| Dear Emacs, please make this -*-Text-*- mode! |
| |
| This file covers NEWS up to the release of R-1.0.0. |
| See 'NEWS.1' for subsequent changes. |
| |
| |
| ************************************************** |
| * * |
| * 0.99 SERIES NEWS * |
| * * |
| ************************************************** |
| |
| |
| CHANGES IN R VERSION 0.99.0 |
| |
| |
| NEW FEATURES |
| |
| o The ``Introduction to R'' manual, in doc/manual. |
| The ``Writing R Extensions'' manual is much enhanced for |
| this release. |
| |
| o The format for save/load has been changed. Workspaces and |
| objects saved in earlier versions can be loaded into this |
| version, but not conversely. Use save() or save.image() with |
| argument oldstyle=TRUE to save in the old format if you need to. |
| |
| o The header files for C code have been reorganised. The |
| preferred header file for user code is now "R.h", and |
| ancillary files such as Arith.h now need to be referred to |
| as "R_ext/Arith.h". The `Writing R Extensions' manual now |
| contains the beginnings of a description of the public API and |
| how to use it. |
| |
| o Many of the exported symbols have been remapped or hidden. This |
| means that code using Rdefines.h or Rinternals.h or Mathlib.h |
| will need to be re-compiled, and code using Applic.h may do |
| so. |
| |
| Many packages will need to be re-installed for use with this |
| release. |
| |
| o The random number generation interface has changed, although |
| saved .Random.seed's will work unchanged. The default |
| generator is now Marsaglia's multicarry, and the Mersenne |
| Twister GFSR and Knuth's Fibonacci subtraction are also |
| available. The type of normal generation can be selected by |
| RNGkind() (and is encoded in .Random.seed). |
| |
| The new function set.seed() which uses a single integer to set |
| the random number seeds is now the recommended way to do so. |
| |
| It is now possible for a user to plug-in a new RNG written |
| in C: consult ?Random and ?Random-user for the details. |
| |
| o All the DPQ {probability density quantile} functions have new |
| arguments, "lower_tail = TRUE" and "log{_p} = FALSE". This allows |
| more precise results when values would be close to 0 or 1. |
| |
| o R CMD Rd2dvi has new options --pdf, --title and --output. |
| |
| o New fields Date, URL and Title in the DESCRIPTION file of |
| packages. The Title field replaces the separate TITLE file of |
| packages, which is no longer necessary. |
| |
| o residuals.lm() has a "type" argument, as S does. |
| |
| o The underlying code for nlm has been translated from Fortran |
| to C and made re-entrant (changes contributed by Saikat DebRoy). |
| |
| o optimize() can now be used recursively. |
| |
| o New suite of optimization methods optim(), covering |
| Nelder-Mead, BFGS quasi-Newton and conjugate-gradients methods |
| for unconstrained minimization and maximization with and |
| without derivatives. |
| |
| optim() also allows box constraints (interval bounds on |
| individual variables) in its limited-memory BFGS option. |
| |
| o R now compiles in the GNU version of regex, so regular |
| expressions (grep, sub, gsub, regexpr, "pattern" in ls) are |
| always available. The class of regular expressions supported |
| is now slightly wider on some Unix platforms. |
| |
| o package ctest (for classical tests) is now part of the base |
| distribution, and also contains chisq.test, prop.test and |
| t.test which previously were in package base. These three |
| functions are auto-loaded from ctest. |
| |
| o New utility `R CMD build' for building add-on packages along |
| with some useful testing and cleaning up. |
| |
| o Conversion of .Rd help files to text format is done in Perl, |
| and no longer requires nroff. This makes the conversion 8-bit |
| clean and more accurate. |
| |
| o Building help for a package now removes help files that no |
| longer exist in the source. |
| |
| o strsplit() now uses split regexps, and no longer insists on |
| splitting into non-empty tokens. |
| |
| o Long-named options with arguments such as `--vsize' now use the |
| `--name=VALUE' form; the old `--name VALUE' is deprecated. |
| The old-style command line options `-v' and `-n' are now defunct. |
| |
| o par("cxy") { == par("cin")/par("pin") in user coordinates} |
| for S compatibility. |
| |
| o If R_PAPERSIZE is not specified otherwise, configure now tries |
| to compute it by calling paperconf. |
| |
| o The deprecated alternative RPROFILE is no longer accepted: use |
| R_PROFILE instead. |
| |
| o Added setequal() for set equality. |
| |
| o First argument renamed to "package" for library(), require(), |
| provide(). |
| |
| o model.frame() now accepts data= arguments that can be coerced to |
| data frames. |
| |
| o Help files can now contain \describe groups. |
| |
| o Hyperlinks in help files can now use LaTeX special characters. |
| |
| o rstandard() now also works for glm objects. |
| |
| o glm drops 0-weight observations when fitting so that the |
| output is compatible with lm.influence() and plot.lm(). |
| |
| o New function ftable() for creating and manipulating flat |
| contingency tables. |
| |
| o New function cutree() for cutting hclust trees in package |
| mva. New functions rect.hclust() and identify.hclust(). |
| |
| o Under Unix, the default editor is obtained from the environment |
| variables EDITOR or VISUAL if either is set. |
| |
| o New command line option `--gui' to specify the graphical user |
| interface under Unix. Currently, possible values are `X11' (the |
| (default) and `GNOME', provided that GNOME support is available. |
| Command line options `-g' and `--gnome' are defunct. |
| |
| o power.t.test() and power.prop.test() functions added for power and |
| sample size calculations. |
| |
| o edit() is now generic and a new edit.data.frame() function |
| calls up the spreadsheet data editor. This is still rather |
| rudimentary, since the data editor really only knows about |
| numeric and character vectors. |
| |
| o Modifications to the data editor so that one can use ESC to |
| quit a partial cell entry and entering an empty cell causes |
| the element to be set to NA. |
| |
| o prop.table() and margin.table() functions (these are *really* trivial). |
| |
| o R INSTALL checks the Depends field of DESCRIPTION if the |
| currently running version of R meets an R |
| dependency. old.packages() reports only packages conforming |
| to the current version of R. New function |
| package.dependencies() for parsing and checking dependencies. |
| |
| o options("expressions") now does something, and the evaluation |
| depth is checked on all platforms (not just Macintosh). This |
| will catch infinite recursions gracefully. |
| |
| o The default number of cons cells (`nsize') is now 350k (it |
| was 250k). This reflects the added base code and packages, |
| and increases memory usage by about 2Mb (on a 32-bit machine). |
| |
| o Some simple multiple comparison procedures: p.adjust() for |
| generic adjustment of a set of p values by variants of the |
| Bonferroni method; pairwise.t.test, pairwise.wilcox.test, |
| pairwise.prop.test for pairwise comparisons of grouped data |
| and proportions. |
| |
| o Error / warning calls with a long description of the call are |
| split into two lines. (This helps avoid scrolling in the |
| Windows GUI.) |
| |
| o lapply() is now internal and substantially faster (7% overall |
| speed-up on the tests for the base package). |
| |
| o apply() no longer names the output dimensions unless FUN returns |
| a result with names, and the same names for every result. |
| |
| o contour() can (at last) label contours by level. |
| |
| o persp() labels its axes. |
| |
| o scan() and read.table() now have a dec= argument to set the |
| decimal point character. If sep= is set, quoting of strings is |
| now possible and follows the conventions for comma-separated |
| files. This should make it easier to read the "continental |
| CSV" format (fields separated by semicolon and using comma as |
| decimal point). The set of quoting characters has also been |
| made optional. Variants of read.table(), read.csv() and |
| read.csv2() have been defined |
| |
| o HDF5 support is gone from the R distribution, and provided by an |
| add-on package available from CRAN. |
| |
| o New function getOption() for retrieving the value of a single |
| option. |
| |
| o read.table.url() and related functions now use download.file, |
| which has an extra "socket" method for direct HTTP socket |
| connection. download.file has new option ``quiet''. |
| |
| o pairs.default() has an oma argument to allow users to override |
| the internal setting of that graphics parameter. |
| |
| o princomp() in package mva allows the user to specify the |
| covariance matrix (and hence use, e.g. cov.mve). |
| |
| |
| BUG FIXES |
| |
| o svd(matrix(2,1,0)), |
| arma0f(NULL), cancor(F,F) and prcomp(F[F]) no longer segfault. |
| |
| o loess.smooth(F[F],F[F]) and supsmu(F[F],F[F]) no longer segfault. |
| |
| o save(1, file = ""[F]) no longer segfaults. |
| |
| o stop(list()) and warning(list()) no longer segfault. |
| |
| o system(""[F]) and save(1, file = ""[F]) no longer segfault. |
| |
| o Overflow of the pointer protection stack is handled correctly |
| |
| o predict.glm(, type="link", se.fit=T) works |
| |
| o str() now works with Surv(.) objects from library(survival5). |
| |
| o all.equal(-Inf, -1e5) now gives "Mean absolute difference: Inf" |
| instead of "Mean relative difference: NaN". |
| |
| o strsplit fix broke copy.url. |
| |
| o 0 ^ -1 == Inf and min(NA, NaN) is now always NA |
| |
| o R CMD xxx sets $R_HOME/bin to be first in PATH |
| |
| o Added more warnings to update.packages & friends. New function |
| old.packages for better control of update.packages. |
| |
| o Adding matrices to data frames now happens column by column as |
| documented, so character or logical matrices generate factor |
| columns. |
| |
| o Formulae containing interactions with the response were |
| handled incorrectly by model.matrix, giving wrong answers or crashes. |
| |
| o anova(lm(.)) with 0 weights now works. |
| |
| o plot.lm(), dffits(), covratio() now do the right thing for weighted |
| lm regression. |
| |
| o formatC(as.integer(c(1,0,NA))) now works. PR#394, thanks to Jens O.-A. |
| |
| o format.char(.) is much faster for long vector argument [Jens O.-A.] |
| |
| o \enumerate now enumerates in text conversion of .Rd files. |
| |
| o glm() no longer fails with names<- errors in cases where |
| observations with fits on the mu.eta boundary have been dropped. |
| |
| o Deviance residuals could be NaN instead of 0 by rounding error. |
| |
| o shapiro.test(x) now gives better error messages (eg. x=rep(1,5)) |
| and doesn't print ANYTHING anymore (in some cases). |
| |
| o mode(as.formula(paste("~", paste(1:50, collapse="+")))[2]) now works. |
| |
| o glm() now handles cases with numerically 0 or 1 fitted values in |
| binomial and numerically 0 in poisson correctly. (Previously |
| these observations were dropped even though the variances were |
| also numerically 0.) |
| |
| o (-4 + 0i) ^ (1/2) now gives 2i. |
| |
| o system.time() now does sensible things in the non-HAVE_TIMES |
| case, and that and proc.time() have better documentation. |
| |
| o A couple of bugs in the data editor spreadsheet have been |
| eliminated. |
| |
| o Elapsed time in proc.time() is no longer rounded to whole |
| seconds under Unix. |
| |
| o Assigning character vectors to subsets of data frames now |
| works correctly (it used to assign the numeric codes of factors). |
| |
| o Extensive enhancements and corrections to the help pages. |
| |
| o The possibility of buffer overruns during printing has been |
| much reduced, and eliminated on systems with vsnprintf. |
| |
| |
| ************************************************** |
| * * |
| * 0.90 SERIES NEWS * |
| * * |
| ************************************************** |
| |
| |
| CHANGES IN R VERSION 0.90.1 |
| |
| |
| NEW FEATURES |
| |
| o rect(.) has `lwd' argument. |
| |
| o legend() has a `adj' argument and has been streamlined (and fixed up). |
| |
| o `unname' convenience function [experimental data.frame behavior]. |
| |
| o `examples' sections have been added to the documentation |
| for most of the data sets in the base library. |
| |
| o update.packages & friends have new argument contriburl for |
| incomplete CRAN mirrors. Package bundles such as VR can be |
| directly installed both from the shell and from inside R. |
| |
| o RLIBS is no longer accepted as well as R_LIBS (which has been |
| the documented form since 0.65.0). |
| |
| o demo(nlm) has examples of using analytical gradients and |
| Hessians. |
| |
| o .Platform$OS.type is standardized to be `unix', `mac' or `windows' |
| |
| o setting cex in matplot(matrix(1:25,5), cex=1:5) now works |
| |
| o ar.ols() has separate demean and intercept arguments, uses |
| internal scaling for greater accuracy. |
| |
| o xxxPR functions allow NCHAR=-1 for S compatibility. |
| |
| o `Rcomplex' is preferred to `complex' (a future reserved word |
| in C) for R complex objects passed to C. |
| |
| o new function dir.create() for platform-independence. |
| |
| o help.search() creates a database for faster searching later in |
| the R session. |
| |
| o density() allows for more kernels and has a new argument |
| `give.Rkern' to access the relevant kernel property. |
| |
| o multivariate methods for ar: "yule-walker" (now in C) and |
| "burg" (new) contributed by Martyn Plummer. |
| |
| o New data sets `HairEyeColor' (hair and eye color of statistics |
| students), `Titanic' (survival of passengers on the Titanic), |
| and `UCBAdmissions' (student admissions at UC Berkeley). |
| |
| |
| BUG FIXES |
| |
| o Many help pages have been revised and enhanced. |
| |
| o predict.glm() works again with type="link". |
| |
| o subscripting arrays and matrices no longer loses the names of |
| the dimnames vector. Transpose also preserves the names. |
| |
| o examples in help files containing \testonly are no longer |
| (partially) duplicated. |
| |
| o is.numeric() of a factor is now FALSE |
| |
| o prevent a segfault in plotmath |
| |
| o f <- get("function"); f(,); f(F,F) now "ok" (PR#361). |
| |
| o blank-line reject code in parse.dcf was wrong (Martyn Plummer) |
| |
| o made filled.contour independent of pointsize. Make plot key |
| wider so there's room for a title. Touchup example. |
| |
| o font size fixups for the X11 driver (mainly) |
| |
| o some.list[[NA]] is NULL, following S, rather than giving spurious |
| error messages |
| |
| o segfault when running out of heap |
| |
| o segfault in rbind of a vector without names fixed. cbind, too. |
| |
| o fixed symbol size problems with PostScript driver |
| |
| o unique() & duplicated() only work for atomic vectors; |
| unique(data.frame(""[F])) doesn't segfault anymore. |
| |
| o get("attr<-")(""[0],""[0]) doesn't segfault anymore. |
| |
| o blunder in do_memoryprofile, causing segfault on Alpha machines |
| |
| o erroneous error message in coerceToSymbol |
| |
| o partial workaround for workspace restore problems. This can |
| happen if an environment on the search path is assigned to a |
| variable which gets saved. The error "unresolved node during |
| restore" is turned into a warning, allowing the rest of the |
| workspace to be restored, but the variable contains an empty |
| environment on reload. |
| |
| o density(x) now works also when IQR(x) == 0. |
| density(x, window=...) now works [S compatibility]. |
| |
| o prevent points from being plotted if pch, cex, or col are NA. |
| Does not apply to bg on pch 21--25 (where NA means |
| "transparent") because it would require fixes at the driver |
| level. |
| |
| |
| CHANGES IN R VERSION 0.90.0 |
| |
| NEW FEATURES |
| |
| o packages splines (for regression smoothing splines or |
| interpolating splines) and nls (nonlinear least squares) are |
| part of the base distribution. |
| |
| o New error handling using |
| options ( error = expression(..) , warning.expr = ... ). |
| REPLACING version 0.65.1's options(error.halt = T/F) |
| |
| o collected warnings before an error are no longer lost but |
| are printed after the error message (unless the error makes |
| this impossible). |
| |
| o A couple of substantial graphics changes, esp. in the X11 |
| driver. The scaling of symbols is now linear in cex=, rather |
| than being tied to the available font's size. The fonts on an |
| X11 device also scale linearly with cex= insofar as your X |
| server can do it. On systems with the scalable type 1 |
| PostScript fonts installed, this looks particularly nice. Note |
| that the scaling is linear in the *diameter*, but quadratic in |
| area. The distance between lines of margin text in the X11 |
| device is now proportional to the size given to |
| x11(pointsize). |
| |
| |
| o abline(a,b) now (again) refers to transformed coordinates on |
| plots with log-axes, so that abline(lm(log10(y)~log10(x))) |
| (say) draws a best-fitting line on a log-log plot. The earlier |
| convention (to draw a curve representing a line in original |
| coordinates) is available using a new untf= argument. |
| |
| o barplot.default() has new `axisnames' (and `sub') arguments, easily |
| allowing suppression of bar labeling. |
| |
| o cbind() and rbind() now actually do what deparse.level=1 implies: |
| add column/row names based on the deparsed argument, provided it |
| is a simple symbol. The behaviour is still hardcoded, though. |
| |
| o gc() now reports the total sizes in Mb as well as numbers. |
| |
| o New function help.search() for searching the names, titles, |
| aliases, or keywords in the help system. |
| |
| o image() allows x and y to specify either the boundaries or the |
| midpoints of the cells. If the latter, the whole cells are |
| drawn, rather than the outer cells being half-sized as previously. |
| |
| o NULL extra arguments to model.frame() are now treated as missing |
| (instead of an error). |
| |
| o optimization with nlm() can use analytic gradients and Hessians |
| if they are supplied. |
| |
| o on.exit() allows add=TRUE. |
| |
| o function parse.dcf() for parsing files in debian control file format |
| (DESCRIPTION, CONTENTS, ...) |
| |
| o predict.{g}lm has a type="terms" option, and residual.glm has |
| type="partial" as a step towards plot.gam(). |
| |
| o New arguments to q() and quit() allow the exit status to be set |
| and the execution of .Last() to be skipped. |
| |
| o New function regexpr(), similar to grep but returns the position |
| of the match in each string. (For S-PLUS compatibility.) |
| |
| o scan() now supports complex numbers. |
| |
| o New function sort.list, for S compatibility. (This has argument |
| partial, but always sorts completely.) |
| |
| o storage.mode<- can be used to set "single", and if setting |
| anything other than "single" it removes the "Csingle" attribute. |
| |
| o new function sunflowerplot(). |
| |
| o New function undoc() for listing undocumented objects. |
| |
| |
| o User's .Rprofile now executes in global environment |
| |
| o All HTML pages now use the new style sheet doc/html/R.css |
| |
| o html and text files have now a header line giving the name of |
| the help file and the package. The description section now |
| comes first. |
| |
| o All the standard packages have DESCRIPTION files with |
| "Priority: base", so installed.packages and |
| package.description will work with them. |
| |
| o The R-external manual which describes programming for the |
| .Call and .External interfaces is in the doc/manual directory. |
| |
| o New target `make pdf' in doc/manuals makes hyperlinked PDF |
| documentation. (This is experimental for this release. See |
| doc/manual/README for further details.) |
| |
| |
| o S.h now contains (via Rdefines.h) a MESSAGE macro, and |
| Free NULLs the pointer, for compatibility with S3 (but not S4). |
| |
| o New subroutine REALPR callable from Fortran (like DBLEPR but |
| for real arguments): useful if as.single is in use. |
| |
| o The cex= argument to plot() etc. can be a vector, like pch=. |
| |
| o lty=0 now (again) makes lines invisible. Looks better for |
| barplot label axis. |
| |
| o zero.R tries to find the zero DLL in a system-independent way. |
| |
| |
| BUG FIXES |
| |
| o apply should now work for all un-dimnamed arrays (PR#318). |
| |
| o ar(..., demean=F) works more consistently across methods. |
| |
| o barplot() had lower limits set at -0.01, causing trouble with |
| small heights. Switch to relative scale. (Thanks to Matt Wiener) |
| |
| o density() should work better with NAs and infinite values. See |
| ?density for the current definitions of how these are handled. |
| |
| o diag(x) now works (as pre 0.65.1) for 1-d arrays. |
| |
| o Stored-source was dropped by dump(). |
| |
| o expand.grid returns a data frame even for one arg. |
| |
| o expand.grid(x) now also works for vector arguments x. |
| |
| o factor(list()) or factor(character(0)) *is* now a factor |
| with valid levels(.); |
| ordered does NOT allow an `ordered' argument anymore |
| and is now defined as trivial call to factor. |
| |
| o help page for gc gives correct size of cons cells (20 bytes |
| for 32-bit systems, 36 or more for 64-bit systems). |
| |
| o gcinfo reports correct percentages of heap even for vsize > 200M. |
| |
| o gl(6,3,12) and gl(6,3,2) now both work. |
| |
| o Empty lists now deparse correctly. |
| |
| o na.omit.ts and na.contiguous preserve classes. |
| |
| o plot.factor {plot(<factor>)} now obeys axes=FALSE and xaxt="n". |
| |
| o read.table(as.is = TRUE) would leave everything as character. |
| Now it correctly tries to convert to numeric. |
| |
| o require() now has the warn.conflicts argument of library(). |
| |
| o Fix problems in scan(flush = TRUE). |
| |
| o scan() got confused by trailing whitespace. |
| |
| o split(x,f) now works even when f is a factor with unused levels |
| (PR#294). |
| |
| o mosaicplot() has a formula interface and |
| NULL instead of NA default args. |
| |
| o stars() has "NULL" instead of "NA" defaults. |
| |
| o str() is quite a bit nicer with factors. |
| |
| o ts.union, cbind.ts, arithmetic on ts objects now allow |
| non-integer frequencies. |
| |
| |
| o Switch to <tt> in HTML pages since Linux Netscape mangles |
| Courier. |
| |
| o When documentation is "compiled" (build-help), you now get warnings |
| for multiple (conflicting) \alias{.} or \name{.}s. |
| |
| o making the reference manual with `make dvi' copes better with |
| isolatin1 characters (but not perfectly as these are not in |
| standard TeX fonts). |
| |
| o Rd.sty now uses standard LaTeX constructs like \bm for bold |
| math and \url for URLs. |
| |
| |
| o Protect R_fopen against NULL filename in Unix. |
| |
| o Math text in outer margins didn't work. |
| |
| o Text clipping now works in the X11 device. |
| |
| o Pixel rows sometimes got doubled in rotated text on the X11 device. |
| |
| o par("yaxt") is now ok. |
| |
| o Problems with realloc on some systems in AllocBuffer. |
| |
| o Problem with formatReal on non-IEEE systems. |
| |
| o demos/dynload/Makefile used macros that gave incorrect build |
| on some non-GNU makes. |
| |
| o Windows version copes better with paths with spaces in. |
| |
| o R CMD check had a typo which made the final message fail. |
| |
| o R_EOF redefined as -1, was causing trouble with isxxxx contructions. |
| |
| |
| |
| ************************************************** |
| * * |
| * 0.65 SERIES NEWS * |
| * * |
| ************************************************** |
| |
| |
| CHANGES IN R VERSION 0.65.1 |
| |
| |
| NEW FEATURES |
| |
| o .C, .Fortran. .Call and .External now have an argument PACKAGE |
| to specify the shared library to be used for the symbol. See |
| ?Foreign. Package writers are encouraged to use this. |
| |
| o On startup (unless --no-environ), first .Renviron is looked for in |
| the current directory, and then in $HOME/ (= ~/ ). |
| |
| o New options(error.halt = FALSE) (default is TRUE) allows |
| continuation after an error in batch processing. |
| |
| o In graphics, lty has now 6 instead of 4 predefined line types. |
| |
| o as.hclust.twins() in package mva to convert (and plot) |
| objects from agnes() and daisy() of package cluster. |
| |
| o R INSTALL now can directly install pkg_version.tar.gz files |
| as obtained from CRAN. New function update.packages() |
| & friends for automatically downloading packages from CRAN and |
| install them on the fly (on Unix and Windows). |
| |
| o New function commandArgs() to record the command-line used. |
| |
| o New arguments `local' and `now' to dyn.load. |
| |
| o diag(x) now keeps names when appropriate and barfs when x is an array. |
| |
| o functions source.url, url.show, read.table.url, scan.url to read |
| from an http server instead of a file. |
| |
| o grid() gets useful defaults: grid lines drawn at tick marks. |
| |
| o set operations union(), intersect(), setdiff() and is.element(). |
| |
| o New function stars() for star plots and segment diagrams of |
| multivariate data. |
| |
| o Version info now in the top-level file `VERSION'. |
| |
| o barplot has a "plot = TRUE" argument and now returns locations of |
| all bars even when "beside = TRUE". |
| |
| o hist has an "nclass" argument purely for S compatibility. |
| |
| o Character strings can now, with most compilers, be passed |
| on and from Fortran. See ?Foreign for details. |
| |
| o Functions as.single and single now have the effect with |
| .C and .Fortran of passing a numeric argument as float/REAL |
| rather than as double/DOUBLE PRECISION, by setting the |
| attribute "Csingle". See ?Foreign for details. |
| |
| o Comparison of strings uses the current locale on systems where |
| this is available, and so is always consistent with the ordering |
| used by sort(). |
| |
| o sapply has a new argument USE.NAMES=TRUE and now returns a named |
| result when its input was a character. |
| |
| o plot.stepfun has new arguments lty and lwd. |
| |
| o x labels in boxplot now handled differently, so that math |
| expressions are allowed. |
| |
| o postscript() argument `onefile' now does something, and there |
| is a new paper type `special' and new argument `pagecentre'. |
| See ?postscript for details. |
| |
| o Experimental function dev2bitmap() to copy to a bitmap graphics format. |
| |
| |
| BUG FIXES |
| |
| o centering in text() will be more accurate, particularly on devices |
| with full font metric information (postscript, x11, not windows). |
| |
| o arguments after --no-readline in the Unix version were ignored. |
| |
| o couldn't set attributes in hashed environments. |
| |
| o [<-.data.frame mishandled dfr[1] <- 1 (forgotten drop=FALSE) |
| |
| o sys.on.exit didn't work |
| |
| o sys.parent didn't quite work either for n >= 2. |
| |
| o par("mfg") was wrong, par(mfg=) switched to down columns. Now |
| par(mfrow/mfcol = c(nr, nc)) followed by par(mfg=c(i,j)) is |
| the preferred style. |
| |
| o plot( <aov.object> ) failed after 2nd plot, PR#279 |
| |
| o Several patches for systems with long != int. |
| |
| o approx failed if inputs contained NAs. |
| |
| o weighted lm fits with 1 diml x failed if any weight was zero. |
| |
| o lm.influence failed when there were undetermined coefficients, PR#280. |
| |
| o problem with function()... inside saved functions because arg count |
| increased to accommodate stored source. (Incorrect number of |
| arguments to "lambda") |
| |
| o improvements to generation of HTML help files: should work |
| better on viewers other than Netscape. |
| |
| o stl in package ts could conflict with package leaps: the Fortran |
| symbols have been changed. |
| |
| o help page for factor is improved and corrected. |
| |
| o na.omit.ts and na.contiguous now preserve time-series attributes. |
| |
| o more automatic testing ("make check") using options(error.halt=FALSE) |
| led to the elimination of dozens (!) of seg.fault possibilities. |
| |
| o family quasi handles zero observations with var=mu^2 more correctly. |
| |
| o dynamically-loaded libraries are searched last-loaded first, as |
| documented (under Unix it used to be first-loaded first). |
| |
| o rowsum failed with a matrix and a single group (drop=FALSE needed). |
| |
| o deriv(y ~ <expr>(x)) now works as well as deriv(~ <expr>(x)). |
| |
| o qr over-estimated ranks in some degenerate cases. |
| qr did not work correctly if n < p and the first n cols were |
| rank-deficient. |
| |
| o str() wouldn't work quite right for named characters; doesn't quote |
| symbols anymore. |
| |
| o Colour conversion (rgb, gray, hsv) truncated doubles and so |
| gave machine-dependent results on the examples. It now rounds. |
| |
| o cat() now admits again that it can't handle lists instead of |
| "random" segfaulting. |
| |
| o More accurate rounding (including rounding to even) on platforms |
| without rint (e.g. Windows). |
| |
| o qgeom() is now left-continuous with a tolerance, and so the |
| example on the help page will be platform-independent. |
| |
| o pretty() has been changed to use tolerance around integers and |
| so will be more platform-independent. The exact output has |
| probably changed on all platforms for some input. |
| |
| o image() & filled.contour() now work for 1x1 matrices |
| and with constant z values. |
| |
| |
| CHANGES IN R VERSION 0.65.0 |
| |
| NEW FEATURES |
| |
| o A first step in improving performance has been made. |
| Attached objects, libraries etc are now hashed; performance |
| gains will be particularly apparent if large packages are in use. |
| |
| o First version of package ts for time-series analysis. |
| This has fairly complete S-PLUS compatibility, but more features |
| are planned. See library(help=ts) for details. |
| |
| o warnings can be collected (options(warn=0), the default), printed |
| immediately (options(warn=1)) or turned into errors (options(warn=2)). |
| As a consequence, all warnings and errors now are printed followed |
| by a newline, if one is not supplied. (This should improve the |
| S compatibility of the use of PROBLEM ... in compiled code.) |
| |
| |
| |
| o All R environment variables are now of the form `R_xxx'. In |
| particular, `RHOME', `RLIBS' and `RPROFILE' are now called |
| `R_HOME', `R_LIBS', and `R_PROFILE'. |
| |
| o The handling of q()/quit()/EOF has been changed, with a new option |
| "default". In interactive use this asks unless --save or --no-save |
| has been specified: if these are specified they set the default. |
| |
| o Limited capability for tilde expansion of file names even without |
| readline (on Unix, and on Windows). |
| |
| o New environment variables `R_HISTFILE' and `R_HISTSIZE' for the |
| name and size of the history file. |
| |
| o Attempting to restore (at startup) too large a .RData is now |
| a fatal error. |
| |
| o The loading of shared library on Unix now uses RTLD_NOW not |
| RTLD_LAZY. This means that all symbols must be resolvable |
| when the library is loaded, and R will not terminate later |
| when a missing symbol is called. Code which had missing symbols |
| (including some packages) will need to be re-compiled. |
| |
| |
| |
| o New generic function all.equal(); |
| most useful for numerical comparisons `up to rounding errors'. |
| |
| o New function boxplot.formula() as a formula interface to boxplots. |
| |
| o New functions getwd() and setwd() for getting and setting the R |
| working directory, basename() and dirname() for manipulating paths. |
| |
| o Function locator(, type=) is implemented to plot points or |
| draw lines interactively. |
| |
| o Functions new.env() to create empty environment and local() to |
| allow local evaluation of expressions, with various useful |
| idiomatic uses. |
| |
| o Convenience functions parent.frame() and eval.parent(). |
| |
| |
| |
| o A new scheme for keeping source code with user-defined |
| functions has been implemented. In particular, comments |
| will no longer move about or disappear. The flip side of the |
| coin is that you can no longer rely on R to indent your |
| code for you. The stored-source facility can be turned |
| off with options(keep.source=FALSE), and for an individual |
| function by deleting the "source" attribute. |
| |
| If the source attribute is absent, the function will be |
| deparsed for editing or printing, but any comments will be |
| lost. |
| |
| o expressions have gained semantics that are closer to |
| those of S. They don't get evaluated except when explicitly |
| specified. Example: |
| |
| e <- expression(x); e[[1]] <- expression(123); eval(e) |
| |
| now gives expression(123), not 123. This fixes some problems |
| with expressions in the list argument to do.call(). |
| |
| |
| |
| o contrast() no longer drops colnames for 1DF contrasts. |
| Consequentially, the labels of regression coefficients for binary |
| factors contain level names (again ...). |
| |
| o na.omit() and na.fail() are now generic. |
| |
| o plot.lm() has more options and now does 4 plots by default, should |
| also be okay for "glm" object; all thanks to John Maindonald. |
| |
| o If the dimnames of a table are themselves named, then their names |
| are used to label the respective dimensions in tabular output. |
| |
| o chisq.test() now optionally computes the p-value by Monte Carlo |
| simulation (in the standard case of a 2-d contigency table). |
| |
| o source() has a new argument `chdir' for changing the working |
| directory to that of the file being sourced when evaluating. |
| |
| o If data() loads an R source file, it now changes the working |
| directory (to that containing the file) when evaluating. |
| |
| o Interpret strings NaN and Inf in character to numeric conversions |
| (and thereby in read.table) |
| |
| o The presence of an object `.conflicts.OK' in a package suppresses |
| conflict checking in library() for that package. |
| |
| o uniroot() can now be used recursively. |
| |
| o hdf5{read|write} now allow more kinds of attributes and add support |
| for HDF5 version 1.2 (or newer) thanks to Marcus G. Daniels. |
| Configure checks for HDF5 1.2 availability, older versions will |
| no longer work. |
| |
| |
| |
| BUG FIXES |
| |
| o x ^ y gives proper results when x or y are infinite. |
| |
| o The semantics of <<- have been corrected. The search for |
| a variable binding to modify now begins one level "up" from |
| the current one. Thus S and R semantics in "non-closure" |
| functions will be identical. |
| |
| o .Last() is called when terminating with q() (not just with EOF). |
| |
| o abline() now understands the "lwd" graphics parameter if it |
| is supplied as an inline argument. |
| |
| o axis() now sorts `labels' when it sorts `at'. |
| |
| o Some small changes have made in the axis drawing code to |
| ensure that tick-mark label alignment is correct for |
| non-default values of the "las" parameter. |
| |
| o Improved error message from check.options(). |
| |
| o cm.colors(n) now doesn't append silly "v=1"; works for n=0, n=1. |
| |
| o cooks.distance() now also works for "glm" objects; |
| deviance.lm() now ok for the case of weights. |
| |
| o date() doesn't return a final "\n" (again ...). |
| |
| o diag() and diag<- now handle correctly matrices with zero rows or cols. |
| |
| o help([<-.factor) (etc) work again. |
| |
| o is.recursive(list(.)) is now TRUE [PR#221]. |
| |
| o log(0) gives -Inf on all architectures. |
| |
| o When persp() was the first graphics command given to R it gave |
| the error "plot.new() has not been called yet". This no |
| longer happens. |
| |
| o pgamma() gave 0 or 1 for extreme arguments too soon. |
| |
| o plot(<function>, log="x") doesn't give a silly warning any more. |
| |
| o The internals of postscript() have been changed so that line |
| textures (dotted dashed etc) look better. The use of the |
| PostScript "initclip" operator has been removed so that we |
| can(?) really claim eps compliance. |
| |
| o revsort() misbehaved if n<=1, causing sample(1,1,,1) to |
| segfault |
| |
| o seq(along = v) { and seq(v) when length(v) > 1 } now returns |
| a result of mode "integer". |
| |
| o split.default() now uses subscripting for x with a non-null |
| class, this preserves, e.g., the class of factors |
| |
| o substr/substring(), deparse(), dput(), dump(), print() |
| will work for arbitrarily long strings. |
| |
| o which(x) failed when x had names and contained NAs. |
| |
| o Default editor files (e.g. from fix()) are now removed at termination. |
| |
| o Typos in NegBinomial.Rd (Negative Binomial distrib), thanks to Ch. Gu. |
| |
| o a clipping problem for plots when there non-zero outer margins |
| has been fixed. This problem used to affect coplot() and pairs(). |
| |
| o get("zzz", mode="xxx") missed promise objects. |
| |
| o match.fun failed when a data frame was attached containing a |
| "length" variable (e.g.) |
| |
| |
| ************************************************** |
| * * |
| * 0.64 SERIES NEWS * |
| * * |
| ************************************************** |
| |
| |
| CHANGES IN R VERSION 0.64.2 |
| |
| |
| NEW FEATURES |
| |
| o new target for R installation testing : make strict-tests. |
| |
| o symnum(x) now nicely codes logical x. |
| |
| o convolve() has a new type = c("circular", "open", "filter") |
| argument allowing more than the only circular convolution. |
| |
| o par(xpd) now has three settings: FALSE (clip to plot region), |
| TRUE (clip to figure region), or NA (clip to device region). |
| |
| o zapsmall(x) works for complex x. |
| |
| o new global variable R.version.string (for plots & reports). |
| Deprecated version & Version for new R.version & R.Version. |
| |
| o R CMD Rd2dvi has builtin "Usage" help and works for multiple files. |
| Useful for automatic reference manual of a package. |
| |
| |
| BUG FIXES |
| |
| o power() is now fully implemented and documented. |
| |
| o A couple of problems with group generic operations. |
| |
| o A bug which meant that it was not possible to add elements |
| to zero length lists in the obvious way has been fixed. |
| x <- list(); x[[1]] <- 10 |
| x <- list(); x[["a"]] <- 11 |
| both now work. |
| |
| o save.image() ignored dot-names. (esp. .First()) |
| |
| o lab= argument to plot() misinterpreted by axis() via ... passing |
| |
| o NULL labels in text() caused segfault |
| |
| o matrix(f,...) with f a factor now coerces to character |
| |
| o documentation errors for substitute and is.vector, minor fixups for |
| trig and nlm |
| |
| o Background colours are set properly on X11 devices with |
| colortype="pseudo": sometimes they were not allocated separately. |
| |
| o C() works (again?) for a single argument. |
| |
| o is.na() didn't work properly for "list" arguments. |
| |
| o symnum() sometimes failed with arrays of rank >= 3. |
| |
| o in some cases one could get nonblack color instead of |
| black on 2nd x11() window. |
| |
| o influence.measures(.) $ is.influential was wrong on the |
| cooks.distance. |
| |
| o printing of complex NaN/Inf was wrong as well. |
| |
| o printing of complex named vectors had a wrong initial space. |
| |
| o allow trailing space in character->numeric coercion |
| |
| o library() gave wrong "masked" warnings in some cases. |
| |
| o par(xpd) semantics were not compatible with S. |
| |
| o rect() output was not clipped in PostScript. |
| |
| o par(pin=c(width, height)) was behaving as par(pin=c(width, width)). |
| |
| o Non-blank separated data files didn't have their 1st field |
| handled properly. |
| |
| o "aux" directory moved to "tools" to avoid difficulties on |
| Windows. |
| |
| o structure() clobbered factors with missing levels. |
| |
| o pmatch() misbehaved on duplicate matches. |
| |
| o R CMD Rd2dvi <file.Rd> works again. |
| |
| o logical binops tried to set time series parameters before dimensions. |
| |
| o upped the BUFSIZE in model.c (NOT proper long-term solution). |
| |
| o dput(), dump() and deparse() now always use DBL_DIG (=15) digits |
| for numeric formatting. |
| |
| o chull() now works for vertical borders, such as in chull(c(1,1,2),3:1). |
| |
| |
| CHANGES IN R VERSION 0.64.1 |
| |
| NEW FEATURES |
| |
| o barplot() and boxplot() are now generic |
| |
| o relevel function to reorder levels in factors. |
| |
| o contr.treatment now has a base= argument for selecting the |
| baseline group. |
| |
| o New command line option `--no-environ' (under Unix) to prevent |
| sourcing the `~/.Renviron' file. Implied by `--vanilla'. |
| |
| o Packages can now have a configure script. If a file `configure' |
| is found it is executed before anything else is done by R |
| INSTALL. |
| |
| o If HTML help files are asked for but not available, text help |
| is used. |
| |
| o HTML help file conversion reports unsatisified \link{..}s. |
| |
| o `vsize' and `nsize' can be set by the environment variables |
| R_VSIZE and R_NSIZE respectively, perhaps most conveniently from |
| `~/.Renviron' under Unix or Windows. Command-line settings will |
| take precedence. |
| |
| The defaults have been increased to 6M and 250k. |
| |
| o zip files can be used for storing help and example files. See |
| the help files for "help" and "example" for details. |
| |
| o New submission method "none" (for not sending email) in |
| bug.report(). |
| |
| o `R CMD check' can now also be used for installed packages without |
| the corresponding sources. |
| |
| o The sources for the Windows port are included in src/gnuwin32. |
| See src/gnuwin32/readme. |
| |
| BUG FIXES |
| |
| o deparser left off empty parentheses on e.g. (function(x) x)() |
| |
| o cat() now works on "name" objects |
| |
| o forgot to set jump buffer in return context in one case |
| |
| o parser dropped off tagged missing args on function calls ( f(a=) ) |
| |
| o relops tried to set time series parameters before dimensions |
| |
| o arithmetic tried to set time series parameters before dimensions |
| |
| o mvfft fixes (from Martyn Plummer) - not working with vectors and |
| segfault problem. |
| |
| o Rephrased error message on invalid assignment target. |
| |
| o ifelse() now evaluates yes/no only if needed |
| |
| o PROTECT'ed some memory in NewExtractNames that was getting overwritten |
| during garbage collection. |
| |
| o Crossing factors (`:') works again. |
| |
| o terms.formula used to choke on terms more than 60 characters long |
| |
| o is.nan() should now work correctly on new/old-style lists. |
| |
| o x[[i]] did not work correctly for negative subscripts i. |
| |
| o as.list() didn't work for expressions |
| |
| o x[[i]] <- quote(a) (x generic vector) didn't work |
| |
| o for method functions: many argument name changes, add ... where |
| needed, for consistency with the generic function. |
| |
| o example() will allow (again) aliased topic names. |
| |
| o HTML help file conversions will find hyperlinks in the main |
| library as well as the current library. Links containing `<' |
| or `>' now work properly. |
| |
| o Rdconv conversion of \section{}{}s to Sd corrected. |
| |
| o ppois rounded non-integer `q', should truncate. |
| |
| o pnbinom was wrong for non-integer `q'. |
| |
| o dbinom, dgeom, dnbinom, dpois give 0 with a warning for |
| non-integer arguments. |
| |
| o load / save / data allow unlimited string sizes. |
| |
| o strsplit() allows unlimited string size. |
| |
| o eigen() now should work (again) in all cases. |
| |
| o is.nan() fixed to work (again) in architectures with |
| "unspecified" internal isnan(). |
| |
| |
| CHANGES IN R VERSION 0.64.0 |
| |
| NEW FEATURES |
| |
| o Files BUGS and FAQ are now included with distribution and |
| various "front matter" files have been cleaned up. |
| |
| o readline has now an argument prompt = "" |
| |
| o coplot() now labels levels when conditioning variable is factor |
| (John Maindonald). |
| |
| o A new function filled.contour() has been added. It produces |
| a variant of contour plots where the area between contours |
| is filled with a solid colour. The function (currently) |
| uses the layout() function and so is restricted to a full |
| page display. |
| |
| o The function terrain.colors() has been modified to remove a |
| visual discontinuity (at yellow). In addition, a function |
| cm.colors() which implements a Cleveland-style cyan-magenta |
| palette has been added. |
| |
| o Primitive function .External() to call dynamically loaded |
| `internal'-style functions (code from Jean Meloche). |
| |
| o Function page() to view an R object in a pager. |
| |
| o Support for handling embedded '\n's in text strings |
| handed to low-level graphics functions has been added. |
| Some changes to the PostScript graphics driver were |
| needed to support this, so there may some minor change |
| in the appearance of plots produced in PostScript. |
| |
| o The LaTeX documentation is now split into 2 parts: the (currently |
| almost non-existent) manual and a reference index. |
| Manual: new section on loading C++ code. |
| |
| o [EXPERIMENTAL] Gnome support added. Use ./configure --with-gnome |
| to try it, but don't expect too much yet. |
| |
| o HDF5 support improved. Still not perfect, though. |
| |
| o The X11 graphics driver can now use a variety of strategies |
| for handing color. This means that it is now possible to |
| use black and white or grayscale graphics on color displays. |
| There are two strategies for handing color on pseudocolor |
| displays. The original "allocate-colors-until-they-run-out" |
| strategy has been supplemented by one which allocates a |
| color cube at startup and approximates requested colors |
| by those in the cube. On truecolor displays, there is no |
| limit on the number of colors which can be displayed and |
| you get exactly the color you request. (Note that |
| Directcolor and staticcolor displays are not supported yet). |
| |
| o The persp() function now allows shading of the rendered surface |
| using a simple lighting model. |
| |
| o Many functions providing an interface to the operating system |
| have been made "platform independent". See the manual entries |
| for "file", "list.files" and "file.show" for details of the new |
| interface. The system.file() interface has been changed. |
| |
| o There is a new function "eval.with.vis" which behaves exactly |
| like "eval", but which returns both the result of the evaluation |
| an a logical value indicating whether the value is ``visible''. |
| This has been used to replace some ad-hoc tests for whether |
| value should be printed or not in "source". As a consequence, |
| the "example" and "demo" functions no longer print invisible |
| values when the example script is run. |
| |
| o Index files in data directories in packages should be `00Index' |
| not `index.doc'. |
| |
| o Function interaction() to compute factor interactions. |
| |
| o load() can load to specific environments. |
| |
| o Sockets interface: make/read/write/close.socket() |
| |
| o Function chull() for planar convex hulls |
| |
| o pairs.formula() allows formula notations for scatter plot matrix. |
| |
| o new dataset co2. |
| |
| o documentation for datasets mtcars, plants, pressure, randu and |
| sleep. |
| |
| o the sunspots dataset is now monthly rather than annual. |
| |
| BUG FIXES |
| |
| o strsplit(), scan() and friends use a much larger char buffer |
| (still fixed size; this will change again) |
| |
| o ts() allows a data-frame argument `data'. |
| |
| o anova.lm handles singular models better, and deparses responses. |
| |
| o dump() now uses digits=12 rather than the current setting. |
| |
| o tabulate ignores entries beyond nbins rather than core dumps. |
| |
| o ?.C documents what C/Fortran types R objects correspond to |
| in foreign function calls, which is not what everyone thought. |
| |
| o changed long to int in several .C calls to follow the above rules. |
| |
| o rbind(x1,x2) now does not lose dimnames when xi are |
| character or complex. |
| |
| o readline() accidentally inherited menu()'s prompt. |
| |
| o .C() and .Fortran() now correctly report that there might be |
| NaN/Infs, not just NAs, unless NAOK=TRUE. |
| |
| o Resizing an inactive graphics window to an invalid size left |
| that window active and produced a spurious prompt and newline |
| in the console window. This no longer happens. |
| |
| o poly() rescales x to increase accuracy |
| |
| o apply() preserves names in yet another case [-> new example]. |
| |
| o phyper() now works for larger arguments than before. |
| |
| o Missing values didn't work in log plot |
| |
| o outer() doesn't produce all-empty dimnames any more |
| |
| o quantile.default() works when `probs' has zero length |
| |
| o example() now works again in all cases [AnIndex spaces]. |
| |
| o typos fixed in nlm() message, glm help |
| |
| o pt() now works better for extreme `df' arguments and gives |
| at least an approximate answer for ncp > 37.6. __more to change__ |
| |
| o fixed some glitches with formatC() and its docs. |
| |
| o several fixes in *.c code to make -Wall happy |
| |
| o curve() [and plot.function()] now use proper `x' values with log="x"; |
| `type = "."' now works with curve() and plot.function() |
| |
| o zapped old windows files since they didn't build any more. |
| The sources for the later gnuwin32 version are expected to |
| appear here for 0.64.1. The #ifdef Win32's here are for that |
| version. |
| |
| |
| ************************************************** |
| * * |
| * 0.63 SERIES NEWS * |
| * * |
| ************************************************** |
| |
| |
| CHANGES IN R VERSION 0.63.3 |
| |
| NEW FEATURES |
| |
| o get() and assign() allow position in search list to be a |
| character string. (e.g. get("delete.response","package:base") |
| |
| o HTML search now works for all packages (after new installation). |
| |
| o R INSTALL now also copies DESCRIPTION file to target dir. |
| |
| o offsets should work with lm as well as with glm now |
| |
| o range() is now in the Summary group, trunc() back in the Math |
| group. |
| |
| o Under Unix, R-specific environment variables can now be kept/set |
| in `~/.Renviron'. |
| |
| o New options `latexcmd' and `dvipscmd' for specifying the locations |
| of LaTeX and dvips; corresponding environment variables renamed to |
| `R_LATEXCMD' and `R_DVIPSCMD'. |
| |
| o --vsize & --nsize now both give size in "single units" |
| (bytes/cons cells) with possible |
| suffixes "M" (Mega), "K"ilo (1024) and "k"ilo(1000). |
| |
| o [pdqr]negbin() now also work with non-integer 'size' [by Ben Bolker]. |
| |
| o New standard package `lqs' for resistant regression and |
| covariance estimation, contributed by Brian Ripley. |
| |
| o new functions match.fun() and kronecker() [by Jonathan Rougier] |
| |
| o par(las = 3) is a new option. |
| |
| o new function jitter() [slightly more useful than S's]. |
| |
| BUG FIXES |
| |
| o system(command, intern=FALSE, ignore.errors=FALSE) |
| changed 1st & 3rd argument names and is better documented. |
| |
| o "/Font5 /Symbol findfont definefont" confused some printers |
| |
| o Bounding box rotated 90 deg for landscape (shouldn't be) |
| |
| o Legend skipped symbol for pch=0 |
| |
| o compilation on non-Intel Linux systems no longer looks for __setfpucw |
| |
| o a %% b -- is now periodic instead of symmetric; more S compatible. |
| |
| o locator(n=512) -- default: MANY points, not just one. |
| |
| o qqnorm() uses ppoints() and returns list with x sorted along y. |
| |
| o plot.formula now allows ylab to be set |
| |
| o plotmath had trouble with paste()'ing expressions |
| |
| o plotting math expressions now also works for objects of mode |
| "call" (in particular on the result of substitute()) |
| |
| o locator() on log axes: value antilogged twice |
| |
| o (a real oldie - and trival too) is.recursive now TRUE for |
| expressions |
| |
| o sanitised delete.response |
| |
| o x[["a",]] could crash R |
| |
| o strwidth() crashed R if no device open |
| |
| o predict inconsistencies with offsets straightened out |
| |
| o tapply goofed when FUN returned named scalar |
| |
| o [.factor now retains contrasts attrib. |
| |
| o hist() had trouble with plotting math |
| |
| o HTML indices get only built when installing a package to RHOME |
| |
| o subscripting with a length zero logical no longer bombs. |
| |
| o as.ordered(NULL) now returns an "ordered" object. |
| |
| o --debugger .. now gives a warning if other command line args are used |
| |
| o pt(t, df, ncp) now also works for bigger ncp's |
| |
| o apply(a,d, fun) now passes vectors (rank 1 arrays) to fun. |
| |
| o model.frame() with subset and only one column fixed |
| |
| o boxplot(<data.frame>) now works again. |
| |
| o dyn.load(..) failing gives more informative error message. |
| |
| o Ops.factor: not error, but a warning + NAs |
| |
| o bug.report() keeps report file if can't be e-mailed |
| |
| o Ops.data.frame : things like d.fr < a now return a matrix |
| |
| o data.frame(): duplicated row.names now give a warning when dropped. |
| |
| o boxplot(.., ylim=..) or (.., axes=..) gave erronous warning |
| |
| o glm had wrong init code for models with offsets. Also fixed |
| so that linear predictor includes offset, also when predicting. |
| |
| o predict.glm didn't work with se=T |
| |
| o backsolve(), qr.solve... now return a vector when x (or y) is a vector. |
| |
| o string tags now converted to symbols and strange symbolic |
| tags print as strings, cf. e<-quote(c(F=2, "tail area" = .5)), etc. |
| |
| o row.names(.) <- val doesn't allow duplicated values anymore. |
| |
| o library(mva)'s dist() now works with both "euclidean" & "euclidian" |
| |
| o revised curve function to avoid using grep patterns that caused |
| problems under Solaris 2.6 |
| |
| o coplot() now has 'number' and 'overlap' arguments, and should work |
| in more situations. [by John Maindonald and MM]. |
| |
| o save(..ascii=TRUE) now uses "full precision" for numerics. |
| |
| o as.array() preserves names() |
| |
| o outer() works for general array args and preserves (dim)names. |
| |
| o print.factor and print.ordered now return their args invisibly. |
| |
| |
| CHANGES IN R VERSION 0.63.2 |
| |
| NEW FEATURES |
| |
| o sink() has new `append' argument. |
| |
| o new function rle(). |
| |
| o plot(.) and curve(.) also accept a function as first argument. |
| new `plot.function'. |
| |
| o new function loglin(). |
| |
| o pretty() has new arguments and now better "obeys" its `n' arg. |
| Internal GPretty() [implicitly used by axis(.., at = NULL,..) |
| now uses pretty. |
| |
| o new generic function aggregate() with methods for data frames |
| and time series. |
| |
| o data set `euro' with Euro conversion rates. |
| |
| BUG FIXES |
| |
| o model.frame(,subset=) no longer loses contrasts |
| |
| o `make install' copied the R shell script a second time without |
| getting RHOME right (thus also breaking R CMD check). Fixed. |
| |
| o help() after help.start() did not work if topic was not equal |
| to filename (e.g. rnorm is found in Normal.html) |
| |
| o fix the 0.63.1 fix for abbreviate(.); improved doc. |
| |
| o predict.mlm(.) couldn't have worked with `newdata'. |
| |
| o model.frame/na.omit bug for matrices and Surv objects. |
| |
| o mean( <data.frame> ) now doesn't return sum(.) anymore. |
| |
| o str(.) doesn't give extraneous "..." in rare cases anymore. |
| |
| o Added documentation for group methods ("Math", "Ops","Summary"). |
| |
| o R_PAPERSIZE is used for Rd2dvi and at configure time for the |
| `make dvi' parts. |
| |
| o hist(i) now also works for e.g., i = -1, 0, or 1. |
| |
| o range() now works on dataframes (uses c(..., recursive=T)) |
| |
| o pretty(.) does not loop infinitely anymore in very extreme cases. |
| |
| o math functions should work better on dataframes now |
| |
| o plot(.., type = 'h', log = 'y') now works ... |
| |
| o plot.factor(x, y, ...) of two factors now makes |
| barplot(table(y,x), ...) |
| |
| o use object$prior.weights in add1.glm, drop1.glm (Brian Ripley) |
| |
| o rnorm(1,mean=m,sd=0) returns m, not NaN (Ben Bolker) |
| |
| o runif(n, a,a) now returns rep(a,n) instead of NaNs. |
| |
| |
| CHANGES IN R VERSION 0.63.1 |
| |
| NEW FEATURES |
| |
| o new function mosaicplot(). |
| |
| o xy.coords(.) has a "recycle = FALSE" argument, used in text(). |
| |
| o RNGtype() allows to choose different Random Number Generators. |
| __EXPERIMENTAL__ |
| |
| o print.default(.) now also works with a `right = TRUE' argument. |
| {{ print.matrix(.) is bound to become deprecated... }} |
| |
| o new help page `Memory' on the usage of command line options |
| --vsize and --nsize. Error message if R runs out of memory |
| points to help(Memory). |
| |
| o rowsum() and improved na.omit() added from survival4 |
| |
| o backsolve(.) has new arguments "upper.tri = TRUE, transpose = FALSE" |
| |
| o hist() has new "right = TRUE" argument; |
| "right = FALSE" gives [a,b) intervals |
| |
| o help() has "htmlhelp" argument, allowing to suppress htmlhelp after |
| help.start(). This is desired for ESS. |
| |
| o quantile(.) has an "names = TRUE" argument for speed. |
| It is much better documented now. |
| |
| |
| BUG FIXES |
| |
| o build-help --dosnames should now also work for text help, |
| latex and examples. |
| |
| o seq() should work better now (fuzz-factor 1e-7 inserted) |
| |
| o multiple arguments to return caused value to be a pairlist |
| |
| o data.frame choked on long names from deparse() |
| |
| o data.edit now works (dataedit doesn't need pairlist()s anymore) |
| |
| o as.pairlist(NULL) is ok |
| |
| o ts(1:5, start=2, end=4) now work. Further plot(ts(..), ts(..)) |
| |
| o eigen() returns $vectors in any case [S compat]. |
| |
| o apply(cbind(1,1:9, 2, quantile) doesn't drop quantile names anymore |
| |
| o array(1, dim=(1:3)[c(F,F,F)]) is now valid == array(1,NULL) == c(1); |
| the same for array(a,d, list()) |
| |
| o fix problem with step() and offsets |
| |
| o drop attributes on matrix subsetting |
| |
| o kappa(.) now works [dtrco now in load table (ROUTINES)]. |
| |
| o pmin() and pmax() now preserve attributes. |
| |
| o handle null models arising in drop1(), step, etc. |
| |
| o partial matching problem with $ indexing |
| |
| o matplot(.) works with lwd (vectors) |
| |
| o par("cex.axis") now has the desired effect... |
| |
| o which(.) now omits NAs in its argument. |
| |
| o rbind.data.frame caused character-to-factor coercion a bit too often |
| |
| o couple of messups in dotplot |
| |
| o z[[1]] <- ~x probl fixed as suggested by J.Lindsey |
| |
| o do_modelframe could lose contrast attributes |
| |
| o "make check" needed standardisation of locale |
| |
| o unlist(...,recursive=F) got names wrong |
| |
| o abbreviate(.) does not anymore return random garbage in some |
| cases [by Guido M.] |
| |
| |
| CHANGES IN R VERSION 0.63 |
| |
| NEW FEATURES |
| |
| o library(... , warn.conflicts = TRUE) |
| now prints all conflicts arising from attaching the given package. |
| |
| o new .Platform variable for better modularizing |
| platform dependence. __This_is_"beta"_and_bound_to_be_changed___ |
| |
| o new arguments to colnames(..) and |
| rownames(x, do.NULL = TRUE, prefix = "row"). |
| _ |
| o par(bty = "]") for _| box(.) in plots. |
| |
| o New standard package `modreg' (smoothing and local MODern |
| REGression methods) contributed by B.D. Ripley. |
| |
| o par() has a `no.readonly = FALSE' argument which allows more |
| sensible op <- par(no.readonly = TRUE); on.exit(par(op)). |
| |
| o Real Bessel functions of 1st to 3rd kind, of arbitrary order: |
| besselI(), besselK(), besselJ(), besselY() are the I(), K(), |
| J(), and Y() Bessel functions. |
| |
| o New conflicts() function from B.D. Ripley |
| |
| o uniroot has a new `maxiter' argument and returns #{iter} and |
| precision. |
| |
| o New option `show.coef.Pvalue' (default: TRUE). If FALSE, |
| print.summary.[g]lm does not print P values. |
| |
| o New `R --vanilla' is equivalent to |
| R --no-save --no-restore --no-site-file --no-init-file |
| |
| o gc() has now a `verbose' argument and returns a matrix with free |
| and total n- and v-cells(heap). |
| |
| o New example(<foo>) function runs the \emph{Examples} R code of |
| <foo>. example() calls source() which now has a `verbose' |
| instead of `debug' argument. |
| |
| o experimental functions [as.|is.|]pairlist() for the few old-style |
| dotted pair lists [undocumented]. |
| |
| o options(check.bounds = TRUE) makes sub-assignments which |
| "stretch" a vector give a warning [dropped undocumented |
| check.bounds() function]. |
| |
| o Makefiles should now conform (mostly) with the GNU Coding |
| Standards. In particular, `make install', `make uninstall' |
| and `make install-strip' now work. |
| Also, it is now possible to build R in a non-source directory. |
| |
| o which() preserves names and has a new `arr.ind' argument |
| allowing for array indices. |
| |
| o New functions {d,p,q,r}signrank for the Wilcoxon signed rank |
| distribution, and {d,p,q,r}wilcox for the Wilcoxon (rank sum) |
| distribution. |
| |
| o Command line options GNUified a bit further. |
| New command line option `--verbose' for printing more |
| information about progress. |
| Command line options `--vsize' and `--hsize' as replacements |
| for `-v' and `-n' which are now deprecated. |
| Added `--silent' as synonym for `--quiet'. |
| Short-style option `-V' obsolete. |
| |
| o Added bug.report() to generate & send bug reports from |
| within R. |
| |
| o The PostScript device driver now uses the ISO Latin1 font |
| encoding. This should allow Western Europeans to render |
| their languages correctly. It is likely that additional |
| encodings will be added (e.g. Latin2) when we figure out |
| how to set the correct font encoding in printers. |
| |
| o The mathematical annotation code has been reworked. Italic |
| correction works better. Additional functionality will be |
| added. |
| |
| o "sample" now has an optional "prob" argument which gives the |
| probabilities of sampling each element in the vector being |
| sampled. The present implementation is based on some code |
| from E. S. Venkatraman <venkat@biosta.mskcc.org>. |
| |
| o The internal data structure used to represent lists has |
| changed from being based on dotted pairs to generic vectors. |
| Users should see no changes as a result (with the exception |
| of some efficiency gains in list operations). |
| |
| o Subscripting matches that of S more closely. It is now |
| possible to use subscripting beyond that the end of vectors |
| and lists. |
| |
| o Element labelling in "c" and "unlist" should match that of |
| of S. |
| |
| o Added split.screen etc functions for manipulating multiple |
| screens on a single device |
| |
| o After help.start() the HTML help system is used for all help() |
| requests. The name of the browser is now controlled by |
| options("browser"). |
| |
| o Added kmeans to package mva (donated by B. Ripley) |
| |
| o New persp function added. It is NOT compatible with S (yet) |
| and is subject to internal and interface changes. |
| |
| o gctorture() for torturing the garbage collector to reveal |
| memory protection bugs. (Call GC on every memory allocation). |
| |
| o B. Ripley's aov code (and more) has been added. This includes: |
| |
| - aov() now handles models with Error terms, multiple |
| responses. |
| |
| - proj(), model.tables(), se.contrast(), replications(), |
| eff.aovlist() are implemented for aov fits, and where |
| appropriate for lm fits. |
| |
| - dummy.coef(), with methods for lm and aovlist fits. |
| |
| - add1(), drop1(), step() for stepwise fitting of statistical |
| models, with default, lm and glm methods. |
| |
| - summary() and deviance() -- mlm methods. |
| |
| - kappa() (for estimating condition numbers) |
| |
| - labels() to find a suitable set of labels from an object |
| |
| - C() for setting the contrasts of a factor |
| |
| - anova(), plot(), summary() and deviance() methods for mlm fits |
| |
| o eval() semantics changed when envir= is a list. A 3rd argument is |
| now allowed, specifying the enclosure (i.e. where R looks for |
| variables *not* found in envir=) it defaults to the calling |
| environment (was .GlobalEnv). Note that when used inside a function, |
| it is often desirable to set the enclosure to the parent |
| environment instead. [ eval(e, data, sys.frame(sys.parent())) ] |
| |
| |
| BUG FIXES |
| |
| o min(NULL); max(double()) now give warnings. range() gives NA. |
| |
| o substring("", NULL) no longer segfaults. |
| |
| o formatC(.) now takes default "width = 1" when both width and digits |
| are unspecified. |
| |
| o several fixes in internal axis and tickmarks setup for |
| "extreme" ranges and values, especially for "log" scaling. |
| |
| o seq(a,a, by=b) now works properly. |
| |
| o print.data.frame(.) now calls print.matrix instead of print(.) |
| which finally enables the 'right = TRUE' argument. |
| |
| o R --help gives more |
| |
| o postscript() now uses 'hyphen' instead of 'plusminus' for a minus. |
| |
| o source(..., echo=TRUE) now puts a `"' if necessary after truncation. |
| |
| o Changes to the PostScript device driver mean that the volume |
| of output has been reduced to about a third of what it was. |
| |
| o Fixes and restructuring to name generation in connection with |
| unlist() and c(). |
| |
| o Many bugs found and fixed in the memory allocation / garbage |
| collection area. In particular, the parser was sometimes |
| UNPROTECT()ing the wrong pointers. |
| |
| o lm(y[g=="1"]~x[g=="1"]) caused memory corruption |
| |
| |
| CHANGES IN R VERSION 0.62.4 |
| BUG FIXES |
| |
| o plot.default(.) has now 'sub' argument which eliminates |
| "Warning: parameter "sub" couldn't be set in high-level plot() function" |
| |
| o formatC(numeric(0)) now works. |
| |
| o menu(.) works for empty imput |
| |
| o 0i ^ 2 now gives 0+0i as it should. |
| |
| o ppoints() now behaves like S, and has additional argument 'a' |
| |
| o seq(1,6,by=3) and similar "by" calls now work okay |
| |
| o mahalanobis(.) now fixed; does *NOT* have default arguments for |
| center and cov anymore. |
| |
| o diag(.) doesn't return non-sensical dimnames anymore. |
| |
| |
| CHANGES IN R VERSION 0.62.3 |
| |
| NEW FEATURES |
| |
| o preserve factor levels and contrast settings in model objects |
| |
| o factor[...,drop=T] reduces level set |
| |
| o added dblepr, intpr |
| |
| o do_modelmatrix(model.c): Set rownames from data argument. |
| |
| o New generic function preplot(). |
| |
| o A new R BATCH interface for non-interactive execution. |
| |
| o Added `offline' argument to help() for producing hardcopy via |
| latex and dvips. |
| |
| o glm.fit.null now calculates AIC and print.glm.null prints it |
| |
| o effects.lm implemented |
| |
| o new class "mlm" for multivariate "lm", predict.mlm to go with it |
| |
| o "Details" section added to .Rd format |
| |
| o R_PRINTCMD and R_PAPERSIZE can now be set via users' environment, |
| overriding setting in startup script. |
| |
| o enhanced identify() |
| |
| o new function print.coefmat() |
| |
| o added unix() as .Deprecated("system") |
| |
| o date() replacing system.date() |
| |
| |
| BUG FIXES |
| |
| o substitute would re-substitute after expanding ... |
| |
| o indexing modified object in some cases |
| |
| o sweep should work again on dataframes |
| |
| o minor changes in aov() |
| |
| o builds should now actually work on systems that do not add |
| underscores to Fortran symbols |
| |
| o biplot[.default]() was redundant in "base" package; now only in "mva". |
| |
| o unix(..) now helps the user to find system(..) instead. |
| |
| o apropos("[") and methods("[") now both work (even though "[" is not |
| a valid regular expression). |
| |
| o row.names<-.default now exists. Converts object to data |
| frame and then adds row names |
| |
| o codes() now distinguishes between ordered and unordered factors |
| |
| o codes() had *opposite* semantics of Splus. Now it's the same. |
| |
| o replicating factors now yields factors (again) |
| |
| o print.summary.xxx functions more consistent, using new function |
| print.coefmat(). |
| |
| o Changed many `T' to `TRUE' and `F' to `FALSE' in the base package. |
| |
| o binary operation on 1x1 matrix lost dimension |
| |
| o fix anova.glm for null model |
| |
| o glm.fit.null: ensure df.residual == df.null for a null model |
| |
| o summary.glm: correlations in saturated cases |
| |
| o stat.anova: use match.arg and labeled switch statement |
| |
| o Major cleanup of glm iteration code |
| |
| o Correct reordering of glm coefficients if pivoting |
| |
| o Rownames on contrast matrices |
| |
| o factor() and [.factor preserves class "ordered" |
| |
| o Code rearrangement in predict.lm (avoid unnecessary computation) |
| + let rownames through on predictions |
| |
| o model.matrix.default: Initial code to define model frame |
| simplified considerably after defaulting data argument to |
| sys.frame(sys.parent()). This also removes the problem where |
| data.frame mangles I(x^2) and similar names, so that the |
| "reorder" sanity check at the end fails. |
| |
| o The handling of extra FORTRAN libraries (f2c-related and BLAS) |
| should now be correct. Via SHLIBLDFLAGS, add-ons will also be |
| linked against these libraries. |
| |
| o Modified makefiles so configure followed by "make distclean" |
| should restore the source tree to its original form. |
| |
| o a leftover "colours <- colors" caused trouble when collating |
| sequence changes caused files to go into the "base" file in a |
| different order |
| |
| CHANGES IN R VERSION 0.62.2 |
| |
| (The new functions predict.glm, poly, aov, alias, biplot.default and |
| biplot.princop, update.default and rug all come from Brian D. Ripley, |
| who is also responsible for finding and/or fixing a lot of the bugs) |
| |
| NEW FEATURES |
| |
| o predict.glm() added. |
| |
| o text() is generic. |
| |
| o update.default() (replaces update.glm() and update.lm()). |
| (This will only work if you comment out update.lm and |
| update.glm in the sources, or disable them with |
| update.lm<-function(object,...)NextMethod(), etc.) |
| |
| o predict.lm() changed towards S-plus compatibility. Intervals are |
| still available via interval= argument. |
| |
| o zapsmall() function. |
| |
| o polygon() now handles NAs |
| |
| o options(show.signif.stars = TRUE). If FALSE, |
| summary.lm and similar functions do *not* print significance stars |
| anymore. |
| |
| o poly() for [g]lm modelling. |
| |
| o aov() for Analysis Of Variance [anova]. |
| |
| o alias() for displaying ``aliased'' factor levels in (>=2)way anova. |
| |
| o mva: Now has biplot and biplot.princomp |
| |
| o rug() plot. |
| |
| o new src/library/profile/Common.R for OS-independent intialization. |
| |
| o new date stamp mechanism (ensures that prerelease versions carry |
| correct date) |
| |
| BUG FIXES |
| |
| o abbreviate() now always retains the first letter. |
| |
| o attr() partial matches for attribute name. |
| |
| o axis() accepts graphical parameters. |
| |
| o binomial() accepts factor responses. |
| |
| o cbind() works with data frames. |
| |
| o contrasts() gives simpler labels (like S) for factors with |
| two levels. |
| |
| o contrasts<-() now has a how.many= argument. |
| |
| o contour() and image() can accept a list to specify the matrix. |
| |
| o contr.poly() uses orthogonal polynomials (like S) not raw |
| polynomials. |
| |
| o data() could fail with a partial match to the dataset name. |
| |
| o density() works correctly if from= or to= are used. |
| n= can now take any value, not just a large power of 2. |
| |
| o expand.grid() now accepts more than two arguments, |
| or a list of factors. |
| |
| o factor() and ordered() handle their levels argument better. |
| |
| o family.glm() now returns the correct family (including link etc). |
| |
| o legend() now knows about lwd. |
| |
| o match.args() works correctly for default arguments. |
| |
| o model.frame.lm() did not invoke `lm'. |
| |
| o model.matrix() calls model.frame() if needed. |
| |
| o model.response() now returns names, so glm() gives names to |
| residuals, fitted values, etc. |
| |
| o quasi() works in glm() (was missing aic component). |
| |
| o seq() sometimes omitted the final value due to rounding error. |
| |
| o terms.formula() and update.formula() now resolve `.' in formulae |
| and tidy up `(a + b) - b' etc. |
| |
| o ... is now passed down correctly to functions inside functions. |
| |
| o save.image didn't work (Martyn Plummer) |
| |
| o abs() instead of fabs() in seq.c crashed R on Digital Unix |
| |
| o model.matrix() gagged on variables with complicated names |
| |
| o saturated models acting up in glm |
| |
| o various improvement of build procedures |
| |
| o rbind(NULL, matrix) core dump |
| |
| o density() default 'bw' now 0.9*(...) instead of 1.06*(...) |
| [=Silverman's rule of thumb]. |
| |
| o detach(2) now works. |
| |
| o format() doesn't drop names anymore. |
| |
| o format.pval() works with NAs. |
| |
| o print.[summary.][g]lm() functions print numbers better formatted. |
| |
| o legend() now also works properly in log coordinates. |
| |
| o backsolve() now working; bakslv.c not depending on |
| Fortran_underscores. |
| |
| o Tick marks acting up on log axes in postscript (fix from Martyn |
| Plummer) |
| |
| o The Rd format has a new section \details{} (needed for proper |
| Sd2Rd translation). \R was not understood for nroff |
| conversions, longer dashes (-- and --- in latex syntax) are |
| now converted properly. |
| |
| o prompt.default() now carries "\details{}". |
| |
| o R [ SHLIB | COMPILE ] were broken on some Solaris systems |
| due to use of bash syntax. R [ INSTALL | COMPILE | SHLIB ] |
| now use a MAKE environment variable if present. |
| R INSTALL only rebuilds man pages if they are not already |
| up to date. |
| |
| |
| CHANGES IN R VERSION 0.62.1 |
| |
| BUG FIXES |
| |
| o Accidentally shipped R-0.62 without the tests and etc/Rdoc |
| directories. |
| |
| |
| CHANGES IN R VERSION 0.62 |
| |
| NEW FEATURES |
| |
| o Many more help(.) pages. |
| |
| o The top level Makefile now supports the usual |
| ./configure; make; make install |
| procedure (new make targets `all' and `install'). |
| |
| o The HTML help pages can now be searched for keywords. |
| |
| o Conversion of functions to and from lists. formals<- and body<-. |
| The alist() function makes it easier to construct argument lists, |
| etc. Added expression-->list coercion. |
| |
| o complex(.) now has optional 'argument' and 'modulus' arguments, |
| allowing ``polar coordinate'' specifications. |
| |
| o layout() documented and improved: starts default device if needed, and |
| returns number of figures. |
| |
| o New find() function [relying on apropos(..)]. |
| |
| o objects(<integer>) now works, being equivalent to |
| objects(pos=<int.>). |
| |
| o storage.mode() and related functions now return |
| "double" instead of "real", for compatibility. |
| "real" is still allowed as synomym for "double". |
| |
| o A `tests' directory has been added (in the source), and "make |
| tests" has been modified to run more than all the examples from |
| the base package. The exact `make tests' behavior is still |
| bound to change. |
| |
| o An experimental directory `etc/Rdoc' has been added with a perl5 |
| module to parse R documentation files. Sample perl programs |
| to use this module are also included. |
| |
| o All internal mechanisms to support factors and data.frames have |
| been removed. These are now entirely supported by interpreted |
| code! `is.unordered' has been eliminated. Thanks to John |
| Chambers for allowing the distribution of his StatLib code. |
| |
| o "pmatch" is now completely S compatible and is not just another |
| name for "charmatch". |
| |
| o There is now a function called ".Alias" which can be used to |
| provide multiple names for the same object. Example: |
| lm2 <- .Alias(lm) |
| This is dangerous because it can be used to defeat the |
| call-by-value illusion. |
| |
| o Many functions changed from <primitive> to .Internal(..). |
| Currently, new .Internal(.)s in ..library/base/R/New-Internal.R |
| Primitive functions are now printed as ``.Primitive(..)''. |
| |
| o [dpqr]hyper(.) now also work with some 0 arguments. |
| |
| o C-code: Many "-Wall" fixes (MM & DB). |
| |
| o mva's dist() now takes arguments diag and upper which control |
| how the distance matrix is printed. plot.hclust() now takes a |
| labels argument. |
| |
| o Attributes are now propagated correctly in binary operations. |
| Changes from: |
| Steve Oncley and Gordon Maclean |
| National Center for Atmospheric Research |
| Boulder, Colorado USA |
| |
| o configure now also checks for fort77. |
| |
| o Usage of R INSTALL now is |
| R INSTALL [options] [-l lib] pkg_1 ... pkg_n |
| The +/- options were replaced by GNU-style `--no-docs' and |
| `--no-text', `--no-html', and `--no-latex'. |
| |
| o Usage of R REMOVE now is |
| R REMOVE [options] [-l lib] pkg_1 ... pkg_n |
| |
| o Usage of R COMPILE now is R COMPILE [options] srcfiles, where |
| through options one can set e.g. CFLAGS or FFLAGS. |
| |
| o Usage of R SHLIB now is R SHLIB [-o libname] files, where the |
| file names can be that of source or object files. |
| |
| o A new R CMD interface allows invokation of executables in |
| $RHOME/{etc,cmd} without installing them or setting paths. |
| |
| o Data files are now also documented using the Rd format, all |
| data documentation in the base package has been converted |
| accordingly. Rd files for data have a \keyword{datasets} as |
| identifier. |
| |
| o new function mahalanobis() for Mahalanobis distance |
| |
| o quantile.default() now handles Inf's correctly. |
| |
| o New command line options `--enable-blas' and `--enable-readline' |
| to configure. |
| |
| o pretty(x) is more reasonable when max(x)-min(x) < 1e-10 max(|x|), |
| and has a new argument "shrink.sml" for that case. |
| |
| o formatC(.) supports a new "fg" format for flexible |
| non-exponential formatting. |
| |
| o etc/build-htmlpkglist has been integrated into etc/build-help |
| (option --htmllists) |
| |
| o family gaussian(.) and inverse.gaussian(.) both accept several |
| link arguments [J.Lindsey]. |
| |
| o The graphics function "tck" now produces effects just |
| like those in S (e.g. par(tck=1) now produces grid lines). |
| Since using "tck" produces nasty results in some circumstances |
| there is also an alternative parameter "tcl" which defines |
| the tick length in terms of lines of text. The default |
| setting is par(tcl=-0.5). |
| |
| o menu() now takes additional arguments `graphics' (currently |
| unused) and `title'. |
| |
| o New function plot.formula(). |
| plot.factor() now produces boxplots when given 2 arguments. |
| |
| o New function write.table(). |
| |
| o signif() now has a `digits' default of 6. |
| |
| o Old-style long command line options (`-save' etc) changed to |
| GNU-style (`--save' etc). |
| Debugging options (`-ddd', `-gdb', `-xxgdb') unified into the |
| new `--debugger' (`-d'). |
| New command line options `--version' (`-V') and `--help' (`-h') |
| which print useful information and exit. |
| |
| o The loading of profiles at startup now works as follows. |
| Unless the new `--no-site-file' was given, a site profile is |
| sought (as specified via the environment variable `RPROFILE', |
| or if this is unset defaulting to `${RHOME}/etc/Rprofile'. |
| Then, unless the new `--no-init-file' was given, the user |
| profiles (`.Rprofile' and `~/.Rprofile') are sought. |
| |
| o New functions subset() and transform() intended primarily to |
| make life with dataframes easier. |
| |
| o debian directory has been added so Debian GNU/Linux packages can be |
| created from raw source. |
| |
| o The graphics system has been through a major overhaul. |
| It is now possible to have multiple active device drivers |
| and to control them with full suite of dev.xxx() functions |
| available in S. Display lists are now kept for interactive |
| devices. When an on-screen graphics window is resized, |
| the content of that window is redrawn at the new size. |
| At present only X11 and PostScript graphics device drivers |
| are available, but more are on the way. |
| |
| o On systems using IEEE arithmetic, the builtin Inf and NaN |
| values are now recognised and used. NA and NaN should |
| propagate correctly in computations, with NA dominating |
| in computations involving both quantities. |
| E.g. NA+NaN is NA. |
| |
| o Some of the t, F, and chisq distribution/probability functions |
| now allow a noncentrality parameter `ncp'. |
| |
| o Functions ptukey() and qtukey() provide the distribution and |
| quantile functions for the maximum of several studentized |
| ranges. |
| |
| o system.file() [now documented] returns all files matched by |
| wildcards. |
| |
| o data() now supports more file formats: .RData for binary |
| files, .txt or .tab for data to be read by |
| `read.table(file, header=TRUE)' and .csv for data to be read |
| by `read.table(file, header=TRUE, sep=";")' |
| |
| o Rdconv: new tabular environment, new sections `\format' and |
| `\source', new output format `-type Sd' for S documentation |
| |
| o .First.lib() now implemented; called by library() after loading |
| a package. |
| |
| o print.summary.[g]lm() now give `significance stars' and a symbolic |
| correlation matrix. |
| |
| o new is.R() function. |
| |
| o glm() now also returns an AIC value [from JL]. |
| print..glm methods indicate the options()$contrasts in some cases. |
| In summary.glm(..., correlation=..), the default has been changed to |
| corr. = FALSE which is consistent with summary.lm(). |
| predict() now works again for glm objects. |
| |
| o the `flag' argument in formatC(.) can now have more than one |
| character. |
| |
| o nlm() returns the number of iterations used [from J.Lindsey]. |
| |
| o cut, diff, hist, mean, quantile, seq, trunc() are now all generic. |
| cut() has an `include.lowest' argument as S. |
| |
| o save.image() as short-cut to save the current session in .RData. |
| |
| o new design of HTML help pages, including an index of all |
| functions from all installed packages. |
| |
| o new editor function pico() |
| |
| o matrices and arrays can have zero extents |
| |
| BUG FIXES (many of which resulted from the added features...) |
| |
| o atanh(.) now works |
| |
| o summary(glm) and summary(lm) now use compatible names. |
| |
| o [pq]tukey(.) now working. |
| |
| o title() now handles main=, sub=, xlab=, ylab= with embedded |
| newlines correctly. This is partly a change in title and |
| partly a change in the underlying graphics code. |
| |
| o min(.), max(.), sum(.) now return integer for integer arguments. |
| |
| o which(.) now returns integer. |
| |
| o Rd files: leading whitespace of lines in user-defined sections |
| was not correctly removed by Rdconv |
| |
| o sign(.) works again. |
| |
| o [.data.frame segfaulted if arg. wasn't a data frame |
| |
| o "R --no-readline" now again gives proper prompts. |
| |
| o demos/zero.R dyn.load(.) now should be working more easily. |
| |
| o mode(.) now returns "(" for a "parentheses 'call'". |
| |
| o Bug fix in mva dist.c for method binary (gave "invalid |
| distance"). plot.hclust failed for data without row names. |
| |
| o R INSTALL should work (again) now when `pkg' is a relative file |
| name. |
| |
| o .not.yet.implemented() now takes an arbitrary number of args. |
| |
| o Plotting of dendrograms is working again. |
| |
| o data.frame(.) now uses "1:n" as default row.names. |
| |
| o image(.) and contour(.) now also work called as, e.g., ``image(z)''. |
| |
| o the first argument of axis(.) is now called `side' as in S. |
| |
| o format(NULL) now works. |
| |
| o minor fix in symnum. |
| |
| o hist() now is more compatible to S, has a new `labels' argument, |
| and should work ok for non-equidistant breaks. |
| |
| o plot(-1) now labels properly. |
| |
| o Many small code changes (eliminating extraneous variables, nested |
| comm.) in C code in order to satisfy `gcc -Wall' [Doug Bates]. |
| |
| o model.extract() will now extract arbitrary model frame arguments. |
| |
| |
| o list of currently loaded libraries (.Dyn.libs) not saved |
| from session to session (really, this time) |
| |
| o rhyper works with vectorisation, degenerate cases. |
| |
| o printing of objects in lists now dispatches methods correctly |
| |
| CHANGES IN R VERSION 0.61.2 |
| |
| BUG FIXES |
| |
| o pretty(999) resulted in an infinite loop due to integer overflow. |
| pretty(.) now sometimes returns different results than before. |
| |
| o pi:6 returned integer, instead of real. |
| |
| o [.data.frame caused segfault if called with non-dataframe argument |
| |
| o hist() now is more compatible to S, has a new `labels' argument, |
| and should work ok for non-equidistant breaks. |
| |
| o lgamma(-1e7) segfaulted. |
| gamma(.) and lgamma(.) now give proper results for negative integers. |
| |
| o formatC(pi,dig=20,wid=2) segfaulted. |
| |
| o quantile(..., pr = c(1,2,5)/1000) gave all names as "0%". |
| |
| o In 0.61.1, model.matrix was fixed to pay attention to the names of |
| the names of its data arg, but the data arg was defaulting to an |
| unnamed list, so model.matrix(~x) failed... |
| |
| o Indexing with [[]] and a zero-length vector segfaulted. |
| |
| o Coercion of factors as in S-plus |
| |
| o dyn.load statement in demos/dynload/zero.R fixed |
| |
| o Factors could get allocated without the OBJECT bit, which |
| nearly drove Kurt mad trying to write plot.factor... |
| |
| o Fixed confidence limit problem in t.test |
| |
| CHANGES IN R VERSION 0.61.1 |
| |
| NEW FEATURES |
| |
| o None (by definition, x.y.z releases are bugfix releases now) |
| |
| BUG FIXES |
| |
| o Return statements of the form return(x,y) will now return |
| a list with named components. |
| |
| o Parsing of nested "if" statments was broken. This is fixed now. |
| (Reported by Paul Gilbert). |
| |
| o Wrong declaration of ConsoleBufCnt in src/main/scan.c caused crash |
| in Irix (George White <gwhite@bodnext.bio.dfo.ca>) |
| |
| o if(nmatch = 0) bug in src/main/character.c fixed (Doug Bates) |
| |
| o R_alloc/S_alloc fixes. The former allocated 4 times more than |
| needed, the latter zeroed half of what it got, sizeof() mistakes |
| in both cases. |
| |
| o c(ordered factor) caused segfault (uninitalised pointer), now |
| fixed. |
| |
| o behaviour of as.numeric() on factors changed recently; now |
| documented. |
| |
| o model.matrix() now pays attention to the names on its dataframe |
| argument. |
| |
| o Fixes to group methods. |
| |
| o autoload() caused infinite loop if function wasn't found in |
| library on loading |
| |
| o The pager ate the rest of stdin in batch mode, now fixed. Also, |
| stdout was not flushed before call to system(). "make tests" |
| should work now. |
| |
| o Empty directories now created by configure (so that it doesn't |
| matter that "CVS export" doesn't do it) |
| |
| o as.name() made idempotent (i.e. if is.name(x) then as.name(x)==x) |
| |
| o 3 problems with glm, 2 in glm.fit and a one in print.glm fixed |
| [Jim Lindsey] |
| |
| o binomial (family) now works when 'n=0'. [J.Lindsey] |
| |
| o split() now also works in split(1:10,1:2) |
| |
| o strsplit() now also works for strsplit(c,NULL) |
| |
| o A LANG='..' environment variable no longer affects scan()ing of |
| numbers. |
| |
| o seq(.) doesn't segfault anymore in gl(2,3):gl(1,6) |
| |
| o contour(.) now also works with integer arguments |
| |
| |
| CHANGES IN R VERSION 0.61 |
| |
| We try to make development more flexible by creating a "CVS branch". This |
| should make it easier to produce patches for obvious bugs in the releases, |
| without having to wait for changes in other areas to stabilize. |
| |
| NEW FEATURES |
| |
| o New functions "all.vars" and "all.names" added. |
| |
| o There has been a small change in the include file structure. |
| All include files now live in RHOME/src/include and are |
| copied to RHOME/include when needed. |
| |
| o The "noquote" functions are now documented. |
| |
| o A new `language' demo, "is.things", is provided. |
| |
| o symnum(.) function |
| |
| o The files in R/library/base/data have had a .R suffix added. |
| |
| BUG_FIXES |
| |
| o A nasty bug which showed when attempt was made to create |
| a zero length call has been fixed. |
| |
| o model.matrix(.) now allows a contrasts argument. |
| |
| o barplot(.) now also works for barplot(table(rpois(100,3))). |
| |
| o make clean ; make now should work; ./Makefile.in eliminated |
| |
| o format(.) is now generic; the default method has a `digits' argument. |
| |
| |
| CHANGES IN R VERSION 0.60.1 |
| |
| NEW FEATURES |
| |
| o "split" is now a generic function, with a method for data frames. |
| (contributed by Doug Bates). |
| |
| o S compatible functions "all.names" and "all.vars" added. |
| |
| |
| |
| BUG FIXES |
| |
| o A file was closed multiple times if an error message occurred |
| after sourcing a file. In some versions of Linux this caused |
| a core dump. |
| |
| o The inclusion <readline/history.h> was causing problems with |
| some versions of readline because the file did not exist. |
| This is now detected by configure. |
| |
| |
| |
| CHANGES IN R VERSION 0.60 |
| |
| R is about to become an official part of the GNU project. |
| To quote RMS (Richard Stallman) |
| |
| ``I hereby dub R GNU software!'' |
| |
| |
| NEW FEATURES |
| |
| o There has been a major change in directory structure |
| masterminded by Kurt Hornik. |
| library(.) now attaches ``package''s which are better |
| integrated, see "?library". Packages may be available from outside |
| the RHOME path via the .lib.loc variable. |
| |
| o The documentation format (of files in src/library/<package>/man/ ) |
| has changed to a more easily parsable LaTeX like format. |
| The doc files now all end in `.Rd'. |
| etc/Rman2Rd can be used to translate old-style documentation to |
| the new one. |
| The translation to *roff, LaTeX and HTML is now done using |
| etc/Rdconv, written in Perl by Fritz Leisch. |
| |
| The HTML online help produced has now links which work. |
| The manual (in doc/manual/) now includes a section on the |
| documentation format and on mathematical text in graphs. |
| |
| etc/ further contains `Sd2Rd' for (partial) translation of S `.d' |
| documentation to Rd, and |
| `Rd2txt' and `Rd2dvi' for easy previewing of single Rd files. |
| |
| o The use of "names" on one dimensional arrays will now produce |
| sensible results. This means that for most purposes, |
| one dimensional arrays can be treated like vectors. |
| |
| o We have a applied a patch from mward@wolf.hip.berkeley.edu |
| which should substantially improve the speed of (vector) |
| arithmetic. |
| |
| o The modeling formula handler has been expanded so that it |
| accepts y ~ 0 + x as a "through the origin" specification. |
| models with no parameters are now acceptable. |
| |
| o "cov", "cor" and "var" now produce a matrix result if either |
| of their x or y arguments is a matrix. Dimnames are propagated |
| in a sensible fashion. |
| |
| o New chisq.test(.) and prop.test() from Kurt Hornik. |
| |
| o New read.fwf(.) for reading fixed width format (KH). |
| |
| o New str(.) [alternative to summary(.) for programmers] (MM). |
| |
| o New example data sets "esoph", "infert" and "anscombe" (TL), |
| "iris3" (KH) and "stackloss" (MM). |
| |
| o source(.) has several new arguments, notably ``echo = FALSE''. |
| This is applied in the new function demo(.) which runs all the |
| code in demos/ (but dynload). |
| |
| o strheight(.) is new, accompanying strwidth(.). |
| Both now work for mathematical expressions (Paul Murrell). |
| |
| o The LaTeX version of the manual (-> doc/manual/) now has an index. |
| |
| o EVERY *.Rd file in src/library/base/man/ has now at least one \keyword |
| |
| o New package (`library(.)') "stepfun" for step functions, incl. |
| empirical distributions. |
| |
| |
| BUG FIXES |
| |
| o Regular expression matching is now done with system versions |
| of the regexp library. This should fix compilation problems |
| on some platforms. |
| |
| o "approx" and "approxfun", have had some minor adjustments. |
| which fix the interpretation of the rule= argument. The |
| code for piecewise constant case is now internal C code |
| that than interpreted. This should boost performance in |
| this case. |
| |
| o There has been a minor fixup of "model.frame" to ensure that |
| subsets, weights, etc are handled properly. |
| |
| o Model fitting of the form |
| |
| lm(y~., data=df) |
| glm(y~., data=df) |
| |
| will now work. The RHS of the model will consist of an |
| additive model containing all (non-response) variables in the |
| given data frame. |
| |
| o The following type of assignment to data frame subsets |
| |
| z <- data.frame(x=rnorm(10),y=rnorm(10),z=rnorm(10)) |
| z[,1:2] <- matrix(1:20,nc=2) |
| |
| was producing incorrect results. The solution was to wrap |
| an implicit "as.data.frame" around the RHS. |
| |
| o "[.data.frame" no longer has a default drop=TRUE argument. |
| This means that subsetting a data frame with "[" will always |
| yield a data frame. |
| |
| o There was a swap of coordinates internally in "mtext" which |
| meant that labels were coming out in the wrong place. Fixed. |
| |
| o Syntax errors in parse(text="...") would cause R to terminate |
| with a segmentation violation. This no longer happens, although |
| the result is still not perfect (the parse() returns). |
| This will be fixed by a future parse rewrite. |
| |
| o rainbow, topo.colors, etc., now also work with n in {1,2}; |
| don't return duplicate neighbor colors anymore. |
| |
| o legend has new `text.width' argument and now also works with |
| mathematical expressions as text. |
| |
| o hist() now works better, has a `plot = TRUE' argument, and returns |
| something useful. |
| |
| o barplot() improved for `names', now returns vector of midpoints. |
| |
| o lm(), lm.fit, lm.wfit (was `lm.w.fit'): Made more compatible. |
| Dealing with (close to) collinear situations is still not flexible |
| enough. |
| |
| o internal postscript() improved (missing lines in boxplot(.)). |
| |
| o Improvement to many (even most ?) documentation (.Rd) files. |
| |
| o Numerous other fixes of minor things ... |
| |
| |
| |
| CHANGES IN R VERSION 0.50 |
| |
| WARNING!!! |
| |
| o A change in the way that "expressions" are implemented means that |
| saved data images which contain expressions will probably not |
| restore properly. |
| |
| NEW FEATURES |
| |
| o The installation of documentation has now been streamlined. |
| Many manual entries have been revised. |
| |
| o "expressions" are now implemented as a basic type rather than as |
| a class of object. This change was made as move toward compatibility |
| with S and also to implement mathematical annotation in graphs. |
| For some examples of the latter, see ?text and ?title. |
| |
| o "eigen" can now handle complex and non-symmetric matrices. |
| |
| o Libraries are now attached by loading their code into newly created |
| environment frames on the search path rather than in with the general |
| system code. This means that libraries can be unloaded as well as |
| loaded. They can also have .First.lib and .Last.lib functions. |
| The variable .Libraries has been replaced by .library() but should not |
| be needed much anymore. |
| |
| o There is now an experimental function called "delay" which creates |
| a promise to evaluate an expression. This provides direct access |
| to the lazy evaluation mechanism used by R. |
| |
| o >>>> 'make tests' allows to test--run all the help() examples. |
| |
| o New functions matplot / matpoints / matlines. |
| |
| o cut has 2 new arguments. 'right = TRUE' gives intervals closed on the |
| right, open to the left (as S); 'right = FALSE' allows to reverse |
| this. The code for default label construction has been enhanced, |
| and can be controlled by the new argument 'dig.lab'. |
| |
| o legend(.) has 2 new arguments 'cex' (obvious) and 'merge = FALSE'. |
| -> ?legend. |
| o deparse has a 2nd argument allowing for a kind of line width. |
| o There is now print.density (method). |
| |
| o many help(.) pages have been updated with working examples, |
| and several new ones have been created. |
| |
| o influence.measures() and lm.influence now allow to get at the usual |
| regression diagnostics. |
| |
| BUG FIXES |
| |
| o The "is.object" function has been with drawn. |
| |
| o A bug which prevented the "pictex" graphics driver from working |
| has been fixed. |
| |
| o Regression diagnostics obtained with "lm.influence" now work when |
| there are weights. This means they should work for glms. |
| |
| o There was a problem in parsing files from statements which were |
| separated from following statements by ";" (e.g. data(iris); iris). |
| This is fixed. |
| |
| o Comments are handled better in functions. The rule is that they |
| are shifted to just before their statements. Comments after the |
| last statement of a function are lost. |
| |
| o It is now possible to perform complicated mutations of expressions. |
| For example |
| e <- quote(f(x=1,y=2)) |
| names(e)[[2]] <- "a" |
| will change the x= argument tag into a=. In the past this produced |
| odd error messages. |
| |
| o The length function now tries to return a "sensible" value for all |
| the built-in types. For example, symbols now have length 1. |
| |
| o "update" should now work in both "lm" and "glm" models. |
| |
| o The functions Re, Im, Mod, Arg and Conj will now accept real-valued |
| arguments and return the obvious results. |
| |
| o Minor graphics cleanup. |
| |
| o A fix for convergence problems in glm from Thomas Lumley included. |
| |
| o A new version of qt() should not take infinitely long to get an |
| answer in the large degrees if freedom case. The underlying code |
| (Hill 1970, CACM) appears to be much faster and more accurate than |
| Splus. |
| |
| o A final Newton step has been added to give a final "polish" to |
| the quantiles produced by pnorm(). These should be close to full |
| accuracy now. |
| |
| o A bug in qbeta found by Martin Maechler has been fixed. This should |
| speed up quantile computation for the F and Beta distributions. |
| Further improvements in qbeta(.) by MM. No infinite loops anymore. |
| |
| o rainbow(.) now allows "start > end" indexing the "color circle". |
| topo.colors(n), terrain.colors(n), heat.colors(n) now also work for n=1,2. |
| |
| o ?"+" now works. |
| |
| o tapply has been fixed as indicated by T. Lumley. |