************************************************** * * * 0.64 SERIES NEWS * * * ************************************************** BUG FIXES o seq(along = v) { and seq(v) when length(v) > 1 } now returns integer. o which(x) failed when x had names and NAs. o Typos in NegBinomial.Rd (Negative Binomial distrib), thanks to Ch.Gu. o revsort() misbehaved if n<=1, causing sample(1,1,,1) to segfault o Improved error message from check.options(). CHANGES IN R VERSION 0.64.2 NEW FEATURES o new target for R installation testing : make strict-tests. o symnum(x) now nicely codes logical x. o convolve() has a new type = c("circular", "open", "filter") argument allowing more than the only circular convolution. o par(xpd) now has three settings: FALSE (clip to plot region), TRUE (clip to figure region), or NA (clip to device region). o zapsmall(x) works for complex x. o new global variable R.version.string (for plots & reports). Deprecated version & Version for new R.version & R.Version. o R CMD Rd2dvi has builtin "Usage" help and works for multiple files. Useful for automatic reference manual of a package. (doc/manual/lib2tex is more efficient for installed packages, however). BUG FIXES o power() is now fully implemented and documented. o A couple of problems with group generic operations. o A bug which meant that it was not possible to add elements to zero length lists in the obvious way has been fixed. x <- list(); x[[1]] <- 10 x <- list(); x[["a"]] <- 11 both now work. o save.image() ignored dot-names. (esp. .First()) o lab= argument to plot() misinterpreted by axis() via ... passing o NULL labels in text() caused segfault o matrix(f,...) with f a factor now coerces to character o documentation errors for substitute and is.vector, minor fixups for trig and nlm o Background colours are set properly on X11 devices with colortype="pseudo": sometimes they were not allocated separately. o C() works (again?) for a single argument. o is.na() didn't work properly for "list" arguments. o symnum() sometimes failed with arrays of rank >= 3. o in some cases one could get nonblack color instead of black on 2nd x11() window. o influence.measures(.) $ is.influential was wrong on the cooks.distance. o printing of complex NaN/Inf was wrong as well. o printing of complex named vectors had a wrong initial space. o allow trailing space in character->numeric coercion o library() gave wrong "masked" warnings in some cases. o par(xpd) semantics were not compatible with S. o rect() output was not clipped in PostScript. o par(pin=c(width, height)) was behaving as par(pin=c(width, width)). o Non-blank separated data files didn't have their 1st field handled properly. o "aux" directory moved to "tools" to avoid difficulties on Windows. o structure() clobbered factors with missing levels. o pmatch() misbehaved on duplicate matches. o R CMD Rd2dvi works again. o logical binops tried to set time series parameters before dimensions. o upped the BUFSIZE in model.c (NOT proper long-term solution). o dput(), dump() and deparse() now always use DBL_DIG (=15) digits for numeric formatting. o chull() now works for vertical borders, such as in chull(c(1,1,2),3:1). CHANGES IN R VERSION 0.64.1 NEW FEATURES o barplot() and boxplot() are now generic o relevel function to reorder levels in factors. o contr.treatment now has a base= argument for selecting the baseline group. o New command line option `--no-environ' (under Unix) to prevent sourcing the `~/.Renviron' file. Implied by `--vanilla'. o Packages can now have a configure script. If a file `configure' is found it is executed before anything else is done by R INSTALL. o If HTML help files are asked for but not available, text help is used. o HTML help file conversion reports unsatisified \link{..}s. o `vsize' and `nsize' can be set by the environment variables R_VSIZE and R_NSIZE respectively, perhaps most conveniently from `~/.Renviron' under Unix or Windows. Command-line settings will take precedence. The defaults have been increased to 6M and 250k. o zip files can be used for storing help and example files. See the help files for "help" and "example" for details. o New submission method "none" (for not sending email) in bug.report(). o `R CMD check' can now also be used for installed packages without the corresponding sources. o The sources for the Windows port are included in src/gnuwin32. See src/gnuwin32/readme. BUG FIXES o deparser left off empty parentheses on e.g. (function(x) x)() o cat() now works on "name" objects o forgot to set jump buffer in return context in one case o parser dropped off tagged missing args on function calls ( f(a=) ) o relops tried to set time series parameters before dimensions o arithmetic tried to set time series parameters before dimensions o mvfft fixes (from Martyn Plummer) - not working with vectors and segfault problem. o Rephrased error message on invalid assignment target. o ifelse() now evaluates yes/no only if needed o PROTECT'ed some memory in NewExtractNames that was getting overwritten during garbage collection. o Crossing factors (`:') works again. o terms.formula used to choke on terms more than 60 characters long o is.nan() should now work correctly on new/old-style lists. o x[[i]] did not work correctly for negative subscripts i. o as.list() didn't work for expressions o x[[i]] <- quote(a) (x generic vector) didn't work o for method functions: many argument name changes, add ... where needed, for consistency with the generic function. o example() will allow (again) aliased topic names. o HTML help file conversions will find hyperlinks in the main library as well as the current library. Links containing `<' or `>' now work properly. o Rdconv conversion of \section{}{}s to Sd corrected. o ppois rounded non-integer `q', should truncate. o pnbinom was wrong for non-integer `q'. o dbinom, dgeom, dnbinom, dpois give 0 with a warning for non-integer arguments. o load / save / data allow unlimited string sizes. o strsplit() allows unlimited string size. o eigen() now should work (again) in all cases. o is.nan() fixed to work (again) in architectures with "unspecified" internal isnan(). CHANGES IN R VERSION 0.64.0 NEW FEATURES o Files BUGS and FAQ are now included with distribution and various "front matter" files have been cleaned up. o readline has now an argument prompt = "" o coplot() now labels levels when conditioning variable is factor (John Maindonald). o A new function filled.contour() has been added. It produces a variant of contour plots where the area between contours is filled with a solid colour. The function (currently) uses the layout() function and so is restricted to a full page display. o The function terrain.colors() has been modified to remove a visual discontinuity (at yellow). In addition, a function cm.colors() which implements a Cleveland-style cyan-magenta palette has been added. o Primitive function .External() to call dynamically loaded `internal'-style functions (code from Jean Meloche). o Function page() to view an R object in a pager. o Support for handling embedded '\n's in text strings handed to low-level graphics functions has been added. Some changes to the PostScript graphics driver were needed to support this, so there may some minor change in the appearance of plots produced in PostScript. o The LaTeX documentation is now split into 2 parts: the (currently almost non-existent) manual and a reference index. Manual: new section on loading C++ code. o [EXPERIMENTAL] Gnome support added. Use ./configure --with-gnome to try it, but don't expect too much yet. o HDF5 support improved. Still not perfect, though. o The X11 graphics driver can now use a variety of strategies for handing color. This means that it is now possible to use black and white or grayscale graphics on color displays. There are two strategies for handing color on pseudocolor displays. The original "allocate-colors-until-they-run-out" strategy has been supplemented by one which allocates a color cube at startup and approximates requested colors by those in the cube. On truecolor displays, there is no limit on the number of colors which can be displayed and you get exactly the color you request. (Note that Directcolor and staticcolor displays are not supported yet). o The persp() function now allows shading of the rendered surface using a simple lighting model. o Many functions providing an interface to the operating system have been made "platform independent". See the manual entries for "file", "list.files" and "file.show" for details of the new interface. The system.file() interface has been changed. o There is a new function "eval.with.vis" which behaves exactly like "eval", but which returns both the result of the evaluation an a logical value indicating whether the value is ``visible''. This has been used to replace some ad-hoc tests for whether value should be printed or not in "source". As a consequence, the "example" and "demo" functions no longer print invisible values when the example script is run. o Index files in data directories in packages should be `00Index' not `index.doc'. o Function interaction() to compute factor interactions. o load() can load to specific environments. o Sockets interface: make/read/write/close.socket() o Function chull() for planar convex hulls o pairs.formula() allows formula notations for scatter plot matrix. o new dataset co2. o documentation for datasets mtcars, plants, pressure, randu and sleep. o the sunspots dataset is now monthly rather than annual. BUG FIXES o strsplit(), scan() and friends use a much larger char buffer (still fixed size; this will change again) o ts() allows a data-frame argument `data'. o anova.lm handles singular models better, and deparses responses. o dump() now uses digits=12 rather than the current setting. o tabulate ignores entries beyond nbins rather than core dumps. o ?.C documents what C/Fortran types R objects correspond to in foreign function calls, which is not what everyone thought. o changed long to int in several .C calls to follow the above rules. o rbind(x1,x2) now does not lose dimnames when xi are character or complex. o readline() accidentally inherited menu()'s prompt. o .C() and .Fortran() now correctly report that there might be NaN/Infs, not just NAs, unless NAOK=TRUE. o Resizing an inactive graphics window to an invalid size left that window active and produced a spurious prompt and newline in the console window. This no longer happens. o poly() rescales x to increase accuracy o apply() preserves names in yet another case [-> new example]. o phyper() now works for larger arguments than before. o Missing values didn't work in log plot o outer() doesn't produce all-empty dimnames any more o quantile.default() works when `probs' has zero length o example() now works again in all cases [AnIndex spaces]. o typos fixed in nlm() message, glm help o pt() now works better for extreme `df' arguments and gives at least an approximate answer for ncp > 37.6. __more to change__ o fixed some glitches with formatC() and its docs. o several fixes in *.c code to make -Wall happy o curve() [and plot.function()] now use proper `x' values with log="x"; `type = "."' now works with curve() and plot.function() o zapped old windows files since they didn't build any more. The sources for the later gnuwin32 version are expected to appear here for 0.64.1. The #ifdef Win32's here are for that version. ************************************************** * * * 0.63 SERIES NEWS * * * ************************************************** CHANGES IN R VERSION 0.63.3 NEW FEATURES o get() and assign() allow position in search list to be a character string. (e.g. get("delete.response","package:base") o HTML search now works for all packages (after new installation). o R INSTALL now also copies DESCRIPTION file to target dir. o offsets should work with lm as well as with glm now o range() is now in the Summary group, trunc() back in the Math group. o Under Unix, R-specific environment variables can now be kept/set in `~/.Renviron'. o New options `latexcmd' and `dvipscmd' for specifying the locations of LaTeX and dvips; corresponding environment variables renamed to `R_LATEXCMD' and `R_DVIPSCMD'. o --vsize & --nsize now both give size in "single units" (bytes/cons cells) with possible suffixes "M" (Mega), "K"ilo (1024) and "k"ilo(1000). o [pdqr]negbin() now also work with non-integer 'size' [by Ben Bolker]. o New standard package `lqs' for resistant regression and covariance estimation, contributed by Brian Ripley. o new functions match.fun() and kronecker() [by Jonathan Rougier] o par(las = 3) is a new option. o new function jitter() [slightly more useful than S's]. BUG FIXES o system(command, intern=FALSE, ignore.errors=FALSE) changed 1st & 3rd argument names and is better documented. o "/Font5 /Symbol findfont definefont" confused some printers o Bounding box rotated 90 deg for landscape (shouldn't be) o Legend skipped symbol for pch=0 o compilation on non-Intel Linux systems no longer looks for __setfpucw o a %% b -- is now periodic instead of symmetric; more S compatible. o locator(n=512) -- default: MANY points, not just one. o qqnorm() uses ppoints() and returns list with x sorted along y. o plot.formula now allows ylab to be set o plotmath had trouble with paste()'ing expressions o plotting math expressions now also works for objects of mode "call" (in particular on the result of substitute()) o locator() on log axes: value antilogged twice o (a real oldie - and trival too) is.recursive now TRUE for expressions o sanitised delete.response o x[["a",]] could crash R o strwidth() crashed R if no device open o predict inconsistencies with offsets straightened out o tapply goofed when FUN returned named scalar o [.factor now retains contrasts attrib. o hist() had trouble with plotting math o HTML indices get only built when installing a package to RHOME o subscripting with a length zero logical no longer bombs. o as.ordered(NULL) now returns an "ordered" object. o --debugger .. now gives a warning if other command line args are used o pt(t, df, ncp) now also works for bigger ncp's o apply(a,d, fun) now passes vectors (rank 1 arrays) to fun. o model.frame() with subset and only one column fixed o boxplot() now works again. o dyn.load(..) failing gives more informative error message. o Ops.factor: not error, but a warning + NAs o bug.report() keeps report file if can't be e-mailed o Ops.data.frame : things like d.fr < a now return a matrix o data.frame(): duplicated row.names now give a warning when dropped. o boxplot(.., ylim=..) or (.., axes=..) gave erronous warning o glm had wrong init code for models with offsets. Also fixed so that linear predictor includes offset, also when predicting. o predict.glm didn't work with se=T o backsolve(), qr.solve... now return a vector when x (or y) is a vector. o string tags now converted to symbols and strange symbolic tags print as strings, cf. e<-quote(c(F=2, "tail area" = .5)), etc. o row.names(.) <- val doesn't allow duplicated values anymore. o library(mva)'s dist() now works with both "euclidean" & "euclidian" o revised curve function to avoid using grep patterns that caused problems under Solaris 2.6 o coplot() now has 'number' and 'overlap' arguments, and should work in more situations. [by John Maindonald and MM]. o save(..ascii=TRUE) now uses "full precision" for numerics. o as.array() preserves names() o outer() works for general array args and preserves (dim)names. o print.factor and print.ordered now return their args invisibly. CHANGES IN R VERSION 0.63.2 NEW FEATURES o sink() has new `append' argument. o new function rle(). o plot(.) and curve(.) also accept a function as first argument. new `plot.function'. o new function loglin(). o pretty() has new arguments and now better "obeys" its `n' arg. Internal GPretty() [implicitly used by axis(.., at = NULL,..) now uses pretty. o new generic function aggregate() with methods for data frames and time series. o data set `euro' with Euro conversion rates. BUG FIXES o model.frame(,subset=) no longer loses contrasts o `make install' copied the R shell script a second time without getting RHOME right (thus also breaking R CMD check). Fixed. o help() after help.start() did not work if topic was not equal to filename (e.g. rnorm is found in Normal.html) o fix the 0.63.1 fix for abbreviate(.); improved doc. o predict.mlm(.) couldn't have worked with `newdata'. o model.frame/na.omit bug for matrices and Surv objects. o mean( ) now doesn't return sum(.) anymore. o str(.) doesn't give extraneous "..." in rare cases anymore. o Added documentation for group methods ("Math", "Ops","Summary"). o R_PAPERSIZE is used for Rd2dvi and at configure time for the `make dvi' parts. o hist(i) now also works for e.g., i = -1, 0, or 1. o range() now works on dataframes (uses c(..., recursive=T)) o pretty(.) does not loop infinitely anymore in very extreme cases. o math functions should work better on dataframes now o plot(.., type = 'h', log = 'y') now works ... o plot.factor(x, y, ...) of two factors now makes barplot(table(y,x), ...) o use object$prior.weights in add1.glm, drop1.glm (Brian Ripley) o rnorm(1,mean=m,sd=0) returns m, not NaN (Ben Bolker) o runif(n, a,a) now returns rep(a,n) instead of NaNs. CHANGES IN R VERSION 0.63.1 NEW FEATURES o new function mosaicplot(). o xy.coords(.) has a "recycle = FALSE" argument, used in text(). o RNGtype() allows to choose different Random Number Generators. __EXPERIMENTAL__ o print.default(.) now also works with a `right = TRUE' argument. {{ print.matrix(.) is bound to become deprecated... }} o new help page `Memory' on the usage of command line options --vsize and --nsize. Error message if R runs out of memory points to help(Memory). o rowsum() and improved na.omit() added from survival4 o backsolve(.) has new arguments "upper.tri = TRUE, transpose = FALSE" o hist() has new "right = TRUE" argument; "right = FALSE" gives [a,b) intervals o help() has "htmlhelp" argument, allowing to suppress htmlhelp after help.start(). This is desired for ESS. o quantile(.) has an "names = TRUE" argument for speed. It is much better documented now. BUG FIXES o build-help --dosnames should now also work for text help, latex and examples. o seq() should work better now (fuzz-factor 1e-7 inserted) o multiple arguments to return caused value to be a pairlist o data.frame choked on long names from deparse() o data.edit now works (dataedit doesn't need pairlist()s anymore) o as.pairlist(NULL) is ok o ts(1:5, start=2, end=4) now work. Further plot(ts(..), ts(..)) o eigen() returns $vectors in any case [S compat]. o apply(cbind(1,1:9, 2, quantile) doesn't drop quantile names anymore o array(1, dim=(1:3)[c(F,F,F)]) is now valid == array(1,NULL) == c(1); the same for array(a,d, list()) o fix problem with step() and offsets o drop attributes on matrix subsetting o kappa(.) now works [dtrco now in load table (ROUTINES)]. o pmin() and pmax() now preserve attributes. o handle null models arising in drop1(), step, etc. o partial matching problem with $ indexing o matplot(.) works with lwd (vectors) o par("cex.axis") now has the desired effect... o which(.) now omits NAs in its argument. o rbind.data.frame caused character-to-factor coercion a bit too often o couple of messups in dotplot o z[[1]] <- ~x probl fixed as suggested by J.Lindsey o do_modelframe could lose contrast attributes o "make check" needed standardisation of locale o unlist(...,recursive=F) got names wrong o abbreviate(.) does not anymore return random garbage in some cases [by Guido M.] CHANGES IN R VERSION 0.63 NEW FEATURES o library(... , warn.conflicts = TRUE) now prints all conflicts arising from attaching the given package. o new .Platform variable for better modularizing platform dependence. __This_is_"beta"_and_bound_to_be_changed___ o new arguments to colnames(..) and rownames(x, do.NULL = TRUE, prefix = "row"). _ o par(bty = "]") for _| box(.) in plots. o New standard package `modreg' (smoothing and local MODern REGression methods) contributed by B. D. Ripley. o par() has a `no.readonly = FALSE' argument which allows more sensible op <- par(no.readonly = TRUE); on.exit(par(op)). o Real Bessel functions of 1st to 3rd kind, of arbitrary order: besselI(), besselK(), besselJ(), besselY() are the I(), K(), J(), and Y() Bessel functions. o New conflicts() function from B.D.Ripley o uniroot has a new `maxiter' argument and returns #{iter} and precision. o New option `show.coef.Pvalue' (default: TRUE). If FALSE, print.summary.[g]lm does not print P values. o New `R --vanilla' is equivalent to R --no-save --no-restore --no-site-file --no-init-file o gc() has now a `verbose' argument and returns a matrix with free and total n- and v-cells(heap). o New example() function runs the \emph{Examples} R code of . example() calls source() which now has a `verbose' instead of `debug' argument. o experimental functions [as.|is.|]pairlist() for the few old-style dotted pair lists [undocumented]. o options(check.bounds = TRUE) makes sub-assignments which "stretch" a vector give a warning [dropped undocumented check.bounds() function]. o Makefiles should now conform (mostly) with the GNU Coding Standards. In particular, `make install', `make uninstall' and `make install-strip' now work. Also, it is now possible to build R in a non-source directory. o which() preserves names and has a new `arr.ind' argument allowing for array indices. o New functions {d,p,q,r}signrank for the Wilcoxon signed rank distribution, and {d,p,q,r}wilcox for the Wilcoxon (rank sum) distribution. o Command line options GNUified a bit further. New command line option `--verbose' for printing more information about progress. Command line options `--vsize' and `--hsize' as replacements for `-v' and `-n' which are now deprecated. Added `--silent' as synonym for `--quiet'. Short-style option `-V' obsolete. o Added bug.report() to generate & send bug reports from within R. o The PostScript device driver now uses the ISO Latin1 font encoding. This should allow Western Europeans to render their languages correctly. It is likely that additional encodings will be added (e.g. Latin2) when we figure out how to set the correct font encoding in printers. o The mathematical annotation code has been reworked. Italic correction works better. Additional functionality will be added. o "sample" now has an optional "prob" argument which gives the probabilities of sampling each element in the vector being sampled. The present implementation is based on some code from E. S. Venkatraman . o The internal data structure used to represent lists has changed from being based on dotted pairs to generic vectors. Users should see no changes as a result (with the exception of some efficiency gains in list operations). o Subscripting matches that of S more closely. It is now possible to use subscripting beyond that the end of vectors and lists. o Element labelling in "c" and "unlist" should match that of of S. o Added split.screen etc functions for manipulating multiple screens on a single device o After help.start() the HTML help system is used for all help() requests. The name of the browser is now controlled by options("browser"). o Added kmeans to package mva (donated by B. Ripley) o New persp function added. It is NOT compatible with S (yet) and is subject to internal and interface changes. o gctorture() for torturing the garbage collector to reveal memory protection bugs. (Call GC on every memory allocation). o B. Ripley's aov code (and more) has been added. This includes: - aov() now handles models with Error terms, multiple responses. - proj(), model.tables(), se.contrast(), replications(), eff.aovlist() are implemented for aov fits, and where appropriate for lm fits. - dummy.coef(), with methods for lm and aovlist fits. - add1(), drop1(), step() for stepwise fitting of statistical models, with default, lm and glm methods. - summary() and deviance() -- mlm methods. - kappa() for estimating condition numbers) - labels() to find a suitable set of labels from an object - C() for setting the contrasts of a factor - anova(), plot(), summary() and deviance() methods for mlm fits o eval() semantics changed when envir= is a list. A 3rd argument is now allowed, specifying the enclosure (i.e. where R looks for variables *not* found in envir=) it defaults to the calling environment (was .GlobalEnv). Note that when used inside a function, it is often desirable to set the enclosure to the parent environment instead. [ eval(e, data, sys.frame(sys.parent())) ] BUG FIXES o min(NULL); max(double()) now give warnings. range() gives NA. o substring("", NULL) no longer segfaults. o formatC(.) now takes default "width = 1" when both width and digits are unspecified. o several fixes in internal axis and tickmarks setup for "extreme" ranges and values, especially for "log" scaling. o seq(a,a, by=b) now works properly. o print.data.frame(.) now calls print.matrix instead of print(.) which finally enables the 'right = TRUE' argument. o R --help gives more o postscript() now uses 'hyphen' instead of 'plusminus' for a minus. o source(..., echo=TRUE) now puts a `"' if necessary after truncation. o Changes to the PostScript device driver mean that the volume of output has been reduced to about a third of what it was. o Fixes and restructuring to name generation in connection with unlist() and c(). o Many bugs found and fixed in the memory allocation / garbage collection area. In particular, the parser was sometimes UNPROTECT()ing the wrong pointers. o lm(y[g=="1"]~x[g=="1"]) caused memory corruption CHANGES IN R VERSION 0.62.4 BUG FIXES o plot.default(.) has now 'sub' argument which eliminates "Warning: parameter "sub" couldn't be set in high-level plot() function" o formatC(numeric(0)) now works. o menu(.) works for empty imput o 0i ^ 2 now gives 0+0i as it should. o ppoints() now behaves like S, and has additional argument 'a' o seq(1,6,by=3) and similar "by" calls now work okay o mahalanobis(.) now fixed; does *NOT* have default arguments for center and cov anymore. o diag(.) doesn't return non-sensical dimnames anymore. CHANGES IN R VERSION 0.62.3 NEW FEATURES o preserve factor levels and contrast settings in model objects o factor[...,drop=T] reduces level set o added dblepr, intpr o do_modelmatrix(model.c): Set rownames from data argument. o New generic function preplot(). o A new R BATCH interface for non-interactive execution. o Added `offline' argument to help() for producing hardcopy via latex and dvips. o glm.fit.null now calculates AIC and print.glm.null prints it o effects.lm implemented o new class "mlm" for multivariate "lm", predict.mlm to go with it o "Details" section added to .Rd format o R_PRINTCMD and R_PAPERSIZE can now be set via users' environment, overriding setting in startup script. o enhanced identify() o new function print.coefmat() o added unix() as .Deprecated("system") o date() replacing system.date() BUG FIXES o substitute would re-substitute after expanding ... o indexing modified object in some cases o sweep should work again on dataframes o minor changes in aov() o builds should now actually work on systems that do not add underscores to Fortran symbols o biplot[.default]() was redundant in "base" package; now only in "mva". o unix(..) now helps the user to find system(..) instead. o apropos("[") and methods("[") now both work (even though "[" is not a valid regular expression). o row.names<-.default now exists. Converts object to data frame and then adds row names o codes() now distinguishes between ordered and unordered factors o codes() had *opposite* semantics of Splus. Now it's the same. o replicating factors now yields factors (again) o print.summary.xxx functions more consistent, using new function print.coefmat(). o Changed many `T' to `TRUE' and `F' to `FALSE' in the base package. o binary operation on 1x1 matrix lost dimension o fix anova.glm for null model o glm.fit.null: ensure df.residual == df.null for a null model o summary.glm: correlations in saturated cases o stat.anova: use match.arg and labeled switch statement o Major cleanup of glm iteration code o Correct reordering of glm coefficients if pivoting o Rownames on contrast matrices o factor() and [.factor preserves class "ordered" o Code rearrangement in predict.lm (avoid unnecessary computation) + let rownames through on predictions o model.matrix.default: Initial code to define model frame simplified considerably after defaulting data argument to sys.frame(sys.parent()). This also removes the problem where data.frame mangles I(x^2) and similar names, so that the "reorder" sanity check at the end fails. o The handling of extra FORTRAN libraries (f2c-related and BLAS) should now be correct. Via SHLIBLDFLAGS, add-ons will also be linked against these libraries. o Modified makefiles so configure followed by "make distclean" should restore the source tree to its original form. o a leftover "colours <- colors" caused trouble when collating sequence changes caused files to go into the "base" file in a different order CHANGES IN R VERSION 0.62.2 (The new functions predict.glm, poly, aov, alias, biplot.default and biplot.princop, update.default and rug all come from Brian D. Ripley, who is also responsible for finding and/or fixing a lot of the bugs) NEW FEATURES o predict.glm() added. o text() is generic. o update.default() (replaces update.glm() and update.lm()). (This will only work if you comment out update.lm and update.glm in the sources, or disable them with update.lm<-function(object,...)NextMethod(), etc.) o predict.lm() changed towards S-plus compatibility. Intervals are still available via interval= argument. o zapsmall() function. o polygon() now handles NAs o options(show.signif.stars = TRUE). If FALSE, summary.lm and similar functions do *not* print significance stars anymore. o poly() for [g]lm modelling. o aov() for Analysis Of Variance [anova]. o alias() for displaying ``aliased'' factor levels in (>=2)way anova. o mva: Now has biplot and biplot.princomp o rug() plot. o new src/library/profile/Common.R for OS-independent intialization. o new date stamp mechanism (ensures that prerelease versions carry correct date) BUG FIXES o abbreviate() now always retains the first letter. o attr() partial matches for attribute name. o axis() accepts graphical parameters. o binomial() accepts factor responses. o cbind() works with data frames. o contrasts() gives simpler labels (like S) for factors with two levels. o contrasts<-() now has a how.many= argument. o contour() and image() can accept a list to specify the matrix. o contr.poly() uses orthogonal polynomials (like S) not raw polynomials. o data() could fail with a partial match to the dataset name. o density() works correctly if from= or to= are used. n= can now take any value, not just a large power of 2. o expand.grid() now accepts more than two arguments, or a list of factors. o factor() and ordered() handle their levels argument better. o family.glm() now returns the correct family (including link etc). o legend() now knows about lwd. o match.args() works correctly for default arguments. o model.frame.lm() did not invoke `lm'. o model.matrix() calls model.frame() if needed. o model.response() now returns names, so glm() gives names to residuals, fitted values, etc. o quasi() works in glm() (was missing aic component). o seq() sometimes omitted the final value due to rounding error. o terms.formula() and update.formula() now resolve `.' in formulae and tidy up `(a + b) - b' etc. o ... is now passed down correctly to functions inside functions. o save.image didn't work (Martyn Plummer) o abs() instead of fabs() in seq.c crashed R on Digital Unix o model.matrix() gagged on variables with complicated names o saturated models acting up in glm o various improvement of build procedures o rbind(NULL, matrix) core dump o density() default 'bw' now 0.9*(...) instead of 1.06*(...) [=Silverman's rule of thumb]. o detach(2) now works. o format() doesn't drop names anymore. o format.pval() works with NAs. o print.[summary.][g]lm() functions print numbers better formatted. o legend() now also works properly in log coordinates. o backsolve() now working; bakslv.c not depending on Fortran_underscores. o Tick marks acting up on log axes in postscript (fix from Martyn Plummer) o The Rd format has a new section \details{} (needed for proper Sd2Rd translation). \R was not understood for nroff conversions, longer dashes (-- and --- in latex syntax) are now converted properly. o prompt.default() now carries "\details{}". o R [ SHLIB | COMPILE ] were broken on some Solaris systems due to use of bash syntax. R [ INSTALL | COMPILE | SHLIB ] now use a MAKE environment variable if present. R INSTALL only rebuilds man pages if they are not already up to date. CHANGES IN R VERSION 0.62.1 BUG FIXES o Accidentally shipped R-0.62 without the tests and etc/Rdoc directories. 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.