initial trial package

R-package/DESCRIPTION

@@ -0,0 +1,15 @@
+Package: xgboost
+Type: Package
+Title: R wrapper of xgboost
+Version: 0.3-0
+Date: 2014-08-23
+Author: Tianqi Chen
+Maintainer: Tianqi Chen <tianqi.tchen@gmail.com>
+Description: xgboost
+License: See LICENSE file
+URL: https://github.com/tqchen/xgboost
+BugReports: https://github.com/tqchen/xgboost/issues
+Depends:
+    R (>= 2.0.2)
+Imports:
+    Matrix (>= 1.1-0)

R-package/LICENSE

@@ -0,0 +1,13 @@
+Copyright (c) 2014 by Tianqi Chen and Contributors 
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+    
+   http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

R-package/R/xgboost.R

@@ -0,0 +1,222 @@
+# depends on matrix
+.onLoad <- function(libname, pkgname) {
+  library.dynam("xgboost", pkgname, libname);
+}
+.onUnload <- function(libpath) {
+  library.dynam.unload("xgboost", libpath);
+}
+
+# constructing DMatrix
+xgb.DMatrix <- function(data, info=list(), missing=0.0) {
+  if (typeof(data) == "character") {
+    handle <- .Call("XGDMatrixCreateFromFile_R", data, as.integer(FALSE))
+  } else if(is.matrix(data)) {
+    handle <- .Call("XGDMatrixCreateFromMat_R", data, missing)
+  } else if(class(data) == "dgCMatrix") {
+    handle <- .Call("XGDMatrixCreateFromCSC_R", data@p, data@i, data@x)
+  } else {
+    stop(paste("xgb.DMatrix: does not support to construct from ", typeof(data)))
+  }
+  dmat <- structure(handle, class="xgb.DMatrix")
+  if (length(info) != 0) {
+    for (i in 1:length(info)) {
+      p <- info[i]
+      xgb.setinfo(dmat, names(p), p[[1]])
+    }
+  }
+  return(dmat)
+}
+# get information from dmatrix
+xgb.getinfo <- function(dmat, name) {
+  if (typeof(name) != "character") {
+    stop("xgb.getinfo: name must be character")
+  }
+  if (class(dmat) != "xgb.DMatrix") {
+    stop("xgb.setinfo: first argument dtrain must be xgb.DMatrix");
+  }
+  if (name != "label" &&
+      name != "weight" &&
+      name != "base_margin" ) {
+    stop(paste("xgb.getinfo: unknown info name", name))
+  }
+  ret <- .Call("XGDMatrixGetInfo_R", dmat, name)
+  return(ret)
+}
+# set information into dmatrix, this mutate dmatrix
+xgb.setinfo <- function(dmat, name, info) {
+  if (class(dmat) != "xgb.DMatrix") {
+    stop("xgb.setinfo: first argument dtrain must be xgb.DMatrix");
+  }
+  if (name == "label") {
+    .Call("XGDMatrixSetInfo_R", dmat, name, as.numeric(info))
+    return(TRUE)
+  }
+  if (name == "weight") {
+    .Call("XGDMatrixSetInfo_R", dmat, name, as.numeric(info))
+    return(TRUE)
+  }
+  if (name == "base_margin") {
+    .Call("XGDMatrixSetInfo_R", dmat, name, as.numeric(info))
+    return(TRUE)
+  }
+  if (name == "group") {
+    .Call("XGDMatrixSetInfo_R", dmat, name, as.integer(info))
+    return(TRUE)
+  }
+  stop(pase("xgb.setinfo: unknown info name", name))
+  return(FALSE)
+}
+# construct a Booster from cachelist
+xgb.Booster <- function(params = list(), cachelist = list(), modelfile = NULL) {
+  if (typeof(cachelist) != "list") {
+    stop("xgb.Booster: only accepts list of DMatrix as cachelist")
+  }
+  for (dm in cachelist) {
+    if (class(dm) != "xgb.DMatrix") {
+      stop("xgb.Booster: only accepts list of DMatrix as cachelist")
+    }
+  }
+  handle <- .Call("XGBoosterCreate_R", cachelist)
+  .Call("XGBoosterSetParam_R", handle, "seed", "0")
+  if (length(params) != 0) {
+    for (i in 1:length(params)) {
+      p <- params[i]
+      .Call("XGBoosterSetParam_R", handle, names(p), as.character(p))
+    }
+  }
+  if (!is.null(modelfile)) {
+    if (typeof(modelfile) != "character"){
+      stop("xgb.Booster: modelfile must be character");
+    }
+    .Call("XGBoosterLoadModel_R", handle, modelfile)
+  }
+  return(structure(handle, class="xgb.Booster"))
+}
+# train a model using given parameters
+xgb.train <- function(params, dtrain, nrounds=10, watchlist=list(), obj=NULL, feval=NULL) {
+  if (typeof(params) != "list") {
+    stop("xgb.train: first argument params must be list");
+  }
+  if (class(dtrain) != "xgb.DMatrix") {
+    stop("xgb.train: second argument dtrain must be xgb.DMatrix");
+  }
+  bst <- xgb.Booster(params, append(watchlist,dtrain))
+  for (i in 1:nrounds) {
+    if (is.null(obj)) {
+      succ <- xgb.iter.update(bst, dtrain, i-1)
+    } else {
+      pred <- xgb.predict(bst, dtrain)
+      gpair <- obj(pred, dtrain)
+      succ <- xgb.iter.boost(bst, dtrain, gpair)
+    }
+    if (length(watchlist) != 0) {
+      if (is.null(feval)) {      
+        msg <- xgb.iter.eval(bst, watchlist, i-1)
+        cat(msg); cat("\n")
+      } else {
+        cat("["); cat(i); cat("]");
+        for (j in 1:length(watchlist)) {
+          w <- watchlist[j]
+          if (length(names(w)) == 0) {
+            stop("xgb.eval: name tag must be presented for every elements in watchlist")
+          }
+          ret <- feval(xgb.predict(bst, w[[1]]), w[[1]])
+          cat("\t"); cat(names(w)); cat("-"); cat(ret$metric); 
+          cat(":"); cat(ret$value)
+        }
+        cat("\n")        
+      }
+    }
+  }
+  return(bst)
+}
+# save model or DMatrix to file 
+xgb.save <- function(handle, fname) {
+  if (typeof(fname) != "character") {
+    stop("xgb.save: fname must be character");
+  }
+  if (class(handle) == "xgb.Booster") {
+    .Call("XGBoosterSaveModel_R", handle, fname);
+    return(TRUE)
+  }
+  if (class(handle) == "xgb.DMatrix") {
+    .Call("XGDMatrixSaveBinary_R", handle, fname, as.integer(FALSE))
+    return(TRUE)
+  }
+  stop("xgb.save: the input must be either xgb.DMatrix or xgb.Booster")
+  return(FALSE)
+}
+# predict 
+xgb.predict <- function(booster, dmat, outputmargin = FALSE) {
+  if (class(booster) != "xgb.Booster") {
+    stop("xgb.predict: first argument must be type xgb.Booster")
+  }
+  if (class(dmat) != "xgb.DMatrix") {
+    stop("xgb.predict: second argument must be type xgb.DMatrix")
+  }
+  ret <- .Call("XGBoosterPredict_R", booster, dmat, as.integer(outputmargin))
+  return(ret)
+}
+# dump model
+xgb.dump <- function(booster, fname, fmap = "") {
+  if (class(booster) != "xgb.Booster") {
+    stop("xgb.dump: first argument must be type xgb.Booster")
+  }
+  if (typeof(fname) != "character"){
+    stop("xgb.dump: second argument must be type character")
+  }
+  .Call("XGBoosterDumpModel_R", booster, fname, fmap)
+  return(TRUE)
+}
+##--------------------------------------
+# the following are low level iteratively function, not needed
+# if you do not want to use them
+#---------------------------------------
+# iteratively update booster with dtrain
+xgb.iter.update <- function(booster, dtrain, iter) {
+  if (class(booster) != "xgb.Booster") {
+    stop("xgb.iter.update: first argument must be type xgb.Booster")
+  }
+  if (class(dtrain) != "xgb.DMatrix") {
+    stop("xgb.iter.update: second argument must be type xgb.DMatrix")
+  }
+  .Call("XGBoosterUpdateOneIter_R", booster, as.integer(iter), dtrain)
+  return(TRUE)
+}
+# iteratively update booster with customized statistics
+xgb.iter.boost <- function(booster, dtrain, gpair) {
+  if (class(booster) != "xgb.Booster") {
+    stop("xgb.iter.update: first argument must be type xgb.Booster")
+  }
+  if (class(dtrain) != "xgb.DMatrix") {
+    stop("xgb.iter.update: second argument must be type xgb.DMatrix")
+  }
+  .Call("XGBoosterBoostOneIter_R", booster, dtrain, gpair$grad, gpair$hess)
+  return(TRUE)
+}
+# iteratively evaluate one iteration
+xgb.iter.eval <- function(booster, watchlist, iter) {
+  if (class(booster) != "xgb.Booster") {
+    stop("xgb.eval: first argument must be type xgb.Booster")
+  }
+  if (typeof(watchlist) != "list") {
+    stop("xgb.eval: only accepts list of DMatrix as watchlist")
+  }
+  for (w in watchlist) {
+    if (class(w) != "xgb.DMatrix") {
+      stop("xgb.eval: watch list can only contain xgb.DMatrix")
+    }
+  }
+  evnames <- list()
+  if (length(watchlist) != 0) {
+    for (i in 1:length(watchlist)) {
+      w <- watchlist[i]
+      if (length(names(w)) == 0) {
+        stop("xgb.eval: name tag must be presented for every elements in watchlist")
+      }
+      evnames <- append(evnames, names(w))     
+    }
+  }
+  msg <- .Call("XGBoosterEvalOneIter_R", booster, as.integer(iter), watchlist, evnames)
+  return(msg)
+}

R-package/README.md

@@ -0,0 +1,3 @@
+This is subfolder for experimental version of R package
+Not yet ready
+

R-package/inst/examples/demo.R

@@ -0,0 +1,127 @@
+# load xgboost library
+require(xgboost)
+require(methods)
+
+# helper function to read libsvm format
+# this is very badly written, load in dense, and convert to sparse
+# use this only for demo purpose
+# adopted from https://github.com/zygmuntz/r-libsvm-format-read-write/blob/master/f_read.libsvm.r
+read.libsvm <- function(fname, maxcol) {
+  content <- readLines(fname)
+  nline <- length(content)
+  label <- numeric(nline)
+  mat <- matrix(0, nline, maxcol+1)
+  for (i in 1:nline) {
+    arr <- as.vector(strsplit(content[i], " ")[[1]])
+    label[i] <- as.numeric(arr[[1]])
+    for (j in 2:length(arr)) {
+      kv <- strsplit(arr[j], ":")[[1]]
+      # to avoid 0 index
+      findex <- as.integer(kv[1]) + 1
+      fvalue <- as.numeric(kv[2])
+      mat[i,findex] <- fvalue
+    }
+  }
+  mat <- as(mat, "sparseMatrix")
+  return(list(label=label, data=mat))
+}
+
+# test code here
+dtrain <- xgb.DMatrix("agaricus.txt.train")
+dtest <- xgb.DMatrix("agaricus.txt.test")
+param = list("bst:max_depth"=2, "bst:eta"=1, "silent"=1, "objective"="binary:logistic")
+watchlist <- list("eval"=dtest,"train"=dtrain)
+# training xgboost model
+bst <- xgb.train(param, dtrain, nround=2, watchlist=watchlist)
+# make prediction
+preds <- xgb.predict(bst, dtest)
+labels <- xgb.getinfo(dtest, "label")
+err <- as.numeric(sum(as.integer(preds > 0.5) != labels)) / length(labels)
+# print error rate
+print(paste("error=",err))
+
+# dump model
+xgb.dump(bst, "dump.raw.txt")
+# dump model with feature map
+xgb.dump(bst, "dump.nice.txt", "featmap.txt")
+
+# save dmatrix into binary buffer
+succ <- xgb.save(dtest, "dtest.buffer")
+# save model into file
+succ <- xgb.save(bst, "xgb.model")
+# load model and data in 
+bst2 <- xgb.Booster(modelfile="xgb.model")
+dtest2 <- xgb.DMatrix("dtest.buffer")
+preds2 <- xgb.predict(bst2, dtest2)
+# assert they are the same
+stopifnot(sum(abs(preds2-preds)) == 0)
+
+###
+# build dmatrix from sparseMatrix
+###
+print ('start running example of build DMatrix from R.sparseMatrix')
+csc <- read.libsvm("agaricus.txt.train", 126)
+label <- csc$label
+data <- csc$data
+dtrain <- xgb.DMatrix(data, info=list(label=label) )
+watchlist <- list("eval"=dtest,"train"=dtrain)
+bst <- xgb.train(param, dtrain, nround=2, watchlist=watchlist)
+
+###
+# build dmatrix from dense matrix
+###
+print ('start running example of build DMatrix from R.Matrix')
+mat = as.matrix(data)
+dtrain <- xgb.DMatrix(mat, info=list(label=label) )
+watchlist <- list("eval"=dtest,"train"=dtrain)
+bst <- xgb.train(param, dtrain, nround=2, watchlist=watchlist)
+
+###
+# advanced: cutomsized loss function
+# 
+print("start running example to used cutomized objective function")
+# 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("bst:max_depth" = 2, "bst:eta" = 1, "silent" =1)
+# user define objective function, given prediction, return gradient and second order gradient
+# this is loglikelihood loss
+logregobj <- function(preds, dtrain) {
+  labels <- xgb.getinfo(dtrain, "label")
+  preds <- 1.0 / (1.0 + exp(-preds))
+  grad <- preds - labels
+  hess <- preds * (1.0-preds)
+  return(list(grad=grad, hess=hess))
+}
+# user defined evaluation function, return a list(metric="metric-name", value="metric-value")
+# NOTE: when you do customized loss function, the default prediction value is margin
+# this may make buildin evalution metric not function properly
+# for example, we are doing logistic loss, the prediction is score before logistic transformation
+# the buildin 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 <- xgb.getinfo(dtrain, "label")
+  err <- as.numeric(sum(labels != (preds > 0.0))) / length(labels)
+  return(list(metric="error", value=err))
+}
+
+# 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, nround=2, watchlist, logregobj, evalerror)
+
+###
+# advanced: start from a initial base prediction
+#
+print ("start running example to start from a initial prediction")
+# specify parameters via map, definition are same as c++ version
+param = list("bst:max_depth"=2, "bst:eta"=1, "silent"=1, "objective"="binary:logistic")
+# train xgboost for 1 round
+bst <- xgb.train( param, dtrain, 1, watchlist )
+# 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 <- xgb.predict(bst, dtrain, outputmargin=TRUE)
+ptest <- xgb.predict(bst, dtest, outputmargin=TRUE)
+succ <- xgb.setinfo(dtrain, "base_margin", ptrain)
+succ <- xgb.setinfo(dtest, "base_margin", ptest)
+print ("this is result of running from initial prediction")
+bst <- xgb.train( param, dtrain, 1, watchlist )

R-package/inst/examples/featmap.txt

@@ -0,0 +1,126 @@
+0	cap-shape=bell	i
+1	cap-shape=conical	i
+2	cap-shape=convex	i
+3	cap-shape=flat	i
+4	cap-shape=knobbed	i
+5	cap-shape=sunken	i
+6	cap-surface=fibrous	i
+7	cap-surface=grooves	i
+8	cap-surface=scaly	i
+9	cap-surface=smooth	i
+10	cap-color=brown	i
+11	cap-color=buff	i
+12	cap-color=cinnamon	i
+13	cap-color=gray	i
+14	cap-color=green	i
+15	cap-color=pink	i
+16	cap-color=purple	i
+17	cap-color=red	i
+18	cap-color=white	i
+19	cap-color=yellow	i
+20	bruises?=bruises	i
+21	bruises?=no	i
+22	odor=almond	i
+23	odor=anise	i
+24	odor=creosote	i
+25	odor=fishy	i
+26	odor=foul	i
+27	odor=musty	i
+28	odor=none	i
+29	odor=pungent	i
+30	odor=spicy	i
+31	gill-attachment=attached	i
+32	gill-attachment=descending	i
+33	gill-attachment=free	i
+34	gill-attachment=notched	i
+35	gill-spacing=close	i
+36	gill-spacing=crowded	i
+37	gill-spacing=distant	i
+38	gill-size=broad	i
+39	gill-size=narrow	i
+40	gill-color=black	i
+41	gill-color=brown	i
+42	gill-color=buff	i
+43	gill-color=chocolate	i
+44	gill-color=gray	i
+45	gill-color=green	i
+46	gill-color=orange	i
+47	gill-color=pink	i
+48	gill-color=purple	i
+49	gill-color=red	i
+50	gill-color=white	i
+51	gill-color=yellow	i
+52	stalk-shape=enlarging	i
+53	stalk-shape=tapering	i
+54	stalk-root=bulbous	i
+55	stalk-root=club	i
+56	stalk-root=cup	i
+57	stalk-root=equal	i
+58	stalk-root=rhizomorphs	i
+59	stalk-root=rooted	i
+60	stalk-root=missing	i
+61	stalk-surface-above-ring=fibrous	i
+62	stalk-surface-above-ring=scaly	i
+63	stalk-surface-above-ring=silky	i
+64	stalk-surface-above-ring=smooth	i
+65	stalk-surface-below-ring=fibrous	i
+66	stalk-surface-below-ring=scaly	i
+67	stalk-surface-below-ring=silky	i
+68	stalk-surface-below-ring=smooth	i
+69	stalk-color-above-ring=brown	i
+70	stalk-color-above-ring=buff	i
+71	stalk-color-above-ring=cinnamon	i
+72	stalk-color-above-ring=gray	i
+73	stalk-color-above-ring=orange	i
+74	stalk-color-above-ring=pink	i
+75	stalk-color-above-ring=red	i
+76	stalk-color-above-ring=white	i
+77	stalk-color-above-ring=yellow	i
+78	stalk-color-below-ring=brown	i
+79	stalk-color-below-ring=buff	i
+80	stalk-color-below-ring=cinnamon	i
+81	stalk-color-below-ring=gray	i
+82	stalk-color-below-ring=orange	i
+83	stalk-color-below-ring=pink	i
+84	stalk-color-below-ring=red	i
+85	stalk-color-below-ring=white	i
+86	stalk-color-below-ring=yellow	i
+87	veil-type=partial	i
+88	veil-type=universal	i
+89	veil-color=brown	i
+90	veil-color=orange	i
+91	veil-color=white	i
+92	veil-color=yellow	i
+93	ring-number=none	i
+94	ring-number=one	i
+95	ring-number=two	i
+96	ring-type=cobwebby	i
+97	ring-type=evanescent	i
+98	ring-type=flaring	i
+99	ring-type=large	i
+100	ring-type=none	i
+101	ring-type=pendant	i
+102	ring-type=sheathing	i
+103	ring-type=zone	i
+104	spore-print-color=black	i
+105	spore-print-color=brown	i
+106	spore-print-color=buff	i
+107	spore-print-color=chocolate	i
+108	spore-print-color=green	i
+109	spore-print-color=orange	i
+110	spore-print-color=purple	i
+111	spore-print-color=white	i
+112	spore-print-color=yellow	i
+113	population=abundant	i
+114	population=clustered	i
+115	population=numerous	i
+116	population=scattered	i
+117	population=several	i
+118	population=solitary	i
+119	habitat=grasses	i
+120	habitat=leaves	i
+121	habitat=meadows	i
+122	habitat=paths	i
+123	habitat=urban	i
+124	habitat=waste	i
+125	habitat=woods	i

R-package/src/Makevars

@@ -0,0 +1,27 @@
+# _*_ mode: Makefile; _*_
+export CC  = gcc
+export CXX = g++
+
+# expose these flags to R CMD SHLIB
+PKG_CPPFLAGS = -O3 -Wno-unknown-pragmas  -DXGBOOST_CUSTOMIZE_ERROR_ -fopenmp -fPIC
+
+ifeq ($(no_omp),1)
+	PKG_CPPFLAGS += -D -DDISABLE_OPENMP 
+endif
+
+CXXOBJ= xgboost_wrapper.o xgboost_io.o
+OBJECTS= xgboost_R.o $(CXXOBJ)
+
+.PHONY: all clean
+all: $(SHLIB)
+$(SHLIB): $(OBJECTS)
+
+xgboost_wrapper.o: ../../wrapper/xgboost_wrapper.cpp
+xgboost_io.o: ../../src/io/io.cpp
+
+$(CXXOBJ) : 
+	$(CXX) -c $(PKG_CPPFLAGS) -o $@ $(firstword $(filter %.cpp %.c, $^) )
+
+clean:
+	rm -rf *.so *.o *~ *.dll
+

R-package/src/xgboost_R.cpp

@@ -0,0 +1,221 @@
+#include <vector>
+#include <string>
+#include <utility>
+#include <cstring>
+#include "xgboost_R.h"
+#include "../../wrapper/xgboost_wrapper.h"
+#include "../../src/utils/utils.h"
+#include "../../src/utils/omp.h"
+#include "../../src/utils/matrix_csr.h"
+
+using namespace xgboost;
+// implements error handling
+namespace xgboost {
+namespace utils {
+void HandleAssertError(const char *msg) {
+  error("%s", msg);
+}
+void HandleCheckError(const char *msg) {
+  error("%s", msg);
+}
+}  // namespace utils
+}  // namespace xgboost
+
+extern "C" {
+  void _DMatrixFinalizer(SEXP ext) {    
+    if (R_ExternalPtrAddr(ext) == NULL) return;
+    XGDMatrixFree(R_ExternalPtrAddr(ext));
+    R_ClearExternalPtr(ext);
+  }
+  SEXP XGDMatrixCreateFromFile_R(SEXP fname, SEXP silent) {
+    void *handle = XGDMatrixCreateFromFile(CHAR(asChar(fname)), asInteger(silent));
+    SEXP ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
+    R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
+    UNPROTECT(1);
+    return ret;
+  }
+  SEXP XGDMatrixCreateFromMat_R(SEXP mat, 
+                                SEXP missing) {
+    SEXP dim = getAttrib(mat, R_DimSymbol);
+    int nrow = INTEGER(dim)[0];
+    int ncol = INTEGER(dim)[1];    
+    double *din = REAL(mat);
+    std::vector<float> data(nrow * ncol);
+    #pragma omp parallel for schedule(static)
+    for (int i = 0; i < nrow; ++i) {
+      for (int j = 0; j < ncol; ++j) {
+        data[i * ncol +j] = din[i + nrow * j];
+      }
+    }
+    void *handle = XGDMatrixCreateFromMat(&data[0], nrow, ncol, asReal(missing));
+    SEXP ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
+    R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
+    UNPROTECT(1);
+    return ret;    
+  }
+  SEXP XGDMatrixCreateFromCSC_R(SEXP indptr,
+                                SEXP indices,
+                                SEXP data) {
+    const int *col_ptr = INTEGER(indptr);
+    const int *row_index = INTEGER(indices);
+    const double *col_data = REAL(data);
+    int ncol = length(indptr) - 1;
+    int ndata = length(data);
+    // transform into CSR format
+    std::vector<size_t> row_ptr;
+    std::vector< std::pair<unsigned, float> > csr_data;
+    utils::SparseCSRMBuilder< std::pair<unsigned,float> > builder(row_ptr, csr_data);
+    builder.InitBudget();
+    for (int i = 0; i < ncol; ++i) {
+      for (int j = col_ptr[i]; j < col_ptr[i+1]; ++j) {
+        builder.AddBudget(row_index[j]);
+      }
+    }
+    builder.InitStorage();
+    for (int i = 0; i < ncol; ++i) {
+      for (int j = col_ptr[i]; j < col_ptr[i+1]; ++j) {
+        builder.PushElem(row_index[j], std::make_pair(i, col_data[j]));
+      }
+    }
+    utils::Assert(csr_data.size() == static_cast<size_t>(ndata), "BUG CreateFromCSC");
+    std::vector<float> row_data(ndata);
+    std::vector<unsigned> col_index(ndata);
+    #pragma omp parallel for schedule(static)
+    for (int i = 0; i < ndata; ++i) {
+      col_index[i] = csr_data[i].first;
+      row_data[i] = csr_data[i].second;      
+    }
+    void *handle = XGDMatrixCreateFromCSR(&row_ptr[0], &col_index[0], &row_data[0], row_ptr.size(), ndata );
+    SEXP ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
+    R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
+    UNPROTECT(1);
+    return ret;
+  }
+  void XGDMatrixSaveBinary_R(SEXP handle, SEXP fname, SEXP silent) {
+    XGDMatrixSaveBinary(R_ExternalPtrAddr(handle),
+                        CHAR(asChar(fname)), asInteger(silent));
+  }
+  void XGDMatrixSetInfo_R(SEXP handle, SEXP field, SEXP array) {
+    int len = length(array);
+    const char *name = CHAR(asChar(field));
+    if (!strcmp("group", name)) {
+      std::vector<unsigned> vec(len);
+      #pragma omp parallel for schedule(static)      
+      for (int i = 0; i < len; ++i) {
+        vec[i] = static_cast<unsigned>(INTEGER(array)[i]);
+      }
+      XGDMatrixSetGroup(R_ExternalPtrAddr(handle), &vec[0], len);
+      return;
+    }
+    {
+      std::vector<float> vec(len);
+      #pragma omp parallel for schedule(static)
+      for (int i = 0; i < len; ++i) {
+        vec[i] = REAL(array)[i];
+      }
+      XGDMatrixSetFloatInfo(R_ExternalPtrAddr(handle), 
+                            CHAR(asChar(field)),
+                            &vec[0], len);
+    }
+  }
+  SEXP XGDMatrixGetInfo_R(SEXP handle, SEXP field) {
+    size_t olen;
+    const float *res = XGDMatrixGetFloatInfo(R_ExternalPtrAddr(handle),
+                                             CHAR(asChar(field)), &olen);
+    SEXP ret = PROTECT(allocVector(REALSXP, olen));
+    for (size_t i = 0; i < olen; ++i) {
+      REAL(ret)[i] = res[i];
+    }
+    UNPROTECT(1);
+    return ret;
+  }
+  // functions related to booster
+  void _BoosterFinalizer(SEXP ext) {    
+    if (R_ExternalPtrAddr(ext) == NULL) return;
+    XGBoosterFree(R_ExternalPtrAddr(ext));
+    R_ClearExternalPtr(ext);
+  }
+  SEXP XGBoosterCreate_R(SEXP dmats) {
+    int len = length(dmats);
+    std::vector<void*> dvec;
+    for (int i = 0; i < len; ++i){
+      dvec.push_back(R_ExternalPtrAddr(VECTOR_ELT(dmats, i)));
+    }
+    void *handle = XGBoosterCreate(&dvec[0], dvec.size());
+    SEXP ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
+    R_RegisterCFinalizerEx(ret, _BoosterFinalizer, TRUE);
+    UNPROTECT(1);
+    return ret;
+  }
+  void XGBoosterSetParam_R(SEXP handle, SEXP name, SEXP val) {
+    XGBoosterSetParam(R_ExternalPtrAddr(handle),
+                      CHAR(asChar(name)),
+                      CHAR(asChar(val)));
+  }
+  void XGBoosterUpdateOneIter_R(SEXP handle, SEXP iter, SEXP dtrain) {
+    XGBoosterUpdateOneIter(R_ExternalPtrAddr(handle),
+                           asInteger(iter),
+                           R_ExternalPtrAddr(dtrain));
+  }
+  void XGBoosterBoostOneIter_R(SEXP handle, SEXP dtrain, SEXP grad, SEXP hess) {
+    utils::Check(length(grad) == length(hess), "gradient and hess must have same length");
+    int len = length(grad);
+    std::vector<float> tgrad(len), thess(len);
+    #pragma omp parallel for schedule(static)
+    for (int j = 0; j < len; ++j) {
+      tgrad[j] = REAL(grad)[j];
+      thess[j] = REAL(hess)[j];
+    }
+    XGBoosterBoostOneIter(R_ExternalPtrAddr(handle),
+                          R_ExternalPtrAddr(dtrain),
+                          &tgrad[0], &thess[0], len);
+  }
+  SEXP XGBoosterEvalOneIter_R(SEXP handle, SEXP iter, SEXP dmats, SEXP evnames) {
+    utils::Check(length(dmats) == length(evnames), "dmats and evnams must have same length");
+    int len = length(dmats);
+    std::vector<void*> vec_dmats;
+    std::vector<std::string> vec_names;
+    std::vector<const char*> vec_sptr;
+    for (int i = 0; i < len; ++i) {
+      vec_dmats.push_back(R_ExternalPtrAddr(VECTOR_ELT(dmats, i)));
+      vec_names.push_back(std::string(CHAR(asChar(VECTOR_ELT(evnames, i)))));
+    }
+    for (int i = 0; i < len; ++i) {
+      vec_sptr.push_back(vec_names[i].c_str());
+    }
+    return mkString(XGBoosterEvalOneIter(R_ExternalPtrAddr(handle),
+                                         asInteger(iter),
+                                         &vec_dmats[0], &vec_sptr[0], len));
+  }
+  SEXP XGBoosterPredict_R(SEXP handle, SEXP dmat, SEXP output_margin) {
+    size_t olen;
+    const float *res = XGBoosterPredict(R_ExternalPtrAddr(handle),
+                                        R_ExternalPtrAddr(dmat),
+                                        asInteger(output_margin),
+                                        &olen);
+    SEXP ret = PROTECT(allocVector(REALSXP, olen));
+    for (size_t i = 0; i < olen; ++i) {
+      REAL(ret)[i] = res[i];
+    }
+    UNPROTECT(1);
+    return ret;
+  }
+  void XGBoosterLoadModel_R(SEXP handle, SEXP fname) {
+    XGBoosterLoadModel(R_ExternalPtrAddr(handle), CHAR(asChar(fname)));
+  }
+  void XGBoosterSaveModel_R(SEXP handle, SEXP fname) {
+    XGBoosterSaveModel(R_ExternalPtrAddr(handle), CHAR(asChar(fname)));
+  }
+  void XGBoosterDumpModel_R(SEXP handle, SEXP fname, SEXP fmap) {
+    size_t olen;
+    const char **res = XGBoosterDumpModel(R_ExternalPtrAddr(handle),
+                                          CHAR(asChar(fmap)),
+                                          &olen);
+    FILE *fo = utils::FopenCheck(CHAR(asChar(fname)), "w");
+    for (size_t i = 0; i < olen; ++i) {
+      fprintf(fo, "booster[%lu]:\n", i);
+      fprintf(fo, "%s", res[i]);
+    }
+    fclose(fo);
+  }
+}

R-package/src/xgboost_R.h

@@ -0,0 +1,124 @@
+#ifndef XGBOOST_WRAPPER_R_H_
+#define XGBOOST_WRAPPER_R_H_
+/*!
+ * \file xgboost_wrapper_R.h
+ * \author Tianqi Chen
+ * \brief R wrapper of xgboost
+ */
+extern "C" {
+#include <Rinternals.h>
+}
+
+extern "C" {
+  /*!
+   * \brief load a data matrix 
+   * \param fname name of the content
+   * \param silent whether print messages
+   * \return a loaded data matrix
+   */
+  SEXP XGDMatrixCreateFromFile_R(SEXP fname, SEXP silent);
+  /*!
+   * \brief create matrix content from dense matrix
+   * This assumes the matrix is stored in column major format
+   * \param data R Matrix object
+   * \param missing which value to represent missing value
+   * \return created dmatrix
+   */
+  SEXP XGDMatrixCreateFromMat_R(SEXP mat, 
+                                SEXP missing);
+  /*! 
+   * \brief create a matrix content from CSC format
+   * \param indptr pointer to column headers
+   * \param indices row indices
+   * \param data content of the data
+   * \return created dmatrix
+   */
+  SEXP XGDMatrixCreateFromCSC_R(SEXP indptr,
+                                SEXP indices,
+                                SEXP data);
+  /*!
+   * \brief load a data matrix into binary file
+   * \param handle a instance of data matrix
+   * \param fname file name
+   * \param silent print statistics when saving
+   */
+  void XGDMatrixSaveBinary_R(SEXP handle, SEXP fname, SEXP silent);
+  /*!
+   * \brief set information to dmatrix
+   * \param handle a instance of data matrix
+   * \param field field name, can be label, weight
+   * \param array pointer to float vector
+   */
+  void XGDMatrixSetInfo_R(SEXP handle, SEXP field, SEXP array);
+  /*!
+   * \brief get info vector from matrix
+   * \param handle a instance of data matrix
+   * \param field field name
+   * \return info vector
+   */  
+  SEXP XGDMatrixGetInfo_R(SEXP handle, SEXP field);
+  /*! 
+   * \brief create xgboost learner 
+   * \param dmats a list of dmatrix handles that will be cached
+   */  
+  SEXP XGBoosterCreate_R(SEXP dmats);
+  /*! 
+   * \brief set parameters 
+   * \param handle handle
+   * \param name  parameter name
+   * \param val value of parameter
+   */
+  void XGBoosterSetParam_R(SEXP handle, SEXP name, SEXP val);
+  /*! 
+   * \brief update the model in one round using dtrain
+   * \param handle handle
+   * \param iter current iteration rounds
+   * \param dtrain training data
+   */
+  void XGBoosterUpdateOneIter_R(SEXP ext, SEXP iter, SEXP dtrain);
+  /*!
+   * \brief update the model, by directly specify gradient and second order gradient,
+   *        this can be used to replace UpdateOneIter, to support customized loss function
+   * \param handle handle
+   * \param dtrain training data
+   * \param grad gradient statistics
+   * \param hess second order gradient statistics
+   */
+  void XGBoosterBoostOneIter_R(SEXP handle, SEXP dtrain, SEXP grad, SEXP hess);
+  /*!
+   * \brief get evaluation statistics for xgboost
+   * \param handle handle
+   * \param iter current iteration rounds
+   * \param dmats list of handles to dmatrices
+   * \param evname name of evaluation
+   * \return the string containing evaluation stati
+   */
+  SEXP XGBoosterEvalOneIter_R(SEXP handle, SEXP iter, SEXP dmats, SEXP evnames);
+  /*!
+   * \brief make prediction based on dmat
+   * \param handle handle
+   * \param dmat data matrix
+   * \param output_margin whether only output raw margin value
+   */
+  SEXP XGBoosterPredict_R(SEXP handle, SEXP dmat, SEXP output_margin);
+  /*!
+   * \brief load model from existing file
+   * \param handle handle
+   * \param fname file name
+   */
+  void XGBoosterLoadModel_R(SEXP handle, SEXP fname);
+  /*!
+   * \brief save model into existing file
+   * \param handle handle
+   * \param fname file name
+   */    
+  void XGBoosterSaveModel_R(SEXP handle, SEXP fname);
+  /*!
+   * \brief dump model into text file 
+   * \param handle handle
+   * \param fname file name of model that can be dumped into
+   * \param fmap  name to fmap can be empty string
+   */
+  void XGBoosterDumpModel_R(SEXP handle, SEXP fname, SEXP fmap);
+};
+#endif  // XGBOOST_WRAPPER_R_H_