CHANGES IN R VERSION 0.62 NEW FEATURES o Many more help(.) pages. o The top level Makefile now supports the usual ./configure; make; make install procedure (new make targets `all' and `install'). o The HTML help pages can now be searched for keywords. o Conversion of functions to and from lists. formals<- and body<-. The alist() function makes it easier to construct argument lists, etc. Added expression-->list coercion. o complex(.) now has optional 'argument' and 'modulus' arguments, allowing ``polar coordinate'' specifications. o layout() documented and improved: starts default device if needed, and returns number of figures. o New find() function [relying on apropos(..)]. o objects() now works, being equivalent to objects(pos=). o storage.mode() and related functions now return "double" instead of "real", for compatibility. "real" is still allowed as synomym for "double". o A tests/ directory has been added (in the source), and "make tests" has been modified to run more than all the examples from the base package. The exact 'make tests' behavior is still bound to change. o An experimental directory etc/Rdoc has been added with a perl5 module to parse R documentation files. Sample perl programs to use this module are also included. o All internal mechanisms to support factors and data.frames have been removed. These are now entirely supported by interpreted code! `is.unordered' has been eliminated. Thanks to John Chambers for allowing the distribution of his StatLib code. o "pmatch" is now completely S compatible and is not just another name for "charmatch". o There is now a function called ".Alias" which can be used to provide multiple names for the same object. Example: lm2 <- .Alias(lm) This is dangerous because it can be used to defeat the call-by-value illusion. o Many functions changed from to .Internal(..). Currently, new .Internal(.)s in ..library/base/R/New-Internal.R Primitive functions are now printed as ``.Primitive(..)''. o [dpqr]hyper(.) now also work with some 0 arguments. o C-code: Many "-Wall" fixes (MM & DB). o mva's dist() now takes arguments diag and upper which control how the distance matrix is printed. plot.hclust() now takes a labels argument. o Attributes are now propagated correctly in binary operations. Changes from: Steve Oncley and Gordon Maclean National Center for Atmospheric Research Boulder, Colorado USA o configure now also checks for fort77. o Usage of R INSTALL now is R INSTALL [options] [-l lib] pkg_1 ... pkg_n The +/- options were replaced by GNU-style `--no-docs' and `--no-text', `--no-html', and `--no-latex'. o Usage of R REMOVE now is R REMOVE [options] [-l lib] pkg_1 ... pkg_n o Usage of R COMPILE now is R COMPILE [options] srcfiles, where through options one can set e.g. CFLAGS or FFLAGS. o Usage of R SHLIB now is R SHLIB [-o libname] files, where the file names can be that of source or object files. o A new R CMD interface allows invokation of executables in $RHOME/{etc,cmd} without installing them or setting paths. o Data files are now also documented using the Rd format, all data documentation in the base package has been converted accordingly. Rd files for data have a \keyword{datasets} as identifier. o new function mahalanobis() for Mahalanobis distance o quantile.default() now handles Inf's correctly. o New command line options `--enable-blas' and `--enable-readline' to configure. o pretty(x) is more reasonable when max(x)-min(x) < 1e-10 max(|x|), and has a new argument "shrink.sml" for that case. o formatC(.) supports a new "fg" format for flexible non-exponential formatting. o etc/build-htmlpkglist has been integrated into etc/build-help (option --htmllists) o family gaussian(.) and inverse.gaussian(.) both accept several link arguments [J.Lindsey]. o The graphics function "tck" now produces effects just like those in S (e.g. par(tck=1) now produces grid lines). Since using "tck" produces nasty results in some circumstances there is also an alternative parameter "tcl" which defines the tick length in terms of lines of text. The default setting is par(tcl=-0.5). o menu() now takes additional arguments `graphics' (currently unused) and `title'. o New function plot.formula(). plot.factor() now produces boxplots when given 2 arguments. o New function write.table(). o signif() now has a `digits' default of 6. o Old-style long command line options (`-save' etc) changed to GNU-style (`--save' etc). Debugging options (`-ddd', `-gdb', `-xxgdb') unified into the new `--debugger' (`-d'). New command line options `--version' (`-V') and `--help' (`-h') which print useful information and exit. o The loading of profiles at startup now works as follows. Unless the new `--no-site-file' was given, a site profile is sought (as specified via the environment variable `RPROFILE', or if this is unset defaulting to `${RHOME}/etc/Rprofile'. Then, unless the new `--no-init-file' was given, the user profiles (`.Rprofile' and `~/.Rprofile') are sought. o New functions subset() and transform() intended primarily to make life with dataframes easier. o debian directory has been added so Debian GNU/Linux packages can be created from raw source. o The graphics system has been through a major overhaul. It is now possible to have multiple active device drivers and to control them with full suite of dev.xxx() functions available in S. Display lists are now kept for interactive devices. When an on-screen graphics window is resized, the content of that window is redrawn at the new size. At present only X11 and PostScript graphics device drivers are available, but more are on the way. o On systems using IEEE arithmetic, the builtin Inf and NaN values are now recognised and used. NA and NaN should propagate correctly in computations, with NA dominating in computations involving both quantities. E.g. NA+NaN is NA. o Some of the t, F, and chisq distribution/probability functions now allow a noncentrality parameter `ncp'. o Functions ptukey() and qtukey() provide the distribution and quantile functions for the maximum of several studentized ranges. o system.file() [now documented] returns all files matched by wildcards. o data() now supports more file formats: .RData for binary files, .txt or .tab for data to be read by `read.table(file, header=TRUE)' and .csv for data to be read by `read.table(file, header=TRUE, sep=";")' o Rdconv: new tabular environment, new sections `\format' and `\source', new output format `-type Sd' for S documentation o .First.lib() now implemented; called by library() after loading a package. o print.summary.[g]lm() now give `significance stars' and a symbolic correlation matrix. o new is.R() function. o glm() now also returns an AIC value [from JL]. print..glm methods indicate the options()$contrasts in some cases. In summary.glm(..., correlation=..), the default has been changed to corr. = FALSE which is consistent with summary.lm(). predict() now works again for glm objects. o the `flag' argument in formatC(.) can now have more than one character. o nlm() returns the number of iterations used [from J.Lindsey]. o cut, diff, hist, mean, quantile, seq, trunc() are now all generic. cut() has an `include.lowest' argument as S. o save.image() as short-cut to save the current session in .RData. o new design of HTML help pages, including an index of all functions from all installed packages. o new editor function pico() o matrices and arrays can have zero extents BUG FIXES (many of which resulted from the added features...) o atanh(.) now works o summary(glm) and summary(lm) now use compatible names. o [pq]tukey(.) now working. o title() now handles main=, sub=, xlab=, ylab= with embedded newlines correctly. This is partly a change in title and partly a change in the underlying graphics code. o min(.), max(.), sum(.) now return integer for integer arguments. o which(.) now returns integer. o Rd files: leading whitespace of lines in user-defined sections was not correctly removed by Rdconv o sign(.) works again. o [.data.frame segfaulted if arg. wasn't a data frame o "R --no-readline" now again gives proper prompts. o demos/zero.R dyn.load(.) now should be working more easily. o mode(.) now returns "(" for a "parentheses 'call'". o Bug fix in mva dist.c for method binary (gave "invalid distance"). plot.hclust failed for data without row names. o R INSTALL should work (again) now when `pkg' is a relative file name. o .not.yet.implemented() now takes an arbitrary number of args. o Plotting of dendrograms is working again. o data.frame(.) now uses "1:n" as default row.names. o image(.) and contour(.) now also work called as, e.g., ``image(z)''. o the first argument of axis(.) is now called `side' as in S. o format(NULL) now works. o minor fix in symnum. o hist() now is more compatible to S, has a new `labels' argument, and should work ok for non-equidistant breaks. o plot(-1) now labels properly. o Many small code changes (eliminating extraneous variables, nested comm.) in C code in order to satisfy `gcc -Wall' [Doug Bates]. o model.extract() will now extract arbitrary model frame arguments. o list of currently loaded libraries (.Dyn.libs) not saved from session to session (really, this time) o rhyper works with vectorisation, degenerate cases. o printing of objects in lists now dispatches methods correctly CHANGES IN R VERSION 0.61.2 BUG FIXES o pretty(999) resulted in an infinite loop due to integer overflow. pretty(.) now sometimes returns different results than before. o pi:6 returned integer, instead of real. o [.data.frame caused segfault if called with non-dataframe argument o hist() now is more compatible to S, has a new `labels' argument, and should work ok for non-equidistant breaks. o lgamma(-1e7) segfaulted. gamma(.) and lgamma(.) now give proper results for negative integers. o formatC(pi,dig=20,wid=2) segfaulted. o quantile(..., pr = c(1,2,5)/1000) gave all names as "0%". o In 0.61.1, model.matrix was fixed to pay attention to the names of the names of its data arg, but the data arg was defaulting to an unnamed list, so model.matrix(~x) failed... o Indexing with [[]] and a zero-length vector segfaulted. o Coercion of factors as in S-plus o dyn.load statement in demos/dynload/zero.R fixed o Factors could get allocated without the OBJECT bit, which nearly drove Kurt mad trying to write plot.factor... o Fixed confidence limit problem in t.test CHANGES IN R VERSION 0.61.1 NEW FEATURES o None (by definition, x.y.z releases are bugfix releases now) BUG FIXES o Return statements of the form return(x,y) will now return a list with named components. o Parsing of nested "if" statments was broken. This is fixed now. (Reported by Paul Gilbert). o Wrong declaration of ConsoleBufCnt in src/main/scan.c caused crash in Irix (George White ) o if(nmatch = 0) bug in src/main/character.c fixed (Doug Bates) o R_alloc/S_alloc fixes. The former allocated 4 times more than needed, the latter zeroed half of what it got, sizeof() mistakes in both cases. o c(ordered factor) caused segfault (uninitalised pointer), now fixed. o behaviour of as.numeric() on factors changed recently; now documented. o model.matrix() now pays attention to the names on its dataframe argument. o Fixes to group methods. o autoload() caused infinite loop if function wasn't found in library on loading o The pager ate the rest of stdin in batch mode, now fixed. Also, stdout was not flushed before call to system(). "make tests" should work now. o Empty directories now created by configure (so that it doesn't matter that "CVS export" doesn't do it) o as.name() made idempotent (i.e. if is.name(x) then as.name(x)==x) o 3 problems with glm, 2 in glm.fit and a one in print.glm fixed [Jim Lindsey] o binomial (family) now works when 'n=0'. [J.Lindsey] o split() now also works in split(1:10,1:2) o strsplit() now also works for strsplit(c,NULL) o A LANG='..' environment variable no longer affects scan()ing of numbers. o seq(.) doesn't segfault anymore in gl(2,3):gl(1,6) o contour(.) now also works with integer arguments CHANGES IN R VERSION 0.61 We try to make development more flexible by creating a "CVS branch". This should make it easier to produce patches for obvious bugs in the releases, without having to wait for changes in other areas to stabilize. NEW FEATURES o New functions "all.vars" and "all.names" added. o There has been a small change in the include file structure. All include files now live in RHOME/src/include and are copied to RHOME/include when needed. o The "noquote" functions are now documented. o A new `language' demo, "is.things", is provided. o symnum(.) function o The files in R/library/base/data have had a .R suffix added. BUG_FIXES o A nasty bug which showed when attempt was made to create a zero length call has been fixed. o model.matrix(.) now allows a contrasts argument. o barplot(.) now also works for barplot(table(rpois(100,3))). o make clean ; make now should work; ./Makefile.in eliminated o format(.) is now generic; the default method has a `digits' argument. CHANGES IN R VERSION 0.60.1 NEW FEATURES o "split" is now a generic function, with a method for data frames. (contributed by Doug Bates). o S compatible functions "all.names" and "all.vars" added. BUG FIXES o A file was closed multiple times if an error message occurred after sourcing a file. In some versions of Linux this caused a core dump. o The inclusion was causing problems with some versions of readline because the file did not exist. This is now detected by configure. CHANGES IN R VERSION 0.60 R is about to become an official part of the GNU project. To quote RMS (Richard Stallman) ``I hereby dub R GNU software!'' NEW FEATURES o There has been a major change in directory structure masterminded by Kurt Hornik. library(.) now attaches ``package''s which are better integrated, see "?library". Packages may be available from outside the RHOME path via the .lib.loc variable. o The documentation format (of files in src/library//man/ ) has changed to a more easily parsable LaTeX like format. The doc files now all end in `.Rd'. etc/Rman2Rd can be used to translate old-style documentation to the new one. The translation to *roff, LaTeX and HTML is now done using etc/Rdconv, written in Perl by Fritz Leisch. The HTML online help produced has now links which work. The manual (in doc/manual/) now includes a section on the documentation format and on mathematical text in graphs. etc/ further contains `Sd2Rd' for (partial) translation of S `.d' documentation to Rd, and `Rd2txt' and `Rd2dvi' for easy previewing of single Rd files. o The use of "names" on one dimensional arrays will now produce sensible results. This means that for most purposes, one dimensional arrays can be treated like vectors. o We have a applied a patch from mward@wolf.hip.berkeley.edu which should substantially improve the speed of (vector) arithmetic. o The modeling formula handler has been expanded so that it accepts y ~ 0 + x as a "through the origin" specification. models with no parameters are now acceptable. o "cov", "cor" and "var" now produce a matrix result if either of their x or y arguments is a matrix. Dimnames are propagated in a sensible fashion. o New chisq.test(.) and prop.test() from Kurt Hornik. o New read.fwf(.) for reading fixed width format (KH). o New str(.) [alternative to summary(.) for programmers] (MM). o New example data sets "esoph", "infert" and "anscombe" (TL), "iris3" (KH) and "stackloss" (MM). o source(.) has several new arguments, notably ``echo = FALSE''. This is applied in the new function demo(.) which runs all the code in demos/ (but dynload). o strheight(.) is new, accompanying strwidth(.). Both now work for mathematical expressions (Paul Murrell). o The LaTeX version of the manual (-> doc/manual/) now has an index. o EVERY *.Rd file in src/library/base/man/ has now at least one \keyword o New package (`library(.)') "stepfun" for step functions, incl. empirical distributions. BUG FIXES o Regular expression matching is now done with system versions of the regexp library. This should fix compilation problems on some platforms. o "approx" and "approxfun", have had some minor adjustments. which fix the interpretation of the rule= argument. The code for piecewise constant case is now internal C code that than interpreted. This should boost performance in this case. o There has been a minor fixup of "model.frame" to ensure that subsets, weights, etc are handled properly. o Model fitting of the form lm(y~., data=df) glm(y~., data=df) will now work. The RHS of the model will consist of an additive model containing all (non-response) variables in the given data frame. o The following type of assignment to data frame subsets z <- data.frame(x=rnorm(10),y=rnorm(10),z=rnorm(10)) z[,1:2] <- matrix(1:20,nc=2) was producing incorrect results. The solution was to wrap an implicit "as.data.frame" around the RHS. o "[.data.frame" no longer has a default drop=TRUE argument. This means that subsetting a data frame with "[" will always yield a data frame. o There was a swap of coordinates internally in "mtext" which meant that labels were coming out in the wrong place. Fixed. o Syntax errors in parse(text="...") would cause R to terminate with a segmentation violation. This no longer happens, although the result is still not perfect (the parse() returns). This will be fixed by a future parse rewrite. o rainbow, topo.colors, etc., now also work with n in {1,2}; don't return duplicate neighbor colors anymore. o legend has new `text.width' argument and now also works with mathematical expressions as text. o hist() now works better, has a `plot = TRUE' argument, and returns something useful. o barplot() improved for `names', now returns vector of midpoints. o lm(), lm.fit, lm.wfit (was `lm.w.fit'): Made more compatible. Dealing with (close to) collinear situations is still not flexible enough. o internal postscript() improved (missing lines in boxplot(.)). o Improvement to many (even most ?) documentation (.Rd) files. o Numerous other fixes of minor things ... CHANGES IN R VERSION 0.50 WARNING!!! o A change in the way that "expressions" are implemented means that saved data images which contain expressions will probably not restore properly. NEW FEATURES o The installation of documentation has now been streamlined. Many manual entries have been revised. o "expressions" are now implemented as a basic type rather than as a class of object. This change was made as move toward compatibility with S and also to implement mathematical annotation in graphs. For some examples of the latter, see ?text and ?title. o "eigen" can now handle complex and non-symmetric matrices. o Libraries are now attached by loading their code into newly created environment frames on the search path rather than in with the general system code. This means that libraries can be unloaded as well as loaded. They can also have .First.lib and .Last.lib functions. The variable .Libraries has been replaced by .library() but should not be needed much anymore. o There is now an experimental function called "delay" which creates a promise to evaluate an expression. This provides direct access to the lazy evaluation mechanism used by R. o >>>> 'make tests' allows to test--run all the help() examples. o New functions matplot / matpoints / matlines. o cut has 2 new arguments. 'right = TRUE' gives intervals closed on the right, open to the left (as S); 'right = FALSE' allows to reverse this. The code for default label construction has been enhanced, and can be controlled by the new argument 'dig.lab'. o legend(.) has 2 new arguments 'cex' (obvious) and 'merge = FALSE'. -> ?legend. o deparse has a 2nd argument allowing for a kind of line width. o There is now print.density (method). o many help(.) pages have been updated with working examples, and several new ones have been created. o influence.measures() and lm.influence now allow to get at the usual regression diagnostics. BUG FIXES o The "is.object" function has been with drawn. o A bug which prevented the "pictex" graphics driver from working has been fixed. o Regression diagnostics obtained with "lm.influence" now work when there are weights. This means they should work for glms. o There was a problem in parsing files from statements which were separated from following statements by ";" (e.g. data(iris); iris). This is fixed. o Comments are handled better in functions. The rule is that they are shifted to just before their statements. Comments after the last statement of a function are lost. o It is now possible to perform complicated mutations of expressions. For example e <- quote(f(x=1,y=2)) names(e)[[2]] <- "a" will change the x= argument tag into a=. In the past this produced odd error messages. o The length function now tries to return a "sensible" value for all the built-in types. For example, symbols now have length 1. o "update" should now work in both "lm" and "glm" models. o The functions Re, Im, Mod, Arg and Conj will now accept real-valued arguments and return the obvious results. o Minor graphics cleanup. o A fix for convergence problems in glm from Thomas Lumley included. o A new version of qt() should not take infinitely long to get an answer in the large degrees if freedom case. The underlying code (Hill 1970, CACM) appears to be much faster and more accurate than Splus. o A final Newton step has been added to give a final "polish" to the quantiles produced by pnorm(). These should be close to full accuracy now. o A bug in qbeta found by Martin Maechler has been fixed. This should speed up quantile computation for the F and Beta distributions. Further improvements in qbeta(.) by MM. No infinite loops anymore. o rainbow(.) now allows "start > end" indexing the "color circle". topo.colors(n), terrain.colors(n), heat.colors(n) now also work for n=1,2. o ?"+" now works. o tapply has been fixed as indicated by T. Lumley.