* Fix#3545: XGDMatrixCreateFromCSCEx silently discards empty trailing rows
Description: The bug is triggered when
1. The data matrix has empty rows at the bottom. More precisely, the rows
`n-k+1`, `n-k+2`, ..., `n` of the matrix have missing values in all
dimensions (`n` number of instances, `k` number of trailing rows)
2. The data matrix is given as Compressed Sparse Column (CSC) format.
Diagnosis: When the CSC matrix is converted to Compressed Sparse Row (CSR)
format (this is common format used for DMatrix), the trailing empty rows
are silently ignored. More specifically, the row pointer (`offset`) of the
newly created CSR matrix does not take account of these rows.
Fix: Modify the row pointer.
* Add regression test
* Refactor to allow for custom regularisation methods
* Implement compositional SplitEvaluator framework
* Fixed segfault when no monotone_constraints are supplied.
* Change pid to parentID
* test_monotone_constraints.py now passes
* Refactor ColMaker and DistColMaker to use SplitEvaluator
* Performance optimisation when no monotone_constraints specified
* Fix linter messages
* Fix a few more linter errors
* Update the amalgamation
* Add bounds check
* Add check for leaf node
* Fix linter error in param.h
* Fix clang-tidy errors on CI
* Fix incorrect function name
* Fix clang-tidy error in updater_fast_hist.cc
* Enable SSE2 for Win32 R MinGW
Addresses https://github.com/dmlc/xgboost/pull/3335#issuecomment-400535752
* Add contributor
* Fix print.xgb.Booster
valid_handle should be TRUE when x$handle is NOT null
* Update xgb.Booster.R
Modify is.null.handle to return TRUE for NULL handle
* For CRAN submission, remove all #pragma's that suppress compiler warnings
A few headers in dmlc-core contain #pragma's that disable compiler warnings,
which is against the CRAN submission policy. Fix the problem by removing
the offending #pragma's as part of the command `make Rbuild`.
This addresses issue #3322.
* Fix script to improve Cygwin/MSYS compatibility
We need this to pass rmingw CI test
* Remove remove_warning_suppression_pragma.sh from packaged tarball
* rank_metric: add AUC-PR
Implementation of the AUC-PR calculation for weighted data, proposed by Keilwagen, Grosse and Grau (https://doi.org/10.1371/journal.pone.0092209)
* rank_metric: fix lint warnings
* Implement tests for AUC-PR and fix implementation
* add aucpr to documentation for other languages
* fix rebase conflict
* [core] additional gblinear improvements
* [R] callback for gblinear coefficients history
* force eta=1 for gblinear python tests
* add top_k to GreedyFeatureSelector
* set eta=1 in shotgun test
* [core] fix SparsePage processing in gblinear; col-wise multithreading in greedy updater
* set sorted flag within TryInitColData
* gblinear tests: use scale, add external memory test
* fix multiclass for greedy updater
* fix whitespace
* fix typo
* [R] fix finding R.exe with cmake on WIN when it is in PATH
* [R] appveyor config for R package
* [R] wrap the lines to make R check happier
* [R] install only binary dep-packages in appveyor
* [R] for MSVC appveyor, also build a binary for R package and keep as an artifact
* [R] fix predict contributions for data with no colnames
* [R] add a render parameter for xgb.plot.multi.trees; fixes#2628
* [R] update Rd's
* [R] remove unnecessary dep-package from R cmake install
* silence type warnings; readability
* [R] silence complaint about incomplete line at the end
* [R] initial version of xgb.plot.shap()
* [R] more work on xgb.plot.shap
* [R] enforce black font in xgb.plot.tree; fixes#2640
* [R] if feature names are available, check in predict that they are the same; fixes#2857
* [R] cran check and lint fixes
* remove tabs
* [R] add references; a test for plot.shap
* SHAP values for feature contributions
* Fix commenting error
* New polynomial time SHAP value estimation algorithm
* Update API to support SHAP values
* Fix merge conflicts with updates in master
* Correct submodule hashes
* Fix variable sized stack allocation
* Make lint happy
* Add docs
* Fix typo
* Adjust tolerances
* Remove unneeded def
* Fixed cpp test setup
* Updated R API and cleaned up
* Fixed test typo
* [R] MSVC compatibility
* [GPU] allow seed in BernoulliRng up to size_t and scale to uint32_t
* R package build with cmake and CUDA
* R package CUDA build fixes and cleanups
* always export the R package native initialization routine on windows
* update the install instructions doc
* fix lint
* use static_cast directly to set BernoulliRng seed
* [R] demo for GPU accelerated algorithm
* tidy up the R package cmake stuff
* R pack cmake: installs main dependency packages if needed
* [R] version bump in DESCRIPTION
* update NEWS
* added short missing/sparse values explanations to FAQ
for loop in create.new.tree.features was referencing length(trees) as the upper bound of the loop. trees is a base R dataset and not the model that the code is generating. Changed loop boundary to model$niter which should be the number of trees.
* [gblinear] add features contribution prediction; fix DumpModel bug
* [gbtree] minor changes to PredContrib
* [R] add feature contribution prediction to R
* [R] bump up version; update NEWS
* [gblinear] fix the base_margin issue; fixes#1969
* [R] list of matrices as output of multiclass feature contributions
* [gblinear] make order of DumpModel coefficients consistent: group index changes the fastest
* [R] add native routines registration
* c_api.h needs to include <cstdint> since it uses fixed width integer types
* [R] use registered native routines from R code
* [R] bump version; add info on native routine registration to the contributors guide
* make lint happy
* [R] make sure things work for a single split model; fixes#2191
* [R] add option use_int_id to xgb.model.dt.tree
* [R] add example of exporting tree plot to a file
* [R] set save_period = NULL as default in xgboost() to be the same as in xgb.train; fixes#2182
* [R] it's a good practice after CRAN releases to bump up package version in dev
* [R] allow xgb.DMatrix construction from integer dense matrices
* [R] xgb.DMatrix: silent parameter; improve documentation
* [R] xgb.model.dt.tree code style changes
* [R] update NEWS with parameter changes
* [R] code safety & style; handle non-strict matrix and inherited classes of input and model; fixes#2242
* [R] change to x.y.z.p R-package versioning scheme and set version to 0.6.4.3
* [R] add an R package versioning section to the contributors guide
* [R] R-package/README.md: clean up the redundant old installation instructions, link the contributors guide
* [R] xgb.save must work when handle in nil but raw exists
* [R] print.xgb.Booster should still print other info when handle is nil
* [R] rename internal function xgb.Booster to xgb.Booster.handle to make its intent clear
* [R] rename xgb.Booster.check to xgb.Booster.complete and make it visible; more docs
* [R] storing evaluation_log should depend only on watchlist, not on verbose
* [R] reduce the excessive chattiness of unit tests
* [R] only disable some tests in windows when it's not 64-bit
* [R] clean-up xgb.DMatrix
* [R] test xgb.DMatrix loading from libsvm text file
* [R] store feature_names in xgb.Booster, use them from utility functions
* [R] remove non-functional co-occurence computation from xgb.importance
* [R] verbose=0 is enough without a callback
* [R] added forgotten xgb.Booster.complete.Rd; cran check fixes
* [R] update installation instructions
* fix cran check
* change required R version because of utils::globalVariables
* temporary commit, monotone not working
* fix test
* fix doc
* fix doc
* fix cran note and warning
* improve checks
* fix urls
* fix cran check
* add cleanup and bump up version number
* use clean in build
* Update Makefile
* [R-package] JSON tree dump interface
* [R-package] precision bugfix in xgb.attributes
* [R-package] bugfix for cb.early.stop called from xgb.cv
* [R-package] a bit more clarity on labels checking in xgb.cv
* [R-package] test JSON dump for gblinear as well
* whitespace lint
* [CORE] allow updating trees in an existing model
* [CORE] in refresh updater, allow keeping old leaf values and update stats only
* [R-package] xgb.train mod to allow updating trees in an existing model
* [R-package] added check for nrounds when is_update
* [CORE] merge parameter declaration changes; unify their code style
* [CORE] move the update-process trees initialization to Configure; rename default process_type to 'default'; fix the trees and trees_to_update sizes comparison check
* [R-package] unit tests for the update process type
* [DOC] documentation for process_type parameter; improved docs for updater, Gamma and Tweedie; added some parameter aliases; metrics indentation and some were non-documented
* fix my sloppy merge conflict resolutions
* [CORE] add a TreeProcessType enum
* whitespace fix
* fix cran check
* change required R version because of utils::globalVariables
* temporary commit, monotone not working
* fix test
* fix doc
* fix doc
* fix cran note and warning
* improve checks
* fix urls
