test ${ac_cv_c_bigendian+y}
-then :
-  printf %s "(cached) " >&6
-else $as_nop
-  ac_cv_c_bigendian=unknown
-    # See if we're dealing with a universal compiler.
-    cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-#ifndef __APPLE_CC__
-	       not a universal capable compiler
-	     #endif
-	     typedef int dummy;
-
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"
-then :
-
-	# Check for potential -arch flags.  It is not universal unless
-	# there are at least two -arch flags with different values.
-	ac_arch=
-	ac_prev=
-	for ac_word in $CC $CFLAGS $CPPFLAGS $LDFLAGS; do
-	 if test -n "$ac_prev"; then
-	   case $ac_word in
-	     i?86 | x86_64 | ppc | ppc64)
-	       if test -z "$ac_arch" || test "$ac_arch" = "$ac_word"; then
-		 ac_arch=$ac_word
-	       else
-		 ac_cv_c_bigendian=universal
-		 break
-	       fi
-	       ;;
-	   esac
-	   ac_prev=
-	 elif test "x$ac_word" = "x-arch"; then
-	   ac_prev=arch
-	 fi
-       done
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
-    if test $ac_cv_c_bigendian = unknown; then
-      # See if sys/param.h defines the BYTE_ORDER macro.
-      cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-#include <sys/types.h>
-	     #include <sys/param.h>
-
-int
-main (void)
-{
-#if ! (defined BYTE_ORDER && defined BIG_ENDIAN \
-		     && defined LITTLE_ENDIAN && BYTE_ORDER && BIG_ENDIAN \
-		     && LITTLE_ENDIAN)
-	      bogus endian macros
-	     #endif
-
-  ;
-  return 0;
-}
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"
-then :
-  # It does; now see whether it defined to BIG_ENDIAN or not.
-	 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-#include <sys/types.h>
-		#include <sys/param.h>
-
-int
-main (void)
-{
-#if BYTE_ORDER != BIG_ENDIAN
-		 not big endian
-		#endif
-
-  ;
-  return 0;
-}
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"
-then :
-  ac_cv_c_bigendian=yes
-else $as_nop
-  ac_cv_c_bigendian=no
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
-    fi
-    if test $ac_cv_c_bigendian = unknown; then
-      # See if <limits.h> defines _LITTLE_ENDIAN or _BIG_ENDIAN (e.g., Solaris).
-      cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-#include <limits.h>
-
-int
-main (void)
-{
-#if ! (defined _LITTLE_ENDIAN || defined _BIG_ENDIAN)
-	      bogus endian macros
-	     #endif
-
-  ;
-  return 0;
-}
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"
-then :
-  # It does; now see whether it defined to _BIG_ENDIAN or not.
-	 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-#include <limits.h>
-
-int
-main (void)
-{
-#ifndef _BIG_ENDIAN
-		 not big endian
-		#endif
-
-  ;
-  return 0;
-}
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"
-then :
-  ac_cv_c_bigendian=yes
-else $as_nop
-  ac_cv_c_bigendian=no
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
-    fi
-    if test $ac_cv_c_bigendian = unknown; then
-      # Compile a test program.
-      if test "$cross_compiling" = yes
-then :
-  # Try to guess by grepping values from an object file.
-	 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-unsigned short int ascii_mm[] =
-		  { 0x4249, 0x4765, 0x6E44, 0x6961, 0x6E53, 0x7953, 0 };
-		unsigned short int ascii_ii[] =
-		  { 0x694C, 0x5454, 0x656C, 0x6E45, 0x6944, 0x6E61, 0 };
-		int use_ascii (int i) {
-		  return ascii_mm[i] + ascii_ii[i];
-		}
-		unsigned short int ebcdic_ii[] =
-		  { 0x89D3, 0xE3E3, 0x8593, 0x95C5, 0x89C4, 0x9581, 0 };
-		unsigned short int ebcdic_mm[] =
-		  { 0xC2C9, 0xC785, 0x95C4, 0x8981, 0x95E2, 0xA8E2, 0 };
-		int use_ebcdic (int i) {
-		  return ebcdic_mm[i] + ebcdic_ii[i];
-		}
-		extern int foo;
-
-int
-main (void)
-{
-return use_ascii (foo) == use_ebcdic (foo);
-  ;
-  return 0;
-}
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"
-then :
-  if grep BIGenDianSyS conftest.$ac_objext >/dev/null; then
-	      ac_cv_c_bigendian=yes
-	    fi
-	    if grep LiTTleEnDian conftest.$ac_objext >/dev/null ; then
-	      if test "$ac_cv_c_bigendian" = unknown; then
-		ac_cv_c_bigendian=no
-	      else
-		# finding both strings is unlikely to happen, but who knows?
-		ac_cv_c_bigendian=unknown
-	      fi
-	    fi
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
+  { { printf "%s\n" "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+printf "%s\n" "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot run test program while cross compiling
+See \`config.log' for more details" "$LINENO" 5; }
 else $as_nop
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
-$ac_includes_default
+#include <stdint.h>
 int
 main (void)
 {
-
-	     /* Are we little or big endian?  From Harbison&Steele.  */
-	     union
-	     {
-	       long int l;
-	       char c[sizeof (long int)];
-	     } u;
-	     u.l = 1;
-	     return u.c[sizeof (long int) - 1] == 1;
-
+const uint16_t endianness = 256; return !!(*(const uint8_t *)&endianness);
   ;
   return 0;
 }
 _ACEOF
 if ac_fn_cxx_try_run "$LINENO"
 then :
-  ac_cv_c_bigendian=no
+  ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=1"
 else $as_nop
-  ac_cv_c_bigendian=yes
+  ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=0"
 fi
 rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
   conftest.$ac_objext conftest.beam conftest.$ac_ext
 fi
 
-    fi
-fi
-{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_bigendian" >&5
-printf "%s\n" "$ac_cv_c_bigendian" >&6; }
- case $ac_cv_c_bigendian in #(
-   yes)
-     { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: using big endian" >&5
-printf "%s\n" "using big endian" >&6; }
-     ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=0";; #(
-   no)
-     { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: using little endian" >&5
-printf "%s\n" "using little endian" >&6; }
-     ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=1" ;; #(
-   universal)
-
-printf "%s\n" "#define AC_APPLE_UNIVERSAL_BUILD 1" >>confdefs.h
-
-     ;; #(
-   *)
-     { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: unknown" >&5
-printf "%s\n" "unknown" >&6; }
-     as_fn_error $? "Could not determine endianness. Please set USE_LITTLE_ENDIAN" "$LINENO" 5
-   ;;
- esac
-
-
-else $as_nop
-
-  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: Forcing endianness to: ${USE_LITTLE_ENDIAN}" >&5
-printf "%s\n" "$as_me: Forcing endianness to: ${USE_LITTLE_ENDIAN}" >&6;}
-  ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=${USE_LITTLE_ENDIAN}"
-
-fi
 
 OPENMP_CXXFLAGS=""
 
@@ -3207,8 +2877,6 @@ fi
 
 ac_config_files="$ac_config_files src/Makevars"
 
-ac_config_headers="$ac_config_headers config.h"
-
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
 # tests run on this system so they can be shared between configure
@@ -3299,7 +2967,43 @@ test "x$prefix" = xNONE && prefix=$ac_default_prefix
 # Let make expand exec_prefix.
 test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
 
-DEFS=-DHAVE_CONFIG_H
+# Transform confdefs.h into DEFS.
+# Protect against shell expansion while executing Makefile rules.
+# Protect against Makefile macro expansion.
+#
+# If the first sed substitution is executed (which looks for macros that
+# take arguments), then branch to the quote section.  Otherwise,
+# look for a macro that doesn't take arguments.
+ac_script='
+:mline
+/\\$/{
+ N
+ s,\\\n,,
+ b mline
+}
+t clear
+:clear
+s/^[	 ]*#[	 ]*define[	 ][	 ]*\([^	 (][^	 (]*([^)]*)\)[	 ]*\(.*\)/-D\1=\2/g
+t quote
+s/^[	 ]*#[	 ]*define[	 ][	 ]*\([^	 ][^	 ]*\)[	 ]*\(.*\)/-D\1=\2/g
+t quote
+b any
+:quote
+s/[	 `~#$^&*(){}\\|;'\''"<>?]/\\&/g
+s/\[/\\&/g
+s/\]/\\&/g
+s/\$/$$/g
+H
+:any
+${
+	g
+	s/^\n//
+	s/\n/ /g
+	p
+}
+'
+DEFS=`sed -n "$ac_script" confdefs.h`
+
 
 ac_libobjs=
 ac_ltlibobjs=
@@ -3319,7 +3023,6 @@ LTLIBOBJS=$ac_ltlibobjs
 
 
 
-
 : "${CONFIG_STATUS=./config.status}"
 ac_write_fail=0
 ac_clean_files_save=$ac_clean_files
@@ -3709,7 +3412,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by xgboost $as_me 2.2.0, which was
+This file was extended by xgboost $as_me 2.1.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -3727,15 +3430,11 @@ case $ac_config_files in *"
 "*) set x $ac_config_files; shift; ac_config_files=$*;;
 esac
 
-case $ac_config_headers in *"
-"*) set x $ac_config_headers; shift; ac_config_headers=$*;;
-esac
 
 
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 # Files that config.status was made for.
 config_files="$ac_config_files"
-config_headers="$ac_config_headers"
 
 _ACEOF
 
@@ -3756,15 +3455,10 @@ Usage: $0 [OPTION]... [TAG]...
       --recheck    update $as_me by reconfiguring in the same conditions
       --file=FILE[:TEMPLATE]
                    instantiate the configuration file FILE
-      --header=FILE[:TEMPLATE]
-                   instantiate the configuration header FILE
 
 Configuration files:
 $config_files
 
-Configuration headers:
-$config_headers
-
 Report bugs to the package provider."
 
 _ACEOF
@@ -3773,7 +3467,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-xgboost config.status 2.2.0
+xgboost config.status 2.1.0
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 
@@ -3827,18 +3521,7 @@ do
     esac
     as_fn_append CONFIG_FILES " '$ac_optarg'"
     ac_need_defaults=false;;
-  --header | --heade | --head | --hea )
-    $ac_shift
-    case $ac_optarg in
-    *\'*) ac_optarg=`printf "%s\n" "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
-    esac
-    as_fn_append CONFIG_HEADERS " '$ac_optarg'"
-    ac_need_defaults=false;;
-  --he | --h)
-    # Conflict between --help and --header
-    as_fn_error $? "ambiguous option: \`$1'
-Try \`$0 --help' for more information.";;
-  --help | --hel | -h )
+  --he | --h |  --help | --hel | -h )
     printf "%s\n" "$ac_cs_usage"; exit ;;
   -q | -quiet | --quiet | --quie | --qui | --qu | --q \
   | -silent | --silent | --silen | --sile | --sil | --si | --s)
@@ -3895,7 +3578,6 @@ for ac_config_target in $ac_config_targets
 do
   case $ac_config_target in
     "src/Makevars") CONFIG_FILES="$CONFIG_FILES src/Makevars" ;;
-    "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
 
   *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
   esac
@@ -3908,7 +3590,6 @@ done
 # bizarre bug on SunOS 4.1.3.
 if $ac_need_defaults; then
   test ${CONFIG_FILES+y} || CONFIG_FILES=$config_files
-  test ${CONFIG_HEADERS+y} || CONFIG_HEADERS=$config_headers
 fi
 
 # Have a temporary directory for convenience.  Make it in the build tree
@@ -4096,116 +3777,8 @@ fi
 cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 fi # test -n "$CONFIG_FILES"
 
-# Set up the scripts for CONFIG_HEADERS section.
-# No need to generate them if there are no CONFIG_HEADERS.
-# This happens for instance with `./config.status Makefile'.
-if test -n "$CONFIG_HEADERS"; then
-cat >"$ac_tmp/defines.awk" <<\_ACAWK ||
-BEGIN {
-_ACEOF
 
-# Transform confdefs.h into an awk script `defines.awk', embedded as
-# here-document in config.status, that substitutes the proper values into
-# config.h.in to produce config.h.
-
-# Create a delimiter string that does not exist in confdefs.h, to ease
-# handling of long lines.
-ac_delim='%!_!# '
-for ac_last_try in false false :; do
-  ac_tt=`sed -n "/$ac_delim/p" confdefs.h`
-  if test -z "$ac_tt"; then
-    break
-  elif $ac_last_try; then
-    as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5
-  else
-    ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
-  fi
-done
-
-# For the awk script, D is an array of macro values keyed by name,
-# likewise P contains macro parameters if any.  Preserve backslash
-# newline sequences.
-
-ac_word_re=[_$as_cr_Letters][_$as_cr_alnum]*
-sed -n '
-s/.\{148\}/&'"$ac_delim"'/g
-t rset
-:rset
-s/^[	 ]*#[	 ]*define[	 ][	 ]*/ /
-t def
-d
-:def
-s/\\$//
-t bsnl
-s/["\\]/\\&/g
-s/^ \('"$ac_word_re"'\)\(([^()]*)\)[	 ]*\(.*\)/P["\1"]="\2"\
-D["\1"]=" \3"/p
-s/^ \('"$ac_word_re"'\)[	 ]*\(.*\)/D["\1"]=" \2"/p
-d
-:bsnl
-s/["\\]/\\&/g
-s/^ \('"$ac_word_re"'\)\(([^()]*)\)[	 ]*\(.*\)/P["\1"]="\2"\
-D["\1"]=" \3\\\\\\n"\\/p
-t cont
-s/^ \('"$ac_word_re"'\)[	 ]*\(.*\)/D["\1"]=" \2\\\\\\n"\\/p
-t cont
-d
-:cont
-n
-s/.\{148\}/&'"$ac_delim"'/g
-t clear
-:clear
-s/\\$//
-t bsnlc
-s/["\\]/\\&/g; s/^/"/; s/$/"/p
-d
-:bsnlc
-s/["\\]/\\&/g; s/^/"/; s/$/\\\\\\n"\\/p
-b cont
-' <confdefs.h | sed '
-s/'"$ac_delim"'/"\\\
-"/g' >>$CONFIG_STATUS || ac_write_fail=1
-
-cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
-  for (key in D) D_is_set[key] = 1
-  FS = ""
-}
-/^[\t ]*#[\t ]*(define|undef)[\t ]+$ac_word_re([\t (]|\$)/ {
-  line = \$ 0
-  split(line, arg, " ")
-  if (arg[1] == "#") {
-    defundef = arg[2]
-    mac1 = arg[3]
-  } else {
-    defundef = substr(arg[1], 2)
-    mac1 = arg[2]
-  }
-  split(mac1, mac2, "(") #)
-  macro = mac2[1]
-  prefix = substr(line, 1, index(line, defundef) - 1)
-  if (D_is_set[macro]) {
-    # Preserve the white space surrounding the "#".
-    print prefix "define", macro P[macro] D[macro]
-    next
-  } else {
-    # Replace #undef with comments.  This is necessary, for example,
-    # in the case of _POSIX_SOURCE, which is predefined and required
-    # on some systems where configure will not decide to define it.
-    if (defundef == "undef") {
-      print "/*", prefix defundef, macro, "*/"
-      next
-    }
-  }
-}
-{ print }
-_ACAWK
-_ACEOF
-cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-  as_fn_error $? "could not setup config headers machinery" "$LINENO" 5
-fi # test -n "$CONFIG_HEADERS"
-
-
-eval set X "  :F $CONFIG_FILES  :H $CONFIG_HEADERS    "
+eval set X "  :F $CONFIG_FILES      "
 shift
 for ac_tag
 do
@@ -4413,30 +3986,7 @@ which seems to be undefined.  Please make sure it is defined" >&2;}
   esac \
   || as_fn_error $? "could not create $ac_file" "$LINENO" 5
  ;;
-  :H)
-  #
-  # CONFIG_HEADER
-  #
-  if test x"$ac_file" != x-; then
-    {
-      printf "%s\n" "/* $configure_input  */" >&1 \
-      && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs"
-    } >"$ac_tmp/config.h" \
-      || as_fn_error $? "could not create $ac_file" "$LINENO" 5
-    if diff "$ac_file" "$ac_tmp/config.h" >/dev/null 2>&1; then
-      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
-printf "%s\n" "$as_me: $ac_file is unchanged" >&6;}
-    else
-      rm -f "$ac_file"
-      mv "$ac_tmp/config.h" "$ac_file" \
-	|| as_fn_error $? "could not create $ac_file" "$LINENO" 5
-    fi
-  else
-    printf "%s\n" "/* $configure_input  */" >&1 \
-      && eval '$AWK -f "$ac_tmp/defines.awk"' "$ac_file_inputs" \
-      || as_fn_error $? "could not create -" "$LINENO" 5
-  fi
- ;;
+
 
 
   esac

R-package/configure.ac

@@ -2,7 +2,7 @@
 
 AC_PREREQ(2.69)
 
-AC_INIT([xgboost],[2.2.0],[],[xgboost],[])
+AC_INIT([xgboost],[2.1.0],[],[xgboost],[])
 
 : ${R_HOME=`R RHOME`}
 if test -z "${R_HOME}"; then
@@ -28,22 +28,11 @@ AC_MSG_RESULT([])
 AC_CHECK_LIB([execinfo], [backtrace], [BACKTRACE_LIB=-lexecinfo], [BACKTRACE_LIB=''])
 
 ### Endian detection
-AC_ARG_VAR(USE_LITTLE_ENDIAN, "Whether to build with little endian (checks at compile time if unset)")
-AS_IF([test -z "${USE_LITTLE_ENDIAN+x}"], [
-  AC_MSG_NOTICE([Checking system endianness as USE_LITTLE_ENDIAN is unset])
-  AC_MSG_CHECKING([system endianness])
-  AC_C_BIGENDIAN(
-    [AC_MSG_RESULT([using big endian])
-     ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=0"],
-    [AC_MSG_RESULT([using little endian])
-     ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=1"],
-    [AC_MSG_RESULT([unknown])
-     AC_MSG_ERROR([Could not determine endianness. Please set USE_LITTLE_ENDIAN])]
-  )
-], [
-  AC_MSG_NOTICE([Forcing endianness to: ${USE_LITTLE_ENDIAN}])
-  ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=${USE_LITTLE_ENDIAN}"
-])
+AC_MSG_CHECKING([endian])
+AC_MSG_RESULT([])
+AC_RUN_IFELSE([AC_LANG_PROGRAM([[#include <stdint.h>]], [[const uint16_t endianness = 256; return !!(*(const uint8_t *)&endianness);]])],
+  [ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=1"],
+  [ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=0"])
 
 OPENMP_CXXFLAGS=""
 
@@ -84,5 +73,4 @@ AC_SUBST(OPENMP_LIB)
 AC_SUBST(ENDIAN_FLAG)
 AC_SUBST(BACKTRACE_LIB)
 AC_CONFIG_FILES([src/Makevars])
-AC_CONFIG_HEADERS([config.h])
 AC_OUTPUT

R-package/demo/00Index

@@ -0,0 +1,14 @@
+basic_walkthrough               Basic feature walkthrough
+custom_objective                Customize loss function, and evaluation metric
+boost_from_prediction           Boosting from existing prediction
+predict_first_ntree             Predicting using first n trees
+generalized_linear_model        Generalized Linear Model
+cross_validation                Cross validation
+create_sparse_matrix            Create Sparse Matrix
+predict_leaf_indices            Predicting the corresponding leaves
+early_stopping                  Early Stop in training
+poisson_regression              Poisson regression on count data
+tweedie_regression              Tweedie regression
+gpu_accelerated                 GPU-accelerated tree building algorithms
+interaction_constraints         Interaction constraints among features
+

R-package/demo/README.md

@@ -0,0 +1,19 @@
+XGBoost R Feature Walkthrough
+====
+* [Basic walkthrough of wrappers](basic_walkthrough.R)
+* [Customize loss function, and evaluation metric](custom_objective.R)
+* [Boosting from existing prediction](boost_from_prediction.R)
+* [Predicting using first n trees](predict_first_ntree.R)
+* [Generalized Linear Model](generalized_linear_model.R)
+* [Cross validation](cross_validation.R)
+* [Create a sparse matrix from a dense one](create_sparse_matrix.R)
+* [Use GPU-accelerated tree building algorithms](gpu_accelerated.R)
+
+Benchmarks
+====
+* [Starter script for Kaggle Higgs Boson](../../demo/kaggle-higgs)
+ 
+Notes
+====
+* Contribution of examples, benchmarks is more than welcomed!
+* If you like to share how you use xgboost to solve your problem, send a pull request :)

R-package/demo/basic_walkthrough.R

@@ -0,0 +1,114 @@
+require(xgboost)
+require(methods)
+
+# we load in the agaricus dataset
+# In this example, we are aiming to predict whether a mushroom is edible
+data(agaricus.train, package = 'xgboost')
+data(agaricus.test, package = 'xgboost')
+train <- agaricus.train
+test <- agaricus.test
+# the loaded data is stored in sparseMatrix, and label is a numeric vector in {0,1}
+class(train$label)
+class(train$data)
+
+#-------------Basic Training using XGBoost-----------------
+# this is the basic usage of xgboost you can put matrix in data field
+# note: we are putting in sparse matrix here, xgboost naturally handles sparse input
+# use sparse matrix when your feature is sparse(e.g. when you are using one-hot encoding vector)
+print("Training xgboost with sparseMatrix")
+bst <- xgboost(data = train$data, label = train$label, max_depth = 2, eta = 1, nrounds = 2,
+               nthread = 2, objective = "binary:logistic")
+# alternatively, you can put in dense matrix, i.e. basic R-matrix
+print("Training xgboost with Matrix")
+bst <- xgboost(data = as.matrix(train$data), label = train$label, max_depth = 2, eta = 1, nrounds = 2,
+               nthread = 2, objective = "binary:logistic")
+
+# you can also put in xgb.DMatrix object, which stores label, data and other meta datas needed for advanced features
+print("Training xgboost with xgb.DMatrix")
+dtrain <- xgb.DMatrix(data = train$data, label = train$label)
+bst <- xgboost(data = dtrain, max_depth = 2, eta = 1, nrounds = 2, nthread = 2,
+               objective = "binary:logistic")
+
+# Verbose = 0,1,2
+print("Train xgboost with verbose 0, no message")
+bst <- xgboost(data = dtrain, max_depth = 2, eta = 1, nrounds = 2,
+               nthread = 2, objective = "binary:logistic", verbose = 0)
+print("Train xgboost with verbose 1, print evaluation metric")
+bst <- xgboost(data = dtrain, max_depth = 2, eta = 1, nrounds = 2,
+               nthread = 2, objective = "binary:logistic", verbose = 1)
+print("Train xgboost with verbose 2, also print information about tree")
+bst <- xgboost(data = dtrain, max_depth = 2, eta = 1, nrounds = 2,
+               nthread = 2, objective = "binary:logistic", verbose = 2)
+
+# you can also specify data as file path to a LIBSVM format input
+# since we do not have this file with us, the following line is just for illustration
+# bst <- xgboost(data = 'agaricus.train.svm', max_depth = 2, eta = 1, nrounds = 2,objective = "binary:logistic")
+
+#--------------------basic prediction using xgboost--------------
+# you can do prediction using the following line
+# you can put in Matrix, sparseMatrix, or xgb.DMatrix
+pred <- predict(bst, test$data)
+err <- mean(as.numeric(pred > 0.5) != test$label)
+print(paste("test-error=", err))
+
+#-------------------save and load models-------------------------
+# save model to binary local file
+xgb.save(bst, "xgboost.model")
+# load binary model to R
+# Function doesn't take 'nthreads', but can be set like this:
+RhpcBLASctl::omp_set_num_threads(1)
+bst2 <- xgb.load("xgboost.model")
+pred2 <- predict(bst2, test$data)
+# pred2 should be identical to pred
+print(paste("sum(abs(pred2-pred))=", sum(abs(pred2 - pred))))
+
+# save model to R's raw vector
+raw <- xgb.save.raw(bst)
+# load binary model to R
+bst3 <- xgb.load.raw(raw)
+pred3 <- predict(bst3, test$data)
+# pred3 should be identical to pred
+print(paste("sum(abs(pred3-pred))=", sum(abs(pred3 - pred))))
+
+#----------------Advanced features --------------
+# to use advanced features, we need to put data in xgb.DMatrix
+dtrain <- xgb.DMatrix(data = train$data, label = train$label)
+dtest <- xgb.DMatrix(data = test$data, label = test$label)
+#---------------Using an evaluation set----------------
+# 'evals' is a list of xgb.DMatrix, each of them is tagged with name
+evals <- list(train = dtrain, test = dtest)
+# to train with an evaluation set, use xgb.train, which contains more advanced features
+# 'evals' argument allows us to monitor the evaluation result on all data in the list
+print("Train xgboost using xgb.train with evaluation data")
+bst <- xgb.train(data = dtrain, max_depth = 2, eta = 1, nrounds = 2, evals = evals,
+                 nthread = 2, objective = "binary:logistic")
+# we can change evaluation metrics, or use multiple evaluation metrics
+print("train xgboost using xgb.train with evaluation data, watch logloss and error")
+bst <- xgb.train(data = dtrain, max_depth = 2, eta = 1, nrounds = 2, evals = evals,
+                 eval_metric = "error", eval_metric = "logloss",
+                 nthread = 2, objective = "binary:logistic")
+
+# xgb.DMatrix can also be saved using xgb.DMatrix.save
+xgb.DMatrix.save(dtrain, "dtrain.buffer")
+# to load it in, simply call xgb.DMatrix
+dtrain2 <- xgb.DMatrix("dtrain.buffer")
+bst <- xgb.train(data = dtrain2, max_depth = 2, eta = 1, nrounds = 2, evals = evals,
+                 nthread = 2, objective = "binary:logistic")
+# information can be extracted from xgb.DMatrix using getinfo
+label <- getinfo(dtest, "label")
+pred <- predict(bst, dtest)
+err <- as.numeric(sum(as.integer(pred > 0.5) != label)) / length(label)
+print(paste("test-error=", err))
+
+# You can dump the tree you learned using xgb.dump into a text file
+dump_path <- file.path(tempdir(), 'dump.raw.txt')
+xgb.dump(bst, dump_path, with_stats = TRUE)
+
+# Finally, you can check which features are the most important.
+print("Most important features (look at column Gain):")
+imp_matrix <- xgb.importance(feature_names = colnames(train$data), model = bst)
+print(imp_matrix)
+
+# Feature importance bar plot by gain
+print("Feature importance Plot : ")
+print(xgb.plot.importance(importance_matrix = imp_matrix))

R-package/demo/boost_from_prediction.R

@@ -0,0 +1,26 @@
+require(xgboost)
+# load in the agaricus dataset
+data(agaricus.train, package = 'xgboost')
+data(agaricus.test, package = 'xgboost')
+dtrain <- xgb.DMatrix(agaricus.train$data, label = agaricus.train$label)
+dtest <- xgb.DMatrix(agaricus.test$data, label = agaricus.test$label)
+
+evals <- list(eval = dtest, train = dtrain)
+###
+# advanced: start from a initial base prediction
+#
+print('start running example to start from a initial prediction')
+# train xgboost for 1 round
+param <- list(max_depth = 2, eta = 1, nthread = 2, objective = 'binary:logistic')
+bst <- xgb.train(param, dtrain, 1, evals)
+# Note: we need the margin value instead of transformed prediction in set_base_margin
+# do predict with output_margin=TRUE, will always give you margin values before logistic transformation
+ptrain <- predict(bst, dtrain, outputmargin = TRUE)
+ptest  <- predict(bst, dtest, outputmargin = TRUE)
+# set the base_margin property of dtrain and dtest
+# base margin is the base prediction we will boost from
+setinfo(dtrain, "base_margin", ptrain)
+setinfo(dtest, "base_margin", ptest)
+
+print('this is result of boost from initial prediction')
+bst <- xgb.train(params = param, data = dtrain, nrounds = 1, evals = evals)

R-package/demo/create_sparse_matrix.R

@@ -0,0 +1,117 @@
+require(xgboost)
+require(Matrix)
+require(data.table)
+if (!require(vcd)) {
+  install.packages('vcd') #Available in CRAN. Used for its dataset with categorical values.
+  require(vcd)
+}
+# According to its documentation, XGBoost works only on numbers.
+# Sometimes the dataset we have to work on have categorical data.
+# A categorical variable is one which have a fixed number of values.
+# By example, if for each observation a variable called "Colour" can have only
+# "red", "blue" or "green" as value, it is a categorical variable.
+#
+# In R, categorical variable is called Factor.
+# Type ?factor in console for more information.
+#
+# In this demo we will see how to transform a dense dataframe with categorical variables to a sparse matrix
+# before analyzing it in XGBoost.
+# The method we are going to see is usually called "one hot encoding".
+
+#load Arthritis dataset in memory.
+data(Arthritis)
+
+# create a copy of the dataset with data.table package
+# (data.table is 100% compliant with R dataframe but its syntax is a lot more consistent
+# and its performance are really good).
+df <- data.table(Arthritis, keep.rownames = FALSE)
+
+# Let's have a look to the data.table
+cat("Print the dataset\n")
+print(df)
+
+# 2 columns have factor type, one has ordinal type
+# (ordinal variable is a categorical variable with values which can be ordered, here: None > Some > Marked).
+cat("Structure of the dataset\n")
+str(df)
+
+# Let's add some new categorical features to see if it helps.
+# Of course these feature are highly correlated to the Age feature.
+# Usually it's not a good thing in ML, but Tree algorithms (including boosted trees) are able to select the best features,
+# even in case of highly correlated features.
+
+# For the first feature we create groups of age by rounding the real age.
+# Note that we transform it to factor (categorical data) so the algorithm treat them as independent values.
+df[, AgeDiscret := as.factor(round(Age / 10, 0))]
+
+# Here is an even stronger simplification of the real age with an arbitrary split at 30 years old.
+# I choose this value based on nothing.
+# We will see later if simplifying the information based on arbitrary values is a good strategy
+# (I am sure you already have an idea of how well it will work!).
+df[, AgeCat := as.factor(ifelse(Age > 30, "Old", "Young"))]
+
+# We remove ID as there is nothing to learn from this feature (it will just add some noise as the dataset is small).
+df[, ID := NULL]
+
+# List the different values for the column Treatment: Placebo, Treated.
+cat("Values of the categorical feature Treatment\n")
+print(levels(df[, Treatment]))
+
+# Next step, we will transform the categorical data to dummy variables.
+# This method is also called one hot encoding.
+# The purpose is to transform each value of each categorical feature in one binary feature.
+#
+# Let's take, the column Treatment will be replaced by two columns, Placebo, and Treated.
+# Each of them will be binary.
+# For example an observation which had the value Placebo in column Treatment before the transformation will have, after the transformation,
+# the value 1 in the new column Placebo and the value 0 in the new column  Treated.
+#
+# Formulae Improved~.-1 used below means transform all categorical features but column Improved to binary values.
+# Column Improved is excluded because it will be our output column, the one we want to predict.
+sparse_matrix <- sparse.model.matrix(Improved ~ . - 1, data = df)
+
+cat("Encoding of the sparse Matrix\n")
+print(sparse_matrix)
+
+# Create the output vector (not sparse)
+# 1. Set, for all rows, field in Y column to 0;
+# 2. set Y to 1 when Improved == Marked;
+# 3. Return Y column
+output_vector <- df[, Y := 0][Improved == "Marked", Y := 1][, Y]
+
+# Following is the same process as other demo
+cat("Learning...\n")
+bst <- xgb.train(data = xgb.DMatrix(sparse_matrix, label = output_vector), max_depth = 9,
+                 eta = 1, nthread = 2, nrounds = 10, objective = "binary:logistic")
+
+importance <- xgb.importance(feature_names = colnames(sparse_matrix), model = bst)
+print(importance)
+# According to the matrix below, the most important feature in this dataset to predict if the treatment will work is the Age.
+# The second most important feature is having received a placebo or not.
+# The sex is third.
+# Then we see our generated features (AgeDiscret). We can see that their contribution is very low (Gain column).
+
+# Does these result make sense?
+# Let's check some Chi2 between each of these features and the outcome.
+
+print(chisq.test(df$Age, df$Y))
+# Pearson correlation between Age and illness disappearing is 35
+
+print(chisq.test(df$AgeDiscret, df$Y))
+# Our first simplification of Age gives a Pearson correlation of 8.
+
+print(chisq.test(df$AgeCat, df$Y))
+# The perfectly random split I did between young and old at 30 years old have a low correlation of 2.
+# It's a result we may expect as may be in my mind > 30 years is being old (I am 32 and starting feeling old, this may explain that),
+# but for the illness we are studying, the age to be vulnerable is not the same.
+# Don't let your "gut" lower the quality of your model. In "data science", there is science :-)
+
+# As you can see, in general destroying information by simplifying it won't improve your model.
+# Chi2 just demonstrates that.
+# But in more complex cases, creating a new feature based on existing one which makes link with the outcome
+# more obvious may help the algorithm and improve the model.
+# The case studied here is not enough complex to show that. Check Kaggle forum for some challenging datasets.
+# However it's almost always worse when you add some arbitrary rules.
+# Moreover, you can notice that even if we have added some not useful new features highly correlated with
+# other features, the boosting tree algorithm have been able to choose the best one, which in this case is the Age.
+# Linear model may not be that strong in these scenario.

R-package/demo/cross_validation.R

@@ -0,0 +1,51 @@
+require(xgboost)
+# load in the agaricus dataset
+data(agaricus.train, package = 'xgboost')
+data(agaricus.test, package = 'xgboost')
+dtrain <- xgb.DMatrix(agaricus.train$data, label = agaricus.train$label)
+dtest <- xgb.DMatrix(agaricus.test$data, label = agaricus.test$label)
+
+nrounds <- 2
+param <- list(max_depth = 2, eta = 1, nthread = 2, objective = 'binary:logistic')
+
+cat('running cross validation\n')
+# do cross validation, this will print result out as
+# [iteration]  metric_name:mean_value+std_value
+# std_value is standard deviation of the metric
+xgb.cv(param, dtrain, nrounds, nfold = 5, metrics = 'error')
+
+cat('running cross validation, disable standard deviation display\n')
+# do cross validation, this will print result out as
+# [iteration]  metric_name:mean_value+std_value
+# std_value is standard deviation of the metric
+xgb.cv(param, dtrain, nrounds, nfold = 5,
+       metrics = 'error', showsd = FALSE)
+
+###
+# you can also do cross validation with customized loss function
+# See custom_objective.R
+##
+print('running cross validation, with customized loss function')
+
+logregobj <- function(preds, dtrain) {
+  labels <- getinfo(dtrain, "label")
+  preds <- 1 / (1 + exp(-preds))
+  grad <- preds - labels
+  hess <- preds * (1 - preds)
+  return(list(grad = grad, hess = hess))
+}
+evalerror <- function(preds, dtrain) {
+  labels <- getinfo(dtrain, "label")
+  err <- as.numeric(sum(labels != (preds > 0))) / length(labels)
+  return(list(metric = "error", value = err))
+}
+
+param <- list(max_depth = 2, eta = 1,
+              objective = logregobj, eval_metric = evalerror)
+# train with customized objective
+xgb.cv(params = param, data = dtrain, nrounds = nrounds, nfold = 5)
+
+# do cross validation with prediction values for each fold
+res <- xgb.cv(params = param, data = dtrain, nrounds = nrounds, nfold = 5, prediction = TRUE)
+res$evaluation_log
+length(res$pred)

R-package/demo/custom_objective.R

@@ -0,0 +1,65 @@
+require(xgboost)
+# load in the agaricus dataset
+data(agaricus.train, package = 'xgboost')
+data(agaricus.test, package = 'xgboost')
+dtrain <- xgb.DMatrix(agaricus.train$data, label = agaricus.train$label)
+dtest <- xgb.DMatrix(agaricus.test$data, label = agaricus.test$label)
+
+# note: for customized objective function, we leave objective as default
+# note: what we are getting is margin value in prediction
+# you must know what you are doing
+evals <- list(eval = dtest, train = dtrain)
+num_round <- 2
+
+# user define objective function, given prediction, return gradient and second order gradient
+# this is log likelihood loss
+logregobj <- function(preds, dtrain) {
+  labels <- getinfo(dtrain, "label")
+  preds <- 1 / (1 + exp(-preds))
+  grad <- preds - labels
+  hess <- preds * (1 - preds)
+  return(list(grad = grad, hess = hess))
+}
+
+# user defined evaluation function, return a pair metric_name, result
+# NOTE: when you do customized loss function, the default prediction value is margin
+# this may make builtin evaluation metric not function properly
+# for example, we are doing logistic loss, the prediction is score before logistic transformation
+# the builtin evaluation error assumes input is after logistic transformation
+# Take this in mind when you use the customization, and maybe you need write customized evaluation function
+evalerror <- function(preds, dtrain) {
+  labels <- getinfo(dtrain, "label")
+  err <- as.numeric(sum(labels != (preds > 0))) / length(labels)
+  return(list(metric = "error", value = err))
+}
+
+param <- list(max_depth = 2, eta = 1, nthread  =  2, verbosity = 0,
+              objective = logregobj, eval_metric = evalerror)
+print('start training with user customized objective')
+# training with customized objective, we can also do step by step training
+# simply look at xgboost.py's implementation of train
+bst <- xgb.train(param, dtrain, num_round, evals)
+
+#
+# there can be cases where you want additional information
+# being considered besides the property of DMatrix you can get by getinfo
+# you can set additional information as attributes if DMatrix
+
+# set label attribute of dtrain to be label, we use label as an example, it can be anything
+attr(dtrain, 'label') <- getinfo(dtrain, 'label')
+# this is new customized objective, where you can access things you set
+# same thing applies to customized evaluation function
+logregobjattr <- function(preds, dtrain) {
+  # now you can access the attribute in customized function
+  labels <- attr(dtrain, 'label')
+  preds <- 1 / (1 + exp(-preds))
+  grad <- preds - labels
+  hess <- preds * (1 - preds)
+  return(list(grad = grad, hess = hess))
+}
+param <- list(max_depth = 2, eta = 1, nthread  =  2, verbosity = 0,
+              objective = logregobjattr, eval_metric = evalerror)
+print('start training with user customized objective, with additional attributes in DMatrix')
+# training with customized objective, we can also do step by step training
+# simply look at xgboost.py's implementation of train
+bst <- xgb.train(param, dtrain, num_round, evals)

R-package/demo/early_stopping.R

@@ -0,0 +1,40 @@
+require(xgboost)
+# load in the agaricus dataset
+data(agaricus.train, package = 'xgboost')
+data(agaricus.test, package = 'xgboost')
+dtrain <- xgb.DMatrix(agaricus.train$data, label = agaricus.train$label)
+dtest <- xgb.DMatrix(agaricus.test$data, label = agaricus.test$label)
+# note: for customized objective function, we leave objective as default
+# note: what we are getting is margin value in prediction
+# you must know what you are doing
+param <- list(max_depth = 2, eta = 1, nthread = 2, verbosity = 0)
+evals <- list(eval = dtest)
+num_round <- 20
+# user define objective function, given prediction, return gradient and second order gradient
+# this is log likelihood loss
+logregobj <- function(preds, dtrain) {
+  labels <- getinfo(dtrain, "label")
+  preds <- 1 / (1 + exp(-preds))
+  grad <- preds - labels
+  hess <- preds * (1 - preds)
+  return(list(grad = grad, hess = hess))
+}
+# user defined evaluation function, return a pair metric_name, result
+# NOTE: when you do customized loss function, the default prediction value is margin
+# this may make builtin evaluation metric not function properly
+# for example, we are doing logistic loss, the prediction is score before logistic transformation
+# the builtin evaluation error assumes input is after logistic transformation
+# Take this in mind when you use the customization, and maybe you need write customized evaluation function
+evalerror <- function(preds, dtrain) {
+  labels <- getinfo(dtrain, "label")
+  err <- as.numeric(sum(labels != (preds > 0))) / length(labels)
+  return(list(metric = "error", value = err))
+}
+print('start training with early Stopping setting')
+
+bst <- xgb.train(param, dtrain, num_round, evals,
+                 objective = logregobj, eval_metric = evalerror, maximize = FALSE,
+                 early_stopping_round = 3)
+bst <- xgb.cv(param, dtrain, num_round, nfold = 5,
+              objective = logregobj, eval_metric = evalerror,
+              maximize = FALSE, early_stopping_rounds = 3)

R-package/demo/generalized_linear_model.R

@@ -0,0 +1,33 @@
+require(xgboost)
+# load in the agaricus dataset
+data(agaricus.train, package = 'xgboost')
+data(agaricus.test, package = 'xgboost')
+dtrain <- xgb.DMatrix(agaricus.train$data, label = agaricus.train$label)
+dtest <- xgb.DMatrix(agaricus.test$data, label = agaricus.test$label)
+##
+#  this script demonstrate how to fit generalized linear model in xgboost
+#  basically, we are using linear model, instead of tree for our boosters
+#  you can fit a linear regression, or logistic regression model
+##
+
+# change booster to gblinear, so that we are fitting a linear model
+# alpha is the L1 regularizer
+# lambda is the L2 regularizer
+# you can also set lambda_bias which is L2 regularizer on the bias term
+param <- list(objective = "binary:logistic", booster = "gblinear",
+              nthread = 2, alpha = 0.0001, lambda = 1)
+
+# normally, you do not need to set eta (step_size)
+# XGBoost uses a parallel coordinate descent algorithm (shotgun),
+# there could be affection on convergence with parallelization on certain cases
+# setting eta to be smaller value, e.g 0.5 can make the optimization more stable
+
+##
+# the rest of settings are the same
+##
+evals <- list(eval = dtest, train = dtrain)
+num_round <- 2
+bst <- xgb.train(param, dtrain, num_round, evals)
+ypred <- predict(bst, dtest)
+labels <- getinfo(dtest, 'label')
+cat('error of preds=', mean(as.numeric(ypred > 0.5) != labels), '\n')

R-package/demo/gpu_accelerated.R

@@ -0,0 +1,45 @@
+# An example of using GPU-accelerated tree building algorithms
+#
+# NOTE: it can only run if you have a CUDA-enable GPU and the package was
+#       specially compiled with GPU support.
+#
+# For the current functionality, see
+# https://xgboost.readthedocs.io/en/latest/gpu/index.html
+#
+
+library('xgboost')
+
+# Simulate N x p random matrix with some binomial response dependent on pp columns
+set.seed(111)
+N <- 1000000
+p <- 50
+pp <- 25
+X <- matrix(runif(N * p), ncol = p)
+betas <- 2 * runif(pp) - 1
+sel <- sort(sample(p, pp))
+m <- X[, sel] %*% betas - 1 + rnorm(N)
+y <- rbinom(N, 1, plogis(m))
+
+tr <- sample.int(N, N * 0.75)
+dtrain <- xgb.DMatrix(X[tr, ], label = y[tr])
+dtest <- xgb.DMatrix(X[-tr, ], label = y[-tr])
+evals <- list(train = dtrain, test = dtest)
+
+# An example of running 'gpu_hist' algorithm
+# which is
+# - similar to the 'hist'
+# - the fastest option for moderately large datasets
+# - current limitations: max_depth < 16, does not implement guided loss
+# You can use tree_method = 'gpu_hist' for another GPU accelerated algorithm,
+# which is slower, more memory-hungry, but does not use binning.
+param <- list(objective = 'reg:logistic', eval_metric = 'auc', subsample = 0.5, nthread = 4,
+              max_bin = 64, tree_method = 'gpu_hist')
+pt <- proc.time()
+bst_gpu <- xgb.train(param, dtrain, evals = evals, nrounds = 50)
+proc.time() - pt
+
+# Compare to the 'hist' algorithm:
+param$tree_method <- 'hist'
+pt <- proc.time()
+bst_hist <- xgb.train(param, dtrain, evals = evals, nrounds = 50)
+proc.time() - pt

R-package/demo/interaction_constraints.R

@@ -0,0 +1,113 @@
+library(xgboost)
+library(data.table)
+
+set.seed(1024)
+
+# Function to obtain a list of interactions fitted in trees, requires input of maximum depth
+treeInteractions <- function(input_tree, input_max_depth) {
+  ID_merge <- i.id <- i.feature <- NULL  # Suppress warning "no visible binding for global variable"
+
+  trees <- data.table::copy(input_tree)  # copy tree input to prevent overwriting
+  if (input_max_depth < 2) return(list())  # no interactions if max depth < 2
+  if (nrow(input_tree) == 1) return(list())
+
+  # Attach parent nodes
+  for (i in 2:input_max_depth) {
+    if (i == 2) trees[, ID_merge := ID] else trees[, ID_merge := get(paste0('parent_', i - 2))]
+    parents_left <- trees[!is.na(Split), list(i.id = ID, i.feature = Feature, ID_merge = Yes)]
+    parents_right <- trees[!is.na(Split), list(i.id = ID, i.feature = Feature, ID_merge = No)]
+
+    data.table::setorderv(trees, 'ID_merge')
+    data.table::setorderv(parents_left, 'ID_merge')
+    data.table::setorderv(parents_right, 'ID_merge')
+
+    trees <- merge(trees, parents_left, by = 'ID_merge', all.x = TRUE)
+    trees[!is.na(i.id), c(paste0('parent_', i - 1), paste0('parent_feat_', i - 1))
+          := list(i.id, i.feature)]
+    trees[, c('i.id', 'i.feature') := NULL]
+
+    trees <- merge(trees, parents_right, by = 'ID_merge', all.x = TRUE)
+    trees[!is.na(i.id), c(paste0('parent_', i - 1), paste0('parent_feat_', i - 1))
+          := list(i.id, i.feature)]
+    trees[, c('i.id', 'i.feature') := NULL]
+  }
+
+  # Extract nodes with interactions
+  interaction_trees <- trees[!is.na(Split) & !is.na(parent_1),  # nolint: object_usage_linter
+                             c('Feature', paste0('parent_feat_', 1:(input_max_depth - 1))),
+                             with = FALSE]
+  interaction_trees_split <- split(interaction_trees, seq_len(nrow(interaction_trees)))
+  interaction_list <- lapply(interaction_trees_split, as.character)
+
+  # Remove NAs (no parent interaction)
+  interaction_list <- lapply(interaction_list, function(x) x[!is.na(x)])
+
+  # Remove non-interactions (same variable)
+  interaction_list <- lapply(interaction_list, unique)  # remove same variables
+  interaction_length <- lengths(interaction_list)
+  interaction_list <- interaction_list[interaction_length > 1]
+  interaction_list <- unique(lapply(interaction_list, sort))
+  return(interaction_list)
+}
+
+# Generate sample data
+x <- list()
+for (i in 1:10) {
+  x[[i]] <- i * rnorm(1000, 10)
+}
+x <- as.data.table(x)
+
+y <- -1 * x[, rowSums(.SD)] + x[['V1']] * x[['V2']] + x[['V3']] * x[['V4']] * x[['V5']]
+     + rnorm(1000, 0.001) + 3 * sin(x[['V7']])
+
+train <- as.matrix(x)
+
+# Interaction constraint list (column names form)
+interaction_list <- list(c('V1', 'V2'), c('V3', 'V4', 'V5'))
+
+# Convert interaction constraint list into feature index form
+cols2ids <- function(object, col_names) {
+  LUT <- seq_along(col_names) - 1
+  names(LUT) <- col_names
+  rapply(object, function(x) LUT[x], classes = "character", how = "replace")
+}
+interaction_list_fid <- cols2ids(interaction_list, colnames(train))
+
+# Fit model with interaction constraints
+bst <- xgb.train(data = xgb.DMatrix(train, label = y), max_depth = 4,
+                 eta = 0.1, nthread = 2, nrounds = 1000,
+                 interaction_constraints = interaction_list_fid)
+
+bst_tree <- xgb.model.dt.tree(colnames(train), bst)
+bst_interactions <- treeInteractions(bst_tree, 4)
+  # interactions constrained to combinations of V1*V2 and V3*V4*V5
+
+# Fit model without interaction constraints
+bst2 <- xgb.train(data = xgb.DMatrix(train, label = y), max_depth = 4,
+                  eta = 0.1, nthread = 2, nrounds = 1000)
+
+bst2_tree <- xgb.model.dt.tree(colnames(train), bst2)
+bst2_interactions <- treeInteractions(bst2_tree, 4)  # much more interactions
+
+# Fit model with both interaction and monotonicity constraints
+bst3 <- xgb.train(data = xgb.DMatrix(train, label = y), max_depth = 4,
+                  eta = 0.1, nthread = 2, nrounds = 1000,
+                  interaction_constraints = interaction_list_fid,
+                  monotone_constraints = c(-1, 0, 0, 0, 0, 0, 0, 0, 0, 0))
+
+bst3_tree <- xgb.model.dt.tree(colnames(train), bst3)
+bst3_interactions <- treeInteractions(bst3_tree, 4)
+  # interactions still constrained to combinations of V1*V2 and V3*V4*V5
+
+# Show monotonic constraints still apply by checking scores after incrementing V1
+x1 <- sort(unique(x[['V1']]))
+for (i in seq_along(x1)){
+  testdata <- copy(x[, - ('V1')])
+  testdata[['V1']] <- x1[i]
+  testdata <- testdata[, paste0('V', 1:10), with = FALSE]
+  pred <- predict(bst3, as.matrix(testdata))
+
+  # Should not print out anything due to monotonic constraints
+  if (i > 1) if (any(pred > prev_pred)) print(i)
+  prev_pred <- pred
+}

R-package/demo/poisson_regression.R

@@ -0,0 +1,6 @@
+data(mtcars)
+head(mtcars)
+bst <- xgb.train(data = xgb.DMatrix(as.matrix(mtcars[, -11]), label = mtcars[, 11]),
+                 objective = 'count:poisson', nrounds = 5)
+pred <- predict(bst, as.matrix(mtcars[, -11]))
+sqrt(mean((pred - mtcars[, 11]) ^ 2))

R-package/demo/predict_first_ntree.R

@@ -0,0 +1,23 @@
+require(xgboost)
+# load in the agaricus dataset
+data(agaricus.train, package = 'xgboost')
+data(agaricus.test, package = 'xgboost')
+dtrain <- xgb.DMatrix(agaricus.train$data, label = agaricus.train$label)
+dtest <- xgb.DMatrix(agaricus.test$data, label = agaricus.test$label)
+
+param <- list(max_depth = 2, eta = 1, objective = 'binary:logistic')
+evals <- list(eval = dtest, train = dtrain)
+nrounds <- 2
+
+# training the model for two rounds
+bst <- xgb.train(param, dtrain, nrounds, nthread = 2, evals = evals)
+cat('start testing prediction from first n trees\n')
+labels <- getinfo(dtest, 'label')
+
+### predict using first 1 tree
+ypred1 <- predict(bst, dtest, iterationrange = c(1, 1))
+# by default, we predict using all the trees
+ypred2 <- predict(bst, dtest)
+
+cat('error of ypred1=', mean(as.numeric(ypred1 > 0.5) != labels), '\n')
+cat('error of ypred2=', mean(as.numeric(ypred2 > 0.5) != labels), '\n')

R-package/demo/predict_leaf_indices.R

@@ -0,0 +1,54 @@
+require(xgboost)
+require(data.table)
+require(Matrix)
+
+set.seed(1982)
+
+# load in the agaricus dataset
+data(agaricus.train, package = 'xgboost')
+data(agaricus.test, package = 'xgboost')
+dtrain <- xgb.DMatrix(data = agaricus.train$data, label = agaricus.train$label)
+dtest <- xgb.DMatrix(data = agaricus.test$data, label = agaricus.test$label)
+
+param <- list(max_depth = 2, eta = 1, objective = 'binary:logistic')
+nrounds <- 4
+
+# training the model for two rounds
+bst <- xgb.train(params = param, data = dtrain, nrounds = nrounds, nthread = 2)
+
+# Model accuracy without new features
+accuracy.before <- (sum((predict(bst, agaricus.test$data) >= 0.5) == agaricus.test$label)
+                    / length(agaricus.test$label))
+
+# by default, we predict using all the trees
+pred_with_leaf <- predict(bst, dtest, predleaf = TRUE)
+head(pred_with_leaf)
+
+create.new.tree.features <- function(model, original.features) {
+  pred_with_leaf <- predict(model, original.features, predleaf = TRUE)
+  cols <- list()
+  for (i in 1:xgb.get.num.boosted.rounds(model)) {
+    # max is not the real max but it s not important for the purpose of adding features
+    leaf.id <- sort(unique(pred_with_leaf[, i]))
+    cols[[i]] <- factor(x = pred_with_leaf[, i], level = leaf.id)
+  }
+  cbind(original.features, sparse.model.matrix(~ . - 1, as.data.frame(cols)))
+}
+
+# Convert previous features to one hot encoding
+new.features.train <- create.new.tree.features(bst, agaricus.train$data)
+new.features.test <- create.new.tree.features(bst, agaricus.test$data)
+colnames(new.features.test) <- colnames(new.features.train)
+
+# learning with new features
+new.dtrain <- xgb.DMatrix(data = new.features.train, label = agaricus.train$label)
+new.dtest <- xgb.DMatrix(data = new.features.test, label = agaricus.test$label)
+bst <- xgb.train(params = param, data = new.dtrain, nrounds = nrounds, nthread = 2)
+
+# Model accuracy with new features
+accuracy.after <- (sum((predict(bst, new.dtest) >= 0.5) == agaricus.test$label)
+                   / length(agaricus.test$label))
+
+# Here the accuracy was already good and is now perfect.
+cat(paste("The accuracy was", accuracy.before, "before adding leaf features and it is now",
+          accuracy.after, "!\n"))

R-package/demo/runall.R

@@ -0,0 +1,13 @@
+# running all scripts in demo folder, removed during packaging.
+demo(basic_walkthrough, package = 'xgboost')
+demo(custom_objective, package = 'xgboost')
+demo(boost_from_prediction, package = 'xgboost')
+demo(predict_first_ntree, package = 'xgboost')
+demo(generalized_linear_model, package = 'xgboost')
+demo(cross_validation, package = 'xgboost')
+demo(create_sparse_matrix, package = 'xgboost')
+demo(predict_leaf_indices, package = 'xgboost')
+demo(early_stopping, package = 'xgboost')
+demo(poisson_regression, package = 'xgboost')
+demo(tweedie_regression, package = 'xgboost')
+#demo(gpu_accelerated, package = 'xgboost')  # can only run when built with GPU support

R-package/demo/tweedie_regression.R

@@ -0,0 +1,49 @@
+library(xgboost)
+library(data.table)
+library(cplm)
+
+data(AutoClaim)
+
+# auto insurance dataset analyzed by Yip and Yau (2005)
+dt <- data.table(AutoClaim)
+
+# exclude these columns from the model matrix
+exclude <- c('POLICYNO', 'PLCYDATE', 'CLM_FREQ5', 'CLM_AMT5', 'CLM_FLAG', 'IN_YY')
+
+# retains the missing values
+# NOTE: this dataset is comes ready out of the box
+options(na.action = 'na.pass')
+x <- sparse.model.matrix(~ . - 1, data = dt[, -exclude, with = FALSE])
+options(na.action = 'na.omit')
+
+# response
+y <- dt[, CLM_AMT5]
+
+d_train <- xgb.DMatrix(data = x, label = y, missing = NA)
+
+# the tweedie_variance_power parameter determines the shape of
+# distribution
+# - closer to 1 is more poisson like and the mass
+#   is more concentrated near zero
+# - closer to 2 is more gamma like and the mass spreads to the
+#   the right with less concentration near zero
+
+params <- list(
+  objective = 'reg:tweedie',
+  eval_metric = 'rmse',
+  tweedie_variance_power = 1.4,
+  max_depth = 6,
+  eta = 1)
+
+bst <- xgb.train(
+  data = d_train,
+  params = params,
+  maximize = FALSE,
+  evals = list(train = d_train),
+  nrounds = 20)
+
+var_imp <- xgb.importance(attr(x, 'Dimnames')[[2]], model = bst)
+
+preds <- predict(bst, d_train)
+
+rmse <- sqrt(sum(mean((y - preds) ^ 2)))

R-package/man/a-compatibility-note-for-saveRDS-save.Rd

@@ -5,88 +5,66 @@
 \title{Model Serialization and Compatibility}
 \description{
 When it comes to serializing XGBoost models, it's possible to use R serializers such as
-\code{\link[=save]{save()}} or \code{\link[=saveRDS]{saveRDS()}} to serialize an XGBoost R model, but XGBoost also provides
+\link{save} or \link{saveRDS} to serialize an XGBoost R model, but XGBoost also provides
 its own serializers with better compatibility guarantees, which allow loading
 said models in other language bindings of XGBoost.
 
-Note that an \code{xgb.Booster} object (\strong{as produced by \code{\link[=xgb.train]{xgb.train()}}}, see rest of the doc
-for objects produced by \code{\link[=xgboost]{xgboost()}}), outside of its core components, might also keep:
-\itemize{
-\item Additional model configuration (accessible through \code{\link[=xgb.config]{xgb.config()}}), which includes
-model fitting parameters like \code{max_depth} and runtime parameters like \code{nthread}.
+Note that an \code{xgb.Booster} object, outside of its core components, might also keep:\itemize{
+\item Additional model configuration (accessible through \link{xgb.config}),
+which includes model fitting parameters like \code{max_depth} and runtime parameters like \code{nthread}.
 These are not necessarily useful for prediction/importance/plotting.
-\item Additional R specific attributes  - e.g. results of callbacks, such as evaluation logs,
-which are kept as a \code{data.table} object, accessible through
-\code{attributes(model)$evaluation_log} if present.
+\item Additional R-specific attributes  - e.g. results of callbacks, such as evaluation logs,
+which are kept as a \code{data.table} object, accessible through \code{attributes(model)$evaluation_log}
+if present.
 }
 
 The first one (configurations) does not have the same compatibility guarantees as
-the model itself, including attributes that are set and accessed through
-\code{\link[=xgb.attributes]{xgb.attributes()}} - that is, such configuration might be lost after loading the
-booster in a different XGBoost version, regardless of the serializer that was used.
-These are saved when using \code{\link[=saveRDS]{saveRDS()}}, but will be discarded if loaded into an
-incompatible XGBoost version. They are not saved when using XGBoost's
-serializers from its public interface including \code{\link[=xgb.save]{xgb.save()}} and \code{\link[=xgb.save.raw]{xgb.save.raw()}}.
+the model itself, including attributes that are set and accessed through \link{xgb.attributes} - that is, such configuration
+might be lost after loading the booster in a different XGBoost version, regardless of the
+serializer that was used. These are saved when using \link{saveRDS}, but will be discarded
+if loaded into an incompatible XGBoost version. They are not saved when using XGBoost's
+serializers from its public interface including \link{xgb.save} and \link{xgb.save.raw}.
 
-The second ones (R attributes) are not part of the standard XGBoost model structure,
-and thus are not saved when using XGBoost's own serializers. These attributes are
-only used for informational purposes, such as keeping track of evaluation metrics as
-the model was fit, or saving the R call that produced the model, but are otherwise
-not used for prediction / importance / plotting / etc.
+The second ones (R attributes) are not part of the standard XGBoost model structure, and thus are
+not saved when using XGBoost's own serializers. These attributes are only used for informational
+purposes, such as keeping track of evaluation metrics as the model was fit, or saving the R
+call that produced the model, but are otherwise not used for prediction / importance / plotting / etc.
 These R attributes are only preserved when using R's serializers.
 
-In addition to the regular \code{xgb.Booster} objects producted by \code{\link[=xgb.train]{xgb.train()}}, the
-function \code{\link[=xgboost]{xgboost()}} produces a different subclass \code{xgboost}, which keeps other
-additional metadata as R attributes such as class names in classification problems,
-and which has a dedicated \code{predict} method that uses different defaults. XGBoost's
-own serializers can work with this \code{xgboost} class, but as they do not keep R
-attributes, the resulting object, when deserialized, is downcasted to the regular
-\code{xgb.Booster} class (i.e. it loses the metadata, and the resulting object will use
-\code{predict.xgb.Booster} instead of \code{predict.xgboost}) - for these \code{xgboost} objects,
-\code{saveRDS} might thus be a better option if the extra functionalities are needed.
-
-Note that XGBoost models in R starting from version \verb{2.1.0} and onwards, and
-XGBoost models before version \verb{2.1.0}; have a very different R object structure and
-are incompatible with each other. Hence, models that were saved with R serializers
-like \code{\link[=saveRDS]{saveRDS()}} or \code{\link[=save]{save()}} before version \verb{2.1.0} will not work with latter
-\code{xgboost} versions and vice versa. Be aware that the structure of R model objects
-could in theory change again in the future, so XGBoost's serializers
+Note that XGBoost models in R starting from version \verb{2.1.0} and onwards, and XGBoost models
+before version \verb{2.1.0}; have a very different R object structure and are incompatible with
+each other. Hence, models that were saved with R serializers live \code{saveRDS} or \code{save} before
+version \verb{2.1.0} will not work with latter \code{xgboost} versions and vice versa. Be aware that
+the structure of R model objects could in theory change again in the future, so XGBoost's serializers
 should be preferred for long-term storage.
 
-Furthermore, note that using the package \code{qs} for serialization will require
-version 0.26 or higher of said package, and will have the same compatibility
-restrictions as R serializers.
+Furthermore, note that using the package \code{qs} for serialization will require version 0.26 or
+higher of said package, and will have the same compatibility restrictions as R serializers.
 }
 \details{
-Use \code{\link[=xgb.save]{xgb.save()}} to save the XGBoost model as a stand-alone file. You may opt into
+Use \code{\link{xgb.save}} to save the XGBoost model as a stand-alone file. You may opt into
 the JSON format by specifying the JSON extension. To read the model back, use
-\code{\link[=xgb.load]{xgb.load()}}.
+\code{\link{xgb.load}}.
 
-Use \code{\link[=xgb.save.raw]{xgb.save.raw()}} to save the XGBoost model as a sequence (vector) of raw bytes
+Use \code{\link{xgb.save.raw}} to save the XGBoost model as a sequence (vector) of raw bytes
 in a future-proof manner. Future releases of XGBoost will be able to read the raw bytes and
-re-construct the corresponding model. To read the model back, use \code{\link[=xgb.load.raw]{xgb.load.raw()}}.
-The \code{\link[=xgb.save.raw]{xgb.save.raw()}} function is useful if you would like to persist the XGBoost model
+re-construct the corresponding model. To read the model back, use \code{\link{xgb.load.raw}}.
+The \code{\link{xgb.save.raw}} function is useful if you'd like to persist the XGBoost model
 as part of another R object.
 
-Use \code{\link[=saveRDS]{saveRDS()}} if you require the R-specific attributes that a booster might have, such
-as evaluation logs or the model class \code{xgboost} instead of \code{xgb.Booster}, but note that
-future compatibility of such objects is outside XGBoost's control as it relies on R's
-serialization format (see e.g. the details section in \link{serialize} and \code{\link[=save]{save()}} from base R).
+Use \link{saveRDS} if you require the R-specific attributes that a booster might have, such
+as evaluation logs, but note that future compatibility of such objects is outside XGBoost's
+control as it relies on R's serialization format (see e.g. the details section in
+\link{serialize} and \link{save} from base R).
 
 For more details and explanation about model persistence and archival, consult the page
 \url{https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html}.
 }
 \examples{
-data(agaricus.train, package = "xgboost")
-
-bst <- xgb.train(
-  data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
-  max_depth = 2,
-  eta = 1,
-  nthread = 2,
-  nrounds = 2,
-  objective = "binary:logistic"
-)
+data(agaricus.train, package='xgboost')
+bst <- xgb.train(data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
+                 max_depth = 2, eta = 1, nthread = 2, nrounds = 2,
+                 objective = "binary:logistic")
 
 # Save as a stand-alone file; load it with xgb.load()
 fname <- file.path(tempdir(), "xgb_model.ubj")

R-package/man/agaricus.test.Rd

@@ -16,10 +16,11 @@ This data set is originally from the Mushroom data set,
 UCI Machine Learning Repository.
 }
 \details{
-It includes the following fields:
+This data set includes the following fields:
+
 \itemize{
-\item \code{label}: The label for each record.
-\item \code{data}: A sparse Matrix of 'dgCMatrix' class with 126 columns.
+\item \code{label} the label for each record
+\item \code{data} a sparse Matrix of \code{dgCMatrix} class, with 126 columns.
 }
 }
 \references{

R-package/man/agaricus.train.Rd

@@ -16,10 +16,11 @@ This data set is originally from the Mushroom data set,
 UCI Machine Learning Repository.
 }
 \details{
-It includes the following fields:
+This data set includes the following fields:
+
 \itemize{
-\item \code{label}: The label for each record.
-\item \code{data}: A sparse Matrix of 'dgCMatrix' class with 126 columns.
+\item \code{label} the label for each record
+\item \code{data} a sparse Matrix of \code{dgCMatrix} class, with 126 columns.
 }
 }
 \references{

R-package/man/coef.xgb.Booster.Rd

@@ -12,12 +12,11 @@
 \item{...}{Not used.}
 }
 \value{
-The extracted coefficients:
-\itemize{
-\item If there is only one coefficient per column in the data, will be returned as a
+The extracted coefficients:\itemize{
+\item If there's only one coefficient per column in the data, will be returned as a
 vector, potentially containing the feature names if available, with the intercept
 as first column.
-\item If there is more than one coefficient per column in the data (e.g. when using
+\item If there's more than one coefficient per column in the data (e.g. when using
 \code{objective="multi:softmax"}), will be returned as a matrix with dimensions equal
 to \verb{[num_features, num_cols]}, with the intercepts as first row. Note that the column
 (classes in multi-class classification) dimension will not be named.
@@ -34,19 +33,16 @@ coefficients as used by \link{predict.xgb.Booster}.
 }
 \description{
 Extracts the coefficients from a 'gblinear' booster object,
-as produced by \code{\link[=xgb.train]{xgb.train()}} when using parameter \code{booster="gblinear"}.
+as produced by \code{xgb.train} when using parameter \code{booster="gblinear"}.
 
 Note: this function will error out if passing a booster model
 which is not of "gblinear" type.
 }
 \examples{
 library(xgboost)
-
 data(mtcars)
-
 y <- mtcars[, 1]
 x <- as.matrix(mtcars[, -1])
-
 dm <- xgb.DMatrix(data = x, label = y, nthread = 1)
 params <- list(booster = "gblinear", nthread = 1)
 model <- xgb.train(data = dm, params = params, nrounds = 2)

R-package/man/dim.xgb.DMatrix.Rd

@@ -13,14 +13,13 @@
 Returns a vector of numbers of rows and of columns in an \code{xgb.DMatrix}.
 }
 \details{
-Note: since \code{\link[=nrow]{nrow()}} and \code{\link[=ncol]{ncol()}} internally use \code{\link[=dim]{dim()}}, they can also
+Note: since \code{nrow} and \code{ncol} internally use \code{dim}, they can also
 be directly used with an \code{xgb.DMatrix} object.
 }
 \examples{
-data(agaricus.train, package = "xgboost")
-
+data(agaricus.train, package='xgboost')
 train <- agaricus.train
-dtrain <- xgb.DMatrix(train$data, label = train$label, nthread = 2)
+dtrain <- xgb.DMatrix(train$data, label=train$label, nthread = 2)
 
 stopifnot(nrow(dtrain) == nrow(train$data))
 stopifnot(ncol(dtrain) == ncol(train$data))

R-package/man/dimnames.xgb.DMatrix.Rd

@@ -10,27 +10,26 @@
 \method{dimnames}{xgb.DMatrix}(x) <- value
 }
 \arguments{
-\item{x}{Object of class \code{xgb.DMatrix}.}
+\item{x}{object of class \code{xgb.DMatrix}}
 
-\item{value}{A list of two elements: the first one is ignored
+\item{value}{a list of two elements: the first one is ignored
 and the second one is column names}
 }
 \description{
 Only column names are supported for \code{xgb.DMatrix}, thus setting of
-row names would have no effect and returned row names would be \code{NULL}.
+row names would have no effect and returned row names would be NULL.
 }
 \details{
-Generic \code{\link[=dimnames]{dimnames()}} methods are used by \code{\link[=colnames]{colnames()}}.
-Since row names are irrelevant, it is recommended to use \code{\link[=colnames]{colnames()}} directly.
+Generic \code{dimnames} methods are used by \code{colnames}.
+Since row names are irrelevant, it is recommended to use \code{colnames} directly.
 }
 \examples{
-data(agaricus.train, package = "xgboost")
-
+data(agaricus.train, package='xgboost')
 train <- agaricus.train
-dtrain <- xgb.DMatrix(train$data, label = train$label, nthread = 2)
+dtrain <- xgb.DMatrix(train$data, label=train$label, nthread = 2)
 dimnames(dtrain)
 colnames(dtrain)
 colnames(dtrain) <- make.names(1:ncol(train$data))
-print(dtrain, verbose = TRUE)
+print(dtrain, verbose=TRUE)
 
 }

R-package/man/getinfo.Rd

@@ -22,34 +22,34 @@ setinfo(object, name, info)
 \method{setinfo}{xgb.DMatrix}(object, name, info)
 }
 \arguments{
-\item{object}{Object of class \code{xgb.DMatrix} or \code{xgb.Booster}.}
+\item{object}{Object of class \code{xgb.DMatrix} of \code{xgb.Booster}.}
 
-\item{name}{The name of the information field to get (see details).}
+\item{name}{the name of the information field to get (see details)}
 
-\item{info}{The specific field of information to set.}
+\item{info}{the specific field of information to set}
 }
 \value{
-For \code{getinfo()}, will return the requested field. For \code{setinfo()},
-will always return value \code{TRUE} if it succeeds.
+For \code{getinfo}, will return the requested field. For \code{setinfo}, will always return value \code{TRUE}
+if it succeeds.
 }
 \description{
 Get or set information of xgb.DMatrix and xgb.Booster objects
 }
 \details{
 The \code{name} field can be one of the following for \code{xgb.DMatrix}:
-\itemize{
-\item label
-\item weight
-\item base_margin
-\item label_lower_bound
-\item label_upper_bound
-\item group
-\item feature_type
-\item feature_name
-\item nrow
-}
 
-See the documentation for \code{\link[=xgb.DMatrix]{xgb.DMatrix()}} for more information about these fields.
+\itemize{
+\item \code{label}
+\item \code{weight}
+\item \code{base_margin}
+\item \code{label_lower_bound}
+\item \code{label_upper_bound}
+\item \code{group}
+\item \code{feature_type}
+\item \code{feature_name}
+\item \code{nrow}
+}
+See the documentation for \link{xgb.DMatrix} for more information about these fields.
 
 For \code{xgb.Booster}, can be one of the following:
 \itemize{
@@ -57,18 +57,17 @@ For \code{xgb.Booster}, can be one of the following:
 \item \code{feature_name}
 }
 
-Note that, while 'qid' cannot be retrieved, it is possible to get the equivalent 'group'
+Note that, while 'qid' cannot be retrieved, it's possible to get the equivalent 'group'
 for a DMatrix that had 'qid' assigned.
 
-\strong{Important}: when calling \code{\link[=setinfo]{setinfo()}}, the objects are modified in-place. See
-\code{\link[=xgb.copy.Booster]{xgb.copy.Booster()}} for an idea of this in-place assignment works.
+\bold{Important}: when calling \code{setinfo}, the objects are modified in-place. See
+\link{xgb.copy.Booster} for an idea of this in-place assignment works.
 
-See the documentation for \code{\link[=xgb.DMatrix]{xgb.DMatrix()}} for possible fields that can be set
+See the documentation for \link{xgb.DMatrix} for possible fields that can be set
 (which correspond to arguments in that function).
 
 Note that the following fields are allowed in the construction of an \code{xgb.DMatrix}
-but \strong{are not} allowed here:
-\itemize{
+but \bold{aren't} allowed here:\itemize{
 \item data
 \item missing
 \item silent
@@ -76,22 +75,19 @@ but \strong{are not} allowed here:
 }
 }
 \examples{
-data(agaricus.train, package = "xgboost")
-
+data(agaricus.train, package='xgboost')
 dtrain <- with(agaricus.train, xgb.DMatrix(data, label = label, nthread = 2))
 
-labels <- getinfo(dtrain, "label")
-setinfo(dtrain, "label", 1 - labels)
-
-labels2 <- getinfo(dtrain, "label")
-stopifnot(all(labels2 == 1 - labels))
-data(agaricus.train, package = "xgboost")
+labels <- getinfo(dtrain, 'label')
+setinfo(dtrain, 'label', 1-labels)
 
+labels2 <- getinfo(dtrain, 'label')
+stopifnot(all(labels2 == 1-labels))
+data(agaricus.train, package='xgboost')
 dtrain <- with(agaricus.train, xgb.DMatrix(data, label = label, nthread = 2))
 
-labels <- getinfo(dtrain, "label")
-setinfo(dtrain, "label", 1 - labels)
-
-labels2 <- getinfo(dtrain, "label")
-stopifnot(all.equal(labels2, 1 - labels))
+labels <- getinfo(dtrain, 'label')
+setinfo(dtrain, 'label', 1-labels)
+labels2 <- getinfo(dtrain, 'label')
+stopifnot(all.equal(labels2, 1-labels))
 }

R-package/man/predict.xgb.Booster.Rd

@@ -13,10 +13,10 @@
   predcontrib = FALSE,
   approxcontrib = FALSE,
   predinteraction = FALSE,
+  reshape = FALSE,
   training = FALSE,
   iterationrange = NULL,
   strict_shape = FALSE,
-  avoid_transpose = FALSE,
   validate_features = FALSE,
   base_margin = NULL,
   ...
@@ -28,36 +28,35 @@
 \item{newdata}{Takes \code{data.frame}, \code{matrix}, \code{dgCMatrix}, \code{dgRMatrix}, \code{dsparseVector},
 local data file, or \code{xgb.DMatrix}.
 
-For single-row predictions on sparse data, it is recommended to use CSR format. If passing
-a sparse vector, it will take it as a row vector.
+\if{html}{\out{<div class="sourceCode">}}\preformatted{   For single-row predictions on sparse data, it's recommended to use CSR format. If passing
+   a sparse vector, it will take it as a row vector.
 
-Note that, for repeated predictions on the same data, one might want to create a DMatrix to
-pass here instead of passing R types like matrices or data frames, as predictions will be
-faster on DMatrix.
+   Note that, for repeated predictions on the same data, one might want to create a DMatrix to
+   pass here instead of passing R types like matrices or data frames, as predictions will be
+   faster on DMatrix.
 
-If \code{newdata} is a \code{data.frame}, be aware that:
-\itemize{
-\item Columns will be converted to numeric if they aren't already, which could potentially make
-the operation slower than in an equivalent \code{matrix} object.
-\item The order of the columns must match with that of the data from which the model was fitted
-(i.e. columns will not be referenced by their names, just by their order in the data).
-\item If the model was fitted to data with categorical columns, these columns must be of
-\code{factor} type here, and must use the same encoding (i.e. have the same levels).
-\item If \code{newdata} contains any \code{factor} columns, they will be converted to base-0
-encoding (same as during DMatrix creation) - hence, one should not pass a \code{factor}
-under a column which during training had a different type.
-}}
+   If `newdata` is a `data.frame`, be aware that:\\itemize\{
+   \\item Columns will be converted to numeric if they aren't already, which could potentially make
+         the operation slower than in an equivalent `matrix` object.
+   \\item The order of the columns must match with that of the data from which the model was fitted
+         (i.e. columns will not be referenced by their names, just by their order in the data).
+   \\item If the model was fitted to data with categorical columns, these columns must be of
+         `factor` type here, and must use the same encoding (i.e. have the same levels).
+   \\item If `newdata` contains any `factor` columns, they will be converted to base-0
+         encoding (same as during DMatrix creation) - hence, one should not pass a `factor`
+         under a column which during training had a different type.
+   \}
+}\if{html}{\out{</div>}}}
 
-\item{missing}{Float value that represents missing values in data
-(e.g., 0 or some other extreme value).
+\item{missing}{Float value that represents missing values in data (e.g., 0 or some other extreme value).
 
-This parameter is not used when \code{newdata} is an \code{xgb.DMatrix} - in such cases,
-should pass this as an argument to the DMatrix constructor instead.}
+\if{html}{\out{<div class="sourceCode">}}\preformatted{   This parameter is not used when `newdata` is an `xgb.DMatrix` - in such cases, should pass
+   this as an argument to the DMatrix constructor instead.
+}\if{html}{\out{</div>}}}
 
-\item{outputmargin}{Whether the prediction should be returned in the form of
-original untransformed sum of predictions from boosting iterations' results.
-E.g., setting \code{outputmargin = TRUE} for logistic regression would return log-odds
-instead of probabilities.}
+\item{outputmargin}{Whether the prediction should be returned in the form of original untransformed
+sum of predictions from boosting iterations' results. E.g., setting \code{outputmargin=TRUE} for
+logistic regression would return log-odds instead of probabilities.}
 
 \item{predleaf}{Whether to predict per-tree leaf indices.}
 
@@ -67,6 +66,10 @@ instead of probabilities.}
 
 \item{predinteraction}{Whether to return contributions of feature interactions to individual predictions (see Details).}
 
+\item{reshape}{Whether to reshape the vector of predictions to matrix form when there are several
+prediction outputs per case. No effect if \code{predleaf}, \code{predcontrib},
+or \code{predinteraction} is \code{TRUE}.}
+
 \item{training}{Whether the prediction result is used for training. For dart booster,
 training predicting will perform dropout.}
 
@@ -74,103 +77,74 @@ training predicting will perform dropout.}
 a two-dimensional vector with the start and end numbers in the sequence (same format as R's \code{seq} - i.e.
 base-1 indexing, and inclusive of both ends).
 
-For example, passing \code{c(1,20)} will predict using the first twenty iterations, while passing \code{c(1,1)} will
-predict using only the first one.
+\if{html}{\out{<div class="sourceCode">}}\preformatted{   For example, passing `c(1,20)` will predict using the first twenty iterations, while passing `c(1,1)` will
+   predict using only the first one.
 
-If passing \code{NULL}, will either stop at the best iteration if the model used early stopping, or use all
-of the iterations (rounds) otherwise.
+   If passing `NULL`, will either stop at the best iteration if the model used early stopping, or use all
+   of the iterations (rounds) otherwise.
 
-If passing "all", will use all of the rounds regardless of whether the model had early stopping or not.}
+   If passing "all", will use all of the rounds regardless of whether the model had early stopping or not.
+}\if{html}{\out{</div>}}}
 
-\item{strict_shape}{Whether to always return an array with the same dimensions for the given prediction mode
-regardless of the model type - meaning that, for example, both a multi-class and a binary classification
-model would generate output arrays with the same number of dimensions, with the 'class' dimension having
-size equal to '1' for the binary model.
+\item{strict_shape}{Default is \code{FALSE}. When set to \code{TRUE}, the output
+type and shape of predictions are invariant to the model type.}
 
-If passing \code{FALSE} (the default), dimensions will be simplified according to the model type, so that a
-binary classification model for example would not have a redundant dimension for 'class'.
+\item{validate_features}{When \code{TRUE}, validate that the Booster's and newdata's feature_names
+match (only applicable when both \code{object} and \code{newdata} have feature names).
 
-See documentation for the return type for the exact shape of the output arrays for each prediction mode.}
+\if{html}{\out{<div class="sourceCode">}}\preformatted{   If the column names differ and `newdata` is not an `xgb.DMatrix`, will try to reorder
+   the columns in `newdata` to match with the booster's.
 
-\item{avoid_transpose}{Whether to output the resulting predictions in the same memory layout in which they
-are generated by the core XGBoost library, without transposing them to match the expected output shape.
+   If the booster has feature types and `newdata` is either an `xgb.DMatrix` or `data.frame`,
+   will additionally verify that categorical columns are of the correct type in `newdata`,
+   throwing an error if they do not match.
 
-Internally, XGBoost uses row-major order for the predictions it generates, while R arrays use column-major
-order, hence the result needs to be transposed in order to have the expected shape when represented as
-an R array or matrix, which might be a slow operation.
+   If passing `FALSE`, it is assumed that the feature names and types are the same,
+   and come in the same order as in the training data.
 
-If passing \code{TRUE}, then the result will have dimensions in reverse order - for example, rows
-will be the last dimensions instead of the first dimension.}
-
-\item{validate_features}{When \code{TRUE}, validate that the Booster's and newdata's
-feature_names match (only applicable when both \code{object} and \code{newdata} have feature names).
-
-If the column names differ and \code{newdata} is not an \code{xgb.DMatrix}, will try to reorder
-the columns in \code{newdata} to match with the booster's.
-
-If the booster has feature types and \code{newdata} is either an \code{xgb.DMatrix} or
-\code{data.frame}, will additionally verify that categorical columns are of the
-correct type in \code{newdata}, throwing an error if they do not match.
-
-If passing \code{FALSE}, it is assumed that the feature names and types are the same,
-and come in the same order as in the training data.
-
-Note that this check might add some sizable latency to the predictions, so it's
-recommended to disable it for performance-sensitive applications.}
+   Note that this check might add some sizable latency to the predictions, so it's
+   recommended to disable it for performance-sensitive applications.
+}\if{html}{\out{</div>}}}
 
 \item{base_margin}{Base margin used for boosting from existing model.
 
-Note that, if \code{newdata} is an \code{xgb.DMatrix} object, this argument will
-be ignored as it needs to be added to the DMatrix instead (e.g. by passing it as
-an argument in its constructor, or by calling \code{\link[=setinfo.xgb.DMatrix]{setinfo.xgb.DMatrix()}}.}
+\if{html}{\out{<div class="sourceCode">}}\preformatted{   Note that, if `newdata` is an `xgb.DMatrix` object, this argument will
+   be ignored as it needs to be added to the DMatrix instead (e.g. by passing it as
+   an argument in its constructor, or by calling \link{setinfo.xgb.DMatrix}).
+}\if{html}{\out{</div>}}}
 
 \item{...}{Not used.}
 }
 \value{
-A numeric vector or array, with corresponding dimensions depending on the prediction mode and on
-parameter \code{strict_shape} as follows:
-
-If passing \code{strict_shape=FALSE}:\itemize{
-\item For regression or binary classification: a vector of length \code{nrows}.
-\item For multi-class and multi-target objectives: a matrix of dimensions \verb{[nrows, ngroups]}.
-
-Note that objective variant \code{multi:softmax} defaults towards predicting most likely class (a vector
-\code{nrows}) instead of per-class probabilities.
-\item For \code{predleaf}: a matrix with one column per tree.
-
-For multi-class / multi-target, they will be arranged so that columns in the output will have
-the leafs from one group followed by leafs of the other group (e.g. order will be \code{group1:feat1},
-\code{group1:feat2}, ..., \code{group2:feat1}, \code{group2:feat2}, ...).
-\item For \code{predcontrib}: when not multi-class / multi-target, a matrix with dimensions
-\verb{[nrows, nfeats+1]}. The last "+ 1" column corresponds to the baseline value.
-
-For multi-class and multi-target objectives, will be an array with dimensions \verb{[nrows, ngroups, nfeats+1]}.
-
-The contribution values are on the scale of untransformed margin (e.g., for binary classification,
-the values are log-odds deviations from the baseline).
-\item For \code{predinteraction}: when not multi-class / multi-target, the output is a 3D array of
-dimensions \verb{[nrows, nfeats+1, nfeats+1]}. The off-diagonal (in the last two dimensions)
-elements represent different feature interaction contributions. The array is symmetric w.r.t. the last
-two dimensions. The "+ 1" columns corresponds to the baselines. Summing this array along the last
-dimension should produce practically the same result as \code{predcontrib = TRUE}.
-
-For multi-class and multi-target, will be a 4D array with dimensions \verb{[nrows, ngroups, nfeats+1, nfeats+1]}
-}
-
-If passing \code{strict_shape=FALSE}, the result is always an array:
+The return type depends on \code{strict_shape}. If \code{FALSE} (default):
 \itemize{
-\item For normal predictions, the dimension is \verb{[nrows, ngroups]}.
-\item For \code{predcontrib=TRUE}, the dimension is \verb{[nrows, ngroups, nfeats+1]}.
-\item For \code{predinteraction=TRUE}, the dimension is \verb{[nrows, ngroups, nfeats+1, nfeats+1]}.
-\item For \code{predleaf=TRUE}, the dimension is \verb{[nrows, niter, ngroups, num_parallel_tree]}.
+\item For regression or binary classification: A vector of length \code{nrows(newdata)}.
+\item For multiclass classification: A vector of length \code{num_class * nrows(newdata)} or
+a \verb{(nrows(newdata), num_class)} matrix, depending on the \code{reshape} value.
+\item When \code{predleaf = TRUE}: A matrix with one column per tree.
+\item When \code{predcontrib = TRUE}: When not multiclass, a matrix with
+\code{ num_features + 1} columns. The last "+ 1" column corresponds to the baseline value.
+In the multiclass case, a list of \code{num_class} such matrices.
+The contribution values are on the scale of untransformed margin
+(e.g., for binary classification, the values are log-odds deviations from the baseline).
+\item When \code{predinteraction = TRUE}: When not multiclass, the output is a 3d array of
+dimension \code{c(nrow, num_features + 1, num_features + 1)}. The off-diagonal (in the last two dimensions)
+elements represent different feature interaction contributions. The array is symmetric WRT the last
+two dimensions. The "+ 1" columns corresponds to the baselines. Summing this array along the last dimension should
+produce practically the same result as \code{predcontrib = TRUE}.
+In the multiclass case, a list of \code{num_class} such arrays.
 }
 
-If passing \code{avoid_transpose=TRUE}, then the dimensions in all cases will be in reverse order - for
-example, for \code{predinteraction}, they will be \verb{[nfeats+1, nfeats+1, ngroups, nrows]}
-instead of \verb{[nrows, ngroups, nfeats+1, nfeats+1]}.
+When \code{strict_shape = TRUE}, the output is always an array:
+\itemize{
+\item For normal predictions, the output has dimension \verb{(num_class, nrow(newdata))}.
+\item For \code{predcontrib = TRUE}, the dimension is \verb{(ncol(newdata) + 1, num_class, nrow(newdata))}.
+\item For \code{predinteraction = TRUE}, the dimension is \verb{(ncol(newdata) + 1, ncol(newdata) + 1, num_class, nrow(newdata))}.
+\item For \code{predleaf = TRUE}, the dimension is \verb{(n_trees_in_forest, num_class, n_iterations, nrow(newdata))}.
+}
 }
 \description{
-Predict values on data based on XGBoost model.
+Predict values on data based on xgboost model.
 }
 \details{
 Note that \code{iterationrange} would currently do nothing for predictions from "gblinear",
@@ -237,7 +211,7 @@ str(pred_contr)
 summary(rowSums(pred_contr) - qlogis(pred))
 # for the 1st record, let's inspect its features that had non-zero contribution to prediction:
 contr1 <- pred_contr[1,]
-contr1 <- contr1[-length(contr1)]    # drop intercept
+contr1 <- contr1[-length(contr1)]    # drop BIAS
 contr1 <- contr1[contr1 != 0]        # drop non-contributing features
 contr1 <- contr1[order(abs(contr1))] # order by contribution magnitude
 old_mar <- par("mar")
@@ -267,6 +241,8 @@ bst <- xgb.train(
 # predict for softmax returns num_class probability numbers per case:
 pred <- predict(bst, as.matrix(iris[, -5]))
 str(pred)
+# reshape it to a num_class-columns matrix
+pred <- matrix(pred, ncol = num_class, byrow = TRUE)
 # convert the probabilities to softmax labels
 pred_labels <- max.col(pred) - 1
 # the following should result in the same error as seen in the last iteration

R-package/man/print.xgb.Booster.Rd

@@ -21,8 +21,9 @@ Print information about \code{xgb.Booster}.
 data(agaricus.train, package = "xgboost")
 train <- agaricus.train
 
-bst <- xgb.train(
-  data = xgb.DMatrix(train$data, label = train$label),
+bst <- xgboost(
+  data = train$data,
+  label = train$label,
   max_depth = 2,
   eta = 1,
   nthread = 2,
@@ -33,4 +34,5 @@ bst <- xgb.train(
 attr(bst, "myattr") <- "memo"
 
 print(bst)
+
 }

R-package/man/print.xgb.DMatrix.Rd

@@ -7,22 +7,21 @@
 \method{print}{xgb.DMatrix}(x, verbose = FALSE, ...)
 }
 \arguments{
-\item{x}{An xgb.DMatrix object.}
+\item{x}{an xgb.DMatrix object}
 
-\item{verbose}{Whether to print colnames (when present).}
+\item{verbose}{whether to print colnames (when present)}
 
-\item{...}{Not currently used.}
+\item{...}{not currently used}
 }
 \description{
 Print information about xgb.DMatrix.
 Currently it displays dimensions and presence of info-fields and colnames.
 }
 \examples{
-data(agaricus.train, package = "xgboost")
-
+data(agaricus.train, package='xgboost')
 dtrain <- with(agaricus.train, xgb.DMatrix(data, label = label, nthread = 2))
-dtrain
 
-print(dtrain, verbose = TRUE)
+dtrain
+print(dtrain, verbose=TRUE)
 
 }

R-package/man/print.xgb.cv.Rd

@@ -7,33 +7,25 @@
 \method{print}{xgb.cv.synchronous}(x, verbose = FALSE, ...)
 }
 \arguments{
-\item{x}{An \code{xgb.cv.synchronous} object.}
+\item{x}{an \code{xgb.cv.synchronous} object}
 
-\item{verbose}{Whether to print detailed data.}
+\item{verbose}{whether to print detailed data}
 
-\item{...}{Passed to \code{data.table.print()}.}
+\item{...}{passed to \code{data.table.print}}
 }
 \description{
-Prints formatted results of \code{\link[=xgb.cv]{xgb.cv()}}.
+Prints formatted results of \code{xgb.cv}.
 }
 \details{
 When not verbose, it would only print the evaluation results,
 including the best iteration (when available).
 }
 \examples{
-data(agaricus.train, package = "xgboost")
-
+data(agaricus.train, package='xgboost')
 train <- agaricus.train
-cv <- xgb.cv(
-  data = xgb.DMatrix(train$data, label = train$label),
-  nfold = 5,
-  max_depth = 2,
-  eta = 1,
-  nthread = 2,
-  nrounds = 2,
-  objective = "binary:logistic"
-)
+cv <- xgb.cv(data = xgb.DMatrix(train$data, label = train$label), nfold = 5, max_depth = 2,
+             eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic")
 print(cv)
-print(cv, verbose = TRUE)
+print(cv, verbose=TRUE)
 
 }

R-package/man/variable.names.xgb.Booster.Rd

@@ -13,8 +13,8 @@
 }
 \description{
 Returns the feature / variable / column names from a fitted
-booster object, which are set automatically during the call to \code{\link[=xgb.train]{xgb.train()}}
-from the DMatrix names, or which can be set manually through \code{\link[=setinfo]{setinfo()}}.
+booster object, which are set automatically during the call to \link{xgb.train}
+from the DMatrix names, or which can be set manually through \link{setinfo}.
 
 If the object doesn't have feature names, will return \code{NULL}.
 

R-package/man/xgb.Callback.Rd

@@ -53,12 +53,12 @@ Return values of \code{NULL} will be interpreted as \code{FALSE}.}
 \item{f_after_training}{A function that will be executed after training is finished.
 
 This function can optionally output something non-NULL, which will become part of the R
-attributes of the booster (assuming one passes \code{keep_extra_attributes=TRUE} to \code{\link[=xgb.train]{xgb.train()}})
-under the name supplied for parameter \code{cb_name} imn the case of \code{\link[=xgb.train]{xgb.train()}}; or a part
-of the named elements in the result of \code{\link[=xgb.cv]{xgb.cv()}}.}
+attributes of the booster (assuming one passes \code{keep_extra_attributes=TRUE} to \link{xgb.train})
+under the name supplied for parameter \code{cb_name} imn the case of \link{xgb.train}; or a part
+of the named elements in the result of \link{xgb.cv}.}
 }
 \value{
-An \code{xgb.Callback} object, which can be passed to \code{\link[=xgb.train]{xgb.train()}} or \code{\link[=xgb.cv]{xgb.cv()}}.
+An \code{xgb.Callback} object, which can be passed to \link{xgb.train} or \link{xgb.cv}.
 }
 \description{
 Constructor for defining the structure of callback functions that can be executed
@@ -66,8 +66,8 @@ at different stages of model training (before / after training, before / after e
 iteration).
 }
 \details{
-Arguments that will be passed to the supplied functions are as follows:
-\itemize{
+Arguments that will be passed to the supplied functions are as follows:\itemize{
+
 \item env The same environment that is passed under argument \code{env}.
 
 It may be modified by the functions in order to e.g. keep tracking of what happens
@@ -75,10 +75,11 @@ across iterations or similar.
 
 This environment is only used by the functions supplied to the callback, and will
 not be kept after the model fitting function terminates (see parameter \code{f_after_training}).
-\item model The booster object when using \code{\link[=xgb.train]{xgb.train()}}, or the folds when using \code{\link[=xgb.cv]{xgb.cv()}}.
 
-For \code{\link[=xgb.cv]{xgb.cv()}}, folds are a list with a structure as follows:
-\itemize{
+\item model The booster object when using \link{xgb.train}, or the folds when using
+\link{xgb.cv}.
+
+For \link{xgb.cv}, folds are a list with a structure as follows:\itemize{
 \item \code{dtrain}: The training data for the fold (as an \code{xgb.DMatrix} object).
 \item \code{bst}: Rhe \code{xgb.Booster} object for the fold.
 \item \code{evals}: A list containing two DMatrices, with names \code{train} and \code{test}
@@ -87,71 +88,79 @@ For \code{\link[=xgb.cv]{xgb.cv()}}, folds are a list with a structure as follow
 from which the \code{test} entry in \code{evals} was obtained.
 }
 
-This object should \strong{not} be in-place modified in ways that conflict with the
+This object should \bold{not} be in-place modified in ways that conflict with the
 training (e.g. resetting the parameters for a training update in a way that resets
 the number of rounds to zero in order to overwrite rounds).
 
 Note that any R attributes that are assigned to the booster during the callback functions,
 will not be kept thereafter as the booster object variable is not re-assigned during
 training. It is however possible to set C-level attributes of the booster through
-\code{\link[=xgb.attr]{xgb.attr()}} or \code{\link[=xgb.attributes]{xgb.attributes()}}, which should remain available for the rest
+\link{xgb.attr} or \link{xgb.attributes}, which should remain available for the rest
 of the iterations and after the training is done.
 
 For keeping variables across iterations, it's recommended to use \code{env} instead.
 \item data The data to which the model is being fit, as an \code{xgb.DMatrix} object.
 
-Note that, for \code{\link[=xgb.cv]{xgb.cv()}}, this will be the full data, while data for the specific
+Note that, for \link{xgb.cv}, this will be the full data, while data for the specific
 folds can be found in the \code{model} object.
-\item evals The evaluation data, as passed under argument \code{evals} to \code{\link[=xgb.train]{xgb.train()}}.
 
-For \code{\link[=xgb.cv]{xgb.cv()}}, this will always be \code{NULL}.
-\item begin_iteration Index of the first boosting iteration that will be executed (base-1 indexing).
+\item evals The evaluation data, as passed under argument \code{evals} to
+\link{xgb.train}.
+
+For \link{xgb.cv}, this will always be \code{NULL}.
+
+\item begin_iteration Index of the first boosting iteration that will be executed
+(base-1 indexing).
 
 This will typically be '1', but when using training continuation, depending on the
 parameters for updates, boosting rounds will be continued from where the previous
 model ended, in which case this will be larger than 1.
+
 \item end_iteration Index of the last boostign iteration that will be executed
 (base-1 indexing, inclusive of this end).
 
-It should match with argument \code{nrounds} passed to \code{\link[=xgb.train]{xgb.train()}} or \code{\link[=xgb.cv]{xgb.cv()}}.
+It should match with argument \code{nrounds} passed to \link{xgb.train} or \link{xgb.cv}.
 
 Note that boosting might be interrupted before reaching this last iteration, for
-example by using the early stopping callback \code{\link[=xgb.cb.early.stop]{xgb.cb.early.stop()}}.
+example by using the early stopping callback \link{xgb.cb.early.stop}.
+
 \item iteration Index of the iteration number that is being executed (first iteration
 will be the same as parameter \code{begin_iteration}, then next one will add +1, and so on).
+
 \item iter_feval Evaluation metrics for \code{evals} that were supplied, either
 determined by the objective, or by parameter \code{feval}.
 
-For \code{\link[=xgb.train]{xgb.train()}}, this will be a named vector with one entry per element in
+For \link{xgb.train}, this will be a named vector with one entry per element in
 \code{evals}, where the names are determined as 'evals name' + '-' + 'metric name' - for
 example, if \code{evals} contains an entry named "tr" and the metric is "rmse",
 this will be a one-element vector with name "tr-rmse".
 
-For \code{\link[=xgb.cv]{xgb.cv()}}, this will be a 2d matrix with dimensions \verb{[length(evals), nfolds]},
+For \link{xgb.cv}, this will be a 2d matrix with dimensions \verb{[length(evals), nfolds]},
 where the row names will follow the same naming logic as the one-dimensional vector
-that is passed in \code{\link[=xgb.train]{xgb.train()}}.
+that is passed in \link{xgb.train}.
 
 Note that, internally, the built-in callbacks such as \link{xgb.cb.print.evaluation} summarize
 this table by calculating the row-wise means and standard deviations.
+
 \item final_feval The evaluation results after the last boosting round is executed
 (same format as \code{iter_feval}, and will be the exact same input as passed under
 \code{iter_feval} to the last round that is executed during model fitting).
+
 \item prev_cb_res Result from a previous run of a callback sharing the same name
 (as given by parameter \code{cb_name}) when conducting training continuation, if there
 was any in the booster R attributes.
 
-Sometimes, one might want to append the new results to the previous one, and this will
+Some times, one might want to append the new results to the previous one, and this will
 be done automatically by the built-in callbacks such as \link{xgb.cb.evaluation.log},
 which will append the new rows to the previous table.
 
 If no such previous callback result is available (which it never will when fitting
 a model from start instead of updating an existing model), this will be \code{NULL}.
 
-For \code{\link[=xgb.cv]{xgb.cv()}}, which doesn't support training continuation, this will always be \code{NULL}.
+For \link{xgb.cv}, which doesn't support training continuation, this will always be \code{NULL}.
 }
 
-The following names (\code{cb_name} values) are reserved for internal callbacks:
-\itemize{
+The following names (\code{cb_name} values) are reserved for internal callbacks:\itemize{
 \item print_evaluation
 \item evaluation_log
 \item reset_parameters
@@ -161,8 +170,7 @@ The following names (\code{cb_name} values) are reserved for internal callbacks:
 \item gblinear_history
 }
 
-The following names are reserved for other non-callback attributes:
-\itemize{
+The following names are reserved for other non-callback attributes:\itemize{
 \item names
 \item class
 \item call
@@ -213,10 +221,8 @@ ssq_callback <- xgb.Callback(
 )
 
 data(mtcars)
-
 y <- mtcars$mpg
 x <- as.matrix(mtcars[, -1])
-
 dm <- xgb.DMatrix(x, label = y, nthread = 1)
 model <- xgb.train(
   data = dm,
@@ -230,8 +236,7 @@ model <- xgb.train(
 attributes(model)$ssq
 }
 \seealso{
-Built-in callbacks:
-\itemize{
+Built-in callbacks:\itemize{
 \item \link{xgb.cb.print.evaluation}
 \item \link{xgb.cb.evaluation.log}
 \item \link{xgb.cb.reset.parameters}

R-package/man/xgb.DMatrix.Rd

@@ -57,20 +57,20 @@ was constructed.
 
 Other column types are not supported.
 \item CSR matrices, as class \code{dgRMatrix} from package \code{Matrix}.
-\item CSC matrices, as class \code{dgCMatrix} from package \code{Matrix}. These are \strong{not} supported for
+\item CSC matrices, as class \code{dgCMatrix} from package \code{Matrix}. These are \bold{not} supported for
 'xgb.QuantileDMatrix'.
 \item Single-row CSR matrices, as class \code{dsparseVector} from package \code{Matrix}, which is interpreted
 as a single row (only when making predictions from a fitted model).
 \item Text files in a supported format, passed as a \code{character} variable containing the URI path to
 the file, with an optional format specifier.
 
-These are \strong{not} supported for \code{xgb.QuantileDMatrix}. Supported formats are:\itemize{
-\item XGBoost's own binary format for DMatrices, as produced by \code{\link[=xgb.DMatrix.save]{xgb.DMatrix.save()}}.
+These are \bold{not} supported for \code{xgb.QuantileDMatrix}. Supported formats are:\itemize{
+\item XGBoost's own binary format for DMatrices, as produced by \link{xgb.DMatrix.save}.
 \item SVMLight (a.k.a. LibSVM) format for CSR matrices. This format can be signaled by suffix
 \code{?format=libsvm} at the end of the file path. It will be the default format if not
 otherwise specified.
 \item CSV files (comma-separated values). This format can be specified by adding suffix
-\code{?format=csv} at the end ofthe file path. It will \strong{not} be auto-deduced from file extensions.
+\code{?format=csv} at the end ofthe file path. It will \bold{not} be auto-deduced from file extensions.
 }
 
 Be aware that the format of the file will not be auto-deduced - for example, if a file is named 'file.csv',
@@ -96,27 +96,30 @@ so it doesn't make sense to assign weights to individual data points.}
 
 \item{base_margin}{Base margin used for boosting from existing model.
 
-In the case of multi-output models, one can also pass multi-dimensional base_margin.}
+\if{html}{\out{<div class="sourceCode">}}\preformatted{   In the case of multi-output models, one can also pass multi-dimensional base_margin.
+}\if{html}{\out{</div>}}}
 
 \item{missing}{A float value to represents missing values in data (not used when creating DMatrix
-from text files). It is useful to change when a zero, infinite, or some other
-extreme value represents missing values in data.}
+from text files).
+It is useful to change when a zero, infinite, or some other extreme value represents missing
+values in data.}
 
 \item{silent}{whether to suppress printing an informational message after loading from a file.}
 
-\item{feature_names}{Set names for features. Overrides column names in data frame and matrix.
+\item{feature_names}{Set names for features. Overrides column names in data
+frame and matrix.
 
-Note: columns are not referenced by name when calling \code{predict}, so the column order there
-must be the same as in the DMatrix construction, regardless of the column names.}
+\if{html}{\out{<div class="sourceCode">}}\preformatted{   Note: columns are not referenced by name when calling `predict`, so the column order there
+   must be the same as in the DMatrix construction, regardless of the column names.
+}\if{html}{\out{</div>}}}
 
 \item{feature_types}{Set types for features.
 
-If \code{data} is a \code{data.frame} and passing \code{feature_types} is not supplied,
-feature types will be deduced automatically from the column types.
+If \code{data} is a \code{data.frame} and passing \code{feature_types} is not supplied, feature types will be deduced
+automatically from the column types.
 
 Otherwise, one can pass a character vector with the same length as number of columns in \code{data},
-with the following possible values:
-\itemize{
+with the following possible values:\itemize{
 \item "c", which represents categorical columns.
 \item "q", which represents numeric columns.
 \item "int", which represents integer columns.
@@ -127,9 +130,9 @@ Note that, while categorical types are treated differently from the rest for mod
 purposes, the other types do not influence the generated model, but have effects in other
 functionalities such as feature importances.
 
-\strong{Important}: Categorical features, if specified manually through \code{feature_types}, must
+\bold{Important}: categorical features, if specified manually through \code{feature_types}, must
 be encoded as integers with numeration starting at zero, and the same encoding needs to be
-applied when passing data to \code{\link[=predict]{predict()}}. Even if passing \code{factor} types, the encoding will
+applied when passing data to \code{predict}. Even if passing \code{factor} types, the encoding will
 not be saved, so make sure that \code{factor} columns passed to \code{predict} have the same \code{levels}.}
 
 \item{nthread}{Number of threads used for creating DMatrix.}
@@ -153,7 +156,7 @@ how the file was split beforehand. Default to row.
 This is not used when \code{data} is not a URI.}
 
 \item{ref}{The training dataset that provides quantile information, needed when creating
-validation/test dataset with \code{\link[=xgb.QuantileDMatrix]{xgb.QuantileDMatrix()}}. Supplying the training DMatrix
+validation/test dataset with \code{xgb.QuantileDMatrix}. Supplying the training DMatrix
 as a reference means that the same quantisation applied to the training data is
 applied to the validation/test data}
 
@@ -168,24 +171,23 @@ subclass 'xgb.QuantileDMatrix'.
 }
 \description{
 Construct an 'xgb.DMatrix' object from a given data source, which can then be passed to functions
-such as \code{\link[=xgb.train]{xgb.train()}} or \code{\link[=predict]{predict()}}.
+such as \link{xgb.train} or \link{predict.xgb.Booster}.
 }
 \details{
-Function \code{xgb.QuantileDMatrix()} will construct a DMatrix with quantization for the histogram
+Function 'xgb.QuantileDMatrix' will construct a DMatrix with quantization for the histogram
 method already applied to it, which can be used to reduce memory usage (compared to using a
 a regular DMatrix first and then creating a quantization out of it) when using the histogram
 method (\code{tree_method = "hist"}, which is the default algorithm), but is not usable for the
 sorted-indices method (\code{tree_method = "exact"}), nor for the approximate method
 (\code{tree_method = "approx"}).
 
-Note that DMatrix objects are not serializable through R functions such as \code{\link[=saveRDS]{saveRDS()}} or \code{\link[=save]{save()}}.
+Note that DMatrix objects are not serializable through R functions such as \code{saveRDS} or \code{save}.
 If a DMatrix gets serialized and then de-serialized (for example, when saving data in an R session or caching
 chunks in an Rmd file), the resulting object will not be usable anymore and will need to be reconstructed
 from the original source of data.
 }
 \examples{
-data(agaricus.train, package = "xgboost")
-
+data(agaricus.train, package='xgboost')
 ## Keep the number of threads to 1 for examples
 nthread <- 1
 data.table::setDTthreads(nthread)

R-package/man/xgb.DMatrix.hasinfo.Rd

@@ -16,10 +16,11 @@ Checks whether an xgb.DMatrix object has a given field assigned to
 it, such as weights, labels, etc.
 }
 \examples{
+library(xgboost)
 x <- matrix(1:10, nrow = 5)
 dm <- xgb.DMatrix(x, nthread = 1)
 
-# 'dm' so far does not have any fields set
+# 'dm' so far doesn't have any fields set
 xgb.DMatrix.hasinfo(dm, "label")
 
 # Fields can be added after construction
@@ -27,5 +28,5 @@ setinfo(dm, "label", 1:5)
 xgb.DMatrix.hasinfo(dm, "label")
 }
 \seealso{
-\code{\link[=xgb.DMatrix]{xgb.DMatrix()}}, \code{\link[=getinfo.xgb.DMatrix]{getinfo.xgb.DMatrix()}}, \code{\link[=setinfo.xgb.DMatrix]{setinfo.xgb.DMatrix()}}
+\link{xgb.DMatrix}, \link{getinfo.xgb.DMatrix}, \link{setinfo.xgb.DMatrix}
 }

R-package/man/xgb.DMatrix.save.Rd

@@ -16,8 +16,7 @@ Save xgb.DMatrix object to binary file
 }
 \examples{
 \dontshow{RhpcBLASctl::omp_set_num_threads(1)}
-data(agaricus.train, package = "xgboost")
-
+data(agaricus.train, package='xgboost')
 dtrain <- with(agaricus.train, xgb.DMatrix(data, label = label, nthread = 2))
 fname <- file.path(tempdir(), "xgb.DMatrix.data")
 xgb.DMatrix.save(dtrain, fname)

R-package/man/xgb.DataBatch.Rd

@@ -21,17 +21,16 @@ xgb.DataBatch(
 \arguments{
 \item{data}{Batch of data belonging to this batch.
 
-Note that not all of the input types supported by \code{\link[=xgb.DMatrix]{xgb.DMatrix()}} are possible
-to pass here. Supported types are:
-\itemize{
+Note that not all of the input types supported by \link{xgb.DMatrix} are possible
+to pass here. Supported types are:\itemize{
 \item \code{matrix}, with types \code{numeric}, \code{integer}, and \code{logical}. Note that for types
 \code{integer} and \code{logical}, missing values might not be automatically recognized as
-as such - see the documentation for parameter \code{missing} in \code{\link[=xgb.ExtMemDMatrix]{xgb.ExtMemDMatrix()}}
+as such - see the documentation for parameter \code{missing} in \link{xgb.ExternalDMatrix}
 for details on this.
 \item \code{data.frame}, with the same types as supported by 'xgb.DMatrix' and same
 conversions applied to it. See the documentation for parameter \code{data} in
-\code{\link[=xgb.DMatrix]{xgb.DMatrix()}} for details on it.
-\item CSR matrices, as class \code{dgRMatrix} from package "Matrix".
+\link{xgb.DMatrix} for details on it.
+\item CSR matrices, as class \code{dgRMatrix} from package \code{Matrix}.
 }}
 
 \item{label}{Label of the training data. For classification problems, should be passed encoded as
@@ -46,21 +45,23 @@ so it doesn't make sense to assign weights to individual data points.}
 
 \item{base_margin}{Base margin used for boosting from existing model.
 
-In the case of multi-output models, one can also pass multi-dimensional base_margin.}
+\if{html}{\out{<div class="sourceCode">}}\preformatted{   In the case of multi-output models, one can also pass multi-dimensional base_margin.
+}\if{html}{\out{</div>}}}
 
-\item{feature_names}{Set names for features. Overrides column names in data frame and matrix.
+\item{feature_names}{Set names for features. Overrides column names in data
+frame and matrix.
 
-Note: columns are not referenced by name when calling \code{predict}, so the column order there
-must be the same as in the DMatrix construction, regardless of the column names.}
+\if{html}{\out{<div class="sourceCode">}}\preformatted{   Note: columns are not referenced by name when calling `predict`, so the column order there
+   must be the same as in the DMatrix construction, regardless of the column names.
+}\if{html}{\out{</div>}}}
 
 \item{feature_types}{Set types for features.
 
-If \code{data} is a \code{data.frame} and passing \code{feature_types} is not supplied,
-feature types will be deduced automatically from the column types.
+If \code{data} is a \code{data.frame} and passing \code{feature_types} is not supplied, feature types will be deduced
+automatically from the column types.
 
 Otherwise, one can pass a character vector with the same length as number of columns in \code{data},
-with the following possible values:
-\itemize{
+with the following possible values:\itemize{
 \item "c", which represents categorical columns.
 \item "q", which represents numeric columns.
 \item "int", which represents integer columns.
@@ -71,9 +72,9 @@ Note that, while categorical types are treated differently from the rest for mod
 purposes, the other types do not influence the generated model, but have effects in other
 functionalities such as feature importances.
 
-\strong{Important}: Categorical features, if specified manually through \code{feature_types}, must
+\bold{Important}: categorical features, if specified manually through \code{feature_types}, must
 be encoded as integers with numeration starting at zero, and the same encoding needs to be
-applied when passing data to \code{\link[=predict]{predict()}}. Even if passing \code{factor} types, the encoding will
+applied when passing data to \code{predict}. Even if passing \code{factor} types, the encoding will
 not be saved, so make sure that \code{factor} columns passed to \code{predict} have the same \code{levels}.}
 
 \item{group}{Group size for all ranking group.}
@@ -88,24 +89,24 @@ not be saved, so make sure that \code{factor} columns passed to \code{predict} h
 }
 \value{
 An object of class \code{xgb.DataBatch}, which is just a list containing the
-data and parameters passed here. It does \strong{not} inherit from \code{xgb.DMatrix}.
+data and parameters passed here. It does \bold{not} inherit from \code{xgb.DMatrix}.
 }
 \description{
 Helper function to supply data in batches of a data iterator when
-constructing a DMatrix from external memory through \code{\link[=xgb.ExtMemDMatrix]{xgb.ExtMemDMatrix()}}
-or through \code{\link[=xgb.QuantileDMatrix.from_iterator]{xgb.QuantileDMatrix.from_iterator()}}.
+constructing a DMatrix from external memory through \link{xgb.ExternalDMatrix}
+or through \link{xgb.QuantileDMatrix.from_iterator}.
 
-This function is \strong{only} meant to be called inside of a callback function (which
-is passed as argument to function \code{\link[=xgb.DataIter]{xgb.DataIter()}} to construct a data iterator)
+This function is \bold{only} meant to be called inside of a callback function (which
+is passed as argument to function \link{xgb.DataIter} to construct a data iterator)
 when constructing a DMatrix through external memory - otherwise, one should call
-\code{\link[=xgb.DMatrix]{xgb.DMatrix()}} or \code{\link[=xgb.QuantileDMatrix]{xgb.QuantileDMatrix()}}.
+\link{xgb.DMatrix} or \link{xgb.QuantileDMatrix}.
 
-The object that results from calling this function directly is \strong{not} like
+The object that results from calling this function directly is \bold{not} like
 an \code{xgb.DMatrix} - i.e. cannot be used to train a model, nor to get predictions - only
 possible usage is to supply data to an iterator, from which a DMatrix is then constructed.
 
-For more information and for example usage, see the documentation for \code{\link[=xgb.ExtMemDMatrix]{xgb.ExtMemDMatrix()}}.
+For more information and for example usage, see the documentation for \link{xgb.ExternalDMatrix}.
 }
 \seealso{
-\code{\link[=xgb.DataIter]{xgb.DataIter()}}, \code{\link[=xgb.ExtMemDMatrix]{xgb.ExtMemDMatrix()}}.
+\link{xgb.DataIter}, \link{xgb.ExternalDMatrix}.
 }

R-package/man/xgb.DataIter.Rd

@@ -13,15 +13,14 @@ used to keep track of variables to determine how to handle the batches.
 For example, one might want to keep track of an iteration number in this environment in order
 to know which part of the data to pass next.}
 
-\item{f_next}{\verb{function(env)} which is responsible for:
-\itemize{
+\item{f_next}{\verb{function(env)} which is responsible for:\itemize{
 \item Accessing or retrieving the next batch of data in the iterator.
-\item Supplying this data by calling function \code{\link[=xgb.DataBatch]{xgb.DataBatch()}} on it and returning the result.
+\item Supplying this data by calling function \link{xgb.DataBatch} on it and returning the result.
 \item Keeping track of where in the iterator batch it is or will go next, which can for example
 be done by modifiying variables in the \code{env} variable that is passed here.
 \item Signaling whether there are more batches to be consumed or not, by returning \code{NULL}
 when the stream of data ends (all batches in the iterator have been consumed), or the result from
-calling \code{\link[=xgb.DataBatch]{xgb.DataBatch()}} when there are more batches in the line to be consumed.
+calling \link{xgb.DataBatch} when there are more batches in the line to be consumed.
 }}
 
 \item{f_reset}{\verb{function(env)} which is responsible for reseting the data iterator
@@ -33,7 +32,7 @@ Note that, after resetting the iterator, the batches will be accessed again, so
 }
 \value{
 An \code{xgb.DataIter} object, containing the same inputs supplied here, which can then
-be passed to \code{\link[=xgb.ExtMemDMatrix]{xgb.ExtMemDMatrix()}}.
+be passed to \link{xgb.ExternalDMatrix}.
 }
 \description{
 Interface to create a custom data iterator in order to construct a DMatrix
@@ -42,11 +41,11 @@ from external memory.
 This function is responsible for generating an R object structure containing callback
 functions and an environment shared with them.
 
-The output structure from this function is then meant to be passed to \code{\link[=xgb.ExtMemDMatrix]{xgb.ExtMemDMatrix()}},
+The output structure from this function is then meant to be passed to \link{xgb.ExternalDMatrix},
 which will consume the data and create a DMatrix from it by executing the callback functions.
 
-For more information, and for a usage example, see the documentation for \code{\link[=xgb.ExtMemDMatrix]{xgb.ExtMemDMatrix()}}.
+For more information, and for a usage example, see the documentation for \link{xgb.ExternalDMatrix}.
 }
 \seealso{
-\code{\link[=xgb.ExtMemDMatrix]{xgb.ExtMemDMatrix()}}, \code{\link[=xgb.DataBatch]{xgb.DataBatch()}}.
+\link{xgb.ExternalDMatrix}, \link{xgb.DataBatch}.
 }

R-package/man/xgb.ExternalDMatrix.Rd

@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/xgb.DMatrix.R
-\name{xgb.ExtMemDMatrix}
-\alias{xgb.ExtMemDMatrix}
+\name{xgb.ExternalDMatrix}
+\alias{xgb.ExternalDMatrix}
 \title{DMatrix from External Data}
 \usage{
-xgb.ExtMemDMatrix(
+xgb.ExternalDMatrix(
   data_iterator,
   cache_prefix = tempdir(),
   missing = NA,
@@ -12,7 +12,7 @@ xgb.ExtMemDMatrix(
 )
 }
 \arguments{
-\item{data_iterator}{A data iterator structure as returned by \code{\link[=xgb.DataIter]{xgb.DataIter()}},
+\item{data_iterator}{A data iterator structure as returned by \link{xgb.DataIter},
 which includes an environment shared between function calls, and functions to access
 the data in batches on-demand.}
 
@@ -20,39 +20,40 @@ the data in batches on-demand.}
 
 \item{missing}{A float value to represents missing values in data.
 
-Note that, while functions like \code{\link[=xgb.DMatrix]{xgb.DMatrix()}} can take a generic \code{NA} and interpret it
+Note that, while functions like \link{xgb.DMatrix} can take a generic \code{NA} and interpret it
 correctly for different types like \code{numeric} and \code{integer}, if an \code{NA} value is passed here,
 it will not be adapted for different input types.
 
 For example, in R \code{integer} types, missing values are represented by integer number \code{-2147483648}
 (since machine 'integer' types do not have an inherent 'NA' value) - hence, if one passes \code{NA},
-which is interpreted as a floating-point NaN by \code{\link[=xgb.ExtMemDMatrix]{xgb.ExtMemDMatrix()}} and by
-\code{\link[=xgb.QuantileDMatrix.from_iterator]{xgb.QuantileDMatrix.from_iterator()}}, these integer missing values will not be treated as missing.
+which is interpreted as a floating-point NaN by 'xgb.ExternalDMatrix' and by
+'xgb.QuantileDMatrix.from_iterator', these integer missing values will not be treated as missing.
 This should not pose any problem for \code{numeric} types, since they do have an inheret NaN value.}
 
 \item{nthread}{Number of threads used for creating DMatrix.}
 }
 \value{
-An 'xgb.DMatrix' object, with subclass 'xgb.ExtMemDMatrix', in which the data is not
+An 'xgb.DMatrix' object, with subclass 'xgb.ExternalDMatrix', in which the data is not
 held internally but accessed through the iterator when needed.
 }
 \description{
-Create a special type of XGBoost 'DMatrix' object from external data
-supplied by an \code{\link[=xgb.DataIter]{xgb.DataIter()}} object, potentially passed in batches from a
+Create a special type of xgboost 'DMatrix' object from external data
+supplied by an \link{xgb.DataIter} object, potentially passed in batches from a
 bigger set that might not fit entirely in memory.
 
 The data supplied by the iterator is accessed on-demand as needed, multiple times,
-without being concatenated, but note that fields like 'label' \strong{will} be
+without being concatenated, but note that fields like 'label' \bold{will} be
 concatenated from multiple calls to the data iterator.
 
 For more information, see the guide 'Using XGBoost External Memory Version':
 \url{https://xgboost.readthedocs.io/en/stable/tutorials/external_memory.html}
 }
 \examples{
+library(xgboost)
 data(mtcars)
 
-# This custom environment will be passed to the iterator
-# functions at each call. It is up to the user to keep
+# this custom environment will be passed to the iterator
+# functions at each call. It's up to the user to keep
 # track of the iteration number in this environment.
 iterator_env <- as.environment(
   list(
@@ -105,7 +106,7 @@ data_iterator <- xgb.DataIter(
 cache_prefix <- tempdir()
 
 # DMatrix will be constructed from the iterator's batches
-dm <- xgb.ExtMemDMatrix(data_iterator, cache_prefix, nthread = 1)
+dm <- xgb.ExternalDMatrix(data_iterator, cache_prefix, nthread = 1)
 
 # After construction, can be used as a regular DMatrix
 params <- list(nthread = 1, objective = "reg:squarederror")
@@ -117,5 +118,5 @@ pred_dm <- predict(model, dm)
 pred_mat <- predict(model, as.matrix(mtcars[, -1]))
 }
 \seealso{
-\code{\link[=xgb.DataIter]{xgb.DataIter()}}, \code{\link[=xgb.DataBatch]{xgb.DataBatch()}}, \code{\link[=xgb.QuantileDMatrix.from_iterator]{xgb.QuantileDMatrix.from_iterator()}}
+\link{xgb.DataIter}, \link{xgb.DataBatch}, \link{xgb.QuantileDMatrix.from_iterator}
 }

R-package/man/xgb.QuantileDMatrix.from_iterator.Rd

@@ -13,26 +13,26 @@ xgb.QuantileDMatrix.from_iterator(
 )
 }
 \arguments{
-\item{data_iterator}{A data iterator structure as returned by \code{\link[=xgb.DataIter]{xgb.DataIter()}},
+\item{data_iterator}{A data iterator structure as returned by \link{xgb.DataIter},
 which includes an environment shared between function calls, and functions to access
 the data in batches on-demand.}
 
 \item{missing}{A float value to represents missing values in data.
 
-Note that, while functions like \code{\link[=xgb.DMatrix]{xgb.DMatrix()}} can take a generic \code{NA} and interpret it
+Note that, while functions like \link{xgb.DMatrix} can take a generic \code{NA} and interpret it
 correctly for different types like \code{numeric} and \code{integer}, if an \code{NA} value is passed here,
 it will not be adapted for different input types.
 
 For example, in R \code{integer} types, missing values are represented by integer number \code{-2147483648}
 (since machine 'integer' types do not have an inherent 'NA' value) - hence, if one passes \code{NA},
-which is interpreted as a floating-point NaN by \code{\link[=xgb.ExtMemDMatrix]{xgb.ExtMemDMatrix()}} and by
-\code{\link[=xgb.QuantileDMatrix.from_iterator]{xgb.QuantileDMatrix.from_iterator()}}, these integer missing values will not be treated as missing.
+which is interpreted as a floating-point NaN by 'xgb.ExternalDMatrix' and by
+'xgb.QuantileDMatrix.from_iterator', these integer missing values will not be treated as missing.
 This should not pose any problem for \code{numeric} types, since they do have an inheret NaN value.}
 
 \item{nthread}{Number of threads used for creating DMatrix.}
 
 \item{ref}{The training dataset that provides quantile information, needed when creating
-validation/test dataset with \code{\link[=xgb.QuantileDMatrix]{xgb.QuantileDMatrix()}}. Supplying the training DMatrix
+validation/test dataset with \code{xgb.QuantileDMatrix}. Supplying the training DMatrix
 as a reference means that the same quantisation applied to the training data is
 applied to the validation/test data}
 
@@ -46,20 +46,20 @@ An 'xgb.DMatrix' object, with subclass 'xgb.QuantileDMatrix'.
 }
 \description{
 Create an \code{xgb.QuantileDMatrix} object (exact same class as would be returned by
-calling function \code{\link[=xgb.QuantileDMatrix]{xgb.QuantileDMatrix()}}, with the same advantages and limitations) from
-external data supplied by \code{\link[=xgb.DataIter]{xgb.DataIter()}}, potentially passed in batches from
-a bigger set that might not fit entirely in memory, same way as \code{\link[=xgb.ExtMemDMatrix]{xgb.ExtMemDMatrix()}}.
+calling function \link{xgb.QuantileDMatrix}, with the same advantages and limitations) from
+external data supplied by an \link{xgb.DataIter} object, potentially passed in batches from
+a bigger set that might not fit entirely in memory, same way as \link{xgb.ExternalDMatrix}.
 
 Note that, while external data will only be loaded through the iterator (thus the full data
 might not be held entirely in-memory), the quantized representation of the data will get
 created in-memory, being concatenated from multiple calls to the data iterator. The quantized
 version is typically lighter than the original data, so there might be cases in which this
-representation could potentially fit in memory even if the full data does not.
+representation could potentially fit in memory even if the full data doesn't.
 
 For more information, see the guide 'Using XGBoost External Memory Version':
 \url{https://xgboost.readthedocs.io/en/stable/tutorials/external_memory.html}
 }
 \seealso{
-\code{\link[=xgb.DataIter]{xgb.DataIter()}}, \code{\link[=xgb.DataBatch]{xgb.DataBatch()}}, \code{\link[=xgb.ExtMemDMatrix]{xgb.ExtMemDMatrix()}},
-\code{\link[=xgb.QuantileDMatrix]{xgb.QuantileDMatrix()}}
+\link{xgb.DataIter}, \link{xgb.DataBatch}, \link{xgb.ExternalDMatrix},
+\link{xgb.QuantileDMatrix}
 }

R-package/man/xgb.attr.Rd

@@ -16,7 +16,7 @@ xgb.attributes(object)
 xgb.attributes(object) <- value
 }
 \arguments{
-\item{object}{Object of class \code{xgb.Booster}. \strong{Will be modified in-place} when assigning to it.}
+\item{object}{Object of class \code{xgb.Booster}. \bold{Will be modified in-place} when assigning to it.}
 
 \item{name}{A non-empty character string specifying which attribute is to be accessed.}
 
@@ -36,18 +36,18 @@ or \code{NULL} if a model has no stored attributes.
 }
 }
 \description{
-These methods allow to manipulate the key-value attribute strings of an XGBoost model.
+These methods allow to manipulate the key-value attribute strings of an xgboost model.
 }
 \details{
-The primary purpose of XGBoost model attributes is to store some meta data about the model.
+The primary purpose of xgboost model attributes is to store some meta data about the model.
 Note that they are a separate concept from the object attributes in R.
-Specifically, they refer to key-value strings that can be attached to an XGBoost model,
+Specifically, they refer to key-value strings that can be attached to an xgboost model,
 stored together with the model's binary representation, and accessed later
 (from R or any other interface).
 In contrast, any R attribute assigned to an R object of \code{xgb.Booster} class
-would not be saved by \code{\link[=xgb.save]{xgb.save()}} because an XGBoost model is an external memory object
+would not be saved by \code{\link[=xgb.save]{xgb.save()}} because an xgboost model is an external memory object
 and its serialization is handled externally.
-Also, setting an attribute that has the same name as one of XGBoost's parameters wouldn't
+Also, setting an attribute that has the same name as one of xgboost's parameters wouldn't
 change the value of that parameter for a model.
 Use \code{\link[=xgb.parameters<-]{xgb.parameters<-()}} to set or change model parameters.
 
@@ -57,15 +57,16 @@ but it doesn't delete the other existing attributes.
 Important: since this modifies the booster's C object, semantics for assignment here
 will differ from R's, as any object reference to the same booster will be modified
 too, while assignment of R attributes through \verb{attributes(model)$<attr> <- <value>}
-will follow the usual copy-on-write R semantics (see \code{\link[=xgb.copy.Booster]{xgb.copy.Booster()}} for an
+will follow the usual copy-on-write R semantics (see \link{xgb.copy.Booster} for an
 example of these behaviors).
 }
 \examples{
 data(agaricus.train, package = "xgboost")
 train <- agaricus.train
 
-bst <- xgb.train(
-  data = xgb.DMatrix(train$data, label = train$label),
+bst <- xgboost(
+  data = train$data,
+  label = train$label,
   max_depth = 2,
   eta = 1,
   nthread = 2,

R-package/man/xgb.cb.cv.predict.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/callbacks.R
 \name{xgb.cb.cv.predict}
 \alias{xgb.cb.cv.predict}
-\title{Callback for returning cross-validation based predictions}
+\title{Callback for returning cross-validation based predictions.}
 \usage{
 xgb.cb.cv.predict(save_models = FALSE, outputmargin = FALSE)
 }
@@ -13,8 +13,8 @@ xgb.cb.cv.predict(save_models = FALSE, outputmargin = FALSE)
 parameter to \link{predict.xgb.Booster}).}
 }
 \value{
-An \code{xgb.Callback} object, which can be passed to \code{\link[=xgb.cv]{xgb.cv()}},
-but \strong{not} to \code{\link[=xgb.train]{xgb.train()}}.
+An \code{xgb.Callback} object, which can be passed to \link{xgb.cv},
+but \bold{not} to \link{xgb.train}.
 }
 \description{
 This callback function saves predictions for all of the test folds,
@@ -24,7 +24,7 @@ and also allows to save the folds' models.
 Predictions are saved inside of the \code{pred} element, which is either a vector or a matrix,
 depending on the number of prediction outputs per data row. The order of predictions corresponds
 to the order of rows in the original dataset. Note that when a custom \code{folds} list is
-provided in \code{\link[=xgb.cv]{xgb.cv()}}, the predictions would only be returned properly when this list is a
+provided in \code{xgb.cv}, the predictions would only be returned properly when this list is a
 non-overlapping list of k sets of indices, as in a standard k-fold CV. The predictions would not be
 meaningful when user-provided folds have overlapping indices as in, e.g., random sampling splits.
 When some of the indices in the training dataset are not included into user-provided \code{folds},

R-package/man/xgb.cb.early.stop.Rd

@@ -23,7 +23,7 @@ stopping. If not set, the last column would be used.
 Let's say the test data in \code{evals} was labelled as \code{dtest},
 and one wants to use the AUC in test data for early stopping regardless of where
 it is in the \code{evals}, then one of the following would need to be set:
-\code{metric_name = 'dtest-auc'} or \code{metric_name = 'dtest_auc'}.
+\code{metric_name='dtest-auc'} or \code{metric_name='dtest_auc'}.
 All dash '-' characters in metric names are considered equivalent to '_'.}
 
 \item{verbose}{Whether to print the early stopping information.}
@@ -33,7 +33,7 @@ in the resulting object. If passing \code{FALSE}, will only keep the boosting ro
 up to the detected best iteration, discarding the ones that come after.}
 }
 \value{
-An \code{xgb.Callback} object, which can be passed to \code{\link[=xgb.train]{xgb.train()}} or \code{\link[=xgb.cv]{xgb.cv()}}.
+An \code{xgb.Callback} object, which can be passed to \link{xgb.train} or \link{xgb.cv}.
 }
 \description{
 This callback function determines the condition for early stopping.
@@ -49,7 +49,7 @@ The same values are also stored as R attributes as a result of the callback, plu
 attribute \code{stopped_by_max_rounds} which indicates whether an early stopping by the \code{stopping_rounds}
 condition occurred. Note that the \code{best_iteration} that is stored under R attributes will follow
 base-1 indexing, so it will be larger by '1' than the C-level 'best_iteration' that is accessed
-through \code{\link[=xgb.attr]{xgb.attr()}} or  \code{\link[=xgb.attributes]{xgb.attributes()}}.
+through \link{xgb.attr} or \link{xgb.attributes}.
 
 At least one dataset is required in \code{evals} for early stopping to work.
 }

R-package/man/xgb.cb.evaluation.log.Rd

@@ -7,14 +7,14 @@
 xgb.cb.evaluation.log()
 }
 \value{
-An \code{xgb.Callback} object, which can be passed to \code{\link[=xgb.train]{xgb.train()}} or \code{\link[=xgb.cv]{xgb.cv()}}.
+An \code{xgb.Callback} object, which can be passed to \link{xgb.train} or \link{xgb.cv}.
 }
 \description{
 Callback for logging the evaluation history
 }
 \details{
 This callback creates a table with per-iteration evaluation metrics (see parameters
-\code{evals} and \code{feval} in \code{\link[=xgb.train]{xgb.train()}}).
+\code{evals} and \code{feval} in \link{xgb.train}).
 
 Note: in the column names of the final data.table, the dash '-' character is replaced with
 the underscore '_' in order to make the column names more like regular R identifiers.

R-package/man/xgb.cb.gblinear.history.Rd

@@ -7,13 +7,13 @@
 xgb.cb.gblinear.history(sparse = FALSE)
 }
 \arguments{
-\item{sparse}{When set to \code{FALSE}/\code{TRUE}, a dense/sparse matrix is used to store the result.
+\item{sparse}{when set to \code{FALSE}/\code{TRUE}, a dense/sparse matrix is used to store the result.
 Sparse format is useful when one expects only a subset of coefficients to be non-zero,
 when using the "thrifty" feature selector with fairly small number of top features
 selected per iteration.}
 }
 \value{
-An \code{xgb.Callback} object, which can be passed to \code{\link[=xgb.train]{xgb.train()}} or \code{\link[=xgb.cv]{xgb.cv()}}.
+An \code{xgb.Callback} object, which can be passed to \link{xgb.train} or \link{xgb.cv}.
 }
 \description{
 Callback for collecting coefficients history of a gblinear booster
@@ -37,10 +37,11 @@ will have column names matching with the feature names, otherwise (when there's
 one coefficient per feature) the names will be composed as 'column name' + ':' + 'class index'
 (so e.g. column 'c1' for class '0' will be named 'c1:0').
 
-With \code{\link[=xgb.train]{xgb.train()}}, the output is either a dense or a sparse matrix.
-With with \code{\link[=xgb.cv]{xgb.cv()}}, it is a list (one element per each fold) of such matrices.
+With \code{xgb.train}, the output is either a dense or a sparse matrix.
+With with \code{xgb.cv}, it is a list (one element per each fold) of such
+matrices.
 
-Function \link{xgb.gblinear.history} provides an easy way to retrieve the
+Function \link{xgb.gblinear.history} function provides an easy way to retrieve the
 outputs from this callback.
 }
 \examples{
@@ -52,109 +53,57 @@ data.table::setDTthreads(nthread)
 
 # In the iris dataset, it is hard to linearly separate Versicolor class from the rest
 # without considering the 2nd order interactions:
-x <- model.matrix(Species ~ .^2, iris)[, -1]
+x <- model.matrix(Species ~ .^2, iris)[,-1]
 colnames(x)
-dtrain <- xgb.DMatrix(
-  scale(x),
-  label = 1 * (iris$Species == "versicolor"),
-  nthread = nthread
-)
-param <- list(
-  booster = "gblinear",
-  objective = "reg:logistic",
-  eval_metric = "auc",
-  lambda = 0.0003,
-  alpha = 0.0003,
-  nthread = nthread
-)
-
+dtrain <- xgb.DMatrix(scale(x), label = 1*(iris$Species == "versicolor"), nthread = nthread)
+param <- list(booster = "gblinear", objective = "reg:logistic", eval_metric = "auc",
+              lambda = 0.0003, alpha = 0.0003, nthread = nthread)
 # For 'shotgun', which is a default linear updater, using high eta values may result in
 # unstable behaviour in some datasets. With this simple dataset, however, the high learning
 # rate does not break the convergence, but allows us to illustrate the typical pattern of
 # "stochastic explosion" behaviour of this lock-free algorithm at early boosting iterations.
-bst <- xgb.train(
-  param,
-  dtrain,
-  list(tr = dtrain),
-  nrounds = 200,
-  eta = 1.,
-  callbacks = list(xgb.cb.gblinear.history())
-)
-
+bst <- xgb.train(param, dtrain, list(tr=dtrain), nrounds = 200, eta = 1.,
+                 callbacks = list(xgb.cb.gblinear.history()))
 # Extract the coefficients' path and plot them vs boosting iteration number:
 coef_path <- xgb.gblinear.history(bst)
-matplot(coef_path, type = "l")
+matplot(coef_path, type = 'l')
 
 # With the deterministic coordinate descent updater, it is safer to use higher learning rates.
 # Will try the classical componentwise boosting which selects a single best feature per round:
-bst <- xgb.train(
-  param,
-  dtrain,
-  list(tr = dtrain),
-  nrounds = 200,
-  eta = 0.8,
-  updater = "coord_descent",
-  feature_selector = "thrifty",
-  top_k = 1,
-  callbacks = list(xgb.cb.gblinear.history())
-)
-matplot(xgb.gblinear.history(bst), type = "l")
+bst <- xgb.train(param, dtrain, list(tr=dtrain), nrounds = 200, eta = 0.8,
+                 updater = 'coord_descent', feature_selector = 'thrifty', top_k = 1,
+                 callbacks = list(xgb.cb.gblinear.history()))
+matplot(xgb.gblinear.history(bst), type = 'l')
 #  Componentwise boosting is known to have similar effect to Lasso regularization.
 # Try experimenting with various values of top_k, eta, nrounds,
 # as well as different feature_selectors.
 
 # For xgb.cv:
-bst <- xgb.cv(
-  param,
-  dtrain,
-  nfold = 5,
-  nrounds = 100,
-  eta = 0.8,
-  callbacks = list(xgb.cb.gblinear.history())
-)
+bst <- xgb.cv(param, dtrain, nfold = 5, nrounds = 100, eta = 0.8,
+              callbacks = list(xgb.cb.gblinear.history()))
 # coefficients in the CV fold #3
-matplot(xgb.gblinear.history(bst)[[3]], type = "l")
+matplot(xgb.gblinear.history(bst)[[3]], type = 'l')
 
 
 #### Multiclass classification:
+#
 dtrain <- xgb.DMatrix(scale(x), label = as.numeric(iris$Species) - 1, nthread = nthread)
-
-param <- list(
-  booster = "gblinear",
-  objective = "multi:softprob",
-  num_class = 3,
-  lambda = 0.0003,
-  alpha = 0.0003,
-  nthread = nthread
-)
-
+param <- list(booster = "gblinear", objective = "multi:softprob", num_class = 3,
+              lambda = 0.0003, alpha = 0.0003, nthread = nthread)
 # For the default linear updater 'shotgun' it sometimes is helpful
 # to use smaller eta to reduce instability
-bst <- xgb.train(
-  param,
-  dtrain,
-  list(tr = dtrain),
-  nrounds = 50,
-  eta = 0.5,
-  callbacks = list(xgb.cb.gblinear.history())
-)
-
+bst <- xgb.train(param, dtrain, list(tr=dtrain), nrounds = 50, eta = 0.5,
+                 callbacks = list(xgb.cb.gblinear.history()))
 # Will plot the coefficient paths separately for each class:
-matplot(xgb.gblinear.history(bst, class_index = 0), type = "l")
-matplot(xgb.gblinear.history(bst, class_index = 1), type = "l")
-matplot(xgb.gblinear.history(bst, class_index = 2), type = "l")
+matplot(xgb.gblinear.history(bst, class_index = 0), type = 'l')
+matplot(xgb.gblinear.history(bst, class_index = 1), type = 'l')
+matplot(xgb.gblinear.history(bst, class_index = 2), type = 'l')
 
 # CV:
-bst <- xgb.cv(
-  param,
-  dtrain,
-  nfold = 5,
-  nrounds = 70,
-  eta = 0.5,
-  callbacks = list(xgb.cb.gblinear.history(FALSE))
-)
+bst <- xgb.cv(param, dtrain, nfold = 5, nrounds = 70, eta = 0.5,
+              callbacks = list(xgb.cb.gblinear.history(FALSE)))
 # 1st fold of 1st class
-matplot(xgb.gblinear.history(bst, class_index = 0)[[1]], type = "l")
+matplot(xgb.gblinear.history(bst, class_index = 0)[[1]], type = 'l')
 
 }
 \seealso{

R-package/man/xgb.cb.print.evaluation.Rd

@@ -7,12 +7,12 @@
 xgb.cb.print.evaluation(period = 1, showsd = TRUE)
 }
 \arguments{
-\item{period}{Results would be printed every number of periods.}
+\item{period}{results would be printed every number of periods}
 
-\item{showsd}{Whether standard deviations should be printed (when available).}
+\item{showsd}{whether standard deviations should be printed (when available)}
 }
 \value{
-An \code{xgb.Callback} object, which can be passed to \code{\link[=xgb.train]{xgb.train()}} or \code{\link[=xgb.cv]{xgb.cv()}}.
+An \code{xgb.Callback} object, which can be passed to \link{xgb.train} or \link{xgb.cv}.
 }
 \description{
 The callback function prints the result of evaluation at every \code{period} iterations.

R-package/man/xgb.cb.reset.parameters.Rd

@@ -2,12 +2,12 @@
 % Please edit documentation in R/callbacks.R
 \name{xgb.cb.reset.parameters}
 \alias{xgb.cb.reset.parameters}
-\title{Callback for resetting booster parameters at each iteration}
+\title{Callback for resetting the booster's parameters at each iteration.}
 \usage{
 xgb.cb.reset.parameters(new_params)
 }
 \arguments{
-\item{new_params}{List of parameters needed to be reset.
+\item{new_params}{a list where each element corresponds to a parameter that needs to be reset.
 Each element's value must be either a vector of values of length \code{nrounds}
 to be set at each iteration,
 or a function of two parameters \code{learning_rates(iteration, nrounds)}
@@ -15,10 +15,10 @@ which returns a new parameter value by using the current iteration number
 and the total number of boosting rounds.}
 }
 \value{
-An \code{xgb.Callback} object, which can be passed to \code{\link[=xgb.train]{xgb.train()}} or \code{\link[=xgb.cv]{xgb.cv()}}.
+An \code{xgb.Callback} object, which can be passed to \link{xgb.train} or \link{xgb.cv}.
 }
 \description{
-Callback for resetting booster parameters at each iteration
+Callback for resetting the booster's parameters at each iteration.
 }
 \details{
 Note that when training is resumed from some previous model, and a function is used to

R-package/man/xgb.cb.save.model.Rd

@@ -2,22 +2,23 @@
 % Please edit documentation in R/callbacks.R
 \name{xgb.cb.save.model}
 \alias{xgb.cb.save.model}
-\title{Callback for saving a model file}
+\title{Callback for saving a model file.}
 \usage{
 xgb.cb.save.model(save_period = 0, save_name = "xgboost.ubj")
 }
 \arguments{
-\item{save_period}{Save the model to disk after every \code{save_period} iterations;
-0 means save the model at the end.}
+\item{save_period}{Save the model to disk after every
+\code{save_period} iterations; 0 means save the model at the end.}
 
 \item{save_name}{The name or path for the saved model file.
-It can contain a \code{\link[=sprintf]{sprintf()}} formatting specifier to include the integer
-iteration number in the file name. E.g., with \code{save_name = 'xgboost_\%04d.model'},
+It can contain a \code{\link[base]{sprintf}} formatting specifier
+to include the integer iteration number in the file name.
+E.g., with \code{save_name} = 'xgboost_\%04d.model',
 the file saved at iteration 50 would be named "xgboost_0050.model".}
 }
 \value{
-An \code{xgb.Callback} object, which can be passed to \code{\link[=xgb.train]{xgb.train()}},
-but \strong{not} to \code{\link[=xgb.cv]{xgb.cv()}}.
+An \code{xgb.Callback} object, which can be passed to \link{xgb.train},
+but \bold{not} to \link{xgb.cv}.
 }
 \description{
 This callback function allows to save an xgb-model file, either periodically

R-package/man/xgb.config.Rd

@@ -10,12 +10,12 @@ xgb.config(object)
 xgb.config(object) <- value
 }
 \arguments{
-\item{object}{Object of class \code{xgb.Booster}.\strong{Will be modified in-place} when assigning to it.}
+\item{object}{Object of class \code{xgb.Booster}. \bold{Will be modified in-place} when assigning to it.}
 
-\item{value}{A list.}
+\item{value}{An R list.}
 }
 \value{
-Parameters as a list.
+\code{xgb.config} will return the parameters as an R list.
 }
 \description{
 Accessors for model parameters as JSON string
@@ -25,7 +25,7 @@ Note that assignment is performed in-place on the booster C object, which unlike
 of R attributes, doesn't follow typical copy-on-write semantics for assignment - i.e. all references
 to the same booster will also get updated.
 
-See \code{\link[=xgb.copy.Booster]{xgb.copy.Booster()}} for an example of this behavior.
+See \link{xgb.copy.Booster} for an example of this behavior.
 }
 \examples{
 data(agaricus.train, package = "xgboost")
@@ -35,8 +35,9 @@ nthread <- 1
 data.table::setDTthreads(nthread)
 train <- agaricus.train
 
-bst <- xgb.train(
-  data = xgb.DMatrix(train$data, label = train$label),
+bst <- xgboost(
+  data = train$data,
+  label = train$label,
   max_depth = 2,
   eta = 1,
   nthread = nthread,

R-package/man/xgb.copy.Booster.Rd

@@ -16,18 +16,14 @@ functions called on that copy will not affect the \code{model} variable.
 \description{
 Creates a deep copy of an 'xgb.Booster' object, such that the
 C object pointer contained will be a different object, and hence functions
-like \code{\link[=xgb.attr]{xgb.attr()}} will not affect the object from which it was copied.
+like \link{xgb.attr} will not affect the object from which it was copied.
 }
 \examples{
 library(xgboost)
-
 data(mtcars)
-
 y <- mtcars$mpg
 x <- mtcars[, -1]
-
 dm <- xgb.DMatrix(x, label = y, nthread = 1)
-
 model <- xgb.train(
   data = dm,
   params = list(nthread = 1),

R-package/man/xgb.create.features.Rd

@@ -7,18 +7,17 @@
 xgb.create.features(model, data, ...)
 }
 \arguments{
-\item{model}{Decision tree boosting model learned on the original data.}
+\item{model}{decision tree boosting model learned on the original data}
 
-\item{data}{Original data (usually provided as a \code{dgCMatrix} matrix).}
+\item{data}{original data (usually provided as a \code{dgCMatrix} matrix)}
 
-\item{...}{Currently not used.}
+\item{...}{currently not used}
 }
 \value{
-A \code{dgCMatrix} matrix including both the original data and the new features.
+\code{dgCMatrix} matrix including both the original data and the new features.
 }
 \description{
-May improve the learning by adding new features to the training data based on the
-decision trees from a previously learned model.
+May improve the learning by adding new features to the training data based on the decision trees from a previously learned model.
 }
 \details{
 This is the function inspired from the paragraph 3.1 of the paper:
@@ -45,11 +44,11 @@ For example, consider the boosted tree model in Figure 1 with 2 subtrees,
 where the first subtree has 3 leafs and the second 2 leafs. If an
 instance ends up in leaf 2 in the first subtree and leaf 1 in
 second subtree, the overall input to the linear classifier will
-be the binary vector \verb{[0, 1, 0, 1, 0]}, where the first 3 entries
+be the binary vector \code{[0, 1, 0, 1, 0]}, where the first 3 entries
 correspond to the leaves of the first subtree and last 2 to
 those of the second subtree.
 
-...
+\link{...}
 
 We can understand boosted decision tree
 based transformation as a supervised feature encoding that
@@ -58,16 +57,15 @@ vector. A traversal from root node to a leaf node represents
 a rule on certain features."
 }
 \examples{
-data(agaricus.train, package = "xgboost")
-data(agaricus.test, package = "xgboost")
-
+data(agaricus.train, package='xgboost')
+data(agaricus.test, package='xgboost')
 dtrain <- with(agaricus.train, xgb.DMatrix(data, label = label, nthread = 2))
 dtest <- with(agaricus.test, xgb.DMatrix(data, label = label, nthread = 2))
 
-param <- list(max_depth = 2, eta = 1, objective = 'binary:logistic')
+param <- list(max_depth=2, eta=1, objective='binary:logistic')
 nrounds = 4
 
-bst <- xgb.train(params = param, data = dtrain, nrounds = nrounds, nthread = 2)
+bst = xgb.train(params = param, data = dtrain, nrounds = nrounds, nthread = 2)
 
 # Model accuracy without new features
 accuracy.before <- sum((predict(bst, agaricus.test$data) >= 0.5) == agaricus.test$label) /

R-package/man/xgb.cv.Rd

@@ -26,136 +26,141 @@ xgb.cv(
 )
 }
 \arguments{
-\item{params}{The list of parameters. The complete list of parameters is available in the
-\href{http://xgboost.readthedocs.io/en/latest/parameter.html}{online documentation}.
-Below is a shorter summary:
+\item{params}{the list of parameters. The complete list of parameters is
+available in the \href{http://xgboost.readthedocs.io/en/latest/parameter.html}{online documentation}. Below
+is a shorter summary:
 \itemize{
-\item \code{objective}: Objective function, common ones are
+\item \code{objective} objective function, common ones are
 \itemize{
-\item \code{reg:squarederror}: Regression with squared loss.
-\item \code{binary:logistic}: Logistic regression for classification.
+\item \code{reg:squarederror} Regression with squared loss.
+\item \code{binary:logistic} logistic regression for classification.
+\item See \code{\link[=xgb.train]{xgb.train}()} for complete list of objectives.
+}
+\item \code{eta} step size of each boosting step
+\item \code{max_depth} maximum depth of the tree
+\item \code{nthread} number of thread used in training, if not set, all threads are used
 }
 
-See \code{\link[=xgb.train]{xgb.train()}} for complete list of objectives.
-\item \code{eta}: Step size of each boosting step
-\item \code{max_depth}: Maximum depth of the tree
-\item \code{nthread}: Number of threads used in training. If not set, all threads are used
-}
-
-See \code{\link[=xgb.train]{xgb.train()}} for further details.
-See also demo for walkthrough example in R.
+See \code{\link{xgb.train}} for further details.
+See also demo/ for walkthrough example in R.
 
 Note that, while \code{params} accepts a \code{seed} entry and will use such parameter for model training if
 supplied, this seed is not used for creation of train-test splits, which instead rely on R's own RNG
-system - thus, for reproducible results, one needs to call the \code{\link[=set.seed]{set.seed()}} function beforehand.}
+system - thus, for reproducible results, one needs to call the \code{set.seed} function beforehand.}
 
 \item{data}{An \code{xgb.DMatrix} object, with corresponding fields like \code{label} or bounds as required
 for model training by the objective.
 
-Note that only the basic \code{xgb.DMatrix} class is supported - variants such as \code{xgb.QuantileDMatrix}
-or \code{xgb.ExtMemDMatrix} are not supported here.}
+\if{html}{\out{<div class="sourceCode">}}\preformatted{   Note that only the basic `xgb.DMatrix` class is supported - variants such as `xgb.QuantileDMatrix`
+   or `xgb.ExternalDMatrix` are not supported here.
+}\if{html}{\out{</div>}}}
 
-\item{nrounds}{The max number of iterations.}
+\item{nrounds}{the max number of iterations}
 
-\item{nfold}{The original dataset is randomly partitioned into \code{nfold} equal size subsamples.}
+\item{nfold}{the original dataset is randomly partitioned into \code{nfold} equal size subsamples.}
 
 \item{prediction}{A logical value indicating whether to return the test fold predictions
-from each CV model. This parameter engages the \code{\link[=xgb.cb.cv.predict]{xgb.cb.cv.predict()}} callback.}
+from each CV model. This parameter engages the \code{\link{xgb.cb.cv.predict}} callback.}
 
-\item{showsd}{Logical value whether to show standard deviation of cross validation.}
+\item{showsd}{\code{boolean}, whether to show standard deviation of cross validation}
 
-\item{metrics}{List of evaluation metrics to be used in cross validation,
+\item{metrics, }{list of evaluation metrics to be used in cross validation,
 when it is not specified, the evaluation metric is chosen according to objective function.
 Possible options are:
 \itemize{
-\item \code{error}: Binary classification error rate
-\item \code{rmse}: Root mean square error
-\item \code{logloss}: Negative log-likelihood function
-\item \code{mae}: Mean absolute error
-\item \code{mape}: Mean absolute percentage error
-\item \code{auc}: Area under curve
-\item \code{aucpr}: Area under PR curve
-\item \code{merror}: Exact matching error used to evaluate multi-class classification
+\item \code{error} binary classification error rate
+\item \code{rmse} Rooted mean square error
+\item \code{logloss} negative log-likelihood function
+\item \code{mae} Mean absolute error
+\item \code{mape} Mean absolute percentage error
+\item \code{auc} Area under curve
+\item \code{aucpr} Area under PR curve
+\item \code{merror} Exact matching error, used to evaluate multi-class classification
 }}
 
-\item{obj}{Customized objective function. Returns gradient and second order
+\item{obj}{customized objective function. Returns gradient and second order
 gradient with given prediction and dtrain.}
 
-\item{feval}{Customized evaluation function. Returns
-\code{list(metric='metric-name', value='metric-value')} with given prediction and dtrain.}
+\item{feval}{customized evaluation function. Returns
+\code{list(metric='metric-name', value='metric-value')} with given
+prediction and dtrain.}
 
-\item{stratified}{Logical flag indicating whether sampling of folds should be stratified
+\item{stratified}{A \code{boolean} indicating whether sampling of folds should be stratified
 by the values of outcome labels. For real-valued labels in regression objectives,
 stratification will be done by discretizing the labels into up to 5 buckets beforehand.
 
-If passing "auto", will be set to \code{TRUE} if the objective in \code{params} is a classification
-objective (from XGBoost's built-in objectives, doesn't apply to custom ones), and to
-\code{FALSE} otherwise.
+\if{html}{\out{<div class="sourceCode">}}\preformatted{   If passing "auto", will be set to `TRUE` if the objective in `params` is a classification
+   objective (from XGBoost's built-in objectives, doesn't apply to custom ones), and to
+   `FALSE` otherwise.
 
-This parameter is ignored when \code{data} has a \code{group} field - in such case, the splitting
-will be based on whole groups (note that this might make the folds have different sizes).
+   This parameter is ignored when `data` has a `group` field - in such case, the splitting
+   will be based on whole groups (note that this might make the folds have different sizes).
 
-Value \code{TRUE} here is \strong{not} supported for custom objectives.}
+   Value `TRUE` here is \\bold\{not\} supported for custom objectives.
+}\if{html}{\out{</div>}}}
 
-\item{folds}{List with pre-defined CV folds (each element must be a vector of test fold's indices).
-When folds are supplied, the \code{nfold} and \code{stratified} parameters are ignored.
+\item{folds}{\code{list} provides a possibility to use a list of pre-defined CV folds
+(each element must be a vector of test fold's indices). When folds are supplied,
+the \code{nfold} and \code{stratified} parameters are ignored.
 
-If \code{data} has a \code{group} field and the objective requires this field, each fold (list element)
-must additionally have two attributes (retrievable through \code{attributes}) named \code{group_test}
-and \code{group_train}, which should hold the \code{group} to assign through \code{\link[=setinfo.xgb.DMatrix]{setinfo.xgb.DMatrix()}} to
-the resulting DMatrices.}
+\if{html}{\out{<div class="sourceCode">}}\preformatted{   If `data` has a `group` field and the objective requires this field, each fold (list element)
+   must additionally have two attributes (retrievable through \link{attributes}) named `group_test`
+   and `group_train`, which should hold the `group` to assign through \link{setinfo.xgb.DMatrix} to
+   the resulting DMatrices.
+}\if{html}{\out{</div>}}}
 
-\item{train_folds}{List specifying which indices to use for training. If \code{NULL}
+\item{train_folds}{\code{list} list specifying which indicies to use for training. If \code{NULL}
 (the default) all indices not specified in \code{folds} will be used for training.
 
-This is not supported when \code{data} has \code{group} field.}
+\if{html}{\out{<div class="sourceCode">}}\preformatted{   This is not supported when `data` has `group` field.
+}\if{html}{\out{</div>}}}
 
-\item{verbose}{Logical flag. Should statistics be printed during the process?}
+\item{verbose}{\code{boolean}, print the statistics during the process}
 
-\item{print_every_n}{Print each nth iteration evaluation messages when \code{verbose > 0}.
+\item{print_every_n}{Print each n-th iteration evaluation messages when \code{verbose>0}.
 Default is 1 which means all messages are printed. This parameter is passed to the
-\code{\link[=xgb.cb.print.evaluation]{xgb.cb.print.evaluation()}} callback.}
+\code{\link{xgb.cb.print.evaluation}} callback.}
 
 \item{early_stopping_rounds}{If \code{NULL}, the early stopping function is not triggered.
 If set to an integer \code{k}, training with a validation set will stop if the performance
 doesn't improve for \code{k} rounds.
-Setting this parameter engages the \code{\link[=xgb.cb.early.stop]{xgb.cb.early.stop()}} callback.}
+Setting this parameter engages the \code{\link{xgb.cb.early.stop}} callback.}
 
 \item{maximize}{If \code{feval} and \code{early_stopping_rounds} are set,
 then this parameter must be set as well.
 When it is \code{TRUE}, it means the larger the evaluation score the better.
-This parameter is passed to the \code{\link[=xgb.cb.early.stop]{xgb.cb.early.stop()}} callback.}
+This parameter is passed to the \code{\link{xgb.cb.early.stop}} callback.}
 
-\item{callbacks}{A list of callback functions to perform various task during boosting.
-See \code{\link[=xgb.Callback]{xgb.Callback()}}. Some of the callbacks are automatically created depending on the
+\item{callbacks}{a list of callback functions to perform various task during boosting.
+See \code{\link{xgb.Callback}}. Some of the callbacks are automatically created depending on the
 parameters' values. User can provide either existing or their own callback methods in order
 to customize the training process.}
 
-\item{...}{Other parameters to pass to \code{params}.}
+\item{...}{other parameters to pass to \code{params}.}
 }
 \value{
-An object of class 'xgb.cv.synchronous' with the following elements:
+An object of class \code{xgb.cv.synchronous} with the following elements:
 \itemize{
-\item \code{call}: Function call.
-\item \code{params}: Parameters that were passed to the xgboost library. Note that it does not
-capture parameters changed by the \code{\link[=xgb.cb.reset.parameters]{xgb.cb.reset.parameters()}} callback.
-\item \code{evaluation_log}: Evaluation history stored as a \code{data.table} with the
+\item \code{call} a function call.
+\item \code{params} parameters that were passed to the xgboost library. Note that it does not
+capture parameters changed by the \code{\link{xgb.cb.reset.parameters}} callback.
+\item \code{evaluation_log} evaluation history stored as a \code{data.table} with the
 first column corresponding to iteration number and the rest corresponding to the
 CV-based evaluation means and standard deviations for the training and test CV-sets.
-It is created by the \code{\link[=xgb.cb.evaluation.log]{xgb.cb.evaluation.log()}} callback.
-\item \code{niter}: Number of boosting iterations.
-\item \code{nfeatures}: Number of features in training data.
-\item \code{folds}: The list of CV folds' indices - either those passed through the \code{folds}
+It is created by the \code{\link{xgb.cb.evaluation.log}} callback.
+\item \code{niter} number of boosting iterations.
+\item \code{nfeatures} number of features in training data.
+\item \code{folds} the list of CV folds' indices - either those passed through the \code{folds}
 parameter or randomly generated.
-\item \code{best_iteration}: Iteration number with the best evaluation metric value
+\item \code{best_iteration} iteration number with the best evaluation metric value
 (only available with early stopping).
 }
 
 Plus other potential elements that are the result of callbacks, such as a list \code{cv_predict} with
-a sub-element \code{pred} when passing \code{prediction = TRUE}, which is added by the \code{\link[=xgb.cb.cv.predict]{xgb.cb.cv.predict()}}
+a sub-element \code{pred} when passing \code{prediction = TRUE}, which is added by the \link{xgb.cb.cv.predict}
 callback (note that one can also pass it manually under \code{callbacks} with different settings,
 such as saving also the models created during cross validation); or a list \code{early_stop} which
-will contain elements such as \code{best_iteration} when using the early stopping callback (\code{\link[=xgb.cb.early.stop]{xgb.cb.early.stop()}}).
+will contain elements such as \code{best_iteration} when using the early stopping callback (\link{xgb.cb.early.stop}).
 }
 \description{
 The cross validation function of xgboost.
@@ -174,20 +179,11 @@ All observations are used for both training and validation.
 Adapted from \url{https://en.wikipedia.org/wiki/Cross-validation_\%28statistics\%29}
 }
 \examples{
-data(agaricus.train, package = "xgboost")
-
+data(agaricus.train, package='xgboost')
 dtrain <- with(agaricus.train, xgb.DMatrix(data, label = label, nthread = 2))
-
-cv <- xgb.cv(
-  data = dtrain,
-  nrounds = 3,
-  nthread = 2,
-  nfold = 5,
-  metrics = list("rmse","auc"),
-  max_depth = 3,
-  eta = 1,objective = "binary:logistic"
-)
+cv <- xgb.cv(data = dtrain, nrounds = 3, nthread = 2, nfold = 5, metrics = list("rmse","auc"),
+             max_depth = 3, eta = 1, objective = "binary:logistic")
 print(cv)
-print(cv, verbose = TRUE)
+print(cv, verbose=TRUE)
 
 }

R-package/man/xgb.dump.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/xgb.dump.R
 \name{xgb.dump}
 \alias{xgb.dump}
-\title{Dump an XGBoost model in text format.}
+\title{Dump an xgboost model in text format.}
 \usage{
 xgb.dump(
   model,
@@ -14,51 +14,43 @@ xgb.dump(
 )
 }
 \arguments{
-\item{model}{The model object.}
+\item{model}{the model object.}
 
-\item{fname}{The name of the text file where to save the model text dump.
-If not provided or set to \code{NULL}, the model is returned as a character vector.}
+\item{fname}{the name of the text file where to save the model text dump.
+If not provided or set to \code{NULL}, the model is returned as a \code{character} vector.}
 
-\item{fmap}{Feature map file representing feature types. See demo/ for a walkthrough
-example in R, and \url{https://github.com/dmlc/xgboost/blob/master/demo/data/featmap.txt}
-to see an example of the value.}
+\item{fmap}{feature map file representing feature types.
+See demo/ for walkthrough example in R, and
+\url{https://github.com/dmlc/xgboost/blob/master/demo/data/featmap.txt}
+for example Format.}
 
-\item{with_stats}{Whether to dump some additional statistics about the splits.
+\item{with_stats}{whether to dump some additional statistics about the splits.
 When this option is on, the model dump contains two additional values:
 gain is the approximate loss function gain we get in each split;
 cover is the sum of second order gradient in each node.}
 
-\item{dump_format}{Either 'text', 'json', or 'dot' (graphviz) format could be specified.
+\item{dump_format}{either 'text', 'json', or 'dot' (graphviz) format could be specified.
 
 Format 'dot' for a single tree can be passed directly to packages that consume this format
-for graph visualization, such as function \code{DiagrammeR::grViz()}}
+for graph visualization, such as function \code{\link[DiagrammeR:grViz]{DiagrammeR::grViz()}}}
 
-\item{...}{Currently not used}
+\item{...}{currently not used}
 }
 \value{
 If fname is not provided or set to \code{NULL} the function will return the model
-as a character vector. Otherwise it will return \code{TRUE}.
+as a \code{character} vector. Otherwise it will return \code{TRUE}.
 }
 \description{
-Dump an XGBoost model in text format.
+Dump an xgboost model in text format.
 }
 \examples{
 \dontshow{RhpcBLASctl::omp_set_num_threads(1)}
-data(agaricus.train, package = "xgboost")
-data(agaricus.test, package = "xgboost")
-
+data(agaricus.train, package='xgboost')
+data(agaricus.test, package='xgboost')
 train <- agaricus.train
 test <- agaricus.test
-
-bst <- xgb.train(
-  data = xgb.DMatrix(train$data, label = train$label),
-  max_depth = 2,
-  eta = 1,
-  nthread = 2,
-  nrounds = 2,
-  objective = "binary:logistic"
-)
-
+bst <- xgboost(data = train$data, label = train$label, max_depth = 2,
+               eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic")
 # save the model in file 'xgb.model.dump'
 dump_path = file.path(tempdir(), 'model.dump')
 xgb.dump(bst, dump_path, with_stats = TRUE)
@@ -67,7 +59,7 @@ xgb.dump(bst, dump_path, with_stats = TRUE)
 print(xgb.dump(bst, with_stats = TRUE))
 
 # print in JSON format:
-cat(xgb.dump(bst, with_stats = TRUE, dump_format = "json"))
+cat(xgb.dump(bst, with_stats = TRUE, dump_format='json'))
 
 # plot first tree leveraging the 'dot' format
 if (requireNamespace('DiagrammeR', quietly = TRUE)) {

R-package/man/xgb.gblinear.history.Rd

@@ -2,24 +2,24 @@
 % Please edit documentation in R/callbacks.R
 \name{xgb.gblinear.history}
 \alias{xgb.gblinear.history}
-\title{Extract gblinear coefficients history}
+\title{Extract gblinear coefficients history.}
 \usage{
 xgb.gblinear.history(model, class_index = NULL)
 }
 \arguments{
-\item{model}{Either an \code{xgb.Booster} or a result of \code{\link[=xgb.cv]{xgb.cv()}}, trained
-using the \link{xgb.cb.gblinear.history} callback, but \strong{not} a booster
-loaded from \code{\link[=xgb.load]{xgb.load()}} or \code{\link[=xgb.load.raw]{xgb.load.raw()}}.}
+\item{model}{either an \code{xgb.Booster} or a result of \code{xgb.cv()}, trained
+using the \link{xgb.cb.gblinear.history} callback, but \bold{not} a booster
+loaded from \link{xgb.load} or \link{xgb.load.raw}.}
 
 \item{class_index}{zero-based class index to extract the coefficients for only that
-specific class in a multinomial multiclass model. When it is \code{NULL}, all the
+specific class in a multinomial multiclass model. When it is NULL, all the
 coefficients are returned. Has no effect in non-multiclass models.}
 }
 \value{
-For an \code{\link[=xgb.train]{xgb.train()}} result, a matrix (either dense or sparse) with the columns
+For an \link{xgb.train} result, a matrix (either dense or sparse) with the columns
 corresponding to iteration's coefficients and the rows corresponding to boosting iterations.
 
-For an \code{\link[=xgb.cv]{xgb.cv()}} result, a list of such matrices is returned with the elements
+For an \link{xgb.cv} result, a list of such matrices is returned with the elements
 corresponding to CV folds.
 
 When there is more than one coefficient per feature (e.g. multi-class classification)
@@ -31,15 +31,15 @@ coefficients N+1 through 2N for the second class, and so on).
 \description{
 A helper function to extract the matrix of linear coefficients' history
 from a gblinear model created while using the \link{xgb.cb.gblinear.history}
-callback (which must be added manually as by default it is not used).
+callback (which must be added manually as by default it's not used).
 }
 \details{
 Note that this is an R-specific function that relies on R attributes that
-are not saved when using XGBoost's own serialization functions like \code{\link[=xgb.load]{xgb.load()}}
-or \code{\link[=xgb.load.raw]{xgb.load.raw()}}.
+are not saved when using xgboost's own serialization functions like \link{xgb.load}
+or \link{xgb.load.raw}.
 
 In order for a serialized model to be accepted by this function, one must use R
-serializers such as \code{\link[=saveRDS]{saveRDS()}}.
+serializers such as \link{saveRDS}.
 }
 \seealso{
 \link{xgb.cb.gblinear.history}, \link{coef.xgb.Booster}.

R-package/man/xgb.get.DMatrix.data.Rd

@@ -7,7 +7,7 @@
 xgb.get.DMatrix.data(dmat)
 }
 \arguments{
-\item{dmat}{An \code{xgb.DMatrix} object, as returned by \code{\link[=xgb.DMatrix]{xgb.DMatrix()}}.}
+\item{dmat}{An \code{xgb.DMatrix} object, as returned by \link{xgb.DMatrix}.}
 }
 \value{
 The data held in the DMatrix, as a sparse CSR matrix (class \code{dgRMatrix}

R-package/man/xgb.get.DMatrix.num.non.missing.Rd

@@ -7,10 +7,10 @@
 xgb.get.DMatrix.num.non.missing(dmat)
 }
 \arguments{
-\item{dmat}{An \code{xgb.DMatrix} object, as returned by \code{\link[=xgb.DMatrix]{xgb.DMatrix()}}.}
+\item{dmat}{An \code{xgb.DMatrix} object, as returned by \link{xgb.DMatrix}.}
 }
 \value{
-The number of non-missing entries in the DMatrix.
+The number of non-missing entries in the DMatrix
 }
 \description{
 Get Number of Non-Missing Entries in DMatrix

R-package/man/xgb.get.DMatrix.qcut.Rd

@@ -7,14 +7,15 @@
 xgb.get.DMatrix.qcut(dmat, output = c("list", "arrays"))
 }
 \arguments{
-\item{dmat}{An \code{xgb.DMatrix} object, as returned by \code{\link[=xgb.DMatrix]{xgb.DMatrix()}}.}
+\item{dmat}{An \code{xgb.DMatrix} object, as returned by \link{xgb.DMatrix}.}
 
-\item{output}{Output format for the quantile cuts. Possible options are:
-\itemize{
-\item "list"\verb{will return the output as a list with one entry per column, where each column will have a numeric vector with the cuts. The list will be named if}dmat` has column names assigned to it.
+\item{output}{Output format for the quantile cuts. Possible options are:\itemize{
+\item \code{"list"} will return the output as a list with one entry per column, where
+each column will have a numeric vector with the cuts. The list will be named if
+\code{dmat} has column names assigned to it.
 \item \code{"arrays"} will return a list with entries \code{indptr} (base-0 indexing) and
 \code{data}. Here, the cuts for column 'i' are obtained by slicing 'data' from entries
-\code{   indptr[i]+1} to \code{indptr[i+1]}.
+\code{indptr[i]+1} to \code{indptr[i+1]}.
 }}
 }
 \value{
@@ -22,7 +23,7 @@ The quantile cuts, in the format specified by parameter \code{output}.
 }
 \description{
 Get the quantile cuts (a.k.a. borders) from an \code{xgb.DMatrix}
-that has been quantized for the histogram method (\code{tree_method = "hist"}).
+that has been quantized for the histogram method (\code{tree_method="hist"}).
 
 These cuts are used in order to assign observations to bins - i.e. these are ordered
 boundaries which are used to determine assignment condition \verb{border_low < x < border_high}.
@@ -35,8 +36,8 @@ which will be output in sorted order from lowest to highest.
 Different columns can have different numbers of bins according to their range.
 }
 \examples{
+library(xgboost)
 data(mtcars)
-
 y <- mtcars$mpg
 x <- as.matrix(mtcars[, -1])
 dm <- xgb.DMatrix(x, label = y, nthread = 1)
@@ -44,7 +45,11 @@ dm <- xgb.DMatrix(x, label = y, nthread = 1)
 # DMatrix is not quantized right away, but will be once a hist model is generated
 model <- xgb.train(
   data = dm,
-  params = list(tree_method = "hist", max_bin = 8, nthread = 1),
+  params = list(
+    tree_method = "hist",
+    max_bin = 8,
+    nthread = 1
+  ),
   nrounds = 3
 )
 

R-package/man/xgb.get.num.boosted.rounds.Rd

@@ -13,13 +13,13 @@ xgb.get.num.boosted.rounds(model)
 \item{model, x}{A fitted \code{xgb.Booster} model.}
 }
 \value{
-The number of rounds saved in the model as an integer.
+The number of rounds saved in the model, as an integer.
 }
 \description{
 Get number of boosting in a fitted booster
 }
 \details{
 Note that setting booster parameters related to training
-continuation / updates through \code{\link[=xgb.parameters<-]{xgb.parameters<-()}} will reset the
+continuation / updates through \link{xgb.parameters<-} will reset the
 number of rounds to zero.
 }

R-package/man/xgb.importance.Rd

@@ -70,8 +70,9 @@ be on the same scale (which is also recommended when using L1 or L2 regularizati
 # binomial classification using "gbtree":
 data(agaricus.train, package = "xgboost")
 
-bst <- xgb.train(
-  data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
+bst <- xgboost(
+  data = agaricus.train$data,
+  label = agaricus.train$label,
   max_depth = 2,
   eta = 1,
   nthread = 2,
@@ -82,8 +83,9 @@ bst <- xgb.train(
 xgb.importance(model = bst)
 
 # binomial classification using "gblinear":
-bst <- xgb.train(
-  data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
+bst <- xgboost(
+  data = agaricus.train$data,
+  label = agaricus.train$label,
   booster = "gblinear",
   eta = 0.3,
   nthread = 1,
@@ -95,11 +97,9 @@ xgb.importance(model = bst)
 # multiclass classification using "gbtree":
 nclass <- 3
 nrounds <- 10
-mbst <- xgb.train(
-  data = xgb.DMatrix(
-    as.matrix(iris[, -5]),
-    label = as.numeric(iris$Species) - 1
-  ),
+mbst <- xgboost(
+  data = as.matrix(iris[, -5]),
+  label = as.numeric(iris$Species) - 1,
   max_depth = 3,
   eta = 0.2,
   nthread = 2,
@@ -123,11 +123,9 @@ xgb.importance(
 )
 
 # multiclass classification using "gblinear":
-mbst <- xgb.train(
-  data = xgb.DMatrix(
-    scale(as.matrix(iris[, -5])),
-    label = as.numeric(iris$Species) - 1
-  ),
+mbst <- xgboost(
+  data = scale(as.matrix(iris[, -5])),
+  label = as.numeric(iris$Species) - 1,
   booster = "gblinear",
   eta = 0.2,
   nthread = 1,