version 4.7-1.2

Author: andyliaw-mrk

DESCRIPTION

@@ -1,16 +1,28 @@
 Package: randomForest
-Title: Breiman and Cutler's Random Forests for Classification and
+Title: Breiman and Cutlers Random Forests for Classification and
         Regression
-Version: 4.7-1.1
+Version: 4.7-1.2
 Date: 2022-01-24
 Depends: R (>= 4.1.0), stats
 Suggests: RColorBrewer, MASS
-Author: Fortran original by Leo Breiman and Adele Cutler, R port by Andy Liaw and Matthew Wiener.
+Authors@R: c(person("Leo", "Breiman", role = "aut",
+                    comment = "Fortran original"),
+             person("Adele", "Cutler", role = "aut",
+	            comment = "Fortran original"),
+             person("Andy", "Liaw", role = c("aut", "cre"),
+                    email = "[email protected]",
+		    comment = "R port"),
+             person("Matthew", "Wiener", role = "aut",
+	            comment = "R port"))
 Description: Classification and regression based on a forest of trees using random inputs, based on Breiman (2001) <DOI:10.1023/A:1010933404324>.
-Maintainer: Andy Liaw <[email protected]>
 License: GPL (>= 2)
 URL: https://www.stat.berkeley.edu/~breiman/RandomForests/
 NeedsCompilation: yes
-Packaged: 2022-05-23 08:06:39 UTC; hornik
+Packaged: 2024-09-22 08:30:17 UTC; hornik
 Repository: CRAN
-Date/Publication: 2022-05-23 08:27:49 UTC
+Date/Publication: 2024-09-22 09:14:44 UTC
+Author: Leo Breiman [aut] (Fortran original),
+  Adele Cutler [aut] (Fortran original),
+  Andy Liaw [aut, cre] (R port),
+  Matthew Wiener [aut] (R port)
+Maintainer: Andy Liaw <[email protected]>

MD5

@@ -1,6 +1,6 @@
 393a5ca445f6965873eca0259a17f833 *COPYING
-c7fb0874404c16675bf24630a11e0748 *DESCRIPTION
-978decaa39e75944d88ab2dbe33a726a *NAMESPACE
+a2729aa6dee937053f616b6730882b3a *DESCRIPTION
+47f0c68ce5460bac806e587645925c50 *NAMESPACE
 a025b98c25cb7761c0dbf3f421618a4d *R/MDSplot.R
 eae0c348160c0e1f5c5140169c7610be *R/classCenter.R
 1fcc48ac21e6e66f22dcc5a02cd722d1 *R/combine.R
@@ -25,16 +25,17 @@ e695b3cfc07facf54856bf366870e360 *R/tuneRF.R
 143dac20c44a22e3bd132cad4385e90e *R/varImpPlot.R
 18f94384910772d7babc8354b4ebae17 *R/varUsed.R
 a54ba14b0cb6cc15e4b7687ead9a2bf9 *R/zzz.R
-a7f95178c626d8f7830768e75f0961db *data/imports85.rda
-980aa22e77a4fccedc05d253b65645be *inst/CITATION
+aa5e5a2cbfaea3d9b6cdbe378ac48cee *build/partial.rdb
+c2c56a849b187e54307470cfa2b1da3d *data/imports85.rda
+aad37847b2fb0ead0b6f991ba9185c95 *inst/CITATION
 9e00469f24af18d37dfe36b1ff57654e *inst/NEWS
 b9b69f61e9ed079e1d9d84df6360d522 *man/MDSplot.Rd
 4fcbc72dd2475ff32f5a348bfa71af41 *man/classCenter.Rd
 e25dffb14a3dc288fda639b762757595 *man/combine.Rd
 3e2a6b978a69049e7ea7dc7a306c92fd *man/getTree.Rd
 cd05a7ccb5857db3a60da26503a22ef9 *man/grow.Rd
 3a63f7f925c1b4ca1bf805c5c7eca4f0 *man/importance.Rd
-3720f27c0c909c615d6d7f99826e1d3b *man/imports85.Rd
+110ee15f5d64c221b3995703b18131a1 *man/imports85.Rd
 c901b3cb1b2ad299574e76e5d80859ed *man/margin.Rd
 288befa4e77e572480dab78b686411f0 *man/na.roughfix.Rd
 8ecd590e5b87afb8e84058adea3f8415 *man/outlier.Rd
@@ -49,11 +50,11 @@ ac3d31008c56add22352b609f8cea599 *man/rfcv.Rd
 e7180386828b0d248c172a03915fc187 *man/tuneRF.Rd
 4ef6a1e04cf7e13580922c4f5769de09 *man/varImpPlot.Rd
 1638c2a6ba3ef89fe83321470c6d9386 *man/varUsed.Rd
-8ddc24e3050c344581787ce7ed10d7a5 *src/classTree.c
+6c450c23429e0fd0ab6ce1fe3b31ed89 *src/classTree.c
 adde4a205871318b538e448e6b8db090 *src/init.c
-71d6ddd355af9e2628304b53bcfde18c *src/regTree.c
-65214356bb8b82c817dc50d4b2751c91 *src/regrf.c
-c732a558584798d8d7574710060a2c70 *src/rf.c
+e3dbd6e39a262c4eb9f442d59f8d2b9b *src/regTree.c
+9cd55649aa061ba0bd4851fbdb3d210e *src/regrf.c
+ff7098e03cb8044f9eff4e459aa3ae5b *src/rf.c
 eb0ecd114bb31a940b2c131bd5a111c4 *src/rf.h
 a7656a9f81dafdc4fdf8621dbba47979 *src/rfsub.f
-6878639f320be3254a38999a26d5380e *src/rfutils.c
+ebd0c55f9255ab5d2c499730201fda52 *src/rfutils.c

NAMESPACE

@@ -15,6 +15,11 @@ S3method(importance, randomForest)
 S3method(outlier, randomForest)
 S3method(outlier, default)
 
+S3method(grow, default)
+S3method(importance, default)
+S3method(margin, default)
+S3method(partialPlot, default)
+
 S3method(randomForest, formula)
 S3method(randomForest, default)
 S3method(rfImpute, formula)

build/partial.rdb

@@ -1,18 +1,11 @@
-citHeader("To cite randomForest in publications use:")
-
-citEntry(entry="Article",
+bibentry("Article",
          title = "Classification and Regression by randomForest",
-         author = personList(person(family="Liaw", given="Andy"),
-	                     person(family="Wiener", given="Matthew")),
+         author = c(person(family="Liaw", given="Andy"),
+	            person(family="Wiener", given="Matthew")),
 	 journal = "R News",
          year         = "2002",
          volume       = "2",
          number       = "3",
          pages        = "18-22",
-         url          = "https://CRAN.R-project.org/doc/Rnews/",
-
-         textVersion =
-         paste("A. Liaw and M. Wiener (2002). ",
-               "Classification and Regression by randomForest. ",
-               "R News 2(3), 18--22.",
-               sep=""))
+         url          = "https://CRAN.R-project.org/doc/Rnews/"
+         )

data/imports85.rda

@@ -33,7 +33,7 @@ data(imports85)
   Auto Manuals, Insurance Services Office, and Insurance Collision
   Report, Insurance Institute for Highway Safety.
 
-  The original data is at \url{http://www.ics.uci.edu/~mlearn/MLSummary.html}.
+  The original data is at \doi{10.24432/C5B01C}.
 }
 \references{
   1985 Model Import Car and Truck Specifications, 1985 Ward's Automotive
@@ -62,4 +62,4 @@ numDoors.rf <- randomForest(numOfDoors ~ ., imp85, do.trace=10, ntree=100)
 print(numDoors.rf)
 }
 \author{Andy Liaw}
-\keyword{datasets}
+\keyword{datasets}

inst/CITATION

@@ -3,7 +3,7 @@
 
    This program is free software; you can redistribute it and/or
    modify it under the terms of the GNU General Public License
-   as published by the Free Software Foundation; either version 2
+   as published by the R_Free Software Foundation; either version 2
    of the License, or (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
@@ -305,7 +305,7 @@ void F77_NAME(catmax)(double *parentDen, double *tclasscat,
     int j, k, n, icat[MAX_CAT], nsplit;
     double leftNum, leftDen, rightNum, decGini, *leftCatClassCount;
 
-    leftCatClassCount = (double *) Calloc(*nclass, double);
+    leftCatClassCount = (double *) R_Calloc(*nclass, double);
     *nhit = 0;
     nsplit = *lcat > *ncmax ?
         *ncsplit : (int) pow(2.0, (double) *lcat - 1) - 1;
@@ -348,7 +348,7 @@ void F77_NAME(catmax)(double *parentDen, double *tclasscat,
             *catsp = *lcat > *ncmax ? pack(*lcat, icat) : n + 1;
         }
     }
-    Free(leftCatClassCount);
+    R_Free(leftCatClassCount);
 }
 
 
@@ -424,7 +424,7 @@ void predictClassTree(double *x, int n, int mdim, int *treemap,
 
     /* decode the categorical splits */
     if (maxcat > 1) {
-        cbestsplit = (int *) Calloc(maxcat * treeSize, int);
+        cbestsplit = (int *) R_Calloc(maxcat * treeSize, int);
         zeroInt(cbestsplit, maxcat * treeSize);
         for (i = 0; i < treeSize; ++i) {
             if (nodestatus[i] != NODE_TERMINAL) {
@@ -458,5 +458,5 @@ void predictClassTree(double *x, int n, int mdim, int *treemap,
 		jts[i] = nodeclass[k];
 		nodex[i] = k + 1;
     }
-    if (maxcat > 1) Free(cbestsplit);
+    if (maxcat > 1) R_Free(cbestsplit);
 }

man/imports85.Rd

@@ -3,7 +3,7 @@
 
    This program is free software; you can redistribute it and/or
    modify it under the terms of the GNU General Public License
-   as published by the Free Software Foundation; either version 2
+   as published by the R_Free Software Foundation; either version 2
    of the License, or (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
@@ -35,16 +35,16 @@ void regTree(double *x, double *y, int mdim, int nsample, int *lDaughter,
   int ndstart, ndend, leftChildLastDataPoint, currentNodeCount, splitResult, msplit;
   double label, sumOfSquares, nodeMean, decsplit, ubest, sumOfNodeData;
 
-  nodestart = (int *) Calloc(numNodes, int);
-  numPointsInEachNode   = (int *) Calloc(numNodes, int);
+  nodestart = (int *) R_Calloc(numNodes, int);
+  numPointsInEachNode   = (int *) R_Calloc(numNodes, int);
 
   /* initialize some arrays for the tree */
   zeroInt(nodestatus, numNodes);
   zeroInt(nodestart, numNodes);
   zeroInt(numPointsInEachNode, numNodes);
   zeroDouble(nodeMeans, numNodes);
 
-  rowIndices = (int *) Calloc(nsample, int);
+  rowIndices = (int *) R_Calloc(nsample, int);
   for (i = 1; i <= nsample; ++i){
     rowIndices[i-1] = i;
   }
@@ -164,9 +164,9 @@ void regTree(double *x, double *y, int mdim, int nsample, int *lDaughter,
       nodestatus[k] = NODE_TERMINAL;
     }
   }
-  Free(nodestart);
-  Free(rowIndices);
-  Free(numPointsInEachNode);
+  R_Free(nodestart);
+  R_Free(rowIndices);
+  R_Free(numPointsInEachNode);
 }
 
 /*
@@ -181,13 +181,13 @@ void findBestSplit(double *x, int *jdex, double *y, int mdim, int nsample,
   int i, j, kv, l, *varIndices, *ncase;
   double *xt, *ut, *v, *yl, sumcat[MAX_CAT], avcat[MAX_CAT], tavcat[MAX_CAT], valueAtBestSplit;
   double crit, bestSplitForAllVariables, bestSplitWithinVariable, suml, sumr, d, critParent;
-  /*Calloc is different from calloc, r handles memory allocation instead of os*/
-  ut = (double *) Calloc(nsample, double);
-  xt = (double *) Calloc(nsample, double);
-  v  = (double *) Calloc(nsample, double);
-  yl = (double *) Calloc(nsample, double);
-  varIndices  = (int *) Calloc(mdim, int);
-  ncase = (int *) Calloc(nsample, int);
+  /*R_Calloc is different from calloc, r handles memory allocation instead of os*/
+  ut = (double *) R_Calloc(nsample, double);
+  xt = (double *) R_Calloc(nsample, double);
+  v  = (double *) R_Calloc(nsample, double);
+  yl = (double *) R_Calloc(nsample, double);
+  varIndices  = (int *) R_Calloc(mdim, int);
+  ncase = (int *) R_Calloc(nsample, int);
   zeroDouble(avcat, MAX_CAT);
   zeroDouble(tavcat, MAX_CAT);
 
@@ -346,12 +346,12 @@ void findBestSplit(double *x, int *jdex, double *y, int mdim, int nsample,
     }
   } else *jstat = NODE_TERMINAL;
 
-  Free(ncase);
-  Free(varIndices);
-  Free(v);
-  Free(yl);
-  Free(xt);
-  Free(ut);
+  R_Free(ncase);
+  R_Free(varIndices);
+  R_Free(v);
+  R_Free(yl);
+  R_Free(xt);
+  R_Free(ut);
 }
 
 /*====================================================================*/
@@ -365,7 +365,7 @@ void predictRegTree(double *x, int nsample, int mdim,
 
   /* decode the categorical splits */
   if (maxcat > 1) {
-    cbestsplit = (int *) Calloc(maxcat * treeSize, int);
+    cbestsplit = (int *) R_Calloc(maxcat * treeSize, int);
     zeroInt(cbestsplit, maxcat * treeSize);
     for (i = 0; i < treeSize; ++i) {
       if (nodestatus[i] != NODE_TERMINAL && cat[splitVar[i] - 1] > 1) {
@@ -398,5 +398,5 @@ void predictRegTree(double *x, int nsample, int mdim,
     ypred[i] = nodepred[k];
     nodex[i] = k + 1;
   }
-  if (maxcat > 1) Free(cbestsplit);
+  if (maxcat > 1) R_Free(cbestsplit);
 }

src/classTree.c

@@ -3,7 +3,7 @@
 
    This program is free software; you can redistribute it and/or
    modify it under the terms of the GNU General Public License
-   as published by the Free Software Foundation; either version 2
+   as published by the R_Free Software Foundation; either version 2
    of the License, or (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
@@ -144,7 +144,7 @@ void regRF(double *x, double *y, int *useweights, double *weights, int *xdim, in
     /*************************************
      * Start the loop over trees.
      *************************************/
-    int *sampledIndices = (int*)Calloc(*sampsize,int);
+    int *sampledIndices = (int*)R_Calloc(*sampsize,int);
     zeroInt(sampledIndices, *sampsize);
     for (j = 0; j < *nTree; ++j) {
 		idx = keepF ? j * *nrnodes : 0;

src/regTree.c

@@ -3,7 +3,7 @@ Copyright (C) 2001-2012 Leo Breiman, Adele Cutler and Merck & Co., Inc.
 
 This program is free software; you can redistribute it and/or
 modify it under the terms of the GNU General Public License
-as published by the Free Software Foundation; either version 2
+as published by the R_Free Software Foundation; either version 2
 of the License, or (at your option) any later version.
 
 This program is distributed in the hope that it will be useful,
@@ -12,7 +12,7 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
 
 You should have received a copy of the GNU General Public License
-along with this program; if not, write to the Free Software
+along with this program; if not, write to the R_Free Software
 Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 
 C driver for Breiman & Cutler's random forest code.

src/regrf.c

@@ -3,7 +3,7 @@
 
    This program is free software; you can redistribute it and/or
    modify it under the terms of the GNU General Public License
-   as published by the Free Software Foundation; either version 2
+   as published by the R_Free Software Foundation; either version 2
    of the License, or (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
@@ -64,8 +64,8 @@ void makeA(double *x, const int mdim, const int nsample, int *cat, int *a,
     int i, j, n1, n2, *index;
     double *v;
 
-    v     = (double *) Calloc(nsample, double);
-    index = (int *) Calloc(nsample, int);
+    v     = (double *) R_Calloc(nsample, double);
+    index = (int *) R_Calloc(nsample, int);
 
     for (i = 0; i < mdim; ++i) {
         if (cat[i] == 1) { /* numerical predictor */
@@ -92,8 +92,8 @@ void makeA(double *x, const int mdim, const int nsample, int *cat, int *a,
                 a[i + j*mdim] = (int) x[i + j * mdim];
         }
     }
-    Free(index);
-    Free(v);
+    R_Free(index);
+    R_Free(v);
 }
 
 
@@ -185,7 +185,7 @@ void permuteOOB(int m, double *x, int *in, int nsample, int mdim) {
     double *tp, tmp;
     int i, last, k, nOOB = 0;
 
-    tp = (double *) Calloc(nsample, double);
+    tp = (double *) R_Calloc(nsample, double);
 
     for (i = 0; i < nsample; ++i) {
 		/* make a copy of the OOB part of the data into tp (for permuting) */
@@ -212,7 +212,7 @@ void permuteOOB(int m, double *x, int *in, int nsample, int mdim) {
             nOOB++;
 		}
     }
-    Free(tp);
+    R_Free(tp);
 }
 
 /* Compute proximity. */
@@ -310,7 +310,7 @@ void sampleDataRows(int populationSize, int sampleSize, int useWeights,
 void sampleWithReplacementWithWeights(int sampleSize, int populationSize, double *weights, int *sampledIndices) {
     int mflag = 0;
     int numBoundaries = populationSize + 1;
-    double *boundaries = (double*)Calloc(numBoundaries, double);
+    double *boundaries = (double*)R_Calloc(numBoundaries, double);
     calculateBoundaries(weights, boundaries, populationSize, numBoundaries);
 
     double sample;
@@ -331,14 +331,14 @@ void sampleWithoutReplacementWithWeights(int sampleSize, int populationSize, dou
     }*/
     int mflag = 0;
     int numBoundaries = populationSize + 1;
-    double *weightsForTree = (double*)Calloc(populationSize, double);
+    double *weightsForTree = (double*)R_Calloc(populationSize, double);
 
     /*copy over weights to array so we don't mess with original weights when removing them*/
     for(int i = 0; i < populationSize; i++){
         weightsForTree[i] = weights[i];
     }
-    double *boundaries = (double*)Calloc(numBoundaries, double);
-    int *populationTaken = (int*)Calloc(populationSize, int);
+    double *boundaries = (double*)R_Calloc(numBoundaries, double);
+    int *populationTaken = (int*)R_Calloc(populationSize, int);
     zeroInt(populationTaken, populationSize);
     calculateBoundaries(weightsForTree, boundaries, populationSize, numBoundaries);
     int first;
@@ -365,7 +365,7 @@ void sampleWithReplacement(int sampleSize, int populationSize, int *sampledIndic
 }
 
 void sampleWithoutReplacement(int sampleSize, int populationSize, int *sampledIndices) {
-    int *indices = (int*)Calloc(populationSize, int);
+    int *indices = (int*)R_Calloc(populationSize, int);
     for(int i = 0; i < populationSize; ++i) {
         indices[i] = i;
     }