--- a +++ b/partyMod/inst/NEWS @@ -0,0 +1,649 @@ + + CHANGES IN party VERSION 1.0-16 (2014-08-18) + + o import("grid") + + + CHANGES IN party VERSION 1.0-15 (2014-06-26) + + o allow for missing predictor values in new varimp for + right-censored responses + + o introduce varperm argument to R_get_nodeID + + + CHANGES IN party VERSION 1.0-14 (2014-05-30) + + o add experimental varimp() for right-censored responses + + + CHANGES IN party VERSION 1.0-13 (2014-02-01) + + o deal with protection issues in R-devel + + + CHANGES IN party VERSION 1.0-12 (2014-01-15) + + o mammoexp -> TH.data + + + CHANGES IN party VERSION 1.0-11 (2013-12-13) + + o deal with empty levels for teststat = "quad" + (bug reported by Wei-Yin Loh <loh@stat.wisc.edu>) + + + CHANGES IN party VERSION 1.0-10 (2013-10-24) + + o new demo "strucchange-perm" + + o proximity has newdata argument + + + CHANGES IN party VERSION 1.0-9 (2013-09-02) + + o export initVariableFrame (for usage in RWeka only) + + o fix NAMESPACE problems + + o data is in TH.data, not ipred anymore + + + CHANGES IN party VERSION 1.0-8 (2013-07-11) + + o update mvtdist + + o documentation update + + + CHANGES IN party VERSION 1.0-7 (2013-05-31) + + o ctree and cforest ignored the scores argument for the + response. Spotted and fixed by Silke Janitza + <janitza@ibe.med.uni-muenchen.de>. + + + CHANGES IN party VERSION 1.0-6 (2013-01-09) + + o use hist()$density instead of hist()$Intensities as + reported by R 3.0.0 to be + + + CHANGES IN party VERSION 1.0-5 (2013-01-07) + + o fix class problem reported by R 3.0.0 to be + + + CHANGES IN party VERSION 1.0-4 (2012-12-18) + + o export varimpAUC() + + o add where() method for RandomForest class + + + CHANGES IN party VERSION 1.0-3 (2012-09-26) + + o new function varimpAUC() for AUC-based variable importance measures + + o the `weights' argument in cforest() can now be used to define + alternative case weights for each of the trees in the forest. + + + CHANGES IN party VERSION 1.0-2 (2012-04-26) + + o version 1.0-0 introduced a new bug in plotting Kaplan-Meier curves + when fixing the weight problem in survfit; the x-axis labels where + incorrect. Spotted by Sarah Vowler <Sarah.Vowler@cancer.org.uk>. + + + CHANGES IN party VERSION 1.0-1 (2012-03-23) + + o fix -Werror warnings suggested by Murray Stokely <mstokely@google.com> + + o make sure no factor variables are evaluated as surrogate split + + o fix confusing warning messages in varimp and check + for non-unity weights + + + CHANGES IN party VERSION 1.0-0 (2012-02-17) + + o varimp can now partially deal with missing values + + o Kaplan-Meier curves are now computed _after_ removing + zero case weights (see comment in ?survfit); plots may change + slightly. + + o use cforest_unbiased instead of cforest_control/cforest_classical + in examples and regression tests + + + CHANGES IN party VERSION 0.9-99996 (2011-12-20) + + o don't ship doxygen documentation with package + + o ctree() and cforest() don't handle `-' in formulae, + warning added to Rd files + + + CHANGES IN party VERSION 0.9-99995 (2011-10-27) + + o observations with missing values in newdata might not have gone + with the majority in predict(<ctree>, newdata) when no surrogate + split was applicable. Spotted and fixed by + Vik <viknesh@stat.ufl.edu>. + + + CHANGES IN party VERSION 0.9-99994 (2011-08-22) + + o reuse classes exported by coin + + + CHANGES IN party VERSION 0.9-99993 (2011-07-26) + + o attach NAMESPACE properly in tests + + + CHANGES IN party VERSION 0.9-99992 (2011-05-02) + + o fix partial matching problems + + + CHANGES IN party VERSION 0.9-99991 (2010-11-19) + + o fix tests/ dependencies + + + CHANGES IN party VERSION 0.9-9999 (2010-09-13) + + o add update slots to tree and forest objects (later to be used + for crossvalidation) + + + CHANGES IN party VERSION 0.9-9998 (2010-08-23) + + o allow for internal permutations in predict via R_predict2 + + + CHANGES IN party VERSION 0.9-9997 (2010-07-06) + + o update mvt.f (see mvtnorm) + + + CHANGES IN party VERSION 0.9-9996 (2010-06-24) + + o print progress bar while forest grows (via trace = TRUE + in cforest_control()) + + + CHANGES IN party VERSION 0.9-9995 (2010-05-19) + + o assignment of observations based on surrogate splits + during fitting might have failed; observations went + with majority (in a sub-optimal way) + + + CHANGES IN party VERSION 0.9-9994 (2010-04-14) + + o varimp() gives warning for non-unity weights + + o "no admissible split found" warnings disabled + + + CHANGES IN party VERSION 0.9-9993 (2010-03-04) + + o just internals needed for mboost + + + CHANGES IN party VERSION 0.9-9992 (2010-02-26) + + o Bug fix in mob plotting for anova models + + + CHANGES IN party VERSION 0.9-9991 (2010-01-27) + + o Bug fix in error handling of mob(). + + CHANGES IN party VERSION 0.9-999 (2009-09-24) + + o minbucket was erronously interpreted as minbucket + 1 + + o p-values for teststat = "max" were wrong + in the uncommon case of zero variances + + + CHANGES IN party VERSION 0.9-998 (2009-06-17) + + o mtry may vary with tree depth + + o finding surrogate variables may have failed, fixed. + + + CHANGES IN party VERSION 0.9-997 (2009-06-04) + + o documentation fixes + + + CHANGES IN party VERSION 0.9-996 (2009-03-27) + + o survival fixes + + + CHANGES IN party VERSION 0.9-994 (2009-02-10) + + o fix bug in new varimp function (which was triggered + by splits in categorical variables) + + + CHANGES IN party VERSION 0.9-993 (2009-01-29) + + o new C-level function R_remove_weights + + + CHANGES IN party VERSION 0.9-992 (2009-01-19) + + o update CITATION file + + + CHANGES IN party VERSION 0.9-991 (2009-01-13) + + o new conditional variable importance measure + (Strobl et al., 2008, BMC Bioinformatics) available. + + + CHANGES IN party VERSION 0.9-99 (2008-10-28) + + o a suboptimal split was implemented when the best + split corresponded to the last row of <data> due to + a coding error. This should have happend only very + rarely, however, the glaucoma example is affected. + + + CHANGES IN party VERSION 0.9-98 (2008-10-15) + + o don't compute ordering of censored variables (thanks to + Brian D. Ripley for the report) + + o experimental version of partialPlot for cforests + + o teststat = "quad" and testtype = "Univariate" produced + wrong criteria in the presence of constant exploratory variables. + Spotted by Sebastian Wietzke <Sebastian.Wietzke@axa.de> + + + CHANGES IN party VERSION 0.9-97 (2008-06-26) + + o predictions for new data containing missing values were + wrong. Bug spotted by Wei-Yin Loh <loh@stat.wisc.edu> + + o vignette updates + + + CHANGES IN party VERSION 0.9-96 (2008-06-06) + + o make searching for surrogate splits a little more stable + + + CHANGES IN party VERSION 0.9-95 (2008-02-27) + + o proximity() now gives _relative_ numbers + (similar to `randomForest'), not absolute numbers + long-standing feature request by Henric Nilsson + + + CHANGES IN party VERSION 0.9-94 (2008-01-30) + + o documentation updates + + + CHANGES IN party VERSION 0.9-93 (2007-11-30) + + o It is now an error to ask for more surrogate variables + than actually available. Thanks to Henric Nilsson. + + + CHANGES IN party VERSION 0.9-92 (2007-11-22) + + o predict(<ctree-object>) computed predictions + for observations with zero weights (by passing them down the tree). + This was already done this way by predict(<cforest-object>) but resulted + in an error for ctree()s. + + o minbucket added to ctree_control() + + + CHANGES IN party VERSION 0.9-91 (2007-09-26) + + o bugfix: NAs in factors lead to segfaults on 64bit machines + as reported by Carolin Strobl <carolin.strobl@lmu.de> + + o related to this: be more careful when splitting in + variables containing missing values, especially factors. + + o add examples to regression tests + + o new function `proximity' (feature request by Henric Nilsson) + + + CHANGES IN party VERSION 0.9-90 (2007-09-24) + + o new defaults for `control' argument of `cforest': unbiased + forests are now grown by default + + o new defaults for binary classification tree visualization: + stacked bar charts are used by default. + + + CHANGES IN party VERSION 0.9-14 (2007-07-23) + + o fix problem in `varimp' introduced by new weights handling + + + CHANGES IN party VERSION 0.9-13 (2007-07-23) + + o update `mvt.f' + + o improve the memory footprint of RandomForest objects + substancially (by removing the weights slots from each node). + + More careful revision of the predict and fitting code is needed. + + o predictions for cforest with multivariate response are + now returned in a matrix (should be a data.frame) + + o remove confusing `no admissible split found' warning + (which simply meant that the `minsplit' wasn't met). + + + CHANGES IN party VERSION 0.9-12 (2007-06-28) + + o adjust to coin 0.6-4 + + + CHANGES IN party VERSION 0.9-11 (2007-06-11) + + o populate `where' slot in `mob' objects. + + o `mob_control' now has an `na.action' argument + + o cforest with replace = FALSE, fraction = ... + can now deal with weights (spotted by Carolin Strobl + <carolin.strobl@stat.uni-muenchen.de>) + + o interface to LAPACK (`dgesdd' for computing a SVD) + directly. As a side-effect, the svdmem class can be + simplified and no memory allocation during + tree growing is necessary (which results in a measureable + performance gain) + + + CHANGES IN party VERSION 0.9-10 (2007-02-28) + + o internal infrastructure for fit(x, y) interfaces, + including a VariableFrame method for matrices. + + o deal with factors with only one level and variables where + all observations are NA + + o don't compute design matrices in `ModelEnvFormula' + + + CHANGES IN party VERSION 0.9-9 (2007-02-02) + + o internal changes to data objects: joint transformations + only necessary for response variables (new class `ResponseFrame') + but we need to distinguish between testing (using ranks, for + example) and prediction (means of raw data!). + + Problem spotted by Henric Nilsson <nilsson.henric@gmail.com>. + + + CHANGES IN party VERSION 0.9-8 (2007-01-15) + + o thicker median lines in boxplots + + + CHANGES IN party VERSION 0.9-7 (2007-01-15) + + o fix problems with multivariate response variables + (spotted by Henric Nilsson <henric.nilsson@sorch.se>) + + + CHANGES IN party VERSION 0.9-6 (2006-11-28) + + o R-2.5.0 does not allow to change the storage.mode of factors + + + CHANGES IN party VERSION 0.9-5 (2006-10-27) + + o adjusted p values computed with testtype = "MonteCarlo" + did not take dimensionality of the underlying linear statistics + into account. It is now ensured that _p values_ are resampled, + not test statistics. + + o fix escape problems + + + CHANGES IN party VERSION 0.9-4 (2006-09-15) + + o make sure `maxsurrogates' exceeds number of input variables + + o fix problems reported by valgrind + + + CHANGES IN party VERSION 0.9-3 (2006-09-08) + + o don't call RNG functions in mvt (this is done in C code, once) + + + CHANGES IN party VERSION 0.9-2 (2006-09-07) + + o mob() can't currently handle missing values, + they are removed and a warning is given. + + o add `methods' and `vcd' to Depends: + + + CHANGES IN party VERSION 0.9-0 (2006-08-31) + + o node_barplot() can now also draw stacked barplots. + + o simplify handling of ordinal variables. It is now possible + to have multiple (ordinal) response variables. + + o some documentation updates + + o fix problems with NA handling for factors + + o make sure minsplit criterion applies in the presence of missing + values. Bug spotted by Han Lee <Han.Lee@geodecapital.com>. + + + CHANGES IN party VERSION 0.8-8 (2006-08-23) + + o export `varimp' (variable importance measures for cforest()) + + o documentation updates + + o add codetools checks + + + CHANGES IN party VERSION 0.8-7 (2006-07-17) + + o REAL(NULL) now gives an error in C code and scores could be + potentially NULL: fixed for the time being. + + o add `show' method for BinaryTree and RandomForest objects + + + CHANGES IN party VERSION 0.8-6 (2006-05-22) + + o add some validity checks for hyper parameters + + o add function `varimp' for computing variable importance + measures for some random forests (this is still experimental and + thus not exported yet, so use `party:::varimp') + + + CHANGES IN party VERSION 0.8-5 (2006-04-25) + + o all hyper parameters to `cforest' are now controlled using + objects of a new class `ForestControl' which can be created using + `cforest_control()'. + + o sampling of a fraction of the observations without replacement + is now available for the `cforest' implementation of random forest. + + + CHANGES IN party VERSION 0.8-4 (2006-04-04) + + o renamed argument `teststattype' to `teststat' with defaults + c("quad", "max") in order to be compatible with the `coin' package, + version >= 0.4-5 + + o use `1 - (1 - p)^k' instead of `p * k' for Bonferroni-adjustment. + Node 7 for the `GlaucomaM' data is now splitted in addition (in tms). + + + CHANGES IN party VERSION 0.8-3 (2006-03-20) + + o `predict' returned nonsensical results in case a tree was + fitted to a multivariate response variable. Now a list with one + element for each observation is returned. + + + CHANGES IN party VERSION 0.8-2 (2006-03-01) + + o plotting buglets fixed: improved axis in MOB plots, + correct (transparent) background on jpeg() and png() devices. + + + CHANGES IN `party' VERSION 0.8-1 (2006-02-23) + + o `testtype' can be Bonferroni, MonteCarlo, Univariate and + Teststatistic (instead of Raw) + + o removed unnecessary constraint on weights in `cforest' + + o maximize raw test statistics for random forest by default. + + + CHANGES IN `party' VERSION 0.8-0 (2006-02-15) + + o `cforest', an implementation of Breiman's random forest ensemble + algorithm based on conditional inference trees (`ctree') has been + added. It is somewhat experimental and thus for advanced users only. + + o `mob', an object-oriented implementation of a recently suggested + algorithm for model-based recursive partitioning (Zeileis, Hothorn, + Hornik, 2005) has been added. It works out of the box for partitioning + (generalized) linear regression models, others can be easily plugged + in. A new vignette "MOB" describes the implementation ideas and provides + a few examples. + + o new S3 generic reweight() with methods for (g)linearModel + for re-fitting a model with different weights. + + o new argument `maxdepth' to `ctree_control' which allows for + growing trees of a fixed maximum depth. + + o LazyData: yes + + + CHANGES IN `party' VERSION 0.3-6 (2006-02-06) + + o use a different way to deal with NAMESPACEs during in tests/*.R + following a suggestion by Prof. Brian D. Ripley + + o use LazyLoad: yes instead of SaveImage: yes + + + CHANGES IN `party' VERSION 0.3-5 (2006-02-02) + + o make R CMD check happy and move src/README to inst/README + + + CHANGES IN `party' VERSION 0.3-4 (2006-01-18) + + o documentation updates + + + CHANGES IN `party' VERSION 0.3-3 (2006-01-18) + + o some new convenience functions, not exported + + + CHANGES IN `party' VERSION 0.3-2 (2006-01-12) + + o isequal must not check equality of attributes + + + CHANGES IN `party' VERSION 0.3-1 (2005-12-02) + + o fix bug introduced in version 0.3-0: coin:::factor_trafo applies + treatment contrasts in case of a binary factor but we need the full + design matrix + + o documentation updates + + + CHANGES IN `party' VERSION 0.3-0 (2005-11-29) + + o `ytrafo' and `xtrafo' functions make use of `coin:::trafo' now, + i.e. the handling of influence functions and transformations + has been unified in packages `party' and `coin' + + + CHANGES IN `party' VERSION 0.2-10 (2005-11-08) + + o new slot `data' in BinaryTree objects, slots inputnames and levels + have been removed + + + CHANGES IN `party' VERSION 0.2-9 (2005-10-19) + + o splits in categorical variables could have failed due + to weired internal checks + + + CHANGES IN `party' VERSION 0.2-8 (2005-08-06) + + o fix problems reported by codetools + + + CHANGES IN `party' VERSION 0.2-7 (2005-08-31) + + o extract inputs using menv@get("input", data = newdata) in predict + + + CHANGES IN `party' VERSION 0.2-6 (2005-08-29) + + o make gfortran happy + + + CHANGES IN `party' VERSION 0.2-5 (2005-08-19) + + o ctree() now searches the global environment for variables given + in `formula' when the `data' argument is unspecified. + + + CHANGES IN `party' VERSION 0.2-4 (2005-07-07) + + o names of `criterion' element in `SplittingNode' objects were wrong + + o categorical splits with `ctree_control(testtype = "MonteCarlo")' + were potentially wrong + + + CHANGES IN `party' VERSION 0.2-3 (2005-06-29) + + o print and plot only levels which are available in a node (for nominal + splits) + + + CHANGES IN `party' VERSION 0.2-2 (2005-06-27) + + o ./src/Makedeps will be automatically generated (on Windows) + and must not be part of the source-package. + + o vignette cosmetics