Dear Emacs, please make this -*-Text-*- mode! ************************************************** * * * 1.7 SERIES NEWS * * * ************************************************** CHANGES IN R VERSION 1.7.1 NEW FEATURES o The help pages give appropriate references to the Blue, White or Green books for functions based on the descriptions of S functions given there. (E&OE) o Function getAnywhere() can find non-exported objects, for namespaces or registered methods. DEPRECATED & DEFUNCT o The (unimplemented) argument 'white' of parse() is deprecated. o The tkfilefind demo in the tcltk library is deprecated, since it never worked well, and apparently not at all with Tcl/Tk 8.4. BUG FIXES o print.table() used too much white space in some cases in 1.7.0. o selectMethod() failed if `f' was a non-generic and optional=TRUE, and gave a confusing error message if optional=FALSE. o pchisq(*, ncp) and qchisq(*, ncp) work in more cases for large ncp or quantile and give warning or error messages otherwise. o str(x) now also works when x is an "externalptr" (or "weakref"). o rbeta(), rf(), and rt() now support infinite parameter values; other distributions return NaN instead of NA for such. o Redefining a class is now safer if the new definition generates an error (previously some invalid metadata could be left behind). o A number of errors are now caught in setClass() that previously either went unchecked or waited until new() to appear: - classes may not contain themselves, directly or indirectly; - classes appearing either as slots or as superclasses must themselves be defined; - slot names (direct or inherited) must be unique. In related changes, prototype() now works as documented, and is the recommended way to provide prototype objects. o Sorting an ordered factor would return an unordered one. This caused some trouble with panel.superpose (PR#974). o methods() could return duplicates if a method in a namespace was both exported and registered. o The internal zip.unpack() could crash if more than 500 files were to be extracted. (PR#2818) o The "r+" and "r+b" modes of opening file connections disallowed writing. o library() now warns the user if the chosen package name doesn't match the internal package name, and corrects the error. (PR#2816) o qr(LAPACK=TRUE) (and qr for complex arguments) might have failed to pivot for rank-deficient inputs. (PR#2867) o Only re-mapped symbols are exported by regex.o, to avoid problems with embedded R on RedHat 9. o arima() did not set transform.pars to FALSE if AR parameters were fixed, although it claimed to. o pnorm() was slower than necessary in the outer tails in some cases due to a typo in the improvements from PR#699. (PR#2883) o setGeneric() and setMethod() now catch some examples where the generic and the method have different argument lists; the evaluator checks for internal consistency of these argument lists. o expand.grid(x) {the rare case of one argument} now treats factor levels as in the typical case of two or more arguments. o Some implicit coercions to lists could cause segfaults, e.g. x <- matrix(nrow=20000, ncol=20); x$any <- numeric(0) due to a PROTECT bug. (PR#2923) o The replacement functions for colnames() and rownames() did not work for arrays with more than two dimensions. They could create dimnames of the form list(NULL, NULL) rather than remove the dimnames attribute. o termplot() gave incorrect answers with rug=TRUE or partial=TRUE for factors whose levels were not in lexicographical order. o A serious performance flaw in as() computations was fixed (the methods were not being cached properly.) o model.frame(~1, data) always returned 1 row. (PR#2958) o The data editor was truncating objects to 65535 rows. Pro tem, editing objects with more than 65535 rows is an error, and objects cannot be extended beyond that row. This restriction will be removed in 1.8.0. (PR#2962) o A bug could produce apparent loops in formal method selection when inheritance was restricted (used for the as() function). A related problem sometimes broke attaching a package that had methods for basic functions, such as names(), used in method selection. o Empty expressions as in return(x,) could generate subsequent segfaults: they are now errors. (PR#2880) o The Kinderman-Ramage Normal Random Generator had several problems leading to not-quite normally distributed variates (PR#2846). One problem was traced to an error in the original 1976 JASA paper! Thanks to Josef Leydold and his team for investigating this. The old generator has been retained for reproducibility of older results, under the name "Buggy Kinderman-Ramage". A warning is issued if you select it (also indirectly via RNGversion()). o promptMethods() now puts the \alias lines for methods in the normal place, near the top of the file, and quotes class names in signatures. o getS3method() and methods() were not finding methods for coefficients() and fitted.values() (which dispatch on "coef" and "fitted" respectively). o scan() (and hence read.table) was not finding matches for separator chars with the upper bit set. (PR#3035) o lm.(w)fit failed if the fit had rank 0. o lqs() did not report explicitly that it had failed if all samples gave singular fits. o predict.lm(*, se=TRUE) {w/ weights, w/o newdata} now gives correct SE's. (PR#3043) o cor.test(x, y, method="spearman") now also works for length(x) > 1290. o Matrices were printed mis-aligned if right=TRUE and na.print was specified. (PR#3058) o R CMD check gives now a clearer message when latex produces errors on the package manual. (PR#3070) o isSeekable() was incorrectly returning FALSE on all file connections. o tkpager() wasn't quite using its title and header arguments in the way prescribed by file.show() o legend(*, pch=p, lty=l) now works better when `p' or `l' have NAs. o All braces in regular expressions used by Sweave() are now escaped by a backslash. o unloadNamespace() failed because getNamespaceImports() now coerces a string argument to a name space. o deriv3 gave incorrect Hessians for some very simple expressions such as expression(x*y) (since the comments in the C code were incorrect). (PR#2577) o power.t.test(..., delta=NULL,alternative='two.sided') failed. (PR#2993) o Lines on postscript() plots with thousands of segments might have been plotted inaccurately in 1.7.0. (PR#3132) Solid lines in postscript() output are split into groups of 1000 segments to help some PostScript interpreters (typically old level-1 interpreters). o cut.POSIXt failed when the breaks were date/time objects. (PR#3181) o Usage of methods in dist.Rd is now correctly documented (as.matrix.dist() is not an exported symbol). o The predict() method for ar fits was not retrieving the series from the parent environment. o eigen() and La.eigen() were not returning a matrix of eigenvectors for a 1x1 input. o hsv() and rgb() now return character(0) when one of their args has length 0. This also fixes terrain.color(1). (PR#3233) o [[<-.data.frame checked if a replacment was too short, but not if it was too long. (related to PR#3229) o qt(x, df) was quite inaccurate for df=1+epsilon; it is now much more accurate for df in (1,2) and more precise for other df. (PR#2991) o qbeta() now has slightly improved C code in two places, as suggested in the 2nd followup to PR#2894. CHANGES IN R VERSION 1.7.0 USER-VISIBLE CHANGES o solve(), chol(), eigen() and svd() now use LAPACK routines unless a new back-compatibility option is turned on. The signs and normalization of eigen/singular vectors may change from earlier versions. o The `methods', `modreg', `mva', `nls' and `ts' packages are now attached by default at startup (in addition to `ctest'). The option "defaultPackages" has been added which contains the initial list of packages. See ?Startup and ?options for details. Note that .First() is no longer used by R itself. class() now always (not just when `methods' is attached) gives a non-null class, and UseMethod() always dispatches on the class that class() returns. This means that methods like foo.matrix and foo.integer will be used. Functions oldClass() and oldClass<-() get and set the "class" attribute as R without `methods' used to. o The default random number generators have been changed to `Mersenne-Twister' and `Inversion'. A new RNGversion() function allows you to restore the generators of an earlier R version if reproducibility is required. o Namespaces can now be defined for packages other than `base': see `Writing R Extensions'. This hides some internal objects and changes the search path from objects in a namespace. All the base packages (except methods and tcltk) have namespaces, as well as the recommended packages `KernSmooth', `MASS', `boot', `class', `nnet', `rpart' and `spatial'. o Formulae are not longer automatically simplified when terms() is called, so the formulae in results may still be in the original form rather than the equivalent simplified form (which may have reordered the terms): the results are now much closer to those of S. o The tables for plotmath, Hershey and Japanese have been moved from the help pages (example(plotmath) etc) to demo(plotmath) etc. o Errors and warnings are sent to stderr not stdout on command-line versions of R (Unix and Windows). o The R_X11 module is no longer loaded until it is needed, so do test that x11() works in a new Unix-alike R installation. NEW FEATURES o if() and while() give a warning if called with a vector condition. o Installed packages under Unix without compiled code are no longer stamped with the platform and can be copied to other Unix-alike platforms (but not to other OSes because of potential problems with line endings and OS-specific help files). o The internal random number generators will now never return values of 0 or 1 for runif. This might affect simulation output in extremely rare cases. Note that this is not guaranteed for user-supplied random-number generators, nor when the standalone Rmath library is used. o When assigning names to a vector, a value that is too short is padded by character NAs. (Wishlist part of PR#2358) o It is now recommended to use the 'SystemRequirements:' field in the DESCRIPTION file for specifying dependencies external to the R system. o Output text connections no longer have a line-length limit. o On platforms where vsnprintf does not return the needed buffer size the output line-length limit for fifo(), gzfile() and bzfile() has been raised from 10k to 100k chars. o The Math group generic does not check the number of arguments supplied before dispatch: it used to if the default method had one argument but not if it had two. This allows trunc.POSIXt() to be called via the group generic trunc(). o Logical matrix replacement indexing of data frames is now implemented (interpreted as if the lhs was a matrix). o Recursive indexing of lists is allowed, so x[[c(4,2)]] is shorthand for x[[4]][[2]] etc. (Wishlist PR#1588) o Most of the time series functions now check explicitly for a numeric time series, rather than fail at a later stage. o The postscript output makes use of relative moves, and so is somewhat more compact. o %*% and crossprod() for complex arguments make use of BLAS routines and so may be much faster on some platforms. o arima() has coef(), logLik() (and hence AIC) and vcov() methods. o New function as.difftime() for time-interval data. o basename() and dirname() are now vectorized. o biplot.default() {mva} allows `xlab' and `ylab' parameters to be set (without partially matching to `xlabs' and `ylabs'). (Thanks to Uwe Ligges.) o New function capture.output() to send printed output from an expression to a connection or a text string. o ccf() (pckage ts) now coerces its x and y arguments to class "ts". o chol() and chol2inv() now use LAPACK routines by default. o as.dist(.) is now idempotent, i.e., works for "dist" objects. o Generic function confint() and `lm' method (formerly in package MASS, which has `glm' and `nls' methods). o New function constrOptim() for optimisation under linear inequality constraints. o Add `difftime' subscript method and methods for the group generics. (Thereby fixing PR#2345) o download.file() can now use HTTP proxies which require `basic' username/password authentication. o dump() has a new argument `envir'. The search for named objects now starts by default in the environment from which dump() is called. o The edit.matrix() and edit.data.frame() editors can now handle logical data. o New argument `local' for example() (suggested by Andy Liaw). o New function file.symlink() to create symbolic file links where supported by the OS. o New generic function flush() with a method to flush connections. o New function force() to force evaluation of a formal argument. o New functions getFromNamespace(), fixInNamespace() and getS3method() to facilitate developing code in packages with namespaces. o glm() now accepts `etastart' and `mustart' as alternative ways to express starting values. o New function gzcon() which wraps a connection and provides (de)compression compatible with gzip. load() now uses gzcon(), so can read compressed saves from suitable connections. o help.search() can now reliably match individual aliases and keywords, provided that all packages searched were installed using R 1.7.0 or newer. o hist.default() now returns the nominal break points, not those adjusted for numerical tolerances. To guard against unthinking use, `include.lowest' in hist.default() is now ignored, with a warning, unless `breaks' is a vector. (It either generated an error or had no effect, depending how prettification of the range operated.) o New generic functions influence(), hatvalues() and dfbeta() with lm and glm methods; the previously normal functions rstudent(), rstandard(), cooks.distance() and dfbetas() became generic. These have changed behavior for glm objects -- all originating from John Fox' car package. o interaction.plot() has several new arguments, and the legend is not clipped anymore by default. It internally uses axis(1,*) instead of mtext(). This also addresses "bugs" PR#820, PR#1305, PR#1899. o New isoreg() function and class for isotonic regression (`modreg' package). o La.chol() and La.chol2inv() now give interpretable error messages rather than LAPACK error codes. o legend() has a new `plot' argument. Setting it `FALSE' gives size information without plotting (suggested by U.Ligges). o library() was changed so that when the methods package is attached it no longer complains about formal generic functions not specific to the library. o list.files()/dir() have a new argument `recursive'. o lm.influence() has a new `do.coef' argument allowing *not* to compute casewise changed coefficients. This makes plot.lm() much quicker for large data sets. o load() now returns invisibly a character vector of the names of the objects which were restored. o New convenience function loadURL() to allow loading data files from URLs (requested by Frank Harrell). o New function mapply(), a multivariate lapply(). o New function md5sum() in package tools to calculate MD5 checksums on files (e.g. on parts of the R installation). o medpolish() {package eda} now has an `na.rm' argument (PR#2298). o methods() now looks for registered methods in namespaces, and knows about many objects that look like methods but are not. o mosaicplot() has a new default for `main', and supports the `las' argument (contributed by Uwe Ligges and Wolfram Fischer). o An attempt to open() an already open connection will be detected and ignored with a warning. This avoids improperly closing some types of connections if they are opened repeatedly. o optim(method = "SANN") can now cover combinatorial optimization by supplying a move function as the `gr' argument (contributed by Adrian Trapletti). o PDF files produced by pdf() have more extensive information fields, including the version of R that produced them. o On Unix(-alike) systems the default PDF viewer is now determined during configuration, and available as the 'pdfviewer' option. o pie(...) has always accepted graphical pars but only passed them on to title(). Now pie(, cex=1.5) works. o plot.dendrogram (`mva' package) now draws leaf labels if present by default. o New plot.design() function as in S. o The postscript() and PDF() drivers now allow the title to be set. o New function power.anova.test(), contributed by Claus Ekstrøm. o power.t.test() now behaves correctly for negative delta in the two-tailed case. o power.t.test() and power.prop.test() now have a `strict' argument that includes rejections in the "wrong tail" in the power calculation. (Based in part on code suggested by Ulrich Halekoh.) o prcomp() is now fast for n x m inputs with m >> n. o princomp() no longer allows the use of more variables than units: use prcomp() instead. o princomp.formula() now has principal argument `formula', so update() can be used. o Printing an object with attributes now dispatches on the class(es) of the attributes. See ?print.default for the fine print. (PR#2506) o print.matrix() and prmatrix() are now separate functions. prmatrix() is the old S-compatible function, and print.matrix() is a proper print method, currently identical to print.default(). prmatrix() and the old print.matrix() did not print attributes of a matrix, but the new print.matrix() does. o print.summary.{lm,glm} now default to symbolic.cor = FALSE, but symbolic.cor can be passed to the print methods from the summary methods. print.summary.{lm,glm} print correlations to 2 decimal places, and the symbolic printout avoids abbreviating labels. o If a prompt() method is called with 'filename' as 'NA', a list-style representation of the documentation shell generated is returned. New function promptData() for documenting objects as data sets. o qqnorm() and qqline() have an optional logical argument `datax' to transpose the plot (S-PLUS compatibility). o qr() now has the option to use LAPACK routines, and the results can be used by the helper routines qr.coef(), qr.qy() and qr.qty(). The LAPACK-using versions may be much faster for large matrices (using an optimized BLAS) but are less flexible. o QR objects now have class "qr", and solve.qr() is now just the method for solve() for the class. o New function r2dtable() for generating random samples of two-way tables with given marginals using Patefield's algorithm. o rchisq() now has a non-centrality parameter `ncp', and there's a C API for rnchisq(). o New generic function reorder() with a dendrogram method; new order.dendrogram() and heatmap(). o require() has a new argument, character.only, -- to make it align with library. o New functions rmultinom() and dmultinom(), the first one with a C API. o New function runmed() for fast runnning medians (`modreg' package). o New function slice.index() for identifying indexes with respect to slices of an array. o solve.default(a) now gives the dimnames one would expect. o stepfun() has a new `right' argument for right-continuous step function construction. o str() now shows ordered factors different from unordered ones. It also differentiates "NA" and as.character(NA), also for factor levels. o symnum() has a new logical argument `abbr.colnames'. o summary() now mentions NA's as suggested by Göran Broström. o summaryRprof() now prints times with a precision appropriate to the sampling interval, rather than always to 2dp. o New function Sys.getpid() to get the process ID of the R session. o table() now allows exclude= with factor arguments (requested by Michael Friendly). o The tempfile() function now takes an optional second argument giving the directory name. o The ordering of terms for terms.formula(keep.order=FALSE) is now defined on the help page and used consistently, so that repeated calls will not alter the ordering (which is why delete.response() was failing: see the bug fixes). The formula is not simplified unless the new argument `simplify' is true. o added "[" method for terms objects. o New argument `silent' to try(). o ts() now allows arbitrary values for y in start/end = c(x, y): it always allowed y < 1 but objected to y > frequency. o unique.default() now works for POSIXct objects, and hence so does factor(). o Package tcltk now allows return values from the R side to the Tcl side in callbacks and the R_eval command. If the return value from the R function or expression is of class "tclObj" then it will be returned to Tcl. o A new HIGHLY EXPERIMENTAL graphical user interface using the tcltk package is provided. Currently, little more than a proof of concept. It can be started by calling "R -g Tk" (this may change in later versions) or by evaluating tkStartGUI(). Only Unix-like systems for now. It is not too stable at this point; in particular, signal handling is not working properly. o Changes to support name spaces: - Placing base in a name space can no longer be disabled by defining the environment variable R_NO_BASE_NAMESPACE. - New function topenv() to determine the nearest top level environment (usually .GlobalEnv or a name space environment). - Added name space support for packages that do not use methods. o Formal classes and methods can be `sealed', by using the corresponding argument to setClass or setMethod. New functions isSealedClass() and isSealedMethod() test sealing. o packages can now be loaded with version numbers. This allows for multiple versions of files to be installed (and potentially loaded). Some serious testing will be going on, but it should have no effect unless specifically asked for. INSTALLATION CHANGES o TITLE files in packages are no longer used, the Title field in the DESCRIPTION file being preferred. TITLE files will be ignored in both installed packages and source packages. o When searching for a Fortran 77 compiler, configure by default now also looks for Fujitsu's frt and Compaq's fort, but no longer for cf77 and cft77. o Configure checks that mixed C/Fortran code can be run before checking compatibility on ints and doubles: the latter test was sometimes failing because the Fortran libraries were not found. o PCRE and bzip2 are built from versions in the R sources if the appropriate library is not found. o New configure option --with-lapack to allow high-performance LAPACK libraries to be used: a generic LAPACK library will be used if found. This option is not the default. o New configure options --with-libpng, --with-jpeglib, --with-zlib, --with-bzlib and --with-pcre, principally to allow these libraries to be avoided if they are unsuitable. o If the precious variable R_BROWSER is set at configure time it overrides the automatic selection of the default browser. It should be set to the full path unless the browser appears at different locations on different client machines. o Perl requirements are down again to 5.004 or newer. o Autoconf 2.57 or later is required to build the configure script. o Configure provides a more comprehensive summary of its results. o Index generation now happens when installing source packages using R code in package tools. An existing 'INDEX' file is used as is; otherwise, it is automatically generated from the \name and \title entries in the Rd files. Data, demo and vignette indices are computed from all available files of the respective kind, and the corresponding index information (in the Rd files, the 'demo/00Index' file, and the \VignetteIndexEntry{} entries, respectively). These index files, as well as the package Rd contents data base, are serialized as R objects in the 'Meta' subdirectory of the top-level package directory, allowing for faster and more reliable index-based computations (e.g., in help.search()). o The Rd contents data base is now computed when installing source packages using R code in package tools. The information is represented as a data frame without collapsing the aliases and keywords, and serialized as an R object. (The 'CONTENTS' file in Debian Control Format is still written, as it is used by the HTML search engine.) o A NAMESPACE file in root directory of a source package is copied to the root of the package installation directory. Attempting to install a package with a NAMESPACE file using --save signals an error; this is a temporary measure. DEPRECATED & DEFUNCT o The assignment operator `_' will be removed in the next release and users are now warned on every usage: you may even see multiple warnings for each usage. If environment variable R_NO_UNDERLINE is set to anything of positive length then use of `_' becomes a syntax error. o machine(), Machine() and Platform() are defunct. o restart() is defunct. Use try(), as has long been recommended. o The deprecated arguments `pkg' and `lib' of system.file() have been removed. o printNoClass() {methods} is deprecated (and moved to base, since it was a copy of a base function). o Primitives dataClass() and objWithClass() have been replaced by class() and class<-(); they were internal support functions for use by package methods. o The use of SIGUSR2 to quit a running R process under Unix is deprecated, the signal may need to be reclaimed for other purposes. UTILITIES o R CMD check more compactly displays the tests of DESCRIPTION meta-information. It now reports demos and vignettes without available index information. Unless installation tests are skipped, checking is aborted if the package dependencies cannot be resolved at run time. Rd files are now also explicitly checked for empty \name and \title entries. The examples are always run with T and F redefined to give an error if used instead of TRUE and FALSE. o The Perl code to build help now removes an existing example file if there are no examples in the current help file. o R CMD Rdindex is now deprecated in favor of function Rdindex() in package tools. o Sweave() now encloses the Sinput and Soutput environments of each chunk in an Schunk environment. This allows to fix some vertical spacing problems when using the latex class slides. C-LEVEL FACILITIES o A full double-precision LAPACK shared library is made available as -lRlapack. To use this include $(LAPACK_LIBS) $(BLAS_LIBS) in PKG_LIBS. o Header file R_ext/Lapack.h added. C declarations of BLAS routines moved to R_ext/BLAS.h and included in R_ext/Applic.h and R_ext/Linpack.h for backward compatibility. o R will automatically call initialization and unload routines, if present, in shared libraries/DLLs during dyn.load() and dyn.unload() calls. The routines are named R_init_ and R_unload_, respectively. See the Writing R Extensions Manual for more information. o Routines exported directly from the R executable for use with .C(), .Call(), .Fortran() and .External() are now accessed via the registration mechanism (optionally) used by packages. The ROUTINES file (in src/appl/) and associated scripts to generate FFTab.h and FFDecl.h are no longer used. o Entry point Rf_append is no longer in the installed headers (but is still available). It is apparently unused. o Many conflicts between other headers and R's can be avoided by defining STRICT_R_HEADERS and/or R_NO_REMAP -- see `Writing R Extensions' for details. o New entry point R_GetX11Image and formerly undocumented ptr_R_GetX11Image are in new header R_ext/GetX11Image. These are used by package tkrplot. BUG FIXES o Sys.sleep() on Unix was having trouble with waits of less than 0.5s o The fix to PR#2396 broke read.table() on files with CR line endings. (PR#2469) Separate problem with this on Carbon MacOS build fixed as well. o Converting Sweave files to noweb syntax using SweaveSyntConv() was broken. o Printing numbers near the minimum could get the number of significant figures wrong due to underflow: for example 4e-308 might print as 4.00000e-308. (Seen on some Windows builds, and also on numbers around 1e-317 on Linux.) o wilcox.test() could give integer overflow warnings on very long vectors. Also added tests for numeric inputs, as per the help page. (PR#2453) o Printing unquoted character vectors containing escape characters was computing the wrong length and hence misaligning names. This was due to a bug in Rstrlen which might have had other effects. o if(logical(0)) and while(logical(0)) now report zero length, not `missing value where logical is needed'. o The gaussian() and inverse.gaussian() families were documented to allow only one link, which has not been true in R for at least four years. o prmatrix() forced conversion to character if `na.print' was used, and that conversion neither respected `digits' nor `quote'. o Rprof() might give misleading results for too small values of `interval' and in practice the default 20ms was about as small as is advisable on Linux. Now the interval is forced to be at least one clock tick. o summary.data.frame() was not giving interpretable results when the data frame contained a data frame as a column. (PR#1891) o delete.response() might re-order the rhs terms so prediction might fail or even give incorrect results. (PR#2206) o StructTS() now accepts numeric time series of integer storage mode. o all(), any() now handle NAs as documented. o Subsetting arrays to a result with 0 dimension(s) failed if the array had dimnames. (PR#2507) o If the call to data.frame() included 0-row arguments, it tried to replicate them to the maximum number of rows, and failed if this was 1 or more. o replicate() now understands data frames to which na.omit() has been applied. o is.ts() was too liberal: a time series must have at least one point. o methods() was sorting by package, not by name. o symbols(thermometers=) was often giving a spurious warning about the range. o tcltk was using deprecated internals of the Tcl library when accessing error messages. Not likely to be a user-visible change. o The automatic search for BLAS libs now tries Sun's libsunperf the way the latest versions require. (PR#2530) o str(array(1)) now does show the array. str(Surv(...)) now works again. o step(), add1.default() and drop1.default() now work somewhat better if called from a function. o page() was searching from the wrong environment, and so searching base before the workspace. o crossprod(Z) for complex Z was returning nonsense. o La.chol2inv() gave incorrect results unless the matrix was square. o When the POSIXt date functions were required to guess DST, they sometimes guessed correctly that DST was in force but converted a POSIXlt time as if standard time was given. o c/rbind were not handling zero col/row matrices correctly. (PR#2541 was one symptom.) o approx() and approxfun() now work with 1 knot if method = "constant". stepfun(), ecdf() and plot.stepfun() do so as well. o AIC.lm/default was failing if multiple objects and k were specified. (PR#2518) o removeMethods{methods} was broken. (PR#2519) o summary.glm() had two `aic' components in the returned object. o autoload() was returning the value of its last command, a promise, even though it was documented to have no value. As a result some packages (e.g. nlme) were loading packages they meant to autoload. o Fixes to methods and classes: - show() is consistent with using setOldClass for S3 classes. - several problems with the coerce and replace methods generated by setIs have been fixed. - more thorough tests & informative messages for invalid `def' arguments to setGeneric - setGeneric will now create the generic function even when a generic of the same name already exists (it does issue a warning). o unz() connections could no longer be opened. (PR#2579) o unique(ordered factor) returned an unordered factor. (PR#2591) o x[] <- value coerced x to the mode of value if and only if x had length 0! (Should only happen if x is null: PR#2590) o lm() mislabelled the cols of the qr decomposition. (cause of PR#2586) o data() looks for file extensions in an order prescribed in the help file: previously whether foo.R or foo.csv was used was locale-dependent. o sys.function() now returns the actual function being evaluated in the specified frame rather than one inferred from the call. o match.call() now uses the definition of the actual function being evaluated rather than one inferred from the call. o abbreviate(*, dot = TRUE) now only adds a "." where abbreviations did happen. o Changing timezones in the POSIXt functions was not working on some Linux systems, and this has been corrected. o ks.test() in package ctest had numerical problems in the lower tail of the asymptotic distribution (PR#2571). o Sweave() now handles empty chunks at the end of files correctly. o [<-() lost the object bit if coercion was involved. o package::object wasn't being deparsed properly. o seq.POSIXt() with `by' an object of class "difftime" ignored the units. o rank(c("B", NA)) no longer returns character. o reference to by() added in ?tapply o ?lm describes what happens with matrix response o The X11 device has improved event handling. In particular it used to often miss the last of a series of resize events. o lm.influence() and related functions now work again for the multivariate case and when there are zero weights. o format( ) now always keeps names and dimnames. o table(factor(c(2,NA), exclude=NULL)) prints better now. o predict(foo, type = "terms") and hence residuals(foo, type = "partial") now work for lm and glm objects with weights zero. Further, model.matrix() is now only called once. o R CMD config now works correctly when called from a Makefile using GNU make. o The data.frame method for rbind() was - converting character columns to factors, - converting ordered factor columns to unordered factors, - failing to append correctly a factor to a character column and vice versa. o as.hclust.twins() now does provide proper `labels', `method' and `call' components. o cycle() sometimes failed on a time series which started at a cycle other than 1. o read.dcf() read incorrectly files which did not end in a new line. o read.socket() dropped certain non-alphanumeric characters. (PR#2639) o termplot() handles missing data better (PR#2687, ) o Corrected MacRoman encoding for Icircumflex etc. ************************************************** * * * 1.6 SERIES NEWS * * * ************************************************** CHANGES IN R VERSION 1.6.2 BUG FIXES o plot.stepfun() now obeys a `ylim=.' specification. o removeClass() does a better job of removing inheritance information. o setIs() will not allow mismatched representations between two classes (without an explicit coerce method). o The code underlying polygon drawing contained a memory leak. This showed up in persp, but did not affect other graphics functions. It is now possible to draw big DEMs. o logLik.nls() gave wrong df. (PR#2295) o rbind() with a mixture of data frames and matrices treated the matrices as vectors. (PR#2266) o stripchart(method="stack") was not handling missing values. (PR#2018) o Arithmetic functions such as log() lost the object bit from classed objects if coercion was needed. (PR#2315) o exp_rand would go into an infinite loop if unif_rand returned 0. o formatC(x, format="fg") could return exponential format if rounding pushed x over a positive power of 10. (PR#2299) o attr(x, foo) used partial matching for `foo' (even though not documented to do so), and failed to find `foo' if there were two or more partial matches before the exact match in the list of attributes. o Rdconv now creates direct HTML hyperlinks when linking to documentation in the same package. The code now ensures that links which can be resolved within the package are so resolved, even when there are possible resolutions in other packages. o If readBin(what=character()) is used incorrectly on a file which does not contain C-style character strings, warnings (usually many) are now given. o Building libR.so with the zlib in the R sources was not finding the local zlib headers. o system(intern=TRUE) has an undocumented line length limit of 119 chars both on Unix and Windows. The limit is now 8096 and documented. On Unix (only) every 120th character used to be discarded. o plot.POSIX[cl]t were not passing graphics parameters on to axis.POSIXct. o On some HP-UX systems, installed scripts were not executable when using the BSD-compatible install system program found by configure. We now always use install-sh on HP-UX. (PR#2091) o c() was converting NA names to "NA": now proper NA strings are used wherever possible. (PR#2358) o Checks in the C code prevent possible memory faults when standardGeneric is called invalidly. o Macros NEW_OBJECT (aka NEW) and MAKE_CLASS added; required by the .Call interface to generate arbitrary objects. o A typo was causing segfaults when using data.entry under SuSE. o mostattributes<-() was failing to copy across dimnames when one component was NULL, affecting pmax() and pmin() when the first argument was a matrix. (root cause of PR#2357) o The pdf() device now initialises graphical parameters properly. (PR#2281) o Checks in the C code prevent possible memory faults when standardGeneric is called invalidly. o Macros NEW_OBJECT (aka NEW) and MAKE_CLASS added; required by the .Call interface to generate arbitrary objects. o Problem that prevented package tcltk from working with Tcl/Tk 8.4 (crash on initialization) resolved. (Notice that binaries may still require an older Tcl/Tk, for example on Windows). o type.convert() was not getting the levels right if passed a character vector containing s, and `na.strings' did not contain "NA". This affected read.table(). o Internal match function did not check for nor handle 0-length vectors. (The R function match() did.) This could cause type.convert() to segfault. o The line length limit in output text connections has been raised to 8095 chars. o Sweave now uses anonymous file rather than text connections to avoid the limits of the latter (see previous item). o parsing did not work on connections when pushback was used (as it had never been implemented). (PR#2396) o max.col() only found NAs in the first column (typo). o Added a workaround for recent versions of glibc (e.g. RedHat 8.0) with inconsistent mktime/localtime functions which caused conversion to/from POSIXct times prior to 1970-01-01 to be inconsistent. On such platforms this is a run-time test to allow e.g. R compiled on RH7.2 to run on RH8.0. o Clipping was not being reset properly between plots on the gtk() device (the default under the GNOME interface). (PR#2366) o axis(*, fg= cc) now works (again) the same as axis(*, col = cc). CHANGES IN R VERSION 1.6.1 NEW FEATURES o Added a few "trivial and obviously missing" functions to tcltk: tkchooseDirectory, tkpopup, tkdialog, tkread o barplot() has a new argument `axis.lty', which if set to 1 allows the pre-1.6.0 behaviour of plotting the axis and tick marks for the categorical axis. (This was apparently not intentional, but axis() used to ignore lty=0.) The argument `border' is no longer ".NotYetUsed". BUG FIXES o hist(, cex.axis = f) now works for x-axis too. o prompt() gave wrong \usage{.} for long argument default expressions. o summary(x) gives more information when `x' is a logical (or a data frame with a logical column which is now quite customary). o seq.POSIXt(from, to, length.out= . ) could give too long results o summaryRprof() was counting nested calls to the same function twice. o Printing of objects of mode "expression" did strange things if there were "%" characters in the deparsed expression (PR#2120). o as.matrix.data.frame converted missings to "NA" not character NA. (PR#2130) o spec.pgram() was only interpolating zero freq for one series. (PR#2123) o help(randu) had % unescaped in the example. (PR#2141) o Making html links would fail if packages-head.html was not writeable. (PR#2133) o Sweave.sty was not installed to $R_HOME/share/texmf when builddir != srcdir. On Windows backslashes in latex paths have to be replaced by slashes. o A memory leak in deparsing was introduced when eliminating static variables (thanks to Achim Zeileis for spotting this). A similar problem in loading workspaces has been corrected. o TclInterface.Rd incorrectly used \synopsis for \usage so that the usage section wasn't output. o Readline stack off-by-one error. (PR#2165) o R_ExpandFileName had a memory leak in the case libreadline was used under Unix-alikes. o sys.save.image() now closes all connections so it will work even if the connection list has become full. o loess() had an unstated limit of four predictors: this is now documented and enforced. o ${R_HOME}/etc/Renviron.site is now not read if R_ENVIRON is set, as documented. Previously it was read unless R_ENVIRON pointed to an actual file. o Startup.Rd described the processing under Unix-alikes but incorrectly implied it happened that way on the Windows and MacOS ports. Neither use Renviron.site, for example. o besselK(x,*) now returns 0 instead of Inf for large x. (PR#2179) o The Tcl console code didn't work with Tcl/TK 8.0, and has been #ifdef'd out. (PR#2090) o format.AsIs() was not handling matrices. o sd() was not passing na.rm to var() for matrices and data frames. o dist() {mva} silently treated +/-Inf as NA. o setwd() now returns NULL invisibly. o basename() and dirname() did not check the length of their input and ignored elements after the first. This affected undoc {tools}. o If A had dimnames, eigen(A) had inappropriate dimnames. (PR#2116) o as.POSIXct.dates had a sign error for the origin (PR#2222) o The claim that pie charts should be avoided (in pie.Rd) is now supported by a quote from Cleveland (1985). o The vsnprintf() functions supplied for systems that don't supply their own had a bug in the output of fractional parts, corrupting data if using save() with ascii=TRUE. (PR#2144) o pretty() values close to 0 in some cases which are now 0 (PR#1032 and D.Brahm's mails). o factor.scope() was giving an error rather than a reasonable default in some cases when it was called incorrectly (e.g. via incorrect formula in add1()). BUILD ISSUES o Toplevel Makefile was missing dependency of "docs" on "R" (causing parallel makes to go wrong) o When building with recommended packages those were installed into the first path in R_LIBS, if the environment variable was present. CHANGES IN R VERSION 1.6.0 USER-VISIBLE CHANGES o The default colour palette now has "grey" instead of "white" in location 8. See palette(). o grid(nx) behaves differently (but the same as in R versions <= 0.64). NEW FEATURES o New operator :: in the grammar, for name spaces. o New faster rowsum(), also works on data frames. o grep(), (g)sub() and regexpr() have a new argument `perl' which if TRUE uses Perl-style regexps from PCRE (if installed). New capabilities option "PCRE" to say if PCRE is available. o Preparations for name space support: - Functions in the base package are now defined in a name space. As a temporary measure, you can disable this by defining the environment variable R_NO_BASE_NAMESPACE. - UseMethod dispatching now searches for methods in the environment of the caller of the generic function rather than the environment where the generic is defined. o The objects created in the methods package to represent classes, generic functions, method definitions, and inheritance relations now themselves belong to true classes. In particular, the "classRepresentation" objects follow the description in "Programming with Data" (section 7.6). o Other additions and changes to the methods package: - The function setOldClass() has been added, following the description on page 450 of "Programming with Data". Use it if old-style classes are to be supplied in signatures for setMethod, particularly if the old-style classes have inheritance. Many of the old-style classes in the base package should be pre-specified; try getClass("mlm"), e.g. - The setGeneric() function applies some heuristics to warn about possibly erroneous generic function definitions. (Before, obscure bugs could result.) - The function promptMethods() has been revised to work better and to provide aliases for individual methods. - The behavior of the as() function has been generalized, in particular with a strict= argument, the general goal being to let simple extensions of classes pass through in method dispatch and related computations without altering the objects. More to make method behavior more "natural" than for direct use. - Some inconsistencies following detach("package:methods") have been removed, so it _should_ be possible to detach/re-attach the methods package. o New methods ([[, print, str) and extended plot() method (incl. logical `horiz') for "dendrogram" class. o sprintf() now checks the agreement between formats and object types, and handles special values (NA, Inf, ...) correctly. o chol() now uses a tolerance for non-positive-definiteness and so should give more consistent results across platforms. o New function agrep() for approximate (fuzzy) string matching. o help.search() can now use both approximate (fuzzy) and regular expression matching. By default, if the pattern to be matched consists of only alphanumeric characters, whitespace or a dash, approximate matching is used. o axis() has three new optional arguments `col', `lty', and `lwd' all for drawing the axis line and tick marks. o Function vcov() (formerly in MASS), a generic function to return the variance-covariance matrix of the parameter estimates of a fitted model. o duplicated() and unique() have methods for matrices and arrays (based on ideas from Jens Oehlschlägel). o Internally memory sizes and counts of cons cells are now stored in unsigned longs. This allows memory limits to be set and objects created in the range 2-4Gb on 32-bit platforms, and allows 64-bit platforms to use much larger amounts of memory. o Command-line flags to set memory can now use the suffix `G' for gigabytes. The setting of maximum vsize is now only limited by the platform's address space. o All warning and error messages are truncated to a length set by options(warning.length=), defaulting to 1000. (Previously most (but not quite all) were truncated at 8192 characters.) o [dpqr]gamma() check for shape parameter > 0. o as.POSIX[cl]t can now convert logical NAs. o All installed packages (even those shipped with R) are given a `Built' field in the DESCRIPTION file. o as.data.frame() now coerces logical matrices into logical columns (rather than factors). o [[<-.data.frame no longer coerces character replacement values to factor. This is consistent with using $ to replace and with S4. o library() attempts to detect improperly installed packages, so as from this version an installed package must have a DESCRIPTION file and that file must have been stamped with a `Built:' line (which was introduced in 1.2.0). Under Unix-alikes, the platform is checked against that used for installation. o print.factor() has new arguments `max.levels' (with a smart default) and `width'. print.ordered() is no longer needed. o RNGkind() has an additional option for normal random generators: "Inversion". o data.frame() recycles factors and "AsIs" objects as well as atomic vectors. o predict.lm() warns if `newdata' is supplied and the fit was rank-deficient, as this can be misleading. o rect() accepts additional graphics parameters through a ... argument (in the same way as polygon). o strwidth/strheight() now coerce their first argument in exactly the same way text() does, so a wider range of inputs is allowed. o prompt()'s default and data.frame methods have a new 3rd argument `name' allowing them to used more easily in scripts and loops. o rgb() has a new `maxColorValue' argument, allowing r,g,b in [0,M], particularly in {0:255}, efficiently and non-error-prone. o summaryRprof() provides the functionality of R CMD Rprof in R code, though more slowly. o stop() accepts multiple arguments (which are concatenated) just as warning() does. o scan() now throws an error with incorrect logical input (which was previously taken as FALSE). o pdf() now uses PDF not R code for clipping, which ensures that partially visible text strings are (partially) shown. o Each R session uses a per-session temporary directory which is removed at normal termination. The directory name is given by the tempdir() function, and filenames returned by tempfile() will be within that directory. o help.start() on Unix now uses a .R subdirectory of the per-session temporary directory and not ~/.R. A side effect is that ~/.R is now never deleted by R. This now uses the remote control mechanism only if the X display is local to the R process (as otherwise it might use a browser running on an arbitrary machine). o *Very* experimental browseEnv() for browsing objects in an environment. o cbind/rbind() used to ignore all zero-length vectors, an undocumented quirk for S-compatibility. This caused problems when combining zero-extent matrices and zero-length vectors, and now zero-length vectors are ignored unless the result would have zero rows/columns. o read.table(stdin()) will now work. o plot.spec(x) now also works for other x than AR and Pgram results. o New functions La.chol() and La.chol2inv() for Cholesky decomposition and inverse of positive definite matrices using Lapack. o Changes to the tcltk package - on Unix systems, the Tcl event loop has been integrated with R's own (so that tkwait.variable() no longer halts updates of plot windows). - also on Unix, stubs have been created to divert R's input and output routines to go via Tcl commands. (Nothing uses this at present, but packages might be developed to take advantage of it.) - return value from Tcl commands is no longer invisible. A new print method, print.tclObj(), has been introduced. - Tcl variables created by tclVar() are now explicitly put into Tcl's global namespace, removing potential scoping problems. - The tcltk dynamic library now loads with local=FALSE since the default had trouble when loading Tcl extensions (e.g. Tix) - The tkpager() function had not been updated for the return value change from 1.5.0 o The bmp(), jpeg() and png() devices can produce multiple bitmap files, one for each page. The default filenames have been changed to include a sequence number. o New function axTicks() returning tick mark locations like axis(). o grid() has a more sensible default behavior. Tick axis alignment only happens when no numbers of grid cells are specified. New arguments lwd and equilogs; nx/ny = NA for not drawing, see ?grid. o installed.packages() has a new argument `priority'. o termplot() uses factor levels rather than 1,2,3... for x-axis. o Workaround for optimization bugs on gcc 3.1/2 on 32-bit Solaris. o The trace() function has been robustified and a new function tracingState() added to turn tracing temporarily on and off. o New cophenetic() in "mva" as utility for hierarchical clustering. o p.adjust() has two new methods, 'Hommel' and 'FDR', contributed by Gordon Smyth . o stars() now has add and plot arguments. DEPRECATED & DEFUNCT o The assignment operator `_' is deprecated: a warning is given once per R session. o machine() is deprecated in favour of .Platform$OS.type. Machine() and Platform() are deprecated in favour of .Machine and .Platform. o arima0.diag() (package ts) is defunct. o piechart() is defunct. o print.ordered() has been removed, so print.factor() is used. o The global internal variables .Dyn.libs and .lib.loc are removed in favor of the internal functions .dynLibs() and .libPaths(). o restart() is deprecated in preparation for proper exception handling. Use try(), as has long been recommended. DOCUMENTATION CHANGES o New demo(persp) containing some of the former example(persp) ones and more. C-LEVEL FACILITIES o Rversion.h is no longer automatically included by R.h. Include it explicitly if you need it. o New entry point R_tmpnam in Utils.h. o The Unix event loop interface has been changed to facilitate integration with other loops. R_checkActivity and R_runHandlers should eventually replace getSelectedHandler. INSTALLATION CHANGES o Perl 5.005 or newer is now required. o R CMD INSTALL is now guaranteed to sort the R source files in ASCII order. UTILITIES o R CMD check now tests for mis-use on an installed or binary package, and sets 'T' and 'F' to 'NULL' when running the examples. o New function SweaveSyntConv() converts between Sweave file syntaxes. RweaveLatex() now gets its prompt from options() and uses the text width as linebreak cutoff for deparsing input statements. BUG FIXES o axis() was not respecting par("mgp")[3] by default. (PR#916) o tcltk back-compatibility fix for tcl8.0 o hist.POSIXct(*, breaks) now works for `breaks = #{breaks}' and when `x' has NAs; the latter applies to cut.POSIXct() as well. o The internal download.file() methods were setting the proxy port to 0 unless it was specified. o poly() did not work for >=3 column matrices. o cut.default() was not handling infinite values with infinite breaks. (PR#1694) o ks.test() could fail due to integer overflow if n.x and n.y were both large. o all.equal(3., 3:3) wasn't TRUE when the methods package was present. o read.table() could remap non-syntactic names to duplicates, and did not check for duplicated names. o ls.str(envir = environment(F)) now works (when F is a function). o pie() now has a `border' (and 'lty') argument which allows empty slice borders and makes pie() useable for hundreds of slices. o all.equal.character() now works correctly also when NAs don't match (PR#1767). o all.equal.numeric() now gives character {instead of list} when lengths don't match. o read.dcf() had a memory leak. o Setting "tcl = a" in a highlevel graphic function worked almost as if par(tcl = a) was called (i.e. was persistent). Further, after par(tcl= <.>), highlevel graphic setting of tcl didn't work anymore. "tck" has now S's default of -0.01 (when tcl=NA). o data() was not checking if ./data was a directory before warning. o Assignment beyond the end of character strings was filling with "", whereas changing the length extended with NA_STRING. Now NA_STRING is used for both. o boxplot()s with logarithmic scale in "width-direction" now have proper widths, i.e. typically constant. o Using GNU readline in asynchronous event callbacks (e.g. TclTk or Gtk) works correctly, i.e. doesn't cause readline to abort the process. o Using Q to exit a browser invoked at the top-level could lead to the browser being invoked on all future top-level loops (PR#1721) o step(fit, direction="both") now uses both directions even if no scope is supplied. o strwidth(), strheight() now give 0 on NA strings (as they are no longer plotted). (PR#1739) o mtext(), persp(), plot.hclust() and title() no longer plot NA character strings. o pdf() has been protected against the user who specified non-existent fonts. (PR#1748) o dlnorm() returns zero for negative x argument. (PR#1781) o Printing 0 in octmode gave "" not "0". (PR#1759) o anova.glm() was ignoring a `dispersion' argument if given multiple objects. (PR#1807) o model.matrix() with a `rhs ~ .' formula included columns with duplicated names in the data frame, which caused subsequent confusion (e.g. in prediction from the object). model.matrix() was sometimes incorrectly determining the first factor in a formula without an intercept. o termplot() now needs data= argument more rarely. (PR#828) o abline() on log scale doesn't draw -ve points. (PR#1243) o The Java search engine now works within Mozilla 1.0 and Netscape 6.2.x / 7.0pr1. o unsplit() failed if f was a list of factors. (PR#1843) o The methods package generic version of primitives is now "sealed" and cannot be redefined (it was always a bad idea to do so). o quantile() gave -Inf not NaN in some examples. (Related to PR#1852) o read.table() read too far in checking the file structure if 0 < nrows < 5 and more rows existed on the file. (PR1809) o loess() was not checking for too small a span (so no points were included in the smoothing window). o match() was assuming that there was only one possible bit pattern for a numeric NA, so some matches failed on Solaris under some compiler options. o identical() no longer thinks NaN and as.double(NA) are identical. o pipe() can open in a binary mode even on Linux (where popen cannot). o zero-column matrices were not being printed at all, not even the row names. o polygon()'s `border' argument was incorrectly documented: in particular `border = 0' plots in background colour. o delete.response() was losing the attribute set for safe prediction. (PR#1840) o poly() was checking the degree against the number of points even when predicting. o Comparison of a data frame and list failed due to typo. (PR#1889) o dput() and dump() attempt to check if writing succeeded. (PR#1884) o rep(1:2, 0) and hence array(1:2, 0) fail no longer. o apply(matrix("", 3, 0), 2, length) now works. o order(na.last = NA, decreasing = TRUE) now sorts in decreasing order. (PR#1906) o order(na.last=NA) failed if all args were of length 1 or all were NA. (PR#1913, 1981) o source() would crash if the `keep.source = TRUE' and the input contained a function with a line longer than 1024 chars. (PR#1900) The limits on nesting of functions and on total function size when the source is kept are now enforced. As (incorrectly) the source was always kept, this meant functions longer than 128Kb could crash R, even in packages. o lqs() and cov.rob() check that the quantile argument does not exceed n-1. o grid() now also works with log coordinates active. o plot.table(tab, xlab="X", ylab="Y") now works as expected. o plot.formula(ask=FALSE) now works. (PR#1923) o as.list() now works properly. (PR#1926). o The residual SSq printed from an aov() fit with weights is now the weighted SSq. (PR#1930) o aov() could still fail on multistrata models with very long Error formulae. o try() could fail in BATCH use due to use of fflush(stdin). Only seen on Solaris. (PR#1934) o title(main=list("main")) printed garbage, as did similar calls using quote() instead of expression() for plotmath. (PR#1939) o deparse() dropped parentheses in some case where they were needed. (PR#1119, 1737, 1928, at least) o pdf(onefile = FALSE) never incremented the file number beyond two. o On Unix, protect against broken pipes where popen calls succeed even though the command does not exist (and the glibc manual says it should return NULL). (PR#1959) o data.frame() was allowing explicit row.names with missing values, but row names are required to be unique. o as.character(expression) was silently truncating to 60 characters: the help page claimed 500 which is now true. o as.hclust(x) now also works (as identity) for "hclust" objects. o NextMethod didn't work right in Ops. o dotchart() now obeys `xlim ='. o t(x) behaves when x is a (multivariate) time series. (PR#1998) o parse(text=x) no longer parses from stdin if length(x) is zero o binom.test() miscalculated p-value in some extreme cases o get("print.ts")(1) would segfault. It's now just an error. o cbind(NULL) {and similar} gave an error instead of NULL. o the complex version of solve(a,b) now also works if b is a vector CHANGES IN R VERSION 1.5.1 NEW FEATURES o Enhancements to mathematical annotation of plots: - expressions involving dot() now produce a dot accent above the (initial patch from Ben Bolker). - within an expression, the symbol partialdiff is now converted to a partial differential symbol (greek delta). o smooth.spline() has a new argument `nknots' allowing to set the default number of knots (when `all.knots = FALSE' as per default). BUG FIXES o Rdconv now skips CRs in input files, even on Unix. o readBin() had a (very slow) memory leak if changing size or reading character strings. writeChar() had a memory leak. o polygon() and rect() with lty = "blank" were omitting the fill colour (if present). symbols(circles=, lty="blank") was drawing the border of the disks. o Subsetting non-existent rows in a data frame would produce missing row names, which are not allowed. o On Unix, R_PAPERSIZE was set to '' instead of 'a4' as default on systems without paperconf. o Under GNOME, capabilities() now reports correctly that X11, png and jpeg are available (if they are under X11). o The names of some results of unlist() had the wrong internal length, which confused paste(). Both have been corrected. (PR#1524) o RweaveLatex.Rd had unbalanced braces in section "Supported Options". o merge() with multiple and differently-named match columns failed. (PR#1510) o NAs in right-justified unquoted character matrices were being mis-aligned. This mainly affected printing data frames. o predict.*bSpline() bugs extrapolating for deriv >= 1 (PR#1473), and predict.[bn]s bug e.g. for bs(x), reported by Ch.Sangiorgio. o qr.X was failing if n < p. Fixed, but only in the case when pivoting does not occur. (PR#1519) o xx[, 1:3] was returning a list if xx had only one row, even though xx[1, 1:3] was a data frame. (PR#1530) o nls() was reporting incorrectly the number of iterations if the maximum was reached. o rbind.data.frame() was coercing logical columns to factors. (PR#1536) o Rprof(NULL) or Rprof("") called when not profiling caused a segfault: now silently ignored. (PR#1471) o On systems (e.g. Windows) using R's own code for expm1, the values were wrong for large negative x, and this affected pweibull(), for example. o prettyNum(*, bigmark=*) added extra marks in some cases. (PR#1548) o cut.dendrogram() failed in some cases. (PR#1552) o The links in refman.pdf were broken by a single invalid \alias{}. Now Rdconv checks more comprehensively. (PR#1550) o predict(smooth.spline(x,*), deriv =1) did not predict at all `x' values, and smooth.spline(x,*, all.knots = TRUE) used much too much memory when length(x) was largish. smooth.spline(*, .... trace = TRUE ..) is a bit more self-explaining. o pexp(x, log=TRUE) and pweibull(*) were losing precision for large x. o Workaround for NetBSD bug in compiling dounzip.c. (PR#1565/6) o Conversions to numeric in type.convert were always treating "NA" as missing whatever the setting of na.strings. (PR#1568) o R CMD check now deals correctly with package names containing a '.' in the Depends field of a DESCRIPTION file. (PR#1591) o pbinom() and pbinom() were misssing the "fuzz" that other discrete distributions have in order to guard against truncation. o The "=" assignment operator behaved as "<<-" in some constructions with composite left-hand sides. o Added print.AsIs() method to ensure "AsIs" objects are printed by the method for their real class. (PR#1587) o mosaicplot(*, color = v) now recycles v[] if needed. o Calling dev.control("inhibit") with no graphics device open crashed R. (PR#1605) o read.dcf() was not checking that memory allocation succeeded. o The C function fprec might overflow for > 16 digits, showing up in example(str) on some platforms. o Changes to the methods package: - Nonstandard generic function definitions given to setGeneric now work; these were previously ignored. - Classes that extend matrix, etc. as the data part previously lost their attributes. - There were bugs in distinguishing methods for "missing" from methods for "ANY". - Some coerce methods were not selected correctly when the two classes were related by an "is" relation. - extends() now works correctly if given a class definition rather than a name. - class()<- was leaving in an explicit class attribute for basic data types. - Method signatures including arguments following "..." in the argument list of the generic didn't work. o par(mgp = v) now allows negative `v' (S-compatibly and sensibly). o identify.hclust() masked its `x' argument and so failed. o System rint was never being used in fround.c. o round/trunc.POSIXt were erroneously retaining information on DST. (PR#1543) o tcltk package didn't work with tcl8.0.x. Compatibility code inserted (PR#1640, thanks to René Bertin for helping out with this). o selfStart() {pkg "nls"} now works again when parameter names are not specified (but implicit). o legend() now treats lty="0" properly (as solid). o ARMAacf was failing if 0 < p < q+1: it failed to say that ar needed to be padded with zeroes, and now the code does that. o old.packages() was assuming a bundle was installed in only one library, and so update.packages() would only update a bundle in the first location in lib.loc. o fisher.test() could miscalculate odds ratio and confidence interval for tables with large entries, due to numerical overflow. o Using lty = "1" (or "10") does no longer produce invalid postscript or pdf. Using "0" in a character lty is currently not implemented device-independently and needs more fixing. o ccf(plot = FALSE) was returning a spurious extra 0 at lag 0. o On console-based versions of R (Windows, GNOME, probably MacOS) warning/error messages longer than 8192 chars could crash R. (PR#1651) o Comparisons between objects of mode "call" using "==" now return TRUE if both sides deparse to the same string (as always intended). o HoltWinters() now initializes correctly in the exponential smoothing case, and plot.HoltWinters() allows lty to be set. o fisher.test() crashed due to corruption on some large problems. It also crashed on tables with total one. (PR#1662) o The substitution code for strptime (used e.g. on Windows) cached the month names and so did not recognise locale changes during an R session, as used by get.hist.quote{tseries}. Caching has been supressed. (PR#1116) o Some functions used the non-existing error() function instead of stop(). o vector("complex",n) doesn't return random garbage anymore. CHANGES IN R VERSION 1.5.0 USER-VISIBLE CHANGES o XDR support is now guaranteed to be available, so the default save format will always be XDR binary files, and it is safe to distribute data in that format. (We are unaware of any platform that did not support XDR in recent versions of R.) gzfile() is guaranteed to be available, so the preferred method to distribute sizeable data objects is now via save(compress = TRUE). o pie() replaces piechart() and defaults to using pastel colours. o formatC has new arguments (see below) and formatC(*, d = ) is no longer valid and must be written as formatC(*, digits = ). o Missingness of character strings is treated much more consistently, and the character string "NA" can be used as a non-missing value. o summary.factor() now uses a stable sort, so the output will change where there are ties in the frequencies. NEW FEATURES o Changes in handling missing character strings: - "NA" is no longer automatically coerced to a missing value for a character string. Use as.character(NA) where a missing value is required, and test via is.na(x) not x == "NA". String "NA" is still converted to missing by scan() and read.table() unless `na.strings' is changed from the default. - A missing character string is now printed as `NA' (no quotes) amongst quoted character strings, and `' if amongst unquoted character strings. - axis() and text.default() omit missing values of their `labels' argument (rather than plotting "NA"). - Missing character strings are treated as missing much more consistently, e.g. in logical comparisons and in sorts. identical() now differentiates "NA" from the missing string. o Changes in package methods: - New function validSlotNames(). - Classes can explicitly have a "data part", formally represented as a .Data slot in the class definition, but implemented consistently with informal structures. While the implementation is different, the user-level behavior largely follows the discussion in "Programming with Data". - A "next method" facility has been provided, via the function callNextMethod(). This calls the method that would have been selected if the currently active method didn't exist. See ?callNextMethod(). This is an extension to the API. - Classes can have initialize methods, which will be called when the function new() is used to create an object from the class. See ?initialize. This is an extension to the API. - The logic of setGeneric() has been clarified, simplifying nonstandard generic functions and default methods. o Changes in package tcltk: - Now works with the GNOME user interface. - Several new functions allow access to C level Tcl objects. These are implemented using a new `tclObj' class, and this is now the class of the return value from .Tcl() and tkcmd(). o Changes in package ts: - More emphasis on handling time series with missing values where possible, for example in acf() and in the ARIMA-fitting functions. - New function arima() which will replace arima0() in due course. Meanwhile, arima0() has been enhanced in several ways. Missing values are accepted. Parameter values can be initialized and can held fixed during fitting. There is a new argument `method' giving the option to use conditional-sum-of-squares estimation. - New function arima.sim(). - New datasets AirPassengers, Nile, UKgas and WWWusage, and a expanded version of UKDriverDeaths (as a multiple time series Seatbelts). - New generic function tsdiag() and methods for arima and arima0, to produce diagnostic plots. Supersedes arima0.diag(). - New functions ARMAacf() and ARMAtoMA() to compute theoretical quantities for an ARMA process. - New function acf2AR() to compute the AR process with a given autocorrelation function. - New function StructTS() to fit structural time series, and new generic function tsSmooth() for fixed-interval state-space smoothing of such models. - New function monthplot() (contributed by Duncan Murdoch). - New functions decompose() and HoltWinters() (contributed by David Meyer) for classical seasonal decomposition and exponentially-weighted forecasting. o An extensible approach to safe prediction for models with e.g. poly(), bs() or ns() terms, using the new generic function makepredictcall(). Used by most model-fitting functions including lm() and glm(). See ?poly, ?cars and ?ns for examples. o acosh(), asinh(), atanh() are guaranteed to be available. o axis() now omits labels which are NA (but still draws the tick mark. o Connections to bzip2-ed files via bzfile(). o chol() allows pivoting via new argument `pivot'. o cmdscale() now takes rownames from a dist object `d' as well as from a matrix; it has new arguments `add' (as S) and `x.ret'. o crossprod() handles the case of real matrices with y = x separately (by accepting y = NULL). This gives a small performance gain (suggestion of Jonathan Rougier). o deriv/deriv3() can now handle expressions involving pnorm and dnorm (with a single argument), as in S-PLUS. o New function expm1() both in R and in C API, for accurate exp(x)-1; precision improvement in pexp() and pweibull() in some cases. (PR#1334-5) o New function findInterval() {using new C entry point findInterval, see below}. o formatDL() now also works if both items and descriptions are given in a suitable list or matrix. o gzfile() is guaranteed to be available, and hence the `compress' option to save() and save.image(). o hist() now has a method for date-time objects. o library() now checks the dependence on R version (if any) and warns if the package was built under a later version of R. o library(help = PKG) now also returns the information about the package PKG. o Added function logb(), same as log() but for S-PLUS compatibility (where log now has only one argument). o New na.action function na.pass() passes through NAs unaltered. o piechart() has been renamed to pie(), as piechart is a Trellis function for arrays of pie charts. The default fill colours are now a set of pastel shades, rather than par("bg"). o plclust() in package mva, for more S-PLUS compatibility. o poly() now works with more than one vector or a matrix as input, and has a predict method for objects created from a single vector. o polyroot() now handles coefficient vectors with terminal zeroes (as in S). o New prettyNum() function used in formatC() and format.default() which have new optional arguments `big.mark', `big.interval', `small.mark', `small.interval', and `decimal.mark'. o print.coefmat() has a new argument 'eps.Pvalue' for determining when small P-values should be printed as "< {...}". o The recover() function has been moved to the base package. This is an interactive debugging function, usually a good choice for options(error=). See ?recover. o rep() has a new argument `each' for S-PLUS compatibility. The internal call is made available as rep.int(), again for help in porting code. o New functions rowSums(), colSums(), rowMeans() and colMeans(): versions of apply() optimized for these cases. o rug() now has a "..." argument allowing its location to be specified. o scan() can have NULL elements in `what', useful to save space when columns need to be discarded. o New option by = "DSTday" for seq.POSIXt(). o Changes to sorting: - sort(), sort.list() and order() have a new argument `decreasing' to allow the order to be reversed whilst still preserving ties. - sort() has an option to use quicksort in some cases (currently numeric vectors and increasing order). - The default Shell sort is Sedgewick's variant, around 20% faster, and pre-screening for NAs speeds cases without any NAs several-fold. - sort.list() (and order with just one vector) is several times faster for numeric, integer and logical vectors, and faster for character vectors. o New assignment forms of split(); new function unsplit(). o New sprintf() function for general C like formatting, from Jonathan Rougier. o Argument `split' of summary.{aov,aovlist} is now implemented. o summary.princomp() now has a separate print() method, and `digits' is now an argument to the print method and not to summary.princomp itself. o An extended version of the trace() function is available, compatible with the function in S-PLUS. Calls to R functions can be inserted on entry, on exit, and before any subexpressions. Calls to browser() and recover() are useful. See ?trace. o New function TukeyHSD() for multiple comparisons in the results of aov(). (Formerly function Tukey in package Devore5 by Douglas Bates.) o New read-only connections to files in zip files via unz(). o warning() has new argument `call.', like stop()'s. o zip.file.extract() is no longer provisional and has an "internal" method available on all platforms. o Methods for [, [<- and as.data.frame() for class "POSIXlt". o Much improved printing of matrices and arrays of type "list". o The "Knuth-TAOCP" option for random-number generation has been given an option of using the 2002 revision. See ?RNG for the details: the R usage already protected against the reported `weakness'. o min/max of integer(0) (or NULL) is now Inf/-Inf, not an extreme integer. DEPRECATED & DEFUNCT o .Alias, reshapeLong(), reshapeWide() are defunct. o arima0.diag() (package ts) is deprecated: use tsdiag() instead. o piechart() is deprecated; renamed to pie(). DOCUMENTATION CHANGES o `Writing R Extensions' now has an example of calling R's random numbers from FORTRAN via C. o R itself and all R manuals now have ISBN numbers, please use them when citing R or one of the manuals. INSTALLATION CHANGES o The configure script used when building R from source under Unix is now generated using Autoconf 2.50 or later, which has the following 'visible' consequences: - By default, configure no longer uses a cache file. Use the command line option '--config-cache' (or '-C') to enable caching. - Key configuration variables such as 'CC' are now *precious*, implying that the variables * no longer need to be exported to the environment and can and should be set as command line arguments; * are kept in the cache even if not specified on the command line, and checked for consistency between two configure runs (provided that caching is used, see above); * are kept during automatic reconfiguration as if having been passed as command line arguments, even if no cache is used. See the variable output section of 'configure --help' for a list of all these variables. o Configure variable 'FC' is deprecated, and options '--with-g77', '--with-f77' and '--with-f2c' are defunct. Use configure variable 'F77' to specify the FORTRAN 77 compiler, and 'F2C' to specify the FORTRAN-to-C compiler and/or that it should be used even if a FORTRAN 77 compiler is available. o Non-standard directories containing libraries are specified using configure variable 'LDFLAGS' (not 'LIBS'). UTILITIES o Sweave(), Stangle() and friends in package tools. Sweave allows mixing LaTeX documentation and R code in a single source file: the R code can be replaced by its output (text, figures) to allow automatic report generation. Sweave files found in package subdir 'inst/doc' are automatically tested by R CMD check and converted to PDF by R CMD build, see the section on package vignettes in the 'Writing R Extensions' manual. o Rdconv can convert to the S4 '.sgml' format. o R::Utils.pm masks some platform dependencies in perl code by providing global variables like R_OSTYPE or wrapper functions like R_runR(). o If a directory 'inst/doc' is present in the sources of a package, the HTML index of the installed package has a link to the respective subdirectory. o R CMD check is more stringent: it now also fails on malformed 'Depends' and 'Maintainer' fields in 'DESCRIPTION' files, and on unbalanced braces in Rd files. It now also provides pointers to documentation for problems it reports. o R CMD check, build and INSTALL produce outline-type output. o QC functions in package 'tools' now return the results of their computations as objects with suitable print() methods. By default, output is only produced if a problem was found. o New utility R CMD config to get the values of basic R configure variables, or the header and library flags necessary for linking against R. o Rdindex and maketitle.pl require perl 5.005, as Text::Wrap::fill was only introduced at 5.004_05. C-LEVEL FACILITIES o All the double-precision BLAS routines are now available, and package writers are encouraged not to include their own (so enhanced ones will be used if requested at configuration). o findInterval(xt[],n,x,...) gives the index (or interval number) of x in the sorted sequence xt[]. There's an F77_SUB(interv)(.) to be called from Fortran; this used to be part of predict.smooth.spline's underlying Fortran code. o Substitutes for (v)snprintf will be used if the OS does not supply one, so tests for HAVE_(V)SNPRINTF are no longer needed. o The DUP and NAOK arguments in a .C() call are not passed on to the native routine being invoked. Any code that relied on the old behaviour will need to be modified. o log1p is only provided in Rmath.h if it is not provided by the platform, in which case its name is not remapped, but a back-compatibility entry point Rf_log1p is provided. Applications using libRmath may need to be re-compiled. o The methods used by optim() and integrate() have entry points in R_ext/Applic.h and have a more general interface documented in `Writing R Extensions'. o The bessel_? entry points are now suitable to be called repeatedly from code loaded by .C(). (They did not free memory until .C() returned in earlier versions of R.) o Server sockets on non-Windows platforms now set the SO_REUSEADDR socket option. This allows a server to create simultanous connections to several clients. o New quicksort sorting (for numeric no-NA data), accessible from C as R_qsort() etc and from Fortran as qsort4() and qsort3(). o Rinternals.h no longer includes fcntl.h, as this is not an ISO C header and cannot be guaranteed to exist. o Fortran subroutines are more correctly declared as `extern void' in R_exts/Applic.h and R_exts/Linpack.h. BUG FIXES o The calculation of which axes to label on a persp() plot was incorrect in some cases. o Insufficient information was being recorded in the display list for the identify() function. In particular, the "plot=" argument was ignored when replaying the display list. (PR#1157) o The vertical alignment of mathematical annotations was wrong. When a vertical adjustment was not given, it was bottom-adjusting i.e,. it was treating adj=0 as adj=c(0, 0). It now treats adj=0 as adj=c(0, 0.5) as for "normal" text. (PR#1302) o the man page (doc/R.1) wasn't updated with the proper VERSION. o smooth.spline() had a "df = 5" default which was never used and hence extraneous and misleading. o read.fwf() was interpreting comment chars in its call to scan: replaced by a call to readlines(). (PR#1297/8) o The default has been changed to scan(comment.char="") for consistency with earlier code (as in the previous item). o bxp(*, notch.frac = f) now draws the median line correctly. o Current versions of gs were rotating the output of bitmap(type = "pdfwrite") and when converting the output of postscript() to PDF; this has been circumvented by suppressing the %%Orientation comment for non-standard paper sizes. o plot.ts(x, log = "y") works again when x has 0s, also for matrix x. o add1(), drop1(), step() work again on glm objects with formulae with rhs's containing `.'. (Broken by a `bug fix' (in reality an API change) in 1.2.1.) o optim(method="BFGS") was not reporting reaching `maxit' iterations in the convergence component of the return value. o aov() and model.tables() were failing on multistrata models with excessively long Error formula. (PR#1315) o Transparent backgrounds on png() devices on Unix-alikes had been broken during the driver changes just prior to 1.4.0. (They worked correctly on Windows.) o demo(is.things) didn't work properly when the methods package was attached. o match(), unique() and duplicated() were not declaring all NaNs to be equal, yet not always distinguishing NA and NaN. This was very rare except for data imported as binary numbers. o The error handler recover() protects itself against errors in dump.frames and uses a new utility, limitedLabels, to generate names for the dump that don't inadvertently blow the limit on symbol length. (TODO: either fix dump.frames accordingly or remove the limit--say by truncating very long symbols?) o se.contrasts() works more reliably with multistratum models, and its help page has an example. o summary.lm() was not returning r.squared nor adj.r.squared for intercept-only models, but summary.lm.null() was returning r.squared but not adj.r.squared. Now both are always returned. Neither returned f.statistic, and that is now documented. o Subsetting of matrices of mode list (or other non-atomic modes) was not implemented and gave incorrect results without warning. (PR#1329) Under some circumstances subsetting of a character matrix inserted NA in the wrong place. o abs() was not being treated as member of the Math group generic function, so e.g. its method for data frames was not being used. o set.seed(seed, "default") was not using the `seed' value (only for kind = "default"). o logLik.lm() now uses "df = p + 1" again (`+ sigma'!). o logLik.glm() was incorrect for families with estimated dispersion. o Added strptime() workaround for those platforms (such as Solaris) that returned missing components as 0. Missing days are now detected, but missing years will still be interpreted as 1900 on such platforms. o Inheritance in formal classes (the methods package) works breadth-first as intuition would expect. o The new() function in package `methods' works better (maybe even correctly?) for the various combinations of super-classes and prototypes that can be supplied as unnamed arguments. o Internal code allowed one more connection to be allocated than the table size, leading to segfaults. (PR#1333) o If a user asks to open a connection when it is created and it cannot be opened, the connection is destroyed before returning from the creation call. (related to PR#1333) o Sys.putenv() was not using permanent storage. (PR#1371) o La.svd() was not coercing integer matrices. (PR#1363) o deriv(3) now reports correctly the function it cannot find the derivatives table. o The GNOME user interface was over-enthusiastic about setting locale information. Now only LC_CTYPE, LC_COLLATE and LC_TIME are determined by the user's environment variables (PR#1321) o In X11, locator() would sound the bell even if "xset b off" had been set. o merge() could be confused by inconsistent use of as.character() giving leading spaces. o [pqr]binom() no longer silently round the `size' argument, but return NaN (as dbinom() does). (PR#1377) o Fixed socket writing code to block until all data is written. Fixed socket reading code to properly handle long reads and reads with part of the data in the connection buffer. o Allow sockets to be opened in binary mode with both open="ab" and open="a+b". o levels<-.factor() was using incorrectly list values longer than the number of levels (PR#1394), and incorrectly documented that a character value could not be longer than the existing levels. o The pdf() device was running out of objects before the documented 500 page limit. Now there is no limit. o legend() did not deal correctly with `angle' arguments. (PR#1404) o sum() tried to give an integer result for integer arguments, but (PR#1408) - this was not documented - it sometimes warned on overflow, sometimes not - it was order-dependent for a mixture of integer and numeric args. o mean() gave (numeric) NA if integer overflow occurred in sum(), but now always works internally with numeric (or complex) numbers. o sort.list() and order() were treating NA_STRING as "NA". o sort.list(na.last = NA) was not implemented. o seq.default() was returning only one element for a relative range of less than about 1e-8, which was excessively conservative. (PR#1416) o tsp(x) <- NULL now also works after library(methods). o persp(shade=) was not working correctly with the default col=NULL if this was transparent. (PR#1419) o min/max(complex(0)) was returning a random value. o range() gave c(1, 1). o range(numeric(0)) is now c(Inf, -Inf), as it was documented to be. o print.ts() was occasionally making rounding errors in the labels for multiple calendar time series. o Rdconv was not handling nested \describe{} constructs when converting to HTML (PR#1257) and not fixing up mal-formed \item fields in \describe{} when converting to text (PR#1330). o filled.contour() was not checking consistency of x, y, z. (PR#1432) o persp.default() no longer crashes with non-character labels. (PR#1431) o fft() gave incorrect answers for input sizes 392, 588, 968, 980 .... (PR#1429) o det(method = "qr") gave incorrect results for numerically singular matrices. (PR#1244) o barplot() now allows the user to control `xpd'. (PR#1088, 1398) o library() (with no arguments) no longer fails on empty TITLE files. o glm() was failing if both offset() and start were specified. (PR#1421) o glm() might have gotten confused if both step-shortening and pivoting had occurred (PR#1331). Step-halving to avoid the boundary of feasible values was not working. o Internal representation of logical values was not being treated consistently. (Related to PR#1439) o The c() function sometimes inserted garbage in the name vector for some types of objects, e.g. names(c(ls, a=1)). o Fixed bug in `$' that could cause mutations on assignment (PR#1450). o Some X servers displayed random bytes in the window title of graphics windows (PR#1451) o The X11 data editor would segfault if closed with window manager controls (PR#1453) o Interrupt of Sys.sleep() on UNIX no longer causes subsequent Sys.sleep() calls to segfault due to infinite recusion. o Eliminated a race condition that could cause segfaults when a SIGINT was received while handling an earlier SIGINT. o rect(lty = "blank") was incorrectly drawing with a dashed line. o type.convert() was not reporting incorrectly formatted complex inputs. (PR#1477) o readChar() was not resetting vmax, so causing memory build-up. (PR#1483) ************************************************** * * * 1.4 SERIES NEWS * * * ************************************************** CHANGES IN R VERSION 1.4.1 BUG FIXES o scan(multi.line = FALSE) now always gives an immediate error message if a line is incomplete. (As requested in PR#1210) o read.table() is no longer very slow in processing comments: moved to C code and fewer lines checked. o type.convert() could give stack imbalance warnings if used with as.is = TRUE. o predict.mlm ignored newdata (PR#1226) and also offsets. o demo(tkttest) was inadvertently changed in 1.4.0 so that it would evaluate the requested test, but not display the result. o stars(scale = TRUE) (the default) now works as documented (and as S does). Previously it only scaled the maximum to 1. (PR#1230) o d0 <- data.frame(a = 0); data.matrix(d0[0, 0]) and data.matrix(d0[, 0]) now work. o plot(multiple time series, plot.type = "single") was computing `ylim' from the first series only. o plot.acf() has a new `xpd = par("xpd")' argument which by default *does* clipping (of the horizontal lines) as desired (xpd = NA was used before, erronously in most cases). o predict(smooth.spline(.), deriv = 1) now works. o identify() failed when x is a structure/matrix. (PR#1238) o getMethod() returns NULL when optional=TRUE as promised in the documentation. o setMethod() allows "..." to be one of the arguments omitted in the method definition (but so far no check for ... being missing) o Allow round() to work again on very large numbers (introduced in fixing PR#1138). (PR#1254) o Rinternals.h is now accepted by a C++ compiler. o type.convert() was failing to detect integer overflow. o piechart() was defaulting to foreground colour (black) fills rather than background (as used in 1.3.1 and earlier). Now background is used, but be aware that as from 1.4.0 this may be transparent. o La.eigen(*, only.values=TRUE) does not segfault anymore in one branch (PR#1262). o cut() now produces correct default labels even when include.lowest = TRUE (PR#1263). o reformulate() works properly with a response. o cmdscale(*, k = 1) now works properly. o Options by = "month" and "year" to seq.POSIXt() will always take account of changes to/from daylight savings time: this was not working on some platforms. o glm.fit.null() now accepts all the arguments of glm.fit() (it could be called from glm.fit with arguments it did not accept), and is now documented. o cov.wt(cbind(1), cor = TRUE) now works. o predict(glm.object, se.fit = TRUE) was failing if the fit involved an offset. o detach() on package:base would crash R. (PR#1271) o print or summary on a manova() object with no terms, no names on the response and intercept = FALSE (which is not sensible) would give an error. o seek() on file connections was ignoring the `origin' argument. o Fixed new environment handling in library() to avoid forcing promises created by delay() o arima0() could leak memory: now released via on.exit(). o qr.coef(qr,*) now keeps the names of qr$qr. o read.00Index() no longer fails on data indexes not generated by Rdindex (PR#1274). CHANGES IN R VERSION 1.4.0 USER-VISIBLE CHANGES [This is a new section to highlight changes in behaviour, which may be given in more detail in the following sections. Many bug fixes are also user-visible changes.] o The default save format has been changed, so saved workspaces and objects cannot (by default) be read in earlier versions of R. o The number of bins selected by default in a histogram uses the correct version of Sturges' formula and will usually be one larger. o data.frame() no longer converts logical arguments to factors (following S4 rather than S3). o read.table() has new arguments `nrows' and `colClasses'. If the latter is NA (the default), conversion is attempted to logical, integer, numeric or complex, not just to numeric. o model.matrix() treats logical variables as a factors with levels c(FALSE, TRUE) (rather than 0-1 valued numerical variables). This makes R compatible with all S versions. o Transparency is now supported on most graphics devices. This means that using par("bg"), for example in legend(), will by default give a transparent rather than opaque background. o [dpqr]gamma now has third argument `rate' for S-compatibility (and for compatibility with exponentials). Calls which use positional matching may need to be altered. o The meaning of spar = 0 in smooth.spline() has changed. o substring() and substring()<- do nothing silently on a character vector of length 0, rather than generating an error. This is consistent with other functions and with S. o For compatibility with S4, any arithmetic operation using a zero-length vector has a zero-length result. (This was already true for logical operations, which were compatible with S4 rather than S3.) o undoc() and codoc() have been moved to the new package `tools'. o The name of the site profile now defaults to `R_HOME/etc/Rprofile.site'. o The startup process for setting environment variables now first searches for a site environment file (given by the environment variable `R_ENVIRON' if set or `R_HOME/etc/Renviron.site' if not), *and* then for a user `.Renviron' file in the current or the user's home directory. o Former stars(*, colors = v) must now be stars(*, col.segments = v). o The default methods for La.svd and La.eigen have changed and so there may be sign changes in singular/eigen vectors, including in cancor, cmdscale, factanal, princomp and varimax. NEW FEATURES o Transparency is now supported on most graphics devices. Internally colors include an alpha channel for opacity, but at present there is only visible support for transparent/opaque. The new color "transparent" (or NA or "NA") is transparent, and is the default background color for most devices. Those devices (postscript, XFig, PDF, Windows metafile and printer) that previously treated bg = "white" as transparent now have "transparent" as the default and will actually print "white". (NB: you may have bg = "white" saved in .Postscript.options in your workspace.) o A package `methods' has been added, containing formal classes and methods ("S4" methods), implementing the description in the book "Programming with Data". See "?Methods" and the references there for more information. - In support of this, the "@" operator has been added to the grammar. - Method dispatch for formal methods (the standardGeneric function), is now a primitive. Aside from efficiency issues, this allows S3-style generics to also have formal methods (not really recommended in the long run, but it should at least work). The C-level dispatch is now implemented for primitives that use either DispatchGroup or DispatchOrEval internally. - A version of the function "plot" in the methods package has arguments "x" and "y", to allow methods for either or both. See "?setMethod" for examples of such methods. - The methods package now uses C-level code (from within DispatchOrEval) to dispatch any methods defined for primitive functions. As with S3-style methods, methods can only be defined if the first argument satisfies is.object(x) (not strictly required for formal methods, but imposed for now for simplicity and efficiency). o Changes to the tcltk package: - New interface for accessing Tcl variables, effectively making the R representations lexically scoped. The old form is being deprecated. - Callbacks can now be expressions, with slightly unorthodox semantics. In particular this allows bindings to contain "break" expressions (this is necessary to bind code to e.g. Alt-x without having the key combination also insert an "x" in a text widget.) - A bunch of file handling and dialog functions (previously only available via tkcmd) have been added o The "?" operator is now an actual function. It can be used (as always) as a unary operator (?plot) and the grammar now allows it as a binary operator, planned to allow differentiating documentation on the same name but different type (class?matrix, for example). So far, no such documentation exists. o New methods AIC.default() and logLik.glm(), also fixing AIC(). o axis.POSIXct() allows the label date/times to be specified via the new `at' argument. o arrows() now allows length = 0 (and draws no arrowheads). o Modifications to the access functions for more consistency with S: arguments `name', `pos' and `where' are more flexible in assign(), exists(), get(), ls(), objects(), remove() and rm(). o Three new primitive functions have been added to base: dataClass(), objWithClass(), and as.environment(). The first two are support routines for class() and class<-() in package methods. The third replaces pos.to.env() in the functions get(), exists(), and friends. o barplot() now respects an inline `cex.axis' argument and has a separate `cex.names' argument so names and the numeric axis labels can be scaled separately. Also, graphics parameters intended for axis() such as `las' can now be used. o Shading by lines added to functions barplot(), hist(), legend(), piechart(), polygon() and rect(). o bxp() has a show.names argument allowing labels on a single boxplot; it and hence boxplot() now makes use of pch, cex, and bg for outlier points(). bxp() and boxplot() also have an argument `outline' to suppress outlier drawing {S-PLUS compatibly}. o New capabilities() options "GNOME" and "IEEE754". o New function casefold(), a wrapper for tolower/toupper provided for compatibility with S-PLUS. o contour() is now generic. o cor.test() in package ctest now also gives an asymptotic confidence interval for the Pearson product moment correlation coefficient. o data(), demo() and library() now also return the information about available data sets, demos or packages. Similarly, help.search() returns its results. o density() allows `bw' or `width' to specify a rule to choose the bandwidth, and rules "nrd0" (the previous default), "nrd", "ucv", "bcv", "SJ-ste" and "SJ-dpi" are supplied (based on functions in package MASS). o df.residual() now has a default method, used for classes "lm" and "glm". o New argument `cacheOK' to download.file() to request cache flushing. All methods for download.file() do tilde-expansion on the path name. The internal download.file() etc now allow URLs of the form ftp://user@foo.bar/ and ftp://user:pass@foo.bar/ o duplicated() and unique() are now generic functions with methods for data frames (as well as atomic vectors). o factanal() and princomp() use napredict() on their scores, so na.action = na.exclude is supported. o Function getNativeSymbolInfo() returns details about a native routine, potentially including its address, the library in which it is located, the interface by which it can be called and the number of parameters. o Functions such as help() which perform library or package index searches now use NULL as default for their `lib.loc' argument so that missingness can be propagated more easily. The default corresponds to all currently known libraries as before. o Added function file.rename(). o hist.default() allows `breaks' to specify a rule to choose the number of classes, and rules "Sturges" (the previous default), "Scott" and "FD" (Freedman-Diaconis) are supplied (based on package MASS). o Function identical(), a fast and reliable way to test for exact equality of two objects. o New generic function is.na<-(), from S4. This is by default equivalent to x[value] <- NA but may differ, e.g. for factors where "NA" is a level. o is.xxx reached through do_is are now generic. o La.eigen() and La.svd() have new default methods to use later (and often much faster) LAPACK routines. The difference is most noticeable on systems with optimized BLAS libraries. o length() is now generic. o New function .libPaths() for getting or setting the paths to the library trees R knows about. This is still stored in .lib.loc, which however should no longer be accessed directly. o Using lm/glm/... with `data' a matrix rather than a data frame now gives a specific error message. o loess(), lqs(), nls() and ppr() use the standard NA-handling and so support na.action = na.exclude. o mahalanobis() now has a `tol' argument to be passed to solve(). o mean() has `data frame' method applying mean column-by-column. When applied to non-numeric data mean() now returns NA rather than a confusing error message (for compatibility with S4). Logicals are still coerced to numeric. o The formula interface to mosaicplot() now allows a contingency table as data argument. o new.env() is now internal and allows you to set hashing. Also, parent.env() and parent.env<-() are included to provide direct access to setting and retrieving environments. o Function nsl() to look up IP addresses of hosts: intended as a way to test for internet connectivity. o Ops(), cbind(), diff() and na.omit() methods for time series objects moved from package ts to package base. o New option `download.file.method' can be used to set the default method for download.file() and functions which use it such as update.packages(). o order() and sort.list() now implement na.last = FALSE, NA. o Started work on new package management system: packageStatus() and friends. o page() has a new `method' argument allowing `method = print'. o png(), jpeg() and bmp() devices now have a `bg' argument to set the background color: useful to set "transparent" on png(). o Changes to the postscript() device: - The symbol font can now be set on a postscript() device, and support has been added for using Computer Modern type-1 fonts (including for symbols). (Contributed by Brian D'Urso.) - There is now support for URW font families: this will give access to more characters and more appropriate metrics on PostScript devices using URW fonts (such as ghostscript). - %%IncludeResource comments have been added to the output. (Contributed by Brian D'Urso.) o predict.ppr() now predicts on `newdata' containing NAs. o princomp() now has a formula interface. o readChar() now returns what is available if fewer characters than requested are on the file. o readline() allows up to 256 chars for the prompt. o read.table(), scan() and count.fields() have a new argument `comment.char', default `#', that can be used to start comments on a line. o New function reg.finalizer() to provide R interface to finalization. o reshape() extends reshapeLong, reshapeWide, which are deprecated. o rle() now returns a classed object, has a print method and an inverse. o Changes to save() and friends: - save() now takes an envir argument for specifying where items to be saved are to be found. - A new default format for saved workspaces has been introduced. This format provides support for some new internal data types, produces smaller save files when saving code, and provides a basis for a more flexible serialization mechanism. - Modified `save' internals to improve performance when saving large collections of code. - save() and save.image() now take a `version' argument to specify the workspace file-format version to use. The version used from R 0.99.0 to 1.3.1 is version 1. The new default format is version 2. load() can read a version 2 saved workspace if it is compressed. - save() and save.image() now take a `compress' argument to specify that the saved image should be written using the zlib compression facilities. - save.image() now takes an argument `ascii'. - save.image() now takes an argument `safe'. If TRUE, the default, a temporary file is used for creating the saved workspace. The temporary file is renamed if the save succeeds. This preserves an existing workspace if the save fails, but at the cost of using extra disk space during the save. - save.image() default arguments can be specified in the `save.image.defaults' option. These specifications are used when save.image() is called from q() or GUI analogs. o scan() allows unlimited (by R) lengths of input lines, instead of a limit of 8190 chars. o smooth.spline() has a new `control.spar' argument and returns `lambda' besides `spar'. spar <= 0 is now valid and allows to go more closely towards interpolation (lambda -> 0) than before. This also fixes smooth.spline() behavior for "df ~= n - 2". Better error messages in several situations. Note that spar = 0 is no longer the default and no longer entails cross-validation. o stars() has been enhanced; new `mar' argument uses smaller mar(gins) by default; further `nrow and `ncol' as S-PLUS, `frame.plot', `flip.labels', `lty' and explicit `main', `sub', `xlab' and `ylab'. Note that `colors' has been replaced by `col.segments' and there's a new `col.stars'. stars() now returns the locations invisibly. o step() is now closer to stepAIC() and so handles a wider range of objects (but stepAIC [in MASS] is still more powerful). o symbols() now has automatic xlab and ylab and a main argument which eliminates an incorrect warning. It better checks wrongly scaled arguments. o Sys.setlocale() now issues a warning if it fails. o An enhanced function type.convert() is now a documented function, rather than just internal to read.table(). o warning() allows multiple arguments, following S4's style. o New function with() for evaluating expressions in environments constructed from data. o Unix x11() devices can now have a canvas color set, which can help to distinguish plotting "white" from plotting "transparent". o On Unix, X11(), png() and jpeg() now give informative warnings if they fail to open the device. o The startup processing now interprets escapes in the values of environment variables set in R_HOME/etc/Renviron in a similar way to most shells. o The operator "=" is now allowed as an assignment operator in the grammar, for consistency with other languages, including recent versions of S-PLUS. Assignments with "=" are basically allowed only at top-level and in braced or parenthesized expressions, to make famous errors such as "if(x=0) 1 else 2" illegal in the grammar. (There is a plan to gradually eliminate the underscore as an assignment in future versions of R.) o Finalizers can be registered to be run on system exit for both reachable and unreachable objects. o integer addition, subtraction, and multiplication now return NA's on overflow and issue a warning. o Printing factors with both level "NA" and missing values uses `' for the missing values to distinguish them. o Added an experimental interface for locking environments and individual bindings. Also added support for "active bindings" that link a variable to a function (useful for example for linking an R variable to an internal C global). o GNOME interface now has separate colours for input and output text (like the windows GUI). These can be modified via the properties dialogue. o Output from the GNOME console is block buffered for increased speed o The GNOME console inherits standard emacs-style keyboard shortcuts from the GtkText widget for cursor motion, editing and selection. These have been modified to allow for the prompt at the beginning of the command line. o One can register R functions and C routines to be called at the end of the successful evaluation of each top-level expression, for example to perform auto-saves, update displays, etc. See addTaskCallback() and taskCallbackManager(). See http://developer.r-project.org/TaskHandlers.pdf. DEPRECATED & DEFUNCT o .Alias has been removed from all R sources and deprecated. o reshapeLong(), reshapeWide() are deprecated in favour of reshape(). o Previously deprecated functions read.table.url(), scan.url(), source.url(), httpclient() and parse.dcf() are defunct. Method "socket" for download.file() no longer exists. DOCUMENTATION CHANGES o `Writing R Extensions' has a new chapter on generic/method functions. UTILITIES o New package `tools' for package development and administration tools, containing the QC tools checkFF(), codoc() and undoc() previously in package base, as well as the following new ones: - checkAssignFuns() for checking whether the final argument of assignment functions in a package is named `value'. - checkDocArgs() for checking whether all arguments shown in \usage of Rd files are documented in the corresponding \arguments. - checkMethods() for checking whether all methods defined in a package have all arguments of their generic. - checkTnF() for finding expressions containing the symbols `T' and `F'. o R CMD Rd2dvi has more convenient defaults for its output file. o R CMD check now also fully checks the Depends field in the package DESCRIPTION file. It also tests for syntax errors in the R code, whether all methods in the code have all arguments of the corresponding generic, for arguments shown in \usage but not documented in \arguments, and whether assignment functions have their final argument named `value'. C-LEVEL FACILITIES o arraySubscript and vectorSubscript are now available to package users. All "array-like" packages can use a standard method for calculating subscripts. o The C routine type2symbol, similar to type2str, returns a symbol corresponding to the type supplied as an argument. o The macro SHLIB_EXT now includes `.', e.g. ".so" or ".dll", since the Mac uses "Lib" without a `.'. o New Fortran entry points rwarn() and rexit() for warnings and error exits from compiled Fortran code. o A new serialization mechanism is available that can be used to serialize R objects to connections or to strings. This mechanism is used for the version 2 save format. For now, only an internal C interface is available. o R_tryEval() added for evaluating expressions from C code with errors handled but guaranteed to return to the calling C routine. This is used in embedding R in other applications and languages. o Support for attach()'ing user-defined tables of variables is available and accessed via the RObjectTables package currently at http://www.omegahat.org/RObjectTables. BUG FIXES o Fixed share/perl/massage-examples.pl to detect instances of par() at the very start of a line. o Fixed Pearson residuals for glms with non-canonical link.(PR#1123). Fixed them again for weights (PR#1175). o Fixed an inconsistency in the evaluation context for on.exit expressions between explicit calls to `return' and falling off the end returns. o The code in model.matrix.default() handling contrasts was assuming a response was present, and so without a response was failing to record the contrasts for the first variable if it was a factor. o diffinv() could get the time base wrong in some cases. o file.append() was opening all files in text mode: mattered on Windows and classic Macintosh. (PR#1085) o f[] <- g now works for factor f. o substr<-() was misbehaving if the replacement was too short. o The version of `packages.html' generated when building R or installing packages had an incorrect link to the style sheet. The version used by help.start() was correct. (PR#1090) o rowsum() now gives character (not factor codes) as rownames. (PR#1092) o plot.POSIX[cl]t now respect the `xaxt' parameter. o It is now possible to predict from an intercept-only model: previously model.matrix.default() objected to a 0-column model frame. o c.POSIXct was not setting the right classes in 1.3.x. o cor(*, use = "all.obs") <= 1 is now guaranteed which ensures that sqrt(1 - r^2) is always ok in cor.test(). (PR#1099) o anova.glm() had a missing drop=FALSE and so failed for some intercept-less models. o predict.arima0() now accepts vector as well as matrix `newxreg' arguments. o cbind(d,f) now works for 0-column dataframes. This fixes PR#1102. o plot(ts(0:99), log = "y") now works o method "gnudoit" of bug.report() was incorrectly documented as "gnuclient" (PR#1108) o saving with ascii=TRUE mangled backslashes. (PR#1115) o frac(,) {and others} now adds a gap appropriately. (PR#1101) o logLik.lm() now uses the correct "df" (nlme legacy code). o closeAllConnections() works again, and closes all sink() diversions. o sink(type="message") works again. o sink.number was (accidentally) returning the result invisibly. o as.POSIXct("NA") (or ..lt) now work; hence, merge(*, all=TRUE) now works with dataframes containing POSIXt date columns. o integer(2^30+1) and similar ones do not segfault anymore but duly report allocation errors. o seq(0, 0, 1) now works (PR#1133). o reshapeWide() got it wrong if the "i" factor was not sorted (the function is now deprecated since reshape() is there, but the bug still needed fixing...) o PR#757 was fixed incorrectly, causing improper subsetting of pch etc. in plot.formula(). o library() no longer removes environments of functions that are not defined in the top-level package scope. Also, packages loaded by require() when sourcing package code are now visible in the remaining source evaluations. o names(d) <- v now works (again) for "dist" objects d. (PR#1129) o Workarounds for problems with incompletely specified date-times in strptime() which were seen only on glibc-based systems (PR#1155). o promax() was returning the wrong rotation matrix. (PR#1146) o The [pqr]signrank and [pqr]wilcox functions failed to check that memory has been allocated (PR#1149), and had (often large) memory leaks if interrupted. They now can be interrupted on Windows and MacOS and don't leak memory. o range(numeric(0)) is now c(NA, NA) not NA. o round(x, digits) for digits <= 0 always gives an integral answer. Previously it might not due to rounding errors in fround. (PR#1138/9) o Several memory leaks on interrupting functions have been circumvented. Functions lqs() and mve() can now be interrupted on Windows and MacOS. o image() was finding incorrect breakpoints from irregularly-spaced midpoints. (PR#1160) o Use fuzz in the 2-sample Kolmogorov-Smirnov test in package ctest to avoid rounding errors (PR#1004, follow-up). o Use exact Hodges-Lehmann estimators for the Wilcoxon tests in package ctest (PR#1150). o Arithmetic which coerced types could lose the class information, for example `table - real' had a class attribute but was not treated as a classed object. o Internal ftp client could crash R under error conditions such as failing to parse the URL. o Internal clipping code for circles could attempt to allocate a vector of length -1 (related to PR#1174) o The hash function used internally in match(), unique() and duplicated() was very inefficient for integers stored as numeric, on little-endian chips. It was failing to hash the imaginary part of complex numbers. o fifo() no longer tries to truncate on opening in modes including "w". (Caused the fifo example to fail on HP-UX.) o Output over 1024 characters was discarded from the GNOME console. o rug() now correctly warns about clipped values also for logarithmic axes and has a `quiet' argument for suppressing these (PR#1188). o model.matrix.default was not handling correctly contrasts.arg which did not supply a full set of contrasts (PR#1187). o The `width' argument of density() was only compatible with S for a Gaussian kernel: now it is compatible in all cases. o The rbinom() C code had a transcription error from the original Fortran which led to a small deviation from the intended distribution. (PR#1190) o pt(t, , ncp=0) was wrong if t was +/-Inf. o Subsetting grouping factors gave incorrect degrees of freedom for some tests in package ctests. (PR#1124) o writeBin() had a memory leak. o qbeta(0.25, 0.143891, 0.05) was (incorrectly) 3e-308. (PR#1201) o Fixed alignment problem in ppr.f on Irix. (PR#1002, 1026) o glm() failed on null binomial models. (PR#1216) o La.svd() with nu = 0 or nv = 0 could fail as the matrix passed to DGESVD was not of dimension at least one (it was a vector). o Rownames in xcoef and ycoef of cancor() were wrong if x or y was rank-deficient. o lqs() could give warnings if there was an exact fit. (PR#1184) o aov() didn't find free-floating variables for Error() terms when called from inside another function o write.table() failed if asked to quote a numerical matrix with no row names. (PR#1219) o rlnorm( *, *, sd=0) now returns the mean, rnbinom(*, *, prob=1) gives 0, (PR#1218). ************************************************** * * * 1.3 SERIES NEWS * * * ************************************************** CHANGES IN R VERSION 1.3.1 NEW FEATURES o massage-examples is now a Perl script and about 50x faster. o On Unix(-alike) systems the default pager is now determined during configuration, and is `less' if available, otherwise `more' (and not `more -s' as previously). o configure now tests for strptime functions that fail on inputs before 1970 (found on Irix). It no longer checks for the SCSL and SGIMATH libraries on Irix. o New formula interface to cor.test() in package ctest. o "NA" is now a valid color name (as NA has been a valid integer color). o pairs() function has a new `gap' argument for adjusting the spacing between panels. o R CMD check has a new test for unbalanced braces in Rd files. o readBin() has a new argument `signed' to simplify reading unsigned 8- and 16-bit integers. o New capabilities() option "cledit". o Modified restore code to give clearer error messages in some cases. BUG FIXES o Fixed placement of mtext() output (including tick labels) when text is perpendicular to axis AND axis is logged (PR#997 and PR#865). o rect() and arrows() now respond to setting of par(xpd) o abline() now responds to the setting of par(xpd), including via the "..." argument (PR#750). o Using cat() to a gzfile() connection no longer compresses poorly (at the expense of some latency). o The `exact' p-values for the two-sided two-sample Kolmogorov-Smirnov test in 1.3.0 were for the wrong tail. o In the HTML conversion of .Rd files, \link[foo]{bar} was ignoring [foo] outside \code{} statements. o lm.influence(), plot.lm(), influence.measures() and the related diagnostic measures now handle lm() fits with na.action=na.exclude. o Eliminated segmentation fault in while loops without braces in their bodies. o barplot did not accept NA heights unless ylim was specified. o predict.lm() failed with single-column model matrix (PR#1018). o legend() now also works with 100s of entries (thanks to M. Schlather). o A long-standing bug leading to inaccuracy in polyroot() has been fixed (PR#751) o A very old bug with eval() not handling a numeric `envir' argument according to specifications has been fixed. [This in particular broke ported S-PLUS code that used eval(..., sys.parent())]. Also, eval() now checks that a numeric `envir' has length one to prevent accidental passing of matrices instead of data frames. o The C code underlying nlm(f, *) now also works correctly when f(x) returns +Inf {nlm() itself *did* work!}. o pdfcolor.tex is now included in doc/manual, as pdftex seems no longer to include it. o Fixed protect bug in save() code that might have been responsible for occasionally saving corrupted workspaces. o capabilities("X11") now reports if X11 is available in this session, thereby giving the correct answer if --gui=none was specified. o Rd files with ,, inside \code{} were treating this as a ligature in LaTeX: now corrected in Rdconv. o dlopen on Compaq Tru64 was finding the wrong entry points: worked-around by using different names in the modules. o plot.mts() allows a type argument again (broken in 1.3.0: PR#1010). o scan() has a limit of 8190 on the length of char strings, and now warns if it is exceeded (when the string has always been truncated). o par adj now accepts values of integer mode (such as text(adj=0:1)). o horizontal adj values outside the range [0, 1] are now supported on devices with canHAdj==1 (Windows devices, xfig). o xtabs() without a response was ignoring drop.unused.levels=TRUE. o readLines(ok=FALSE) was not generating an error when it should. o princomp(covmat=) has been broken. o Many documentation clean-ups: formerly undocumented arguments, use of T/F rather than TRUE/FALSE. o df[] <- foo now works for data frames (PR#1047). o nargs() was documented incorrectly. o Using seq.POSIXt(by="2 weeks") was stepping by single weeks (PR#1046). o dummy.coef.lm was not handling complex terms like z:I(x). It now either does or warns and gives NAs (PR#1048). o predict.mlm() was broken (PR#1049). o ksmooth (in package modreg) was using points to the left of the kernel under some circumstances (PR#1050). o attr(x, "class") <- character(0) was segfaulting. Similar problem with "comment" attribute also fixed. o loadings() results from PCA (as well as from factor analysis) are now printed by print.loadings. o Using chol() on an non-positive-definite matrix gave an misleading error message (PR#1061). o as.character() on a language object was truncating to about 70 characters: the internal limit (from the deparse code) is now the maximum possible 500. o X11() device was failing to re-initialize correctly after all devices were shut down, so the colortype could not be changed and some systems showed protocol errors. (PR#1065) o Converting Inf and NaN values by as.character() and reading by scan() was supported by strtod on some platforms and not others: these are now handled by R itself. (PR#1072) o hclust(dist(1)) doesn't loop infinitely but signal an error. o cutree() can now cut outside heights and does not return garbage for h >= max(tree$heights) anymore. (PR#1067) o interaction(...,drop=F) returned an object looking like a factor, but with storage mode "double", confusing model.matrix.default (PR#1003) o splineDesign(*, ord=) and others give better error messages for wrong `ord' (and have slightly improved documentation). CHANGES IN R VERSION 1.3.0 NEW FEATURES o Changes to connections: - New function url() to read from URLs. file() will also accept URL specifications, as will all the functions which use it. - file connections can now be opened for both reading and writing. - Anonymous file connections (via file()) are now supported. - New function gzfile() to read from / write to compressed files. - New function fifo() for connections to / from fifos (on Unix). - Text input from file, pipe, fifo, gzfile and url connections can be read with a user-specified encoding. - New functions readChar() and writeChar() to read character strings with known lengths and no terminators, and to write user-specified lengths from strings. - sink() now has a stack of output connections, following S4. - sink() can also be applied to the message stream, to capture error messages to a connection. Use carefully! - seek() has a new `origin' argument. - New function truncate() to truncate a connection open for writing at the current position. - Socket connections via function socketConnection(). - The `blocking' argument for file, fifo and socket connections is now operational. o Changes to date/time classes and functions: - Date/time objects now all inherit from class "POSIXt". - New function difftime() and corresponding class for date/time differences, and a round() method. - Subtraction and logical comparison of objects from different date/time classes is now supported. NB: the format for the difference of two objects of the same date/time class has changed, but only for objects generated by this version, not those generated by earlier ones. - Methods for cut(), seq(), round() and trunc() for date/time classes. - Convenience generic functions weekdays(), months(), quarters() and julian() with methods for "POSIXt" objects. o Coercion from real to integer now gives NA for out-of-range values, rather than the most extreme integer of the same sign. o The Ansari-Bradley, Bartlett, Fligner-Killeen, Friedman, Kruskal-Wallis, Mood, Quade, t, and Wilcoxon tests as well as var.test() in package ctest now have formula interfaces. o Matrix multiplication functions %*% and crossprod() now use a level-3 BLAS routine dgemm. When R is linked with the ATLAS or other enhanced BLAS libraries this can be substantially faster than the previous code. o New functions La.eigen() and La.svd() for eigenvector and singular value decompositions, based on LAPACK. These are preferred to eigen() and svd() for new projects and can make use of enhanced BLAS routines such as ATLAS. They are used in cancor(), cmdscale(), factanal() and princomp() and this may lead to sign reversals in some of the output of those functions. o Provided the Fortran compiler can handle COMPLEX*16, the following routines now handle complex arguments, based on LAPACK code. qr, qr.coef, qr.solve, qr.qy, qr.qty, solve.default, svd, La.svd. o aperm() uses strides in the internal C code and so is substantially faster (by Jonathan Rougier). o The four bessel[IJKY](x,nu) functions are now defined for nu < 0. o [dpqr]nbinom also accept an alternative parametrization via the mean and the dispersion parameter (thanks to Ben Bolker). o Generalised "birthday paradox" functions [pq]birthday. o boxplot() and bxp() have a new argument `at' o New function capabilities() to report optional capabilities such as jpeg, png, tcltk, gzfile and url support. o New function checkFF() for checking foreign function calls. o New function col2rgb() for color conversion of names, hex, or integer. o coplot() has a new argument `bar.bg' (color of conditioning bars), gives nicer plots when the conditioners are factors, and allows factors for x and y (treated almost as if unclass()ed) using new argument `axlabels'. [original ideas by Thomas Baummann] o `hessian' argument added to deriv() and its methods. A new function deriv3() provides identical capabilities to deriv() except that `hessian' is TRUE by default. deriv(*, *, func = TRUE) for convenience. o New dev.interactive() function, useful for setting defaults for par(ask=*) in multifigure plots. o dist() in package mva can now handle missing values, and zeroes in the Canberra distance. o The default method for download.file() (and functions which use it such as update.packages()) is now "internal", and uses code compiled into R. o eigen() tests for symmetry with a numerical tolerance. o New function formatDL() for formatting description lists. o New argument `nsmall' to format.default(), for S-PLUS compatibility (and used in various packages). o ?/help() now advertises help.search() if it fails to find a topic. o image() is now a generic function. o New function integrate() with S-compatible call. o New function is.unsorted() the C version of which also speeds up .Internal(sort()) for sorted input. o is.loaded() accepts an argument PACKAGE to search within a specific DLL/shared library. o Exact p-values are available for the two-sided two-sample Kolmogorov-Smirnov test. o lm() now passes `...' to the low level functions for regression fitting. o Generic functions logLik() and AIC() moved from packages nls and nlme to base, as well as their *.lm methods. o New components in .Machine give the sizes of long, long long and long double C types (or 0 if they do not exist). o merge.data.frame() has new arguments, `all[.xy]' and `suffixes', for S compatibility. o model.frame() now calls na.action with the terms attribute set on the data frame (needed to distiguish the response, for example). o New generic functions naresid(), napredict() and naprint() (formerly in packages survival5 and MASS, also used in rpart). Also na.exclude(), a variant on na.omit() that is handled differently by naresid() and napredict(). The default, lm and glm methods for fitted, residuals, predict and weights make use of these. o New function oneway.test() in package ctest for testing for equal means in a one-way layout, assuming normality but not necessarily equal variances. o options(error) accepts a function, as an alternative to an expression. (The Blue Book only allows a function; current S-PLUS a function or an expression.) o outer() has a speed-up in the default case of a matrix outer product (by Jonathan Rougier). o package.skeleton() helps with creating new packages. o New pdf() graphics driver. o persp() is now a generic function. o plot.acf() makes better use of white space for `nser > 2', has new optional arguments and uses a much better layout when more than one page of plots is produced. o plot.mts() has a new argument `panel' providing the same functionality as in coplot(). o postscript() allows user-specified encoding, with encoding files supplied for Windows, Mac, Unicode and various others, and with an appropriate platform-specific default. o print.htest() can now handle test names that are longer than one line. o prompt() improved for data sets, particularly non-dataframes. o qqnorm() is now a generic function. o read.fwf() has a new argument `n' for specifying the number of records (lines) read in. o read.table() now uses a single pass through the dataset. o rep() now handles lists (as generic vectors). o scan() has a new argument `multi.line' for S compatibility, but the default remains the opposite of S (records can cross line boundaries by default). o sort(x) now produces an error when x is not atomic instead of just returning x. o split() now allows splitting on a list of factors in which case their interaction defines the grouping. o stl() has more optional arguments for fine tuning, a summary() and an improved plot() method. o New function strwrap() for formatting character strings into paragraphs. o New replacement functions substr<-() and substring<-(). o Dataset swiss now has row names. o Arguments `pkg' and `lib' of system.file() have been renamed to `package' and `lib.loc', respectively, to be consistent with related functions. The old names are deprecated. Argument `package' must now specify a single package. o The Wilcoxon and Ansari-Bradley tests now return point estimators of the location or scale parameter of interest along with confidence intervals for these. o New function write.dcf() for writing data in Debian Control File format. parse.dcf() has been replaced by (much faster) internal read.dcf(). o Contingency tables created by xtabs() or table() now have a summary() method. o Functions httpclient(), read.table.url(), scan.url() and source.url() are now deprecated, and hence method="socket' in download.file() is. Use url connections instead: in particular URLs can be specified for read.table(), scan() and source(). o Formerly deprecated function getenv() is now defunct. o Support for package-specific demo scripts (R code). demo() now has new arguments to specify the location of demos and to allow for running base demos as part of `make check'. o If not explicitly given a library tree to install to or remove from, respectively, R CMD INSTALL and R CMD REMOVE now operate on the first directory given in `R_LIBS' if this is set and non-null, and the default library otherwise. o R CMD INSTALL and package.description() fix some common problems of DESCRIPTION files (blank lines, ...) o The INSTALL command for package installation allows a `--save' option. Using it causes a binary image of the package contents to be created at install time and loaded when the package is attached. This saves time, but also uses a more standard way of source-ing the package. Packages that do more than just assign object definitions may need to install with `--save'. Putting a file `install.R' in the package directory makes `--save' the default behavior. If that file is not empty, its contents should be R commands executed at the end of loading the image. There is also a new command line option `--configure-vals' for passing variables to the configure script of a package. o R CMD check now also checks the keyword entries against the list of standard keywords, for code/documentation mismatches (this can be turned off by the command line option `--no-codoc'), and for sufficient file permissions (Unix only). There is a new check for the correct usage of library.dynam. It also has a new command line option `--use-gct' to use `gctorture(TRUE)' when running R code. o R CMD Rd2dvi has better support for producing reference manuals for packages and package bundles. o configure now tests for the versions of jpeg (>= 6b), libpng (>= 1.0.5) and zlib (>= 1.1.3). It no longer checks for the CXML/DXML BLAS libraries on Alphas. o Perl scripts now use Cwd::cwd() in place of Cwd::getcwd(), as cwd() can be much faster. o R::Dcf.pm can now also handle files with more than one record and checks (a little bit) for continuation lines without leading whitespace. o New manual `R Installation and Administration' with fuller details on the installation process: file `INSTALL' is now a brief introduction referencing that manual. o New keyword `internal' which can be used to hide objects that are not part of the API from indices like the alphabetical lists in the HTML help system. o Under Unix, shlib modules for add-on packages are now linked against R as a shared library (`libR') if this exists. (This allows for improved embedding of R into other applications.) o New mechanism for explicitly registering native routines in a DLL/shared library accessible via .C(), .Call(), .Fortran() and .External(). This is potentially more robust than the existing dynamic lookup, since it checks the number of arguments, type of the routine. o New mechanism allowing registration of C routines for converting R objects to C pointers in .C() calls. Useful for references to data in other languages and libraries (e.g. C and hdf5). o The internal ftp/http access code maintains the event loop, so you can download whilst running tcltk or Rggobi, say. It can be hooked into package XML too. BUG FIXES o boxplot.stats() now returns the correct `n' component in the case of NAs. This also affects `conf', the notch length (PR#967). o the "coef = 0" fix (PR#917) to boxplot.stats() broke boxplot.stats(do.out = FALSE). o curve(* , add = FALSE) now works correctly again if used when par("xlog") is true. o Printing a dataframe with a column called "row.names" or "check.names" omitted the column. o data.frame(a=1, b=2)[1, -(1:2)] now works, giving an empty data frame. as.matrix(df), deparse(), dput() and str() now work for empty data frames. o dbeta() could return zero erroneously on some platforms where roundoff makes e.g. 1.3 - 1 > (1.3 + 1) - 2 (Solaris and HP-UX were affected). (PR#970) o pointer protection in deriv() (PR#953) o expand.data.frame() didn't interpret its subset= argument in the data frame. (PR#979 et al., fix from Greg Warnes) o format() on character arrays was losing the dimensions. o hist.default() was ignoring its `probability' argument for equi-spaced breaks. o Occasionally insane results of is.nan(NULL), is.na(NULL) (PR#952) o ks.test() in package ctest now had the one-sided alternatives in the one-sample case reversed (PR#934). o ls.str() and lsf.str() now work better with pos > 1, and are correctly documented (PR#899). o plot(1:2, xaxs = "i") now gives both "1.0" and "2.0" x-axis labels. o promax() was not using its `m' argument (m=4 was always used). o qr.X() was ignoring pivoting (which happens only in rank-deficient cases). o sign of Pearson residuals was wrong for reciprocal link (PR#862) o The algorithm for determining starting estimates in the SSfpl self-starting model in the nls package was changed following a suggestion by Phillipe Grosjean o svd(x)$v was not a matrix when x had only 1 row (PR#963). o symnum(x) behaves more reasonably for zero length or non-numeric x. o The implementation of sys.function() did not work when the current function was already a function (e.g., a closure). o tapply() had "..." argument after simplify=, which made it incompatible with S when passing additional unnamed arguments to FUN. o use formula environments in xy.coords() (PR#932) o Unused entry points in `src/appl/fortran.c' and `Fortran.h' have been removed. o Unused directory `src/f2clib' and header `src/include/R_ext/f2c.h' have been removed. o The documentation and parts of the parse/deparse mechanism indicated that there was an operator `%'. Corrected (PR#925). o Fixed some cases where the deparser gave code that threw a syntax error when parsed. o Using a pushback with more than two lines at a time could crash. o Eliminate or warn on use of .Last.value in help examples, since .Last.value is only set from top-level expressions (and was incorrectly documented). o asInteger was ignoring integer overflow (PR#929 and others). o approxfun(*, ties = ) could return garbage when there were ties; ties = "ordered" was incorrect--also for approx()-- when there was a tie at the very right. ************************************************** * * * 1.2 SERIES NEWS * * * ************************************************** CHANGES IN R VERSION 1.2.3 NEW FEATURES o Support for configuration and building the Unix version of R under Mac OS X. (The `classic' Macintosh port is `Carbonized' and also runs under that OS.) o dotchart() and stripchart() become the preferred names for dotplot() and stripplot(), respectively. The old names are now deprecated. o Functions in package ctest now consistently use +/-Inf rather than NA for one-sided confidence intervals. BUG FIXES o `Writing R Extensions' incorrectly described an entry point `fmod' which was not included in the R binary on most systems. The entry point has been removed, to avoid any confusion with the standard C entry point of the same name. o Printing of kernels in package ts was unreliable: the internal representation was correct. o A problem with "..." in substitutions has been fixed (PR#860). o Various strangeness with match.call() and "..." has been fixed (PR#813). o sys.function() could return an unevaluated promise, messing up formals() and match.arg() (PR#872) o Deparsing or dumping attributes with non-standard names was not quoting the name (PR#871). o We now use match.fun() in tapply() so that it won't get trapped by non-functions masking FUN. o The `nmax' argument in scan(what=list(...), nmax=300) was counting blank lines, although they were said to be ignored. This affected using read.table on files with blank lines in 1.2.2, and using `n' with `what' a list. o as.numeric(), as.integer(), as.complex() returned zero on completely blank strings. Now they return NA. (PR#870) o Overflow in deparse() in terms(formula) with very long left-hand side fixed. (PR#873) o lowess(c(1:3, 7:5)) now should give the same on different platforms, since now in the C code (int)(f*n + 1e-7) is used. o curve(*, add = TRUE) now works properly with active log scales. o rt() could give different results on different platforms as the order of evaluation of calls to random numbers was not fully defined. This affected the Mac port. o ppr() inside nested calls sometimes failed to find objects due to a typo in the eval call in ppr.formula. o qchisq(0.025, 31, ncp=1, lower.tail=FALSE) now works. (PR#875) o dchisq with integer x, df and ncp sometimes gave incorrect results on i686 Linux. o Cancelling a quit caused quit() not to ask next time it was called. o Some complicated operations with "..." didn't work. o Missingness was not correctly propagated in some cases. o eigen() segfaulted on 0-dimensional matrices. o nls( ~ rhs, ..) now works (formula with empty left hand side). o The fuzz added in hist() for 1.2.2 broke the logic testing for equidistant breakpoints. o Calls to replacement functions ("f<-") lost argument names (PR#888). o is.na() and is.nan() gave random results on lists containing zero-length objects. o cor(), cov() and var() gave a result on a zero-length argument (now an error). cov(x, NULL) and cor(x, NULL) are now errors if x is a vector. (PR#883). o ?smooth.spline now properly describes `spar' which is *not* lambda. smooth.spline(1:20, spar = 50) gives an error instead of silent nonsense. print.smooth.spline() now makes use of a digits argument. o Confidence intervals for wilcox.test() had the samples reversed in the two-sided case (PR#895), and sometimes got continuity correction wrong (PR#896). o Using out-of-range font values in text() on a postscript() device on Windows could crash. .ps.prolog was incorrectly named in some of the documentation. (PR#914) o Warning messages of > 8191 chars could crash R (PR#902), as could errors. Now they are truncated to 8191 chars on machines which have vsnprintf (almost all). o range() now works properly for date-time objects. o contour() could loop infinitely (PR#897). o R-lang manual had precedence of %% wrong (PR#879). o try() constructs lost protection of R_alloc'ed memory (PR#877). o Documented that as.numeric() dispatches to as.double.foo methods (PR#918.1). o httpclient() (and the "socket" method of download.file) skipped ^V rather than ^Z in input (if drop.ctrl.z = TRUE, the default). o boxplot(*, range = 0) and boxplot.stats(*, coef = 0) now don't return outliers anymore (PR#917). o segmentation fault with tmp[[1,]] (PR#904) o incorrect "..." handling in plot.factor (PR#830) CHANGES IN R VERSION 1.2.2 NEW FEATURES o The Macintosh port becomes a full member of the R family and its sources are incorporated as from this release. See `src/macintosh/INSTALL' for how that port is built. o The API header files and export files `R.exp' are released under LGPL rather than GPL to allow dynamically loaded code to be distributed under licences other than GPL. o postscript() and xfig() devices now make use of genuine Adobe afm files, and warn if characters are used in string width or height calculations that are not in the afm files. o Configure now uses a much expanded search list for finding a FORTRAN 77 compiler, and no longer disallows wrapper scripts for this compiler. o New Rd markup \method{GENERIC}{CLASS} for indicating the usage of methods. o print.ftable() and write.ftable() now have a `digits' argument. o undoc() has a new `lib.loc' argument, and its first argument is now called `package'. BUG FIXES o The behaviour of polygon() with NA coordinate values is now documented. o polygon() now correctly recycles the values of border and lty. Thanks to Denis White. o readBin() and writeBin() were not always making good use of long types (such as long double) when available. o The C function fprec was not handling very small denormalized numbers correctly. This affected the way they were printed on Windows, for example. o legend() now draws points after lines allowing "empty dots on lines" thanks to Ben Bolker. o Setting row/column names preserves the names of the dimnames (PR#809). o Using help() after help.start() on Unix was failing to find the linked help files if more than one package was loaded (as now happens by default). o scan now sets the maximal sizes internally when `what' is a list from `nmax' and failing that `nlines'. This uses memory much more efficiently if `nmax' is specified. read.table() makes use of this. o The FORTRAN code used is now much closer to ANSI compliance. o cov.rob() gives a useful error message on nearly-degenerate matrices. o summary() on a data frame was computing results to a precision based on options("digits") (default 4), not its `digits' argument. Now results are computed to full precision but formatted using `digits'. o summary(m, digits=*) also properly works for matrices. o When returning parameters from .C/.Fortran, the OBJECT field was not copied even though class attributes were (PR#834). o There was a spurious warning from the X11 driver on 100 dpi displays (PR#840, fix from Tom Vogels). o scan() was reading all-blank numeric fields as zero. Should be read as NA, and are now. o dnbinom(*, size, *) now works again for size < 1 (PR#842). o dgeom(*, p = 0) and pgeom(*, p = 0) don't give NaN anymore. o smooth.spline() allows zero weights again. o aperm() fix for list arg; aperm(*, resize=FALSE) now works with dimnames (by dropping them). o The xfig() driver was not closing unclosed polygons as the R driver expected (but did not document). o spec.ar() now handles order 1 correctly. o Add fuzz to prevent anomalies with hist(). o print.matrix() checks length of rowlab, collab (PR#850) o add1.glm() was using the wrong weights for binomial glms in cbind(successes, failures) ~ lhs form, since 1.2.0. o Eliminate packing of the `structRstart' structure, which was probably non-ISO C and caused some compilers problems (PR#852). o all.vars() no longer returns empty `names' (PR#829). o dotplot() passes `cex' down to the mtext() calls used for the labels (PR#816). o The pictex() driver was drawing polylines incorrectly (PR#845). o In the event of a fatal X11 error (this can be generated under FVWM by selecting Destroy), the input handler would loop, leaving the "please save work and shut down R" advice useless. There should now be an opportunity for a relatively graceful exit. o polyroot() misbehaved if all coefficients except that of the highest degree term were zero (partial fix for PR#751) o spline(method="natural") was extrapolating incorrectly (both to the left and to the right, for different reasons). (PR#653) o Line clipping was incorrect for log-plots. (PR#839) o Add explicit test for rank-deficient residuals to summary.manova(). o The help search databases did not contain the data from the platform-specific help files. o parse.dcf() and hence package.contents() now work with a warning for empty contents' files. o which.min() and which.max() now properly work for 0-length and NA-only arguments. CHANGES IN R VERSION 1.2.1 NEW FEATURES o New functions factanal(), varimax(), promax() and examples in package mva. o New functions readBin() and writeBin() to transfer binary data to and from connections. o merge() is partially moved to C to reduce its memory usage. o library(help = PKG) now displays the contents of the package's DESCRIPTION file in addition to its INDEX. o Sd2Rd can handle S4-style documentation too: see `Writing R Extensions'. o prompt() now also works with a character argument (useful for producing many *.Rd files in a loop). o The Unix front-end shell script now ignores a value for R_HOME found in the environment. o Connections functions such as file() now accept a description of length > 1, with a warning. o All text-mode connections now accept input with LF, CR or CRLF line endings. This means that readLines() can be used on DOS files and source() on Mac files, for example. Also, CRLF-terminated files can be used as stdin on Unix, and files with last lines without an EOL mark can be used as stdin and source()-ed on Unix and Windows. o DESCRIPTION file has a new recommended `Maintainer:' field. o stars() now uses a larger "cex" for the labels, and cex and lwd are now arguments. Further, the argument names (xlim, ylim, axes) are now consistent with other plot functions. The key symbol is not clipped anymore into the plot region by default. o Date-time quantities are now printed with the timezone, if known. o R CMD build now ignores all files specified (via Perl regexps) in file `.Rbuildignore' in the top-level source directory of a package. o Horizontal boxplots are possible with horizontal = TRUE. o all.equal() on lists now compares them as generic vectors, that is they are equal if have identical names attributes and all components are equal. o Invalid lines in .Renviron now give warnings when R is started. o Argument `na.last' implemented for rank(). BUG FIXES o There have been many small improvements/corrections in the documentation. In particular: The help pages for lm and glm now describe the fitted objects. is.vector() is now correctly documented: complex vectors and lists return TRUE. o The default sortedXyData constructor in the nls package now handles missing values in the response. o On startup, file .RData is now restored *after* the site and user profiles are loaded (if at all). This is as previously documented. o as.POSIXlt (and *ct) operating on a character string only extracted the date (and not the time) in some cases. o as.POSIXct() on character objects was ignoring `tz'. o codoc(ignore.generic.functions = TRUE) works again. o Explicitly close files opened by sink() for OSes (such as Windows) that benefit from it. o Prevent closing the sink connection (which would be a silly thing to do). o showConnections(all = TRUE) was sometimes counting connections incorrectly, and so not showing some closed ones. o ts(1:10, start= c(1999,6), end = c(2000,3), frequency = 12) now prints both years (as it should). o Monthly multivariate time series now print proper month names in all cases. o print.stl(), print.princomp() and print.prcomp() now pass on `digits =' etc. o prompt() now produces a \usage{} line for data frames and other datasets, as documented in `Writing R Extensions'. o glm() now returns correct linear predictor and fitted values for zero-weight cases. o scan(strip.white=TRUE) and readline() could give incorrect answers when an input field was empty or blank. o dchisq() now behaves better for large values of its ncp parameter. o besselJ(*, nu) is now ok for nu < 1; fix improves accuracy of other values by a few bits as well. o The convergence criterion in the Fortran SVD code has been changed to circumvent spurious convergence errors when comparing extended-precision quantities on ix86 Linux (and some compilers and options). o Rdindex now handles multi-line \title{}'s correctly. o Add weights.glm() so that plot.lm() gets the correct weights from glm objects (the ones that go with deviance residuals not the working residuals). o Printing a language object (e.g. a formula) in a list was clobbering the buffer holding the tag labels which then were lost in subsequent lines of printout (PR#746). o aic in family() objects is now computed more precisely using dxxxx(log=TRUE). For binomial fits the value was wrong for models specified via proportions and weights (PR#796). Avoid NaN values in aic where n = 0 occurs. o Using non-integer numbers of successes in a binomial glm (as formerly in demo(lm.glm)) now gives a warning, as the theory and in particular the AIC value is not applicable. o demo(is.things) works again {is.ALL() doesn't call methods anymore}. o persp(*, nticks = nn) now works (better) for too small nn. persp(*, main = t1, sub= t2) now work (as always documented). o Printing of attributes of a list element no longer precedes `attr' by the tag (PR#715). o It is no longer possible to use df[foo] to select non-existent columns in df and so create an invalid object of class "data.frame" (PR#698). o edit.data.frame() was trying to set row.names on a list, which is no longer allowed. o In the \link[pkg]{topic}, `pkg' was not being used if `topic' was found in a package in .lib.loc. Now `pkg' is always used. o plot() with small relative ranges gave an error, which e.g. broke library(ts); plot(stl(ts(rep(1:7, 15), freq = 7), s.win = "per")) o Using scan() with a 0-length `what' argument now gives an error message rather than a segfault. o Loading .Random.seed could extremely rarely and with some generators reject a value as NA_INTEGER when it was valid. o save(..., ascii=TRUE) created broken files when saving strings containing special characters (ASCII code > 127). o mean(c(1,NA,NA,NA)[-1], trim = .1, na.rm = TRUE) doesn't give an error anymore. o As the supplied afm files are not properly in the ISOLatin1 encoding, the font metric for "-" was wrong since 0.63 on a postscript/xfig device, and randomly wrong in 1.2.0. It will now be correct (but the files remain incorrect: C45 is "minus" not "hyphen" and there are missing slots). Metrics for the duplicated characters (acute, dieresis, macron, space) in ISOLatin1 encoding are now correct for both occurrences: previously only one was present. o The data-time functions try harder to guess the DST setting when the OS does not know, as some OSes were printing times in DST if this was marked as unknown. o Setting par(pty=) after par(pin=) or par(plt=) was having no effect until the margins were set. o Nested \describe sections in .Rd files have (again) nested indentation when converted to text. o Concatenation of C strings by ## is no longer used, to avoid spurious warnings from some recent versions of gcc. o dev.copy2eps() allows a `paper' argument to be passed to postscript(). o file.show() handles the case of zero files better. o formula.lm uses object$formula if it exists, in preference to object$terms. o strsplit() is corrected for an empty split pattern. o kronecker() now does a better job when creating dimnames. o Better handling of input dimnames in fourfoldplot(). CHANGES IN R VERSION 1.2.0 NEW FEATURES o There is a new memory management system using a generational garbage collector. This improves performance, sometimes marginally but sometimes by double or more. The workspace is no longer statically sized and both the vector heap and the number of nodes can grow as needed. (They can shrink again, but never below the initially allocated sizes.) See ?Memory for a longer description, including the new command-line options to manage the settings. o values of `--min-nsize' up to 50M (2Gb on 64-bit Solaris) are allowed. o A (preliminary) version of S4-like connections has been added, and most functions which take a "file" argument can now work with a connection as well as a file name. For more details, see the chapter on Connections in the R Data Import/Export manual. o New command-line option `--no-restore-history' implied by `--vanilla'. o Command-line option `--no-restore' is now `--no-restore-data' and `--no-restore' implies `--no-restore-*' (currently `data' and `history'). o The more recent GNU regex from grep-2.4.2 is used. This uses locale-based ordering for ranges on platforms with strcoll. o The print routines now escape " (as \") in a character string only when it is printed as a quoted string. This makes print(, quote=FALSE) and cat() consistent. o The standard methods for add1() and drop1() now attempt to cope with missing values by using a subset of the data that is `cleaned' by na.action for the maximal model under consideration. o anova() for 3 or more lm objects now behaves compatibly with S and anova.glmlist(). The old behaviour is still available by calling anovalist.lm() directly. o anova() for multiple lm and glm objects no longer truncates the formula printed. There is much more extensive documentation for anova() methods. o New method as.data.frame.table() for converting the array-based representation of a contingency table to a data frame containing the classifying factors and the corresponding counts. o New function assocplot() for producing Cohen-Friendly association plots. o autoload() accepts lib.loc and other arguments to library() o bxp() has new argument `frame.plot', as plot.default(). o contour() now has `axes' and `frame.plot' args. o contrasts(, FALSE) now always returns an identity matrix, to make model.matrix compatible with S. This affects models such as lm(y ~ o - 1) where o is an ordered factor. o `where' command added to debug(). o demo(dynload) (which used the superseded call_R interface) has been removed. o Class "dendrogram" in package mva providing general support for tree-like structures (plotting, cutting, ...). o dev.copy2eps() and dev2bitmap() preserve the aspect ratio of the copied device if just one of `width' and `height' is specified. o dump() has new argument append, argument `fileout' has been renamed to `file' (for consistency with all other functions). o edit.default() now checks for an unset `editor' argument, and terminates with an error if the editor cannot be run. o The `mode' argument of exists() and get() is interpreted as mode(x) rather than typeof(x), following S. o New functions file.access() and file.info() for information on files on the user's file systems. o New convenience function file.copy(). o file.show() allows `pager' argument to be an R function, and consequently, the `pager' option can be an R function. o Formatting (and printing) of data.frames with complex objects is improved. toString was added as a new function. o format() has a new argument `justify' controlling the justification of character strings (and factors). o Formula objects now have an environment and code manipulating them needs to take care to preserve it or set an appropriate environment. o New function fourfoldplot() for producing fourfold displays of 2 by 2 by k contingency tables. o gc() now reports the space allocated, not the space free, since the total space is now variable. o New primitive gc.time() to report on time spent in garbage collection. o hclust() takes new argument `members' allowing dissimilarity matrices both for singletons (as until now) and clusters. o help() has an additional `pager' argument which may be passed to file.show() {useful for ESS fans}. o There is now an R `Hershey' list object for Hershey vector font computations and documentation. o hist() now returns a "histogram" object and calls the new function plot.histogram() for plotting. It now also allows character labels. o if(*) now gives a more intelligible error message when "*" cannot be coerced to logical. o inherits() is now an internal function and compatible with S. o New function lag.plot() in package ts. o legend() has a new argument pt.bg. o The commands history can be loaded with loadhistory(), saved with savehistory() and displayed with history(), under Windows and under Unix using the readline or GNOME interfaces. o mad() has new (logical) arguments "low" and "high" (the first giving S compatibility). o New function manova() and summary method. o Function mantelhaen.test() in package ctest now can deal with general I x J x K tables. In addition, in the 2 x 2 x K case, it can also perform an exact conditional test of independence, and gives confidence intervals for the common odds ratio. o model.frame() now uses the environment of its formula argument, rather than the parent environment, to evaluate variables not found in the data argument. See help(formula). o mosaicplot() can now also create extended mosaic plots, which visualize the residuals from a log-linear model using color and outline. o New utility function n2mfrow(). o nlm(check.analyticals = TRUE) now warns if the supplied gradient and/or hessian are of the wrong length. o New function object.size() to give approximate memory allocation. o optim() now checks the length of an analytical gradient at each evaluation. o The L-BFGS-B method of optim() now support tracing, at several levels of detail. o options(check.bounds = TRUE) makes each vector extension by sub-assignment ("x[.] <- .") produce a warning. o options(width) now admits to a limit (previously 200, now 10000) and gives a more informative message if out of range (as it does now for digits and expressions). o Function path.expand() to do tilde-expansion on file paths. This provides an interface to R_ExpandFileName, which is now a documented entry point. o .Platform has new component "endian", useful for binary file manipulations. o plot.function() and curve() now take xlim as default for (from,to) if the former is specified. o plot.hclust() allows arguments main, sub, etc, and has non-empty defaults for these. o plot.ts(x,y) now allows to suppress labels and lines; it is better documented. o The postscript() driver now allows a user-specified family so, for example, one can use the same fonts in diagrams as in running text. o The postscript() driver allows its prolog to be changed (by an expert) via object .ps.prolog. o prop.table() and margin.table() now work with an empty `margin'. o Formerly deprecated function provide() is now defunct. o New functions read.delim() and read.delim2() to make it easier to read delimited files as Windows programs tend to create (usually TAB separated). o New readLines() function to read a file line-by-line. o New functions reshapeLong() and reshapeWide() emulating Stata's reshape command. These are still labeled experimental and might be improved (or removed) in later versions. o row.names() and row.names<-() are now generic functions which call rownames() as their default method and have methods for class "data.frame". o New function Rprof() for profiling R expressions under Unix. Configure with `--enable-R-profiling' (on by default) to make this operational. o save(, oldstyle=TRUE) has been withdrawn. o scan() and read.table() have a new argument `fill' which can be set TRUE to allow reading files with unequal number of fields per line. (Programs like Excel have a habit of creating such files when exporting.) o scan() and read.table() have a new argument `blank.lines.skip' to allow blank lines to be read. o scan() now reads empty character fields as "" not "NA" unless "" is included in na.strings. o smooth() in package eda has a better default (3RS3R instead of 3RSR) and more arguments, e.g. `twiceit' for some S compatibility and `kind = "3R"' for running medians of 3. o strsplit() has a new argument `extended' controlling whether to use extended (the default) or basic regular expressions for splitting. o Sys.getenv() becomes the preferred name for getenv(), which is now deprecated. o New functions Sys.getlocale() and Sys.setlocale() to query and set aspects of the locale of the R process, and Sys.localeconv() to find the default decimal point, etc. o New function Sys.info() for platform, host and user information. o New function Sys.putenv() to set environment variables. o New function Sys.sleep() to suspend execution for a while. o Date-time support functions with classes "POSIXct" and "POSIXlt" to represent dates/times (resolution 1 second) in the POSIX formats. Functions include Sys.time(), as.POSIXct(), strftime(), strptime(), and methods for format, plot, c, .... There are conversion functions for objects from packages `date' and `chron'; unlike those packages these support functions know about time zones (if the OS does). o tcltk package now has tkpager() which is designed to be used by file.show() and shows help pages etc. in separate text widgets. o tcltk is now more careful about removing the objects representing widgets in the R workspace when the windows are destroyed (e.g. using window manager controls) o tcltk package has had several canvas functions implemented. o tcltk now wraps callbacks to R in a try() construct - the nonlocal return from R's error handling could bring the Tk system into a strange state. o New demos for tcltk: tkfaq, tkfilefind, tkcanvas. o termplot() now has an `ask' argument. o terms() creates objects which now inherit from class "formula", so for example as.formula(terms.object) needs to be replaced by formula(terms.object). o traceback() is now printed un-quoted and labelled by the frame number. o New argument `recursive' to unlink(). The default behaviour on Unix is now that of rm -f, not rm -rf. unlink() is now compatible across platforms. o New functions write.ftable() and read.ftable() for writing out and reading in flat contingency tables. o write.table() now quotes factor columns if quote=TRUE, and has a new argument `qmethod' to control the escaping of embedded quotes in character or factor columns. o New function xtabs() providing a formula interface to cross tabulation. o The R Data Import/Export Manual (`R-data.texi') has been added. o The set of valid R names is now described (at last) in R-intro. o The R Language Manual (`R-lang.texi') is now included and built in the same way as the other manuals. o The R manuals (R-intro, R-exts, ...) are converted to HTML format (if the necessary texinfo tools are available) and linked into the top HTML help page. o The header file `R.h' and those included from it are now usable with C++ code. o New header file `R_ext/Boolean.h': Rboolean type with TRUE and FALSE enum constants. o New header file `Rgraphics.h' to allow addons to use graphics structures. o Recommended include file `Rmath.h' replaces `R_ext/Mathlib.h'. o Bessel, beta and gamma functions are now documented as part of the API. Undocumented entry points are no longer in the header files, and some are no longer visible. o Calloc & Realloc failures now give size information. o DESCRIPTION file in installed packages has a new `Built:' field giving build information (R version, platform, date). o Much improved support for C++ code in add-on packages under Unix. New configure/build variables SHLIB_CXXLD and SHLIB_CXXLDFLAGS for specifying the command and flags needed for building shared libraries containing objects from a C++ compiler. Configure tries to get these right in typical cases (GNU tools and/or common platforms). C++ source suffixes `.cpp' and `.C' are now recognized in addition to `.cc'. o Configure/build variables MAINLD and MAINLDFLAGS are renamed to MAIN_LD and MAIN_LDFLAGS for consistency with other MAIN_* vars, similarly for SHLIBLD and SHLIBLDFLAGS. o Configure/build variable FLIBS now only contains the Fortran 77 intrinsic and run-time libraries needed for linking a Fortran 77 program or shared library (as determined by configure). BLAS library detection was extended, with results saved to the Make variable BLAS_LIBS which is also available to add-on packages. o R CMD build and check have been completely re-written in Perl. In addition to running examples, check now also checks the directory structure and control files, makes a temporary installation and runs LaTeX on the help pages. Build has been reduced to cleaning, rewriting indices and creating tar files. The same files of Perl code are now also used under Windows. o Add-ons for utilities like Perl or LaTeX have now a central place in $R_HOME/share. Migration of existing files might take a while, though. o Preliminary support for building R as a shared library (`libR') under Unix. Use configure with option `--enable-R-shlib' or do `make libR' in directory `src/main' to create the shared library. There is also a linker front-end `R CMD LINK' which is useful for creating executable programs linked against the R shared library. BUG FIXES o New "[.AsIs" function fixing PR#665. o Effectively zero-length arrows() are omitted (rather than getting a system- and device-dependent arbitrary angle). o barplot() passes "..." down to plot.window as documented. o bxp(*) now obeys axes, xaxt, yaxt & ylim arguments (again?). o contour(.., labcex = 0.6, .. , vfont = c("sans serif", "plain"), ..) now behaves as it has been documented, PR#740. o D(.) is now more correctly documented, has second argument "name" instead of "namevec" (S compatibility), and gives a warning when name has not length 1. o dbinom() and dpois() now use a the accurate algorithm of C.Loader; e.g., 1 - 2*sum(dbinom(0:999, 1999, 1/2)) is now zero instead of 1e-12. o dbeta(), df(), dt(), dnbinom(), dgeom(), dgamma(), now all use the more accurate algorithms of dbinom() and dpois(); More limits are computed correctly, e.g. dgeom(Inf,*), or dnbinom(*,*,p=0), and integer argument coercion is more consistent. o dbeta(x, a,b) was giving NaN and Inf for large a and b. o The math functions now (again!) return NaN (not NA) when the warning message says so (e.g. gamma(-1)). o Paper sizes for "a4" and "legal" were interchanged in dev.print(). o Improved logic in the re-scaling of plots in dev.print(). o dev.print() and dev.copy2eps() now evaluate arguments as needed, so e.g. dev.print(file="junk.ps", horizontal=F) will work (previously =FALSE was needed). o Now dweibull(0,1) == dexp(0) == 1 for consistency. o Changing column modes from factor/character to numeric in edit.data.frame() (and fix() on data frames) is now allowed. o gctorture() did return a value although documented not to, that of gcinfo. It now returns the previous setting of gctorture. o glm() now follows lm() in dropping unused factor levels when fitting. o hist() now labels y-axis Density rather than Relative Frequency if freq=FALSE. The `intensities' component of the result is now deprecated and `density' should be used instead. o hsv() truncation bug fixed (hopefully correctly this time...) o library.dynam() no longer fails if the library appears more than once in lib.loc. o lm.fit & lm.wfit (and hence lm) now give understandable error messages when there are 0 non-NA cases. o match() does not always use "as.character()" anymore, fixes PR#741. o Trimmed mean() and median() are no longer attempted for complex data. o median() of empty vector is now NA. o model.matrix() can now handle NAs in factors. o model.matrix() now uses ":" not "." in labelling interaction terms, as terms() and the prototype do (PR#701). o old.packages() now sorts version strings correctly by splitting at "." and "-". o optim() has several new precautions against bugs, one of which was an infinite loop in the L-BFGS-B method if the derivatives were inaccurate (or if numerical derivatives were used and the problem was badly scaled). o pairs() now obeys an "cex = " argument, and so does panel.smooth(). o pf() had a bug in the code handling large noncentrality parameters, going all the way back to the original Appl.Stat. algorithm (PR#752). This affected pbeta() as well. o phantom(expr) in plotmath was used to calculate the bounding boxes, but the space was not actually used in typesetting the expression (PR#622). o Problem with subsetting and "..." arguments in plot.formula() (PR#757) o plot.lm() has a better default for its `ask' argument. o plot.new() does *NOT* allow an argument (`ask') anymore. This has not been working (since ~ R 0.49), is low-level and hence should not break anything. o plot.stl() now uses correct time labels for tickmarks of x-axes. o pnorm() is somewhat more accurate (SIXTEN=16; PR#699) and `infinitesimally faster' in some cases, thanks to James M. Rath. o Failure to open a postscript() device now gives diagnostic warnings. o Zero the widths of undefined chars in postscript(). o Make font metrics local to the device in postscript(), so that simultaneous instances of postscript/xfig/bitmap can use different values for `family'. o postscript() no longer uses the initclip operator, which was against the EPSF specifications and broke inclusion of graphics in some documents. o In postscript(), cleaned up the internals to fix some cases where it was unclear whether a variable was meant to set or track device status. o In some cases, emitted postscript violated the PS Document Structuring Conventions since some settings were carried over from one page to the next. (Caused breakage when turning antialiasing on/off in "gv" for instance.) o The DocumentMedia comment in postscript() output was wrong, and the font DSC comments have been changed to the preferred style for DSC 3.0. o pretty(x <- c(2.8,3))[1] - x[1] is now 0; in general, p <- pretty(x) now again fulfills p[1] <= x[] <= p[length(p)]. o print.dist() {mva} now passes "..." to print.default. o print.noquote("ABC") now works. o prompt(fn) uses fn's "source" attribute if it has one. o In prop.test(), the conf.int. now contains the estimate, even when that is 0 or 1 (PR#714). o qnorm(0) and qnorm(1) now give -/+ Inf (again!). o qt(*, log = TRUE) has a somewhat extended working range. o Specifying col.names in read.table() now overrides any header line in the data file. o Bug caused rpois() to generate biased variables in some cases. o scale(scale=TRUE) gave all NAs in any columns containing NAs. o eda's smooth() now computes Tukey's endrule properly. o smooth.spline()'s GCV method now uses a more accurate formula when there are repeated x points. o stars() fix (for 0/NA columns) PR#739. o data(state)'s state.abb has been corrected to use official 2-letter abbrevations. o strsplit() had two memory leaks. o tcltk interface now has better string quoting and no longer breaks on strings with unbalanced braces o tcltk callbacks used to include a "%..." argument on the call if the callback function had a "..." argument. This is no longer the case. o t.test() allows an input vector of length 2. o Method dispatch in primitive functions such as `c' only occurred if they were called by that name, and in particular not if used in lapply or called as .Primitive("c"). It now always occurs. o Method dispatching now forces evaluation of promises, so autoloading works with methods. o c(0.099999994, 0.2) prints as 0.1 0.2 not 0.10 0.20 after correcting the precision calculations. o Internal function fprec was overflowing for numbers around 1e-305. o [internal] .C("strsignif",*) doesn't use fixed size strings anymore (possible overflow). o ff[i] <- r now works for formula (and potentially other non-standard) objects ff. o Errors in argument matching could cause crashes if error handler was used. o NULL == ... now gives logical(0) instead of an error. This fixes a bug with e.g. apply(X,2,median, na.rm = TRUE) and all(NULL == NULL) is now TRUE. o polylines with more than 64K pieces will now work on more X servers with the x11 device. o R CMD Rd2dvi now again works with file names containing "_" or "$". o R CMD Rdconv now handles .rd as input file extension correctly in all cases. o make install could fail if there were no shared libraries to install (e.g. on vanilla Solaris). o Rd's \describe{} constructs are converted better to text output, and \items of >=22 chars now work. o Help aliases "(" and "{" now work, apart from as PDF hyperlinks. o NA || x , NA && y (etc) do not give errors anymore, but work as the "|" and "&" operators and as documented (PR#749). o Coercing lists to functions failed if argument list was empty. (PR#743). Also coercing functions to lists was wrong when the body was a single constant. ************************************************** * * * 1.1 SERIES NEWS * * * ************************************************** CHANGES IN R VERSION 1.1.1 NEW FEATURES o data(), example() and help() now search the loaded packages, then in their .lib.loc argument, the latter as pre-0.99.0. See their help pages for the precise details. o help() has a new argument `try.all.packages' set by the option "help.try.all.packages". If help is not found in the normal path and this is TRUE then a search is made of all packages for possible matches. o Improved detection of Tcl/Tk at configure time. One can either set configure variables TCLTK_CPPFLAGS and TCLTK_LIBS, or give the locations of the tclConfig.sh and tkConfig.sh scripts via the `--with-tcl-config' and `--with-tk-config' arguments. o prop.trend.test() - test for trend in proportions. o write.table() has new argument `dec' for setting the decimal separator (SPSS/Windows and probably others want commas in continental European locales). o Advance warning: save(, oldstyle=TRUE) will no longer be available after this release. o Symbols can now be coerced to expressions, making as.expression(quote(a)) work BUG FIXES o data() now works correctly with data-only packages. o Standalone Mathlib can now be made if builddir = srcdir (working around an undocumented autoconf `feature'). o Check for pre-1.1.0 saved object .Postscript.options in postscript(). o More stringent checks on the arguments to dataentry(). o Specifying xlab as an expression now works again. o dev2bitmap() works again. o Numerous uses of `F' and `T' replaced by `FALSE' and `TRUE'. o bxp() now extends `ylim' properly when notch=TRUE (and a notch is more extreme than other stats). Also, varwidth is okay again, see example(split). o Making manuals without making R first now works. o princomp() now works when some eigenvalues are tiny negative values (which are treated as zero). o SearchEngine.html was not installed when builddir != srcdir. o lm.{w}fit(x,y,..) now work when x has no column names. These functions no longer add and subtract n zeros when there's no offset. They are now documented somewhat. o Some HTML files used src="R.css" instead of href="R.css" causing some browsers to ignore the style sheet. `R.css' now passes the w3c CSS validator and gives the intended results with Internet Explorer. `R.css' is copied to all library directories. o The data editor no longer crashes when entries contain more than 45 characters, and works correctly if the field width is larger than the window width. o Recording plots used to ignore graphics events before the last replay. o plot(), points(), etc now give warnings and error for invalid `type' arguments. o matplot() now allows the same `type's as plot(). o dev.print() and dev.copy2eps() now work when called from a function, such as dev2bitmap(). o anova.glmlist works correctly with decreasing models and test="F" now gets the correct residual df. o Functions created (not just edited) with fix() now get environment .GlobalEnv not the body of fix. o Rdconv was ignoring OS-specific parts of the files with some Perl versions. (This did not affect installing packages.) o R CMD check did not run more than one specific test. o keyword2html omitted items when changing up a level, so the HTML search engine keyword list was missing `data' and `utilities', for example. o aov() with multiple strata was setting some spurious options. o Under UNIX, help(, htmlhelp=TRUE) uses the linked copy of the HTML file in ~/.R if help.start() has been run recently in the session, so the style sheet and hyperlinks should now be found. o dotplot's arguments `color' and `lcolor' are now interpreted correctly if they are vectors of length > 1. (It is not clear from the help that this was ever intended.) o Error messages of e.g. do.call() are now spaced properly. o summary(.matrix | .data.frame) now respects a `digits' argument. o scan() recognises quoted strings by default again. The default for the quote= argument got set wrongly when it was introduced. They are, however, turned off when using sep="\n", since you probably want unprocessed lines of text in that case. o fixed buglet where scan() would double a character following a terminating quote symbol. o kmeans was failing on vector inputs (although not documented to accept such). o fixes in predict.lm (John Maindonald) o NCOL got confused by 1D arrays, which it now reports have 1 column rather than NA. o rep(1:2,c(1,-1)) segfaulted (PR 619) o x[["a"]] <- y rejected some object types for y (e.g. expressions) which were accepted in x$a <- y (PR o data editor froze on empty data frame, and more generally on zero-length cols. o data editor did not handle factors properly in numeric-edit mode. o table() misbehaved on empty (or all-NA) data o data editor now handles empty data frames, allowing data entry to begin with dd<-edit(data.frame()) or dd<-data.frame() ; fix(dd) o plotting math expressions when specified as a LANGSXP or SYMSXP didn't work in several cases: plot(1,main=quote(a)) would segfault and there were problems with title(), text(), and mtext() as well. o optim(): no more segfault for REPORT=0; corrected error msg; .. maxit default is now okay also when "L-*-B" is chosen automatically. Using (abs|rel)tol with that method now gives a warning. o text() did not respect its `xpd' argument, the default of which is still to use par("xpd"); gave a wrong error message in one case. o polygon() had an incorrect documentation and silently disregarded "..." arguments. o predict.loess was giving incorrect results (those for the non-robust fit) in the case of a fit with family = "symmetric" and surface = "direct" and prediction with se = FALSE. The fitted values were missing for such fits. o Better rendering of ^ and ~ in latex in \code{} (and they should not appear outside code and verbatim sections). o Fixed unterminated string problem with lty (PR 584) o Fixed scoping problem with quasi() family (PR 614) CHANGES IN R VERSION 1.1.0 NEW FEATURES o There are several changes to the compile and link flags, and an attempt is made to use /usr/local/include and /usr/local/lib on all platforms. Please read config.site and INSTALL if you have set flags for previous versions. o New package tcltk, providing interface and language bindings for the Tcl/Tk graphical interface toolkit. This makes it possible to do some rather nifty things with buttons and entry fields and so forth in very few lines of code. It is still somewhat experimental so don't go churning out thousands of lines of GUI code and then blame us for changing the API later on. It does not currently work with GNOME because of event loop differences. See demo(tkttest) and demo(tkdensity). o Internally using global R_Expressions [getOption("expressions")] dramatically speeds up eval.c. o The X11 support code is now in a separate shared library, and option `--gui=none' will run R without X11 support (and so x11() and data.entry() will not be available). R BATCH sets --gui=none. o Configuring without X (e.g., `--without-x') does work (at last). configure will report if X11 support has been included. If R has been built without X11 the default GUI is "none". o GNOME support files have moved from src/gnome to src/unix/gnome and the code is now in a separate shared library. Both `--gui=GNOME' and `--gui=gnome' are allowed. The main graphics device for use with GNOME is now called gtk(); the x11() device from the X11 support can also be used. (The gnome() device remains unreliable, and is by default unavailable.) All GNOME support now installs in R_HOME/gnome to make it easier to package separately. o Command line option `-g' can now be used as short version of `--gui'. o The "keep.source" option now defaults to interactive() instead of TRUE. o Many interface enhancements to the data editor, which now uses (by default) variable-width columns and much less redrawing. See ?dataentry for a description of the current user interface. o R under Unix can be sent SIGUSR1 to quit and save or SIGUSR2 to quit and save without running .Last and on.exit expressions. o Added ability to use the graphics device driver to perform horizontal justification of strings. This is used in the x11(), windows(), postscript() and xfig() drivers and will lead to more accurate placing of centred or right-justified strings. o Formulas created with the tilde operator now contain the environment in which they were created. The environment of a formula can be accessed with the environment() function. This facility is still experimental; it is intended to help simplify writing modeling functions. o $ and $<- are now generic functions. o add1.glm() and drop1.glm() now allow test="F", which is appropriate for models with estimated dispersion. o approx() and approxfun() have an extra argument ties= to control handling of tied x values o New function as.symbol(), identical to as.name(). is.symbol and is.name() are now identical by definition; before, they were equivalent by implementation. o attach() now works for R data files. o axis() now has additional arguments. The argument "tick" turns tick drawing on and off (on by default). Additional arguments line, pos, and outer; allow more flexible placement of axes. o New device bitmap(), like dev2bitmap() but a stand-alone device. o boxplot() returns (and bxp() accepts) a list containing the summary statistics for the boxes (changed from a list of elements one for each box). o file="|cmd" is allowed (to pipe output to `cmd'), under cat() and postscript() and functions that use them (for example, write()). o New functions chartr() for general-purpose character translation in character vectors, and tolower() and toupper() for converting alphabetic characters to lower-case and upper-case, respectively. o coplot() has new option subscripts=TRUE to pass the indices to the panel function. o cor.test(method="spearman") might give slightly better P values, since it now relies on pnorm() (with proper tail) instead of alnorm. o dbinom() works for size=0 (where appropriate). o New trivial function det() for determinant computation (the example in ?qr did not seem to be sufficient). o If present in the package, a function .Last.lib will be called when a package is detached. o New function dev.copy2eps() copies the current device to an eps file, taking the size from that of the device. o dev.print() now prints if possible, and takes the size from the device being copied. o edit() or fix() applied to a numeric or character matrix now uses the data editor, if available. o edit.data.frame() edits factors in character mode by default, and will allow the row names to be edited, by default if they are not 1:nrow(name). o expand.model.frame() for adding variables to a model frame. o The handling of estimating the dispersion in glm() fits has been changed for consistency across methods. For `binomial' and `poisson' families the dispersion is always taken as one. For `quasibinomial' and `quasipoisson' families it is always estimated (by residual chisq/residual df). o Using "~" when specifying lib.loc (for example to help() or library()) is now supported. o image() has a new argument "breaks" and divides the zlim range into equal-length intervals. o install.packages() and update.packages() have a new `destdir' argument for the directory to which to download the packages. o New function interaction.plot(). o Internal cleanup of lapply()'s C code. o library(), require(), and sys.source() have a new argument ` keep.source = getOption("keep.source.pkgs") '. This defaults to false, but can be set (also for base) to true by setting the environment variable R_KEEP_PKG_SOURCE to "yes" o Par `lty' in lines() now defaults to par("lty") not "solid", for consistency with plot(). o list.files() [aka dir()]: path argument has now default = "." o locator() allows inline graphics parameters (for the plotting it does with type !="n"). o New function max.col() from MASS, thanks to V&R. o nlm() can now take additional arguments in ... to be passed to f. o par() returns elements in alphabetical order, and "ann" as a logical (not integer). o .Platform has a new component GUI specifying the GUI in use (which might be "unknown"). o plot.formula() searches for a plot method for the left-side of the formula before searching for a plot method for the right-side of the formula. o New bitmap devices png() and jpeg() on Unix/X11. (They were already available on Windows.) o postscript(print.it=TRUE) now does print the plot file. postscript(onefile=FALSE) now produces multiple separate files. o provide() is now deprecated. o New function quade.test() in package ctest for the Quade test for unreplicated blocked data. o quantile(x, probs) now propagates NA/NaN in probs. o Option for user-supplied normal random generator in RNGkind(). o read.fwf() is no longer dependent on Perl. o New arguments check.names and strip.white to read.table() and friends. o Functions recordPlot() and replayPlot() save a plot to an R variable and replay it. o residuals.lm() also allows types "partial" and "response" as residuals.glm(). o Added col option to rug(). o scale() is now generic with scale.default method. o New "call. = TRUE" argument for stop(), and new function stopifnot(.) -- to be used in "make check". o str(.) has a new optional argument "nchar.max = 128" and truncates strings longer than that. Also eliminated a few minor glitches. o The symbols() function is now implemented. o New function termplot() with similar functionality to plot.gam() in S. o The parameters to title() which specify the labels may now be specified as a list containing the parameter together with additional modifying par values (cex, col, font) which affect just that label. title() also has new line and outer arguments which provide functionality which matches that in axis(). o New functions which.min() amd which.max(). o The Wilcoxon and Ansari-Bradley tests now optionally return confidence intervals for the location or scale parameter of interest. o New argument `extend' to window() (and updated documentation). o write.table() can now write CSV files in the format Excel expects. o New device xfig() to produce XFig files. o New xyz.coords() utility function to be used for 3D highlevel plots. o R CMD build now also works for package bundles. o Rdconv allows an output file to be specified. o Initial support for C++ source code in add-on packages under Unix. o Mathlib can be built as a standalone library: see directory src/nmath/standalone. BUG FIXES o The Mathlib functions now use exactly the same values for +/-Inf, NaN and NA as the rest of R in all cases. o Improved automatic remaking. o option keep.source was not set correctly before the base package was loaded: some functions in the base package had the source kept. The memory usage should now be reduced by ca 1Mb. o The base file is no longer closed twice in case of a syntax error (caused segfault on Linux). o The X11 data editor scrolls cells and so allows more than ca 10 characters to be entered. Several interface/redraw errors have been corrected. o Using `destroy' or `close' on the X11 data editor window killed R. o Multiple `destroy' events or X11 errors killed R (PR#400). o Warnings from .Last or closing devices are printed where sensible (e.g. not on GNOME nor Windows console). o add1.glm() and drop1.glm() gave incorrect results in the "Chisq" test option when the scale was estimated. o aggregate() applied to multiple time series lost the series names. o as.hclust.twins() in package mva sets method=NA (PR#538) o ave(1:3) now works (as when is.null(list()) was TRUE years ago). o barplot(c(0.1, 0.5, 1), ylim = c(0, 1)) now works: [xy]axs="i" and exact limits now labels the limits. o by() works when embedded in a function. o The xlab and ylab in coplot() now set the x and y axis labels, as in S. Supply a second component to label the conditioning variables. o count.fields() and read.table() now have the same default quote = "\"'". o guard against segfault in dataentry(x<-1, Modes = plot), and the like. o dev.print() now checks if the current device is replayable (and not all devices were, despite the documentation). o The gtk() device (formerly x11() under GNOME) was incorrectly returning character information, so in particular `*' was wrongly centred as a plotting symbol. o is.qr() checks not only for $qr, but also for $rank & $qraux, PR#482. o library() will not leave the package on the search path if loading fails (including if .First.lib fails). o lqs(, method="S") rounded k0 on passing to C. o na.omit() now handles vectors and matrices as well as data frames. o plot.lm(*, which=4) now works thanks to Marcel Wolbers. o postscript() now uses the options "papersize" and "printcmd" rather than the values of R_PAPERSIZE in the environment and R_PRINTCMD found at build time. o postscript() now makes use of kerning information in computing string widths. o M <- 2 ; print(ppr(.., nterms = M)) now works. o ppr(, sm.method="spline") had an internal limit of 250 rows: this is now 2500 and is now checked. o predict.lm(,type="terms",se.fit=T) gives correct standard errors (thanks to John Maindonald) o print.ftable() now returns its argument. o proj.aovlist() now gives a non-zero result for strata with no fitted effects. o qnorm() is now based on AS 241 instead of AS 111, and should give precise results up to 16 digits precision. o rgeom(, prob=1) gives 0 rather than NA o rpois(*, lambda) now works when lambda > .Machine$integer.max o strheight("X") with no active device would segfault. o system() is now (partially) functional on systems without popen. o Fixed bug in undoc() - requiring new `chdir' argument for sys.source() o Fixed problem in usemethod() where CAR(call) could be non-symbol. o The x11() device no longer crashes R if a font is not found, and will warn if there is a size mismatch of more than 10%. o R CMD Rd2dvi now sorts files alphabetically. o Rdconv now reports if an invalid type is specified (rather than using latex). o Support for Rd conversion to Sd has been reinstated (it was unintentionally removed along with nroff-based conversion to text). o \deqn{} fix in R-exts.texi, PR#523. o Linpack.h now makes clear which routines are actually in R. o Entry-point "pythag" is now loaded even though it is not necessarily used in R. Where "hypot" is available pythag just calls hypot after checking for special values. o call_R will now correctly handle character vector arguments. o The alphabet links on top of HTML function indices with more than 100 entries now contain only the letters which are really first letters of at least one entry. CHANGES IN R VERSION 1.0.1 BUG FIXES o pgamma(Inf, 1, Inf) gives NaN instead of an infinite loop, PR#462. o Inline xaxt and yaxt parameters were ignored. o Setting the normal RNG was not always recorded in .Random.seed. o \link[pkg]{foo} links were wrongly translated to HTML. o Direct use of show.data() with no args was incorrect. o print.coefmat does sensible things if options show.signif.stars and show.coef.Pvalues are not set correctly. o x <- list(a=1, b=2) ; x["c"] <- 3 now (again) stretches the list rather than give a "subscript out of bounds" error. o Models with response appearing on rhs could cause segfault. o as.data.frame.matrix will now ensure the columns added have non-empty names. o Some (strange?) model formulas could cause memory corruption (thanks to John Fox for digging this up). o Matrix multiplication in cases such as 1:3 %*% t(1:2) is accepted. o Options --nsize and --vsize to R CMD check gave warning messages and only one was accepted. o The autoload()s during startup are "wrapped" such that conflicting objects don't break startup. o cor.test(*, meth="spear") {pkg ctest} now works (again) for n <= 6 o scale = 0 in biplot.princomp() now works. o The scores given by princomp(, cor = TRUE) and the rotated values given by prcomp(, scale = TRUE) are now computed from the scaled data. o barplot now works okay when length(col) < length(legend.txt), thanks to Ben Bolker, PR#494. o legend has new args `ncol' and `horiz' thanks to Ben Bolker. o kernel("dirichlet", m=10, r=1) in package ts now works. o save/restore of environments containing "..." object should work now. o qhyper should work better for large N. o qbinom(1-1e-16, n, p) , qpois() and qnbinom(*) looped for ever. o as.matrix.data.frame no longer escapes quotes in character vectors. o R would try to save the readline history at the end of non-interactive sessions, causing crashes on some systems. o Subtle roundoff problems caused arrays to be allocated short in loess.c in some cases, leading to segfaults. o Document that postscript(file="") sends the output directly to the default printer. o ts.union(, dframe=TRUE) had a long-standing typo, now works. o save(, ascii=TRUE) had problem with octal escapes in strings when there was a digit following, should work now. o matpoints() and matlines() now also have a "type =" argument with defaults "p" and "l", respectively; PR#506. o The new Perl 5.6 broke our version-detection mechanism. A better one has been inserted. o X11(colortype="gray") failed to work on 8-bit screens, and more generally when colour allocation failed X11() did not revert to monochrome correctly (and did not say it was doing so). It was not documented in the help that to change the X11 colortype one needs to close all open X11 devices. o loessf.f in modreg defined DSIGN unecessarily and this caused a conflict on AIX. o plot.lm will now work with rlm objects. o start and end behave better when the frequency is not an integer. o aggregate.ts is closer to S-PLUS's aggregate.rts. o quantile(x) now works when x contains several +/- Inf's. o guard against segfault in dataentry(0,0) (or, more realistically, when mistyping data.entry(x,y) as dataentry(x,y)) o fixed special cases that caused bad behavior for methods, particularly with nested use of primitive operators when setMethod had been called. Also fixed some situations that prevented caching methods (and therfore slowed down dispatch seriously) in similar cases. ********************************************************* * * * News of 1.0.0 and earlier is in file `ONEWS' * * * *********************************************************