NEWS

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randomForest 4.7-1 (2022-02-03)

• The long-standing wishlist item of case weights (used only in sampling) is now available (thanks to urging from Robert Tishirani and implementation by Ethan Liaw).

randomForest 4.6-14 (2018-03-25)

• Native routines are now reigstered.

randomForest 4.6-13

• The tie-breaking mechanisms in various places were not implemented correctly. (Thanks to Adele Cutler and Susan Durham for reporting!)
• In unsupervised mode, the synthetic data were generated without updating the index matrix that trees actually operate on.
• In rfcv(), the importance measures were taken from the first column of the $importance component of the randomForest object. Now corrected to use importance(..., type=1).
• Maximum tree size was computed incorrectly, leading to possibly smaller than maxinum possible sized trees grown.
• In classification code, splits on categorical variables with >=32 levels were not encoded correctly.
• Memory usage increase due to .C(..., DUP=FALSE) no longer being supported. Work is underway to transition to .Call() to reduce memory usage.

randomForest 4.6-12 (2015-10-07)

• The "inbag" component of the randomForest object now records the number of times an observation is included in the bootstrap sample, instead of just indicating whether it is included or not.
• The "ncat" component of the "forest" component of the randomForest object now always has names that are the column names of x.
• The "inbag" component is combined properly now in the combine() function.
• Housekeeping: Cleaned up the DESCRIPTION, NAMESPACE, and URLs in help files.

randomForest 4.6-10 (2014-07-17)

• Fixed bugs introduced in 4.6-8 and 4.6-9. Levels for ordered factors in predictors are no longer checked for consistency between training and test data in predict.randomForest(). In 4.6-9 the response is mean centered before running the algorithm (for regression), but the mean was not added back in the $y component of the return object from randomForest().

randomForest 4.6-9

• Categorical predictors are allowed to have up to 53 categories now.

randomForest 4.6-8

• There was a bug in the handling of ordered factors in randomForest.formula(). (Reported by Barry Rawlingson.)
• Changed randomForest.formula() and predict.randomForest() so that predict() without newdata when na.action=na.exclude pads the output with NAs to match the rows in the original data (suggested by Barry Rawlingson.).
• There was a long standing bug in randomForest(..., proximity=TRUE, oob.prox=FALSE) in regression mode. (Thanks to Stefano Romano for the report.)

randomForest 4.6-6 (2012-01-06)

• In randomForest(), proximity matrix is not computed correctly if oob.prox=TRUE. (Thanks to Adele Cutler for the report!)
• In rfcv(), changed the sample-splitting for regression to handle cases when there are many ties in the data.
• The calculation of importanceSD for classification was missing a divisor. (Thanks to Abhishek Jaiantilal for the report.) ? The simulated data in unsupervised randomForest() were not in the right range. (Thanks to Abhishek Jaiantilal for the report.)
• In rfImpute(), padded 1e-8 to the division by sum of proximities to avoid division by 0.
• Some R code clean up to keep R CMD check happy (complete argument names).
• Fixed yet another bug in checking for missing classes in the in-bag sample.

randomForest 4.6-5 (2012-01-04)

• Minor bug fix for drawing samples in classification that was introduced in 4.6-4. (Thanks to Joran Elias for reporting.)

randomForest 4.6-4 (2011-12-20)

• Changed the error condition added in 4.6-3 to the case when there are fewer than two classes present in the in-bag sample.

randomForest 4.6-3 (2011-12-16)

• Fixed bugs in the tie-breaking code in various places. (Thanks to Abhishek Jaiantilal and Nathan Longbotham for the report and Abhishek for the fix.)
• Throw error if some class has no data after 10 sampling attempts in classification. (Thanks to Abhishek Jaiantilal for the report.)

randomForest 4.6-2 (2010-12-20)

• Part of the enhancement in 4.5-37 causes segfault in R-2.12.x. That part has been reverted to the older code for the time being while the problem is investigated further.

randomForest 4.6-1 (2010-12-18)

• The package now includes the rfcv() function for feature selection. See the reference in the help page for details.
• predict.randomForest() was not retaining names of observations in some cases.

randomForest 4.5-37

• Many repeated calls to predict.randomForest() should run faster, thanks to Philip Pham and Rory Martin who pointed out some unnecessary overhead.

randomForest 4.5-36 (2010-07-25)

• outlier() now works when the input matrix to randomForest() has no row names. (Reported by Rau Carrio Gaspar.)
• na.roughfix() is now much faster on some data (fixed based on idea from Hadley Wickham; problem reported by Mike Williamson.)
• Corrected typos in the description of categorical splits in ?getTree.

randomForest 4.5-35 (2010-06-21)

• Fixed an error in partialPlot.randomForest(). Now the partial dependence plots for classification data should be more sensible. (Thanks to Adele Cutler for the bug report and patch.)
• Re-worded part of the help pages regarding variable importance calculation.

randomForest 4.5-34 (2009-12-06)

• Fixed infinite loop when randomForest() is called with non-null maxnodes.
• Fixed a bug in margin.default() that gave nonsensical results.

randomForest 4.5-33 (2009-10-18)

• Fixed a _long standing_ bug (existed since the original Fortran) in randomForest(): If importance=TRUE and proximity=TRUE, the proximity matrix returned is incorrect. Those computed with importance=FALSE, or with predict.randomForest(..., proximity=TRUE) are correct.

randomForest 4.5-32 (2009-10-16)

• Fixed a bug in predict.randomForest(..., predict.all=TRUE) introduced in 4.5-31. Added examples in ?predict.randomForest for the options.

randomForest 4.5-31 (2009-10-15)

• Added a new option ‘maxnodes’ in randomForest() that limits the size of trees.
• margin() is now generic with a method for randomForest objects.
• Fixed the help page for getTree() about how data are split on numeric variables (‘<=’ instead of ‘<’).
• Fixed predict.randomForest() so that if the randomForest object is of type "regression" and built from the formula interface and newdata contains NAs, NAs are returned in the corresponding positions (instead of being dropped altogether).

randomForest 4.5-30 (2009-02-26)

• In regression, cases that had not been out-of-bag now gets NA as prediction (as in classification).

randomForest 4.5-29

• Fixed a couple of benign errors in help pages spotted by the new Rd parser.

randomForest 4.5-28 (2008-10-16)

• randomForest() would segfault if there are 32-level factors among the predictor variables.

randomForest 4.5-27 (2008-09-12)

• Fixed handling of ordered factors in predict.randomForest().

randomForest 4.5-26 (2008-09-12)

• Fix formula parsing so use of functions in formula won't trigger errors.
• predict.randomForest() did not work when given a matrix without column names as the newdata.

randomForest 4.5-25 (2008-04-21)

• In regression, the out-of-bag estimate of MSE and R-squared for the first few trees (for which not all observations have been OOB yet), were computed wrong, leading to gross over-estimates of MSEs for the first few trees. This did not affect the final MSE and R-squared for the whole forest; i.e., the first few elements of the ‘mse’ component (and thus the corresponding elements in ‘rsq’) in the randomForest object are wrong, but others are correct. (Thanks to Ulrike Gromping for pointing out this problem, as well as the one fixed in 4.5-24.)

randomForest 4.5-24 (2008-04-07)

• randomForest.formula() did not exclude terms preceded by -.

randomForest 4.5-23 (2008-01-22)

• Fixed tuneRF() to work with R version > 2.6.1.
• Make predict.randomForest() more backward compatible with randomForest objects created from versions older than 4.5-21.

randomForest 4.5-22 (2007-11-30)

• Allow unsupervised randomForest not to produce a proximity matrix (by specifying proximity=FALSE), suggested by Nick Crookston.

randomForest 4.5-21 (2007-11-27)

• The added check for factor level consistency in predictor variables in 4.5-20 was not working for predictors given in a matrix (reported by Ramon Diaz-Uriate).

randomForest 4.5-20 (2007-11-21)

• Fixed a memory bug in the C code when the test set is given and proximity is requested in regression. (Reported by Clayton Springer.)
• Fixed the one-pass random tie-breaking algorithm in various places.
• Added code to check consistency of levels for factors in the predictors, as well as allowing missing levels of factors and extraneous variables in predict(..., newdata). (Thanks to Nick Crookston for suggesting a patch.)

randomForest 4.5-19 (2007-10-16)

• In classification, if sampsize is small and sampling is not stratified, the actual sample might be larger than specified in some trees. Now fixed.
• Fixed combine() to work on regression randomForest objects and for cases when ntree is small.
• randomForest.default() for regression was unnecessarily creating a matrix of 0s for localImportance when importance=TRUE but localImp=FALSE. (Thanks to Robert McGehee for reporting these bugs.)
• predict.randomForest(..., nodes=TRUE) now works for regression.

randomForest 4.5-18 (2006-12-10)

• Added S-PLUS 8 compatibility.

randomForest 4.5-17

• Added ‘w’ (for weights) to partialPlot.randomForest().

randomForest 4.5-16 (2006-01-24)

• Fixed some typos in the documentation source files (e.g., \note vs. \notes, etc).

randomForest 4.5-15 (2005-09-22)

• Fixed error message call in predict.randomForest().

randomForest 4.5-14

• varImpPlot() was ignoring the ‘type’ argument.
• "<" was used instead of ".lt." in Fortran code, which is not F77-compliant.

randomForest 4.5-13

• Fixed a bug in randomForest() when biasCorr=TRUE for regression.
• Fixed bug in predict.randomForest() when newdata is a matrix with no rownames.

randomForest 4.5-12 (2005-06-21)

• Added the ‘strata’ argument to randomForest, which, in conjunction with ‘sampsize’, allow sampling (with or without replacement) according to a strata variable (which can be something other than the class variable). Currently only works in classification.

randomForest 4.5-11 (2005-05-21)

• Fixed partialPlot.randomForest() so that if x.var is a character, it's taken as the name of the variable.
• Clean up code for importance() and varImpPlot() so that if the randomForest object only contains one importance measure, varImpPlot() will work as intended.

randomForest 4.5-10 (2005-05-04)

• Renamed the first argument of randomForest.formula() to ‘formula’, to be consistent with other formula interfaces.

randomForest 4.5-9 (2005-05-02)

• Fixed a bug with unsupervised randomForest(..., keep.forest=TRUE).
• Fixed a bug in regression that caused crash when proximiy=TRUE.
• Added ‘keep.inbag’ argument to randomForest(), which, if set to TRUE, cause randomForest() to return a matrix of indicators that indicate which case is included in the bootstrap sample to grow the trees.

randomForest 4.5-8 (2005-04-11)

• Added some code in predict.randomForest() so it works with randomForest objects created in older versions of the package.
• Fixed randomForest.default() so that getTree() works when the forest contains only one tree.
• Added the argument ‘labelVar’ (default FALSE) to getTree() for prettier output.

randomForest 4.5-7 (2005-04-06)

• Fixed (another!) bug in splitting on categorical variables, especially impacting data with binary (categorical) variables.

randomForest 4.5-6 (2005-04-06)

• Fixed a bug introduced in 4.5-2 that used the wrong default class weights.

randomForest 4.5-5

• Fixed a couple of bugs in C/Fortran code for splitting on categorical variables in classification trees, which lead to negative or Inf decrease in the Gini index.

randomForest 4.5-4 (2005-03-03)

• Fixed a bug in regression when there are categorical predictors. (The splits can be completely wrong!)

randomForest 4.5-3

• Fixed predict.randomForest() so that it uses the class labels stored in the randomForest object (for classification).

randomForest 4.5-2 (2005-02-01)

• New argument ‘cutoff’ added to predict.randomForest(). The usage is analogous to the same argument to randomForest().
• Added ‘palette’ and ‘pch’ arguments to MDSplot() to allow more user control.
• In randomForest(), allow the forest to be returned in ‘unsupervised’ mode.
• Fixed some inaccuracies in help pages.
• Fixed the way version number of the package is found at start-up.

randomForest 4.5-1 (2004-12-04)

• In classification, split on a categorical predictor with more than 10 categories is made more efficient: For two-class problems, the heuristic presented in Section 4.2.2 of the CART book is used. Otherwise 512 randomly sampled (not necessarily unique) splits are tested, instead of all possible splits.
• New function classCenter() has been added. It takes a proximity matrix and a vector of class labels and compute one prototype per class.
• Added the ‘Automobile’ data from UCI Machine Learning Repository.
• Fixed partialPlot() for categorical predictors (wrong barplot was produced).
• Some re-organization and clean-up of internal C/Fortran code is on-going.

randomForest 4.4-3

• Added the nPerm argument to randomForest(), which controls the number of times the out-of-bag part of each variable is permuted, per tree, for computing variable importance. (Currently only implemented for regression.)
• When computing the out-of-bag MSE for each tree for assessing variable importance in regression, the total number of cases was wrongly used as the divisor.
• Fixed the default and formula methods of randomForest(), so that the ‘call’ component of the returned object calls the generic.
• The ‘% increase in MSE’ measure of variable importance in regression was not being computed correctly (should divide sum of squares by number of out-of-bag samples rather than total number of samples, for each tree).
• Fixed a bug in na.roughfix.default() that gave warning with matrix input.

randomForest 4.4-2 (2004-11-03)

• Fixed two memory leaks in the regression code (introduced in 4.3-1).
• Fixed a bug that sometimes caused crash in regression when nodesize is set to something larger than default (5).
• Changed the tree structure in regression slightly: "treemap" is replaced by "leftDaughter" and "rightDaughter".

randomForest 4.4-1 (2004-10-20)

• Made slight change in regression code so that it won't split ‘pure’ nodes. Also fixed the ‘increase in node purity’ importance measure in regression.
• The outscale option in randomForest() is removed. Use the outlier() function instead. The default outlier() method can be used with other proximity/dissimilarity measures.
• More Fortran subroutines migrated to C.

randomForest 4.3-3 (2004-09-14)

• Fixed randomForest.formula() so that update() will work.
• Fixed up problem in importance(), which was broken in a couple of ways.

randomForest 4.3-2 (2004-09-13)

• Fixed a bug that caused crashes in classification if test set data are supplied.

randomForest 4.3-1

• Fixed bugs in sampling cases and variables without replacement.
• Added the rfNews() function to display the NEWS file. Advertised in the start up banner.
• (Not user-visible.) Translated regression tree building code from Fortran to C. One perhaps noticeable change is less memory usage.

randomForest 4.3-0 (2004-07-07)

• Thanks to Adele Cutler, there's now casewise variable importance measures in classification. Similar feature is also added for regression. Use the new localImp option in randomForest().
• The ‘importance’ component of randomForest object has been changed: The permutation-based measures are not divided by their ‘standard errors’. Instead, the ‘standard errors’ are stored in the ‘importanceSD’ component. One should use the importance() extractor function rather than something like rf.obj$importance for extracting the importance measures.
• The importance() extractor function has been updated: If the permutation-based measures are available, calling importance() with only a randomForest object returns the matrix of variable importance measures. There is the ‘scale’ argument, which defaults to TRUE.
• In predict.randomForest, there is a new argument ‘nodes’ (default to FALSE). For classification, if nodes=TRUE, the returned object has an attribute ‘nodes’, which is an n by ntree matrix of terminal node indicators. This is ignored for regression.

randomForest 4.2-1

• There is now a package name space. Only generics are exported.
• Some function names have been changed: partial.plot -> partialPlot var.imp.plot -> varImpPlot var.used -> varUsed
• There is a new option ‘replace’ in randomForest() (default to TRUE) indicating whether the sampling of cases is with or without replacement.
• In randomForest(), the ‘sampsize’ option now works for both classification and regression, and indicate the number of cases to be drawn to grow each tree. For classification, if sampsize is a vector of length the number of classes, then sampling is stratified by class.
• With the formula interface for randomForest(), the default na.action, na.fail, is effective. I.e., an error is given if there are NAs present in the data. If na.omit is desired, it must be given explicitly.
• For classification, the err.rate component of the randomForest object (and the corresponding one for test set) now is a ntree by (nclass + 1) matrix, the first column of which contains the overall error rate, and the remaining columns the class error rates. The running output now also prints class error rates. The plot method for randomForest will plot the class error rates as well.
• The predict() method now checks whether the variable names in newdata match those from the training data (if the randomForest object is not created from the formula interface).
• partialPlot() and varImpPlot() now have optional arguments xlab, ylab and main for more flexible labelling. Also, if a factor is given as the variable, a real bar plot is produced.
• partialPlot() will now remove rows with NAs from the data frame given.
• For regression, if proximity=FALSE, an n by n array of integers is erroneously allocated but not used (it's only used for proximity calculation, so not needed otherwise).
• Updated combine() to conform to the new randomForest object.
• na.roughfix() was not working correctly for matrices, which in turns causes problem in rfImpute().

randomForest 4.1-0

• In randomForest(), if sampsize is given, the sampling is now done without replacement, in addition to stratified by class. Therefore sampsize can not be larger than the class frequencies.
• In classification randomForest, checks are added to avoid trees with only the root node.
• Fixed a bug in the Fortran code for classification that caused segfault on some system when encountering a tree with only root node.
• The help page for predict.randomForest() now states the fact that when newdata is not specified, the OOB predictions from the randomForest object is returned.
• plot.randomForest() and print.randomForest() were not checking for existence of performance (err.rate or mse) on test data correctly.