From keitt at nceas.ucsb.edu Tue Feb 1 19:58:41 2000 From: keitt at nceas.ucsb.edu (Timothy H. Keitt) Date: Tue, 01 Feb 2000 10:58:41 -0800 Subject: Install problems with RPgSQL Message-ID: <38972CE1.D433532A@nceas.ucsb.edu> If you have had problems with the latest configure script in RPgSQL, please try the version attached to this message. Let me know if you have any problems. Thanks. Tim -- Timothy H. Keitt National Center for Ecological Analysis and Synthesis 735 State Street, Suite 300, Santa Barbara, CA 93101 Phone: 805-892-2519, FAX: 805-892-2510 http://www.nceas.ucsb.edu/~keitt/ -------------- next part -------------- A non-text attachment was scrubbed... Name: RPgSQL-0.4.tar.gz Type: application/x-gzip Size: 31662 bytes Desc: not available URL: From p.dalgaard at biostat.ku.dk Mon Feb 7 13:56:24 2000 From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA) Date: 07 Feb 2000 13:56:24 +0100 Subject: R-0.99.0 is released Message-ID: I've rolled up R-0.99.0.tgz a moment ago. You can get it from ftp://cvs.r-project.org/pub/CRAN/src/base/R-0.99.0.tgz or http://cvs.r-project.org/pub/CRAN/src/base/R-0.99.0.tgz or wait for it to be mirrored at a CRAN site near you within a day or two. There's also a version split in three (!) for floppies if you prefer that. The next release is to be 1.0.0 at the end of this month, and you may consider this as a prerelease of that. I.e. this is your chance to help us making version 1.0.0 as bug-free as possible. Notice that GNOME support is still experimental. In particular, plotting of mathematical formulas is pretty much out of whack at the moment. For the R Core Team, Peter D. Here's the relevant bit of the NEWS file: 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 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. -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From bates at stat.wisc.edu Mon Feb 7 17:53:47 2000 From: bates at stat.wisc.edu (Douglas Bates) Date: 07 Feb 2000 10:53:47 -0600 Subject: R-0.99.0 available from rsync.r-project.org Message-ID: <6rhfflar8k.fsf@franz.stat.wisc.edu> rsync.r-project.org has been updated to serve the sources for R-0.99.0. There are three versions of the R CVS source tree available for anonymous rsync. $ rsync rsync.r-project.org:: r-release R sources (feature-frozen version) CVS tree (approx 12 MB) r-release-patched patched R sources (feature-frozen version) CVS tree (approx 12 MB) r-devel R sources (development version) CVS tree (approx 12 MB) r-manuals Development sources for manuals for R xlispstat xlispstat sources (development version) CVS tree (approx 12 MB) ess ess (Emacs Speaks Statistics) CVS tree (approx 8.5 MB) omega Omega Project for Statistical Computing CVS tree As of today, `r-release' is R-0.99.0. It will not be changed. Minor bug fixes will go into r-release-patched. Development for version 1.0.0 will be carried on in r-devel. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From saikat at stat.wisc.edu Tue Feb 8 17:55:31 2000 From: saikat at stat.wisc.edu (Saikat DebRoy) Date: 08 Feb 2000 10:55:31 -0600 Subject: RMySQL-0.2 available for R-0.99.0 Message-ID: A package to access MySQL databases from R is now available from the development section of CRAN (http://cran.r-project.org/ and its mirrors). This implements a proposed common interface between S like languages and various relational databases. Details about this proposal can be obtained from http://www.omegahat.org/contrib/RS-DBI/. Comments and bugs about the package should be reported to either saikat at stat.wisc.edu. Comments about the SDBI interface should be addressed to omega-devel at omegahat.org and/or r-devel at r-project.org. Saikat DebRoy -- Department of Statistics Email: saikat at stat.wisc.edu University of Wisconsin - Madison Phone: (608) 263 5948 1210 West Dayton Street Fax: (608) 262 0032 Madison, WI 53706-1685 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From p.dalgaard at biostat.ku.dk Wed Feb 9 13:36:56 2000 From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA) Date: 09 Feb 2000 13:36:56 +0100 Subject: R-0.99.0 bugfixes available Message-ID: A couple of bugs turned up immediately after the release, one of them causing nasty memory corruption when strsplit() was used. Therefore, a set of patches has been supplied on ftp://cvs.r-project.org/pub/R/src/base/R-0.99.0-fixes.gz and the rest of CRAN should soon follow. The recipe for patching is (GNU patch assumed) gunzip -dc R-0.99.0-fixes.gz | patch -p 1 For those with broken patch programs or fast connections, there is also a patched distribution in ftp://cvs.r-project.org/pub/R/src/base/R-0.99.0a.tgz Files patched: uncmin.c --> demo(nlm) bug character.c --> strsplit/devPS memory corruption printutils.c --> va_list trouble devGTK.c --> gnome/plotmath fix edit.R --> couldn't edit character vectors -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From keitt at nceas.ucsb.edu Wed Feb 9 20:03:54 2000 From: keitt at nceas.ucsb.edu (Timothy H. Keitt) Date: Wed, 09 Feb 2000 11:03:54 -0800 Subject: RPgSQL and RPMS for 0.99 Message-ID: <38A1BA1A.F75FAAAF@nceas.ucsb.edu> The latest version of RPgSQL and RPMS for R version 0.99 can be found at http://www.nceas.ucsb.edu/~keitt/R/ Cheers, Tim -- Timothy H. Keitt National Center for Ecological Analysis and Synthesis 735 State Street, Suite 300, Santa Barbara, CA 93101 Phone: 805-892-2519, FAX: 805-892-2510 http://www.nceas.ucsb.edu/~keitt/ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From guido at hal.stat.unipd.it Fri Feb 11 11:47:34 2000 From: guido at hal.stat.unipd.it (Guido Masarotto) Date: Fri, 11 Feb 2000 11:47:34 +0100 Subject: R 0.99.0a for Ms Windows (9X/NT) Message-ID: <20000211114734.20126@hal.stat.unipd.it> A binary distribution of R 0.99.0a is available from http://www.r-project.org/bin/windows/windows-NT/base Pre-compiled packages for this version are now available from the Windows contrib area on CRAN (http://www.r-project.org/bin/windows/windows-NT/contrib). In many cases a new version is needed, and all have been rebuilt using the latest improvements in the help conversion. All the changes listed below are due to Brian Ripley. Hence, thank him for them (and blame me if something doesn't work: it means that my testing was not suffcient). guido masarotto (for the R Core Team) New in this release =================== The console and internal pager now have horizontal scollbars. These are disabled (greyed out) if no text is obscured in the current view. Help menu items will be greyed out if the corresponding files are not installed. Many of the menu items now call internal functions and so are much faster, but produce nothing on the console. Help files will be displayed in the internal pager with headings in a contrasting colour. There are new functions winDialog() and winDialogString() to produce dialog boxes, and functions winMenu* (use ?winMenus) to manipulate user menus. Following Unix, the handling of help(, offline=TRUE) has been altered. It will be necessary to adjust helpPRINT.bat to set the TEXINPUTS path to find Rd.sty. TeX processing of these help files normally uses LaTeX package `ae' to handle Latin-1 characters: this can be changed by setting the environment variable R_RD4DVI. The conversion to text help no longer requires groff. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From ripley at stats.ox.ac.uk Thu Feb 17 19:46:02 2000 From: ripley at stats.ox.ac.uk (Prof Brian D Ripley) Date: Thu, 17 Feb 2000 18:46:02 +0000 (GMT) Subject: VR_6.1-7 is out Message-ID: VR_6.1-7.tar.gz is on CRAN in Vienna now, and a Windows version will be there tomorrow morning. This is for R 0.99.0 (and R-devel) only. The main differences are - use of optim - about half the previously commented-out items in the scripts are now working - the help pages can now be processed to dvi and pdf. The problem with the help pages is that they were converted by Sd2Rd and followed the manual, but R would not process the specification its manual gave! This is properly sorted for 1.0.0, but I have managed to make these pages work on 0.99.0 and pre-1.0.0. -- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From erich.neuwirth at univie.ac.at Fri Feb 25 13:26:12 2000 From: erich.neuwirth at univie.ac.at (Erich Neuwirth) Date: Fri, 25 Feb 2000 13:26:12 +0100 Subject: r-excel interface code Message-ID: <38B674E4.70092CEE@univie.ac.at> some of you might be interested. i just uploaded the first release of my r-excel interface package to CRAN. it is in contributed extensions nonstandard extensions erich neuwirth -- Erich Neuwirth, Computer Supported Didactics Working Group Visit our SunSITE at http://sunsite.univie.ac.at Phone: +43-1-4277-38624 Fax: +43-1-4277-9386 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From p.dalgaard at biostat.ku.dk Tue Feb 29 10:51:27 2000 From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA) Date: 29 Feb 2000 10:51:27 +0100 Subject: R-1.0.0 is released Message-ID: I've rolled up R-1.0.0.tgz a short while ago. You can get it from ftp://cvs.r-project.org/pub/CRAN/src/base/R-1.0.0.tgz or http://cvs.r-project.org/pub/CRAN/src/base/R-1.0.0.tgz or wait for it to be mirrored at a CRAN site near you within a day or two. It should get to the CRAN master site within a few hours. There's also a version split in three for floppies if you prefer that. Since this is a major release, we've made a formal release statement this time. Below is an excerpt; full text is available at http://developer.r-project.org/R-release-1.0.0.txt "The release of a current major version indicates that we believe that R has reached a level of stability and maturity that makes it suitable for production use. Also, the release of 1.0.0 marks that the base language and the API for extension writers will remain stable for the foreseeable future. In addition we have taken the opportunity to tie up as many loose ends as we could." For the R Core Team, Peter D. Here's the relevant bit of the NEWS file: CHANGES IN R VERSION 1.0.0 NEW FEATURES o The entry points [dpq]norm no longer exist: the header file R_ext/Mathlib.h must be used and such code re-compiled. o Header files in R_ext must be given explicitly as e.g. "R_ext/Mathlib.h". o New function log1p(x) := log(1 + x) , accurate for |x| << 1. o HTML searches can now select between any combination of titles, keywords and object names. The keyword list of SearchEngine.html is automatically built from KEYWORDS.db. Missing links are now resolved using the search engine. o A data subdirectory of the working directory will be searched for data, by default after all the loaded packages (including base). o Data directories can now be zipped as Rdata.zip, provided a list of contents is provided in file `filelist'. o New function try(expr) which provides a user-friendly wrapper to restart(). o New function geterrmessage() to retrieve the last error message, for use in try() and user's error handlers, and new option "show.error.messages" to control the printing of error messages. o persp() now labels its axes. o ?plotmath documents the plotting expressions facility much more comprehensively, with tables in the examples. o New functions dump.frames() and debugger() allow post-mortem debugging. See the help on debugger. o New functions by() and merge() to split and join data frames. o Generic methods now do "match before dispatch", so plot(pch=2, y ~ x) invokes plot.formula. Notice that this will break user code if it has renamed the dispatch argument and uses the original name for a different argument. o Long-named command-line options also allow `--name VALUE'. o arima0() now uses optim() rather than nlm(), and is thereby normally faster and gives more accurate solutions. Perhaps more importantly, it fails to converge much less often. o Enhanced pairs() function allowing separate upper, lower and diagonal panel functions and control of diagonal labels. (Much of this was contributed by Jens Oehlschlaegel-Akiyoshi.) o Links to R objects in other packages in help files can now be specified explicitly as \link[pkg]{topic} or \link[pkg:maintopic]{topic} o optim() has a new simulated annealing method contributed by Adrian Trapletti. o Hershey vector fonts are available in text() and contour(). Documentation for Hershey vector fonts is in help(Hershey). o The HTML function indices (for packages and for all installed functions) and the index to the reference manual now omit methods for generic functions if they would immediately follow the generic and refer to the same file. This reduces the clutter considerably. o New functions points.formula() and lines.formula() to supplement plot.formula(). The latter has been enhanced so that all arguments are now evaluated in the supplied data frame and all subsettable arguments are subsetted. Notice that the data= argument can no longer be given as a positional argument but must be given in keyword form. o The behaviour of pmatch() has been changed to be S-compatible: in particular the meaning of duplicates.ok=TRUE has changed. The help for pmatch and charmatch now gives more precise descriptions, including of their differences. o print.hclust(), hclust() and dist() now store the method that has been used. o If there are unmatched function argument(s), the first found is named in the message, for example `unused argument(s) (xlabel ...)'. o Conversion from Rd to raw nroff is no longer available. o text() now accepts vector "col", "cex" and "font" arguments. o "default" is now a valid argument to RNGkind(). o nlm() and optim() will now give up immediately they try to step to a non-finite value: nlm at least would go into an infinite loop. o "mostattributes(obj) <- value" utility useful for careful attributes' inheritance; e.g. for fixing pmax/pmin (see below). BUG FIXES o (0.99.0a) The internal code for strsplit no longer destroys other internal structures, e.g. postscript file output on Linux. o (0.99.0a) nlm() no longer segfaults with Hessian specified. o (0.99.0a) Gnome version plotmath works, kind of o (0.99.0a) edit.data.frame() now handles character vectors better, provided they were generated with I(). o (0.99.0a) Attempt to special-case print-buffer allocation with just a format argument was abandoned, since there is no portable way of doing it and it caused compile problem on Alpha. o tempfile("") now works on all Unix platforms, and tempfile("a b c") returns a single name (with spaces in). The file names are now unique across processes (Unix), are guaranteed not to exist and very likely to be unique within an R session. o The search semantics of data(), example() and help() have changed (see their help pages). In particular, they will normally look in the package which was loaded, even if it is not in one of the libraries given in .lib.loc. Autoloads are no longer included in the search (as they searched whole packages, not just the autoloaded objects). o The documentation for .Rd files said & must be entered as \& but only the unescaped form was processed correctly. Now both are accepted but & is preferred. o list.files now skips non-existent/unreadable directories with a warning, rather that failing with an error. o Lots of help examples now tidy up the files they created, and detach data frames and libraries they attach. o library(help=foo) lists only contents of first version if multiple matches are found on lib.loc. o round(2.345e-99, 100) now works (not giving 0). C functions fprec() and fround() [= R's signif() and round()], now use R_pow_di(10.0, n) which is clean and more efficient. This changes some results in the least significant bits. o rpois sometimes had problems with mu=0, now special-cased o Rare memory overrun in rpois fixed. o --nsize and --vsize arguments to R CMD check now work. o plot.stepfun had renamed the dispatch argument and used the original name "x" for a different argument which broke on the new `match & dispatch' code. Changed to "xval". o The return value for par() was incorrectly documented, and in consequence cpgram() was not re-setting "pty". o package.dependencies() printed unnecessary debugging messages (version comparison): these have been removed. o backslashes in examples in help files are now converted correctly to latex. o qchisq with non-centrality parameter now does something. o Greek symbols are now converted correctly in HTML help (but only rendered correctly on a few browsers). o rbind(x, y) works when x has no columns. o \tabular in Rd files is rendered better in latex, and long tabular material is now acceptable (and split over pages). o evaluation depth wasn't properly reset by "next" o Old (pre-0.63.1) .Random.seed would cause problems if used. o Row indexing of data.frames by characters (e.g. y["ab", ]) was wrong, as pmatch was not S-compatible. o Contour labels used to be rounded to integers. o Calling rbinom() repeatedly with the same p but different n gave incorrect results. o Rd2contents assumed the \name field was the file name, so searches could lead to non-existent links. o Assigning functions to list elements is not longer disallowed. o Unified usage statement to R CMD xxx for all commands o Using duplicated new string indices in [<- caused a crash on some platforms, e.g. x <- 1:2; x[c("3", "3")] <- 3; x. o rle() can now handle character vectors, as documented. o print.default failed to reset its settings, so, e.g. na.print could persist when printing a list. o [cr]bind could sometimes return an invisible value. o axis() and rug() sometimes extended the axis line too far. rug() always clipped x values to the plot region, but now admits to doing so with a warning. o plot() and axis() got into trouble with very small relative ranges: these are now required to be at least 100x the machine precision. o split.screen(, erase=TRUE) failed to create a new plot, so failed if it was used on a postscript device before other plots. o plotting with lwd = 0 also set the dash length to 0: now dash lengths are scaled up for lwd > 1 but not reduced for 0 <= lwd < 1. o plotting a " " vertically caused an X11 error with some fonts, (notably URW fonts on RedHat) causing plot.lm to crash R o F distributions with huge DF now behave more sensibly o Crashes could occur if there was an error in inline parameters, because the call was not being recorded. It is now. o Title field of DESCRIPTION now overrides TITLE file. o R now reports `50 or more warnings', not just 50, as it only displays the first 50. o Resetting the RNG state resets the state of the Box-Muller generator too. o Pointer protection bug in load() code. o Assignment with unknown string index caused memory corruption when used on matrices. o It is now possible to call Fortran routines d1mach and 11mach on platforms which do not append underscores. o Additions to plots by identify() and locator() were not being recorded, and so did not appear when a plot was copied or printed. o The defaults for `na.action' arguments were inconsistently documented. In R the default is taken from the options(na.action) setting, and that defaults to `na.omit'. If there is no `na.action' setting, the default is `na.fail'. For consistency, the default for replications() has been changed. o Fix cases with lambda==0 in Poisson distribution o demo(is.things) had been broken by the introduction of is.element. o palette() didn't check for overflow and was limited to 256 colors, so palette(colors()) would segfault. Limit increased to 1024 and check inserted. o C functions fprec() and fround() [= R's signif() and round()], now use R_pow_di(10., n) which is clean and more efficient. This changes some results in the least significant bits. o pmin(c(a=1), 2:3) now works {and pmax(.) too}. -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From bates at stat.wisc.edu Tue Feb 29 13:28:20 2000 From: bates at stat.wisc.edu (Douglas Bates) Date: 29 Feb 2000 06:28:20 -0600 Subject: R-1.0 is available via rsync Message-ID: <6rk8jogpln.fsf@franz.stat.wisc.edu> You can now obtain the R-1.0 sources via rsync from rsync.r-project.org as the r-release module. For example, rsync -aC rsync.r-project.org::r-release ./R-1.0.0 will create a copy of the source tree (minus the CVS subdirectories) in the subdirectory R-1.0.0 The module r-release-patched incorporates any patches that may be made to the current released version. The module r-devel is a copy of the unstable, development version of the CVS tree. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From guido at hal.stat.unipd.it Thu Mar 2 11:13:02 2000 From: guido at hal.stat.unipd.it (Guido Masarotto) Date: Thu, 2 Mar 2000 11:13:02 +0100 Subject: R 1.0.0 for Windows Message-ID: <20000302111302.32118@hal.stat.unipd.it> As Brian Ripley said this morning on 'r-help', a binary distribution of R 1.0.0 to run on Windows 95, 98, NT4.0 and 2000 on Intel/clone chips is available at CRAN (at least in Wien). The URL is http://cran.r-project.org/bin/windows/windows-NT/base/ See 'README.rw1000' for installation instructions and 'CHANGES' for a list of Windows specific news. As always, pre-compiled version of most of the contributed packages are available from http://cran.r-project.org/bin/windows/windows-NT/contrib/ A FAQ for this port of R is included in the distribution and can be read on line at http://www.stats.ox.ac.uk/pub/R/rw-FAQ.html guido masarotto (for the R-Core team) -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From albrecht.gebhardt at uni-klu.ac.at Thu Mar 2 14:00:29 2000 From: albrecht.gebhardt at uni-klu.ac.at (Albrecht Gebhardt) Date: Thu, 2 Mar 2000 14:00:29 +0100 (MET) Subject: R 1.0.0 for SuSE Linux Message-ID: New RPM packages for SuSE Linux are available now at ftp://ftp-stat.uni-klu.ac.at/pub/R/bin/linux/suse/6.3/RPMS/i386/ and should soon arrive at ftp://cvs.r-project.org/pub/R/bin/linux/suse/6.3/RPMS/i386/ They are built on SuSE 6.3, but run also on SuSE 6.2. RPMs for SuSE 5.3 and 6.{0,1} will drop in later this or next week and replace the 0.9x.x versions. NOTE: ----- I changed the installation prefix from /usr/local to /usr, so you cannot mix older contrib RPMs with the new base RPM without explicitly modifying the R_LIBS variable! The ESS package (currently only a xemacs version) will only run on SuSE 6.3, please use the older one (under the suse/6.2 tree) for 6.2. Note for ESS on SuSE 6.3: ------------------------ Do not forget to check that your /dev/pty* devices are world read-writeable !! If necessary execute "chmod o+rw /dev/pty*" or ESS will not work. Of course this may affect your security. See also http://sdb.suse.de/sdb/en/html/ke_devpts-63.html for notes on this topic. The ess-xemacs package creates a new file /etc/profile.d/xemacs-site.sh which sets EMACSLOADPATH=/usr/share/xemacs/site-packages, where it also creates site-start.el with a reference to ESS's start files. I don't know if this interferes with GNU emacs installations. Albrecht Gebhardt ..................................................................... | Albrecht Gebhardt Tel.: (++43 463) 2700/832 | | Institut fuer Mathematik Fax : (++43 463) 2700/834 | | Universitaet Klagenfurt mailto:albrecht.gebhardt at uni-klu.ac.at | | Villacher Str. 161 http://www-stat.uni-klu.ac.at/~agebhard | | A-9020 Klagenfurt, Austria | `--------------------------------------------------------------------' -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From jlindsey at alpha.luc.ac.be Thu Mar 23 18:44:18 2000 From: jlindsey at alpha.luc.ac.be (Jim Lindsey) Date: Thu, 23 Mar 2000 18:44:18 +0100 (MET) Subject: dna library Message-ID: <200003231744.SAA11616@alpha.luc.ac.be> I have just placed version 0.2 alpha of my library, dna, on my web page at www.luc.ac.be/~jlindsey/rcode.html The R functions in this library cover most of the basic methods of dna and protein sequence analysis. The library includes ports of CLUSTAL W for multiple sequence alignment and flip for finding open reading frames in a dna sequence. There are an enormous number of interesting and challenging statistical problems in current molecular biology and I am hoping that making these procedures available to the R community will encourage people to get involved. Some links to useful sites for learning about molecular biology can be found at www.luc.ac.be/~jlindsey/url.html Comments and suggestions for further inclusions in the library are very welcome. Jim -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From p.dalgaard at biostat.ku.dk Fri Apr 14 11:47:09 2000 From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA) Date: 14 Apr 2000 11:47:09 +0200 Subject: R-1.0.1 is released Message-ID: I've rolled up R-1.0.1.tgz a moment ago. You can get it from ftp://cvs.r-project.org/pub/CRAN/src/base/R-1.0.1.tgz or http://cvs.r-project.org/pub/CRAN/src/base/R-1.0.1.tgz or wait for it to be mirrored at a CRAN site near you within a day or two. There's also a version split in three for floppies and a patch file if you prefer that. For the R Core Team, Peter D. Here's the relevant bit of the NEWS file (in fact, the entire thing since we have now moved the pre-1.0.0 news to ONEWS): CHANGES IN R VERSION 1.0.1 BUG FIXES o pgamma(Inf, 1, Inf) gives NaN instead of an infinite loop, PR#462. o Inline xaxt and yaxt parameters were ignored. o Setting the normal RNG was not always recorded in .Random.seed. o \link[pkg]{foo} links were wrongly translated to HTML. o Direct use of show.data() with no args was incorrect. o print.coefmat does sensible things if options show.signif.stars and show.coef.Pvalues are not set correctly. o x <- list(a=1, b=2) ; x["c"] <- 3 now (again) stretches the list rather than give a "subscript out of bounds" error. o Models with response appearing on rhs could cause segfault. o as.data.frame.matrix will now ensure the columns added have non-empty names. o Some (strange?) model formulas could cause memory corruption (thanks to John Fox for digging this up). o Matrix multiplication in cases such as 1:3 %*% t(1:2) is accepted. o Options --nsize and --vsize to R CMD check gave warning messages and only one was accepted. o The autoload()s during startup are "wrapped" such that conflicting objects don't break startup. o cor.test(*, meth="spear") {pkg ctest} now works (again) for n <= 6 o scale = 0 in biplot.princomp() now works. o The scores given by princomp(, cor = TRUE) and the rotated values given by prcomp(, scale = TRUE) are now computed from the scaled data. o barplot now works okay when length(col) < length(legend.txt), thanks to Ben Bolker, PR#494. o kernel("dirichlet", m=10, r=1) in package ts now works. o save/restore of environments containing "..." object should work now. o qhyper should work better for large N. o qbinom(1-1e-16, n, p) , qpois() and qnbinom(*) looped for ever. o as.matrix.data.frame no longer escapes quotes in character vectors. o R would try to save the readline history at the end of non-interactive sessions, causing crashes on some systems. o Subtle roundoff problems caused arrays to be allocated short in loess.c in some cases, leading to segfaults. o Document that postscript(file="") sends the output directly to the default printer. o ts.union(, dframe=TRUE) had a long-standing typo, now works. o save(, ascii=TRUE) had problem with octal escapes in strings when there was a digit following, should work now. o matpoints() and matlines() now also have a "type =" argument with defaults "p" and "l", respectively; PR#506. o The new Perl 5.6 broke our version-detection mechanism. A better one has been inserted. o X11(colortype="gray") failed to work on 8-bit screens, and more generally when colour allocation failed X11() did not revert to monochrome correctly (and did not say it was doing so). It was not documented in the help that to change the X11 colortype one needs to close all open X11 devices. o loessf.f in modreg defined DSIGN unecessarily and this caused a conflict on AIX. o plot.lm will now work with rlm objects. o start and end behave better when the frequency is not an integer. o aggregate.ts is closer to S-PLUS's aggregate.rts. o quantile(x) now works when x contains several +/- Inf's. o guard against segfault in dataentry(0,0) (or, more realistically, when mistyping data.entry(x,y) as dataentry(x,y)) -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From guido at hal.stat.unipd.it Thu Apr 20 11:19:25 2000 From: guido at hal.stat.unipd.it (Guido Masarotto) Date: Thu, 20 Apr 2000 10:19:25 +0100 Subject: New Windows binaries available Message-ID: <20000420101925.47833@hal.stat.unipd.it> Windows binaries at CRAN (in bin/windows/Windows-NT/base) have been updated to R-1.0.1. See below for a list of Windows-specific changes. Happy Easter, guido masarotto Windows-specific changes to R ============================= The installer, rwinst.exe, now checks for ZIP files as well as zip files, as some browsers manage to map filenames to uppercase. There are batch files Rd2txt.bat Rdconv.bat Rdindex.bat Sd2Rd.bat which are the equivalent of the Unix `R CMD foo' utilities mentioned in `Writing R Extensions'. To use these you must have R_HOME set as an environment variable (using the form P:/R/rw1001). There is also a shell script Rd2dvi.sh which you can use if you have sh.exe (as used to compile packages) and latex etc. The environment variable XDVI sets the previewer, defaulting to xdvi.bat. A file `Makevars' in the `src' directory of a package can be used to add to/override the MakeDll makefile used to make foo.dll, as on Unix. (See `Creating shared libraries', section 3.4 of `Writing R Extensions'.) Under rare conditions (lots of very short input lines) the history buffer could overrun and so cause crashes. This has been possible since rw0623, but first caused reported problems in rw1000 and has now been fixed. Certain HP printer drivers (e.g. the 6/6MP-Postscript driver) reset the FPU and so were causing crashes. This has been circumvented in this version by restoring the settings before and after each page. Building on a non-default drive should be more reliable, as Perl is used to find the current drive. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From pgilbert at bank-banque-canada.ca Fri Apr 28 15:14:39 2000 From: pgilbert at bank-banque-canada.ca (Paul Gilbert) Date: Fri, 28 Apr 2000 09:14:39 -0400 Subject: multivariate time series package Message-ID: <39098EBF.433374B5@bank-banque-canada.ca> ANNOUNCEMENT April 28, 2000 An R version of my multivariate time series package (DSE) is now available in the devel area of CRAN. A short description follows below. The DSE bundle requires two other packages which are also available in the devel area of CRAN and may be of interest by themselves. The first, called syskern, provides a kernel of functions for S/R programmers. It is intended to help write code which is independent of operating system differences and some small differences between S and R. Users of different operating systems are encouraged to contribute. It also includes a mechanism for generating the same random sequences in S and R, which can be especially useful for testing other code. The second, called tframe, provides a mechanism to make time series programs independent of a data object's time representation. Using this it is possible to write code which can use new/better/different time representations when they appear. It also provides windowing, splicing, alternative plotting methods and some other utility functions specifically for time series work. DSE implements an object oriented approach to time series models. This means that different model representations can be added with fairly simple extensions to the library. The library includes multi-variate state space and ARMA models (including VAR models). Methods for simulating, estimating, and converting among different model representations form the base part of the library in dse1, the first package of the bundle. Methods for studying estimation methods and for examining the forecasting properties of models are in dse2, the second package in the bundle. The syskern package (and thus tframe and dse) requires R 1.0.1. I have run fairly extensive tests in Solaris and Linux. The code in syskern, tframe, dse1 and dse2 is reasonably stable. The code in dse3 is much less stable (and still largely undocumented). The help documentation has been automatically converted from an older system so that I can start to take advantage of R's capabilities for organizing and testing help documentation. However, the converted help has not yet been extensively examined and the original was out of date in some respects. For this reason I have put the package in the devel area of CRAN. Comments on errors and omissions are appreciated. The User's Guide for DSE is available at . Paul Gilbert Head Statistician, Bank of Canada, Monetary and Financial Analysis Department pgilbert at bank-banque-canada.ca -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From Friedrich.Leisch at ci.tuwien.ac.at Tue May 9 13:15:42 2000 From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich Leisch) Date: Tue, 9 May 2000 13:15:42 +0200 (CEST) Subject: contributed documentation Message-ID: <14615.62302.797487.291706@galadriel.ci.tuwien.ac.at> Hi, as promised I have started a ``user contributed documentation'' section on CRAN. It currently contains a Spanish version of the ``Notes on R'' by Andr?s Gonz?lez and Silvia Gonz?lez and ``Data Analysis and Graphics Using R'' by John Maindonald. All contributions are welcome! Please note that I had a little accident last week (shoulder dislocation) such that CRAN maintainance will be a bit slower for the next 2-3 weeks ... Best, Fritz -- ------------------------------------------------------------------- Friedrich Leisch Institut f?r Statistik Tel: (+43 1) 58801 10715 Technische Universit?t Wien Fax: (+43 1) 58801 10798 Wiedner Hauptstra?e 8-10/1071 Friedrich.Leisch at ci.tuwien.ac.at A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch PGP public key http://www.ci.tuwien.ac.at/~leisch/pgp.key ------------------------------------------------------------------- -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From jlindsey at alpha.luc.ac.be Wed May 17 22:52:59 2000 From: jlindsey at alpha.luc.ac.be (Jim Lindsey) Date: Wed, 17 May 2000 22:52:59 +0200 (MET DST) Subject: Introductory Statistics Message-ID: <200005172052.WAA17183@alpha.luc.ac.be> Following the recent discussion on the R-help list about introductory statistics, I have spent some time updating the R code for my Introductory Statistics book (OUP, 1995). The previous version was over four years old and used R v0.7! (under current numbering that would be 0.07 -- it still used my Fortran implementation of nlm). The R (and GLIM4) code for all examples and answers to the exercises are available at www.luc.ac.be/~jlindsey/books.html and the instructors manual at www.luc.ac.be/~jlindsey/publications.html (A professor using the book at UCLA has also promised Stata code for it.) Errors, comments, and suggestions welcome! Jim -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From paradis at isem.univ-montp2.fr Thu May 18 10:51:48 2000 From: paradis at isem.univ-montp2.fr (Emmanuel Paradis) Date: Thu, 18 May 2000 10:51:48 +0200 (MET DST) Subject: tutorial =?iso-8859-1?Q?=22R_pour_les_d=E9butants=22_?= is available on CRAN Message-ID: <3.0.32.19700101010000.0091a100@162.38.183.200> Dear R-users, Thanks to Friedrich Leisch, my document "R pour les d?butants" is available on CRAN in the contributed documentation section: http://cran.r-project.org/doc/contrib/Rdebuts.pdf. It is written in French. "R pour les d?butants" ("R for beginners") gives a starting point for people with no experience with R (or S). I tried to explain the basics in the simplest way, as well as giving useful details (mostly with tables). Any feed-back would be greatly appreciated. If some people think that an English translation would be useful, I would be ready to consider it. Chers utilisateurs de R, Gr?ce ? Friedrich Leisch, mon document "R pour les d?butants" est disponible sur CRAN dans la section "contributed documentation": http://cran.r-project.org/doc/contrib/Rdebuts.pdf. Le but de "R pour les d?butants" est de fournir un point de d?part pour les utilisateurs qui n'ont aucune exp?rience avec R (ou S). J'ai essay? de simplifier les explications, tout en donnant des d?tails utiles (le plus souvent sous forme de tableaux). Tout commentaire ou suggestion serait grandement appr?ci?. Si certaines personnes pensent qu'une tranduction en anglais serait utile, je serais pr?t ? examiner cette possibilit?. Emmanuel Paradis Laboratoire de Pal?ontologie Institut des Sciences de l'Evolution Universit? Montpellier II F-34095 Montpellier c?dex 05 France phone: +33 4 67 14 39 64 fax: +33 4 67 14 36 10 mailto:paradis at isem.univ-montp2.fr -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From p.dalgaard at biostat.ku.dk Fri May 19 23:18:43 2000 From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA) Date: 19 May 2000 23:18:43 +0200 Subject: New R core member Message-ID: We are pleased to announce that John Chambers has joined the R core team. It is hard to believe that anyone on this list wouldn't know who John is, but just in case: He is the principal designer of the S language and environment, for which he received the ACM Software Systems Award in 1999. John has been very supportive and helpful throughout the development of R. He is joining the core development group to help enhance R as an Open Source project that can efficiently support the development of new approaches and ideas in statistical computing. In his own words: "[...] the focus of much or our research here on statistical computing is in finding high leverage in new computing directions. I'm hoping that we can share related ideas with the rest of the community working on R, and benefit everybody. [...] R seems to be poised to expand its role in statistics, perhaps especially in terms of the audience. As Linux and other open-source software makes its way beyond academia, there is potential for R to appeal to a wider user base. Maybe I can offer a few ideas as this process goes on." -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From mlapsley at sthelier.sghms.ac.uk Wed May 24 09:55:00 2000 From: mlapsley at sthelier.sghms.ac.uk (Michael Lapsley) Date: Wed, 24 May 2000 08:55:00 +0100 Subject: RODBC Message-ID: <20000524085500.A3565@athome.lapsley> Dear R-fans, My database access package RODBC is now available on CRAN. For those who have never used it, odbc is a database and platform independant API which provides an SQL interface to a large number of database engines. The databases supported include not only SQL based RDBMS but also CSV files, foxbase, dBase, MSExcel etc. ODBC has been promoted mainly by Microsoft and this is where the driver support is most widespread and solid. Unix support is available (free) for some of the more common database engines. To my knowledge RODBC works with oracle, MSAccess, Sybase, DB2 and SQLServer on MSWindows platforms, and with MySQL, postgreSQL and oracle (with a slightly buggy beta driver) under unix. With access to the server I have been able to use it with MSAccess from unix as well by installing (free) bridging software. SQL itself is very easy to learn and use in the context of selecting data from a single table; a rather contrived search will look like 'SELECT col1,col2,col3 from MYTABLE where col1 > 999 and col2 = 'exact match' and col3 like '%wildcard match%' There are a number of convenience functions in the package to wrap up some of the more common usages of saving and retrieving dataframes. Please keep me posted with bug reports and suggestions. Michael -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From keitt at nceas.ucsb.edu Thu May 25 22:28:40 2000 From: keitt at nceas.ucsb.edu (Timothy H. Keitt) Date: Thu, 25 May 2000 13:28:40 -0700 Subject: RPgSQL at SourceForge Message-ID: <392D8CF8.7BB4DA29@nceas.ucsb.edu> Hi Folks, I recently moved my RPgSQL package over to http://rpgsql.sourceforge.net/ The package does everything that I need it to do, but I am hoping that others will be interested in maintaining and extending the package. Full instructions on using SourceForge can be found at http://sourceforge.net/ Cheers, Tim -- Timothy H. Keitt National Center for Ecological Analysis and Synthesis 735 State Street, Suite 300, Santa Barbara, CA 93101 Phone: 805-892-2519, FAX: 805-892-2510 http://www.nceas.ucsb.edu/~keitt/ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From p.dalgaard at biostat.ku.dk Thu Jun 15 11:35:23 2000 From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA) Date: 15 Jun 2000 11:35:23 +0200 Subject: R-1.1.0 is released Message-ID: I've rolled up R-1.1.0.tgz a moment ago. You can get it from ftp://cvs.r-project.org/pub/CRAN/src/base/R-1.1.0.tgz or http://cvs.r-project.org/pub/CRAN/src/base/R-1.1.0.tgz or wait for it to be mirrored at a CRAN site near you within a day or two. There's also a version split in three for floppies if you prefer that. For the R Core Team, Peter D. Here's the relevant bit of the NEWS file: CHANGES IN R VERSION 1.1.0 NEW FEATURES o There are several changes to the compile and link flags, and an attempt is made to use /usr/local/include and /usr/local/lib on all platforms. Please read config.site and INSTALL if you have set flags for previous versions. o New package tcltk, providing interface and language bindings for the Tcl/Tk graphical interface toolkit. This makes it possible to do some rather nifty things with buttons and entry fields and so forth in very few lines of code. It is still somewhat experimental so don't go churning out thousands of lines of GUI code and then blame us for changing the API later on. It does not currently work with GNOME because of event loop differences. See demo(tkttest) and demo(tkdensity). o Internally using global R_Expressions [getOption("expressions")] dramatically speeds up eval.c. o The X11 support code is now in a separate shared library, and flag --gui=none will run R without X11 support (and so x11() and data.entry() will not be available). R BATCH sets --gui=none. o Configuring without X (e.g. --without-x) does work (at last). configure will report if X11 support has been included. If R has been built without X11 the default GUI is "none". o GNOME support files have moved from src/gnome to src/unix/gnome and the code is now in a separate shared library. Both --gui=GNOME and --gui=gnome are allowed. The main graphics device for use with GNOME is now called gtk(); the x11() device from the X11 support can also be used. (The gnome() device remains unreliable, and is by default unavailable.) All GNOME support now installs in R_HOME/gnome to make it easier to package separately. o Command line option `-g' can now be used as short version of `--gui'. o The "keep.source" option now defaults to interactive() instead of TRUE. o Many interface enhancements to the data editor, which now uses (by default) variable-width columns and much less redrawing. See ?dataentry for a description of the current user interface. o R under Unix can be sent SIGUSR1 to quit and save or SIGUSR2 to quit and save without running .Last and on.exit expressions. o Added ability to use the graphics device driver to perform horizontal justification of strings. This is used in the x11(), windows(), postscript() and xfig() drivers and will lead to more accurate placing of centred or right-justified strings. o Formulas created with the tilde operator now contain the environment in which they were created. The environment of a formula can be accessed with the environment() function. This facility is still experimental; it is intended to help simplify writing modeling functions. o $ and $<- are now generic functions. o add1.glm() and drop1.glm() now allow test="F", which is appropriate for models with estimated dispersion. o approx() and approxfun() have an extra argument ties= to control handling of tied x values o New function as.symbol(), identical to as.name(). is.symbol and is.name() are now identical by definition; before, they were equivalent by implementation. o attach() now works for R data files. o axis() now has additional arguments. The argument "tick" turns tick drawing on and off (on by default). Additional arguments line, pos, and outer; allow more flexible placement of axes. o New device bitmap(), like dev2bitmap() but a stand-alone device. o boxplot() returns (and bxp() accepts) a list containing the summary statistics for the boxes (changed from a list of elements one for each box). o file="|cmd" is allowed (to pipe output to `cmd'), under cat() and postscript() and functions that use them (for example, write()). o New functions chartr() for general-purpose character translation in character vectors, and tolower() and toupper() for converting alphabetic characters to lower-case and upper-case, respectively. o coplot() has new option subscripts=TRUE to pass the indices to the panel function. o cor.test(method="spearman") might give slightly better P values, since it now relies on pnorm() (with proper tail) instead of alnorm. o dbinom() works for size=0 (where appropriate). o New trivial function det() for determinant computation (the example in ?qr did not seem to be sufficient). o If present in the package, a function .Last.lib will be called when a package is detached. o New function dev.copy2eps() copies the current device to an eps file, taking the size from that of the device. o dev.print() now prints if possible, and takes the size from the device being copied. o edit() or fix() applied to a numeric or character matrix now uses the data editor, if available. o edit.data.frame() edits factors in character mode by default, and will allow the row names to be edited, by default if they are not 1:nrow(name). o expand.model.frame() for adding variables to a model frame. o The handling of estimating the dispersion in glm() fits has been changed for consistency across methods. For `binomial' and `poisson' families the dispersion is always taken as one. For `quasibinomial' and `quasipoisson' families it is always estimated (by residual chisq/residual df). o Using "~" when specifying lib.loc (for example to help() or library()) is now supported. o image() has a new argument "breaks" and divides the zlim range into equal-length intervals. o install.packages() and update.packages() have a new `destdir' argument for the directory to which to download the packages. o New function interaction.plot(). o Internal cleanup of lapply()'s C code. o library(), require(), and sys.source() have a new argument ` keep.source = getOption("keep.source.pkgs") '. This defaults to false, but can be set (also for base) to true by setting the environment variable R_KEEP_PKG_SOURCE to "yes" o Par `lty' in lines() now defaults to par("lty") not "solid", for consistency with plot(). o list.files() [aka dir()]: path argument has now default = "." o locator() allows inline graphics parameters (for the plotting it does with type !="n"). o New function max.col() from MASS, thanks to V&R. o nlm() can now take additional arguments in ... to be passed to f. o par() returns elements in alphabetical order, and "ann" as a logical (not integer). o .Platform has a new component GUI specifying the GUI in use (which might be "unknown"). o plot.formula() searches for a plot method for the left-side of the formula before searching for a plot method for the right-side of the formula. o New bitmap devices png() and jpeg() on Unix/X11. (They were already available on Windows.) o postscript(print.it=TRUE) now does print the plot file. postscript(onefile=FALSE) now produces multiple separate files. o provide() is now deprecated. o New function quade.test() in package ctest for the Quade test for unreplicated blocked data. o quantile(x, probs) now propagates NA/NaN in probs. o Option for user-supplied normal random generator in RNGkind(). o read.fwf() is no longer dependent on Perl. o New arguments check.names and strip.white to read.table() and friends. o Functions recordPlot() and replayPlot() save a plot to an R variable and replay it. o residuals.lm() also allows types "partial" and "response" as residuals.glm(). o Added col option to rug(). o scale() is now generic with scale.default method. o New "call. = TRUE" argument for stop(), and new function stopifnot(.) -- to be used in "make check". o str(.) has a new optional argument "nchar.max = 128" and truncates strings longer than that. Also eliminated a few minor glitches. o The symbols() function is now implemented. o New function termplot() with similar functionality to plot.gam() in S. o The parameters to title() which specify the labels may now be specified as a list containing the parameter together with additional modifying par values (cex, col, font) which affect just that label. title() also has new line and outer arguments which provide functionality which matches that in axis(). o New functions which.min() amd which.max(). o The Wilcoxon and Ansari-Bradley tests now optionally return confidence intervals for the location or scale parameter of interest. o New argument `extend' to window() (and updated documentation). o write.table() can now write CSV files in the format Excel expects. o New device xfig() to produce XFig files. o New xyz.coords() utility function to be used for 3D highlevel plots. o R CMD build now also works for package bundles. o Rdconv allows an output file to be specified. o Initial support for C++ source code in add-on packages under Unix. o Mathlib can be built as a standalone library: see directory src/nmath/standalone. BUG FIXES o The Mathlib functions now use exactly the same values for +/-Inf, NaN and NA as the rest of R in all cases. o Improved automatic remaking. o option keep.source was not set correctly before the base package was loaded: some functions in the base package had the source kept. The memory usage should now be reduced by ca 1Mb. o The base file is no longer closed twice in case of a syntax error (caused segfault on Linux). o The X11 data editor scrolls cells and so allows more than ca 10 characters to be entered. Several interface/redraw errors have been corrected. o Using `destroy' or `close' on the X11 data editor window killed R. o Multiple `destroy' events or X11 errors killed R (PR#400). o Warnings from .Last or closing devices are printed where sensible (e.g. not on GNOME nor Windows console). o add1.glm() and drop1.glm gave() incorrect results in the "Chisq" test option when the scale was estimated. o aggregate() applied to multiple time series lost the series names. o as.hclust.twins() in package mva sets method=NA (PR#538) o ave(1:3) now works (as when is.null(list()) was TRUE years ago). o barplot(c(0.1, 0.5, 1), ylim = c(0, 1)) now works: [xy]axs="i" and exact limits now labels the limits. o by() works when embedded in a function. o The xlab and ylab in coplot() now set the x and y axis labels, as in S. Supply a second component to label the conditioning variables. o count.fields() and read.table() now have the same default quote = "\"'". o guard against segfault in dataentry(x<-1, Modes = plot), and the like. o dev.print() now checks if the current device is replayable (and not all devices were, despite the documentation). o The gtk() device (formerly x11() under GNOME) was incorrectly returning character information, so in particular `*' was wrongly centred as a plotting symbol. o is.qr() checks not only for $qr, but also for $rank & $qraux, PR#482. o library() will not leave the package on the search path if loading fails (including if .First.lib fails). o lqs(, method="S") rounded k0 on passing to C. o na.omit() now handles vectors and matrices as well as data frames. o plot.lm(*, which=4) now works thanks to Marcel Wolbers. o postscript() now uses the options "papersize" and "printcmd" rather than the values of R_PAPERSIZE in the environment and R_PRINTCMD found at build time. o postscript() now makes use of kerning information in computing string widths. o M <- 2 ; print(ppr(.., nterms = M)) now works. o ppr(, sm.method="spline") had an internal limit of 250 rows: this is now 2500 and is now checked. o predict.lm(,type="terms",se.fit=T) gives correct standard errors (thanks to John Maindonald) o print.ftable() now returns its argument. o proj.aovlist() now gives a non-zero result for strata with no fitted effects. o qnorm() is now based on AS 241 instead of AS 111, and should give precise results up to 16 digits precision. o rgeom(, prob=1) gives 0 rather than NA o rpois(*, lambda) now works when lambda > .Machine$integer.max o strheight("X") with no active device would segfault. o system() is now (partially) functional on systems without popen. o Fixed bug in undoc() - requiring new `chdir' argument for sys.source() o Fixed problem in usemethod() where CAR(call) could be non-symbol. o The x11() device no longer crashes R if a font is not found, and will warn if there is a size mismatch of more than 10%. o R CMD Rd2dvi now sorts files alphabetically. o Rdconv now reports if an invalid type is specified (rather than using latex). o Support for Rd conversion to Sd has been reinstated (it was unintentionally removed along with nroff-based conversion to text). o \deqn{} fix in R-exts.texi, PR#523. o Linpack.h now makes clear which routines are actually in R. o Entry-point "pythag" is now loaded even though it is not necessarily used in R. Where "hypot" is available pythag just calls hypot after checking for special values. o call_R will now correctly handle character vector arguments. o The alphabet links on top of HTML function indices with more than 100 entries now contain only the letters which are really first letters of at least one entry. -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From bates at stat.wisc.edu Thu Jun 15 15:24:24 2000 From: bates at stat.wisc.edu (Douglas Bates) Date: 15 Jun 2000 08:24:24 -0500 Subject: R-1.1.0 now available by rsync Message-ID: <6r7lbrcc1j.fsf@franz.stat.wisc.edu> Sources for the 1.1.0 release are now available from rsync.r-project.org via anonymous rsync. $ rsync rsync.r-project.org:: r-release R sources (feature-frozen version) CVS tree (approx 13 MB) r-release-patched patched R sources (feature-frozen version) CVS tree (approx 13 MB) r-devel R sources (development version) CVS tree (approx 13 MB) r-manuals Development sources for manuals for R xlispstat xlispstat sources (development version) CVS tree (approx 12 MB) ess ess (Emacs Speaks Statistics) CVS tree (approx 8.5 MB) omega Omega Project for Statistical Computing CVS tree -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From guido at hal.stat.unipd.it Sat Jun 17 20:39:07 2000 From: guido at hal.stat.unipd.it (Guido Masarotto) Date: Sat, 17 Jun 2000 19:39:07 +0100 Subject: R 1.1.0 for Windows Message-ID: <20000617193907.62739@hal.stat.unipd.it> Windows binaries at CRAN (bin/windows/Windows-NT/base) have been updated to R-1.1.0. See below for a list of Windows-specific changes. We thanks all the people who checked over pre-test versions. guido masarotto (for the R-core team) Windows-specific changes to R ============================= There is now a GUI preferences editor on the Edit menu in Rgui. A data entry editor is now implemented. This is similar to the Unix one (see ?dataentry: that has itself been considerably enhanced in parallel with the Windows version) with the additional features that double-clicking in a cell turns it into an editable field (entered as a new value by navigating away from the cell), and there is a right-click popup menu. Rterm will now load and save the commands history (as Rgui does). There is a new item on the File menu in Rgui to save the commands history at that point in a session, and a new function savehistory() (only applicable in Rgui and Rterm). Colours in Rconsole can be specified as "Windows" and will be taken from the current Windows colour scheme. (The preferences editor will save the actual colour, though.) The placement of multiple pagers is now `random' (so they will not always appear in the exact centre of the screen) and under the MDI interface the pager rows and columns settings are now used. The postscript() device can now spool plots to a printer. You will need a suitable program to send a file to the spooler (or even to send it to ghostscript to interpret PostScript for the printer): the RedMon suite available from http://www.cs.wisc.edu/~ghost/rjl.html and GhostScript distribution sites should provide suitable tools. See ?postscript for further details. The new xfig() device can be used, and a port of xfig to Windows (with an X server and the Cygwin B20.1 environment and X11R6.4 installed) is at ftp.franken.de:/pub/win32/develop/gnuwin32/cygwin/porters/Humblet_Pierre_A/B20 as xfig-3.2.2-cygwin-b20.1-bin.tar.gz. The R DLL and executables now contain standard Windows version information, which will appear on a Version tab of the Properties dialog box in Explorer. The internal unzip and the installer now use unzip5.41, not unzip5.40, and the DLL interface is incompatible. There are changes in the tools needed to build R (see the file INSTALL) and those recommended for building packages from source (see the file readme.packages). New makefile target zipdata-% to zip up data directories in packages. If there is a file `Makefile.win' in a package src directory this will be used rather than MakePkgs (and the tcltk package provides an example). There is an example package `windlgs' in the package sources distribution that shows how to use graphapp to build dialog boxes to be called from menus, with a worked example of a t test done in three ways. More details of graphapp, including a tutorial and a reference manual, are at http://www.cs.usyd.edu.au/~loki/GraphApp. Optional support for the Tcl/Tk interface. To use this you need to install tcl831.exe from dev.scriptics.com, and you will need the Tcl and Tk dlls in your path. Also, you need to set the environment variable TCL_LIBRARY, to something like c:/Program Files/Tcl/lib/tcl8.3. The demos(tk*) will work on Windows. The R mathematical functions can now be built as a DLL for use with your own C programs. See src/nmath/standalone/README in the sources. Rdconv.bat no longer depends on having a Unix-compatible `cat' program in your path. A long-standing bug in the (vertical) alignment of symbols in plotmath has been corrected. Pagers should no longer flash when launched. Launching a pager or data editor or graphics window now brings it to the front, even from Rterm.exe. (Not for Tcl/Tk windows, unfortunately.) Failure to load a DLL with dyn.load now gives extended error information. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From hornik at ci.tuwien.ac.at Wed Jun 28 23:13:32 2000 From: hornik at ci.tuwien.ac.at (Kurt Hornik) Date: Wed, 28 Jun 2000 23:13:32 +0200 Subject: New version of chron Message-ID: <200006282113.XAA23403@aragorn.ci.tuwien.ac.at> A new version of the chron add-on package is now available from CRAN. The previous version introduced code to ensure that chron would work correctly in the 21st century. Of course, the main issue is how to deal with 2-digit dates. To this end, the original author of chron, David James, indicated that the `y' format specifier was always meant to specify the year without the century (i.e., the year modulo 100), as in strftime(3)'s `%y'. Hence, there should be an error when using a number outside the [0, 99] range, such as 1999 or 2000, with the `y' format specifier. Several users have expressed their dislike of the new behavior and that using `y' with 4-digit years used to work, sort of. Hence, the new versions has changed the default behavior as follows. 2-digit years are expanded using 30 as century cutoff, i.e. 00 -> 29 21st century 30 -> 99 20th century All other values are left alone. In the next version, I want to introduce strftime(3) formatting specs, similar to the new timeDate class in S-PLUS 5. Most likely, ISO 8601 format (yyyy-mm-dd hh:mm:ss) will be used as default. -kh -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From torlasz at xenia.sote.hu Mon Jul 3 09:51:22 2000 From: torlasz at xenia.sote.hu (Tornoci Laszlo) Date: Mon, 3 Jul 2000 09:51:22 +0200 (CEST) Subject: A new mirror site in Hungary In-Reply-To: <14681.50931.593674.41223@galadriel.ci.tuwien.ac.at> Message-ID: Hi, I have set up a mirror of CRAN at xenia.sote.hu (193.6.210.44). It is accessible by: ftp://cran.hu.r-project.org/pub/mirrors/CRAN rsync://cran.hu.r-project.org/CRAN http://cran.hu.r-project.org The mirror gets updated daily. If you have any problems accessing it, please inform me: torlasz at xenia.sote.hu Yours: Laszlo ---------------------------------------------------------------------- Laszlo L Tornoci Inst Pathophysiology E-mail: torlasz at xenia.sote.hu Semmelweis Univ Med School torlasz at net.sote.hu Nagyvarad ter 4. fax: (36-1)-210-4409 Budapest, H-1089, Hungary ---------------------------------------------------------------------- -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From keitt at nceas.ucsb.edu Wed Jul 12 23:26:42 2000 From: keitt at nceas.ucsb.edu (Timothy H. Keitt) Date: Wed, 12 Jul 2000 14:26:42 -0700 Subject: New release of RPgSQL Message-ID: <396CE292.AA2D74F8@nceas.ucsb.edu> I've done some major house cleaning on RPgSQL. The latest release is available at http://rpgsql.sourceforge.net/ and should soon appear on CRAN. Cheers, Tim -- Timothy H. Keitt National Center for Ecological Analysis and Synthesis 735 State Street, Suite 300, Santa Barbara, CA 93101 Phone: 805-892-2519, FAX: 805-892-2510 http://www.nceas.ucsb.edu/~keitt/ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From p.dalgaard at biostat.ku.dk Tue Aug 15 11:41:40 2000 From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA) Date: 15 Aug 2000 11:41:40 +0200 Subject: R-1.1.1 is released Message-ID: I've rolled up R-1.1.1.tgz a moment ago. This is expected to be the last release in the 1.1 series unless some truly dreadful error pops up. The 1.2.0 release is scheduled for early December. You can get it from ftp://cvs.r-project.org/pub/CRAN/src/base/R-1.1.1.tgz or http://cvs.r-project.org/pub/CRAN/src/base/R-1.1.1.tgz or wait for it to be mirrored at a CRAN site near you within a day or two. There's also a version split in three for floppies and a patch file if you prefer that. For the R Core Team, Peter D. Here's the relevant part of the NEWS file: NEW FEATURES o data(), example() and help() now search the loaded packages, then in their .lib.loc argument, the latter as pre-0.99.0. See their help pages for the precise details. o help() has a new argument `try.all.packages' set by the option "help.try.all.packages". If help is not found in the normal path and this is TRUE then a search is made of all packages for possible matches. o Improved detection of Tcl/Tk at configure time. One can either set configure variables TCLTK_CPPFLAGS and TCLTK_LIBS, or give the locations of the tclConfig.sh and tkConfig.sh scripts via the `--with-tcl-config' and `--with-tk-config' arguments. o prop.trend.test() - test for trend in proportions. o write.table() has new argument `dec' for setting the decimal separator (SPSS/Windows and probably others want commas in continental European locales). o Advance warning: save(, oldstyle=TRUE) will no longer be available after this release. o Symbols can now be coerced to expressions, making as.expression(quote(a)) work BUG FIXES o data() now works correctly with data-only packages. o Standalone Mathlib can now be made if builddir = srcdir (working around an undocumented autoconf `feature'). o Check for pre-1.1.0 saved object .Postscript.options in postscript(). o More stringent checks on the arguments to dataentry(). o Specifying xlab as an expression now works again. o dev2bitmap() works again. o Numerous uses of `F' and `T' replaced by `FALSE' and `TRUE'. o bxp() now extends `ylim' properly when notch=TRUE (and a notch is more extreme than other stats). Also, varwidth is okay again, see example(split). o Making manuals without making R first now works. o princomp() now works when some eigenvalues are tiny negative values (which are treated as zero). o SearchEngine.html was not installed when builddir != srcdir. o lm.{w}fit(x,y,..) now work when x has no column names. These functions no longer add and subtract n zeros when there's no offset. They are now documented somewhat. o Some HTML files used src="R.css" instead of href="R.css" causing some browsers to ignore the style sheet. R.css now passes the w3c CSS validator and gives the intended results with Internet Explorer. R.css is copied to all library directories. o The data editor no longer crashes when entries contain more than 45 characters, and works correctly if the field width is larger than the window width. o Recording plots used to ignore graphics events before the last replay. o plot(), points(), etc now give warnings and error for invalid `type' arguments. o matplot() now allows the same `type's as plot(). o dev.print() and dev.copy2eps() now work when called from a function, such as dev2bitmap(). o anova.glmlist works correctly with decreasing models and test="F" now gets the correct residual df. o Functions created (not just edited) with fix() now get environment .GlobalEnv not the body of fix. o Rdconv was ignoring OS-specific parts of the files with some Perl versions. (This did not affect installing packages.) o R CMD check did not run more than one specific test. o keyword2html omitted items when changing up a level, so the HTML search engine keyword list was missing `data' and `utilities', for example. o aov() with multiple strata was setting some spurious options. o Under UNIX, help(, htmlhelp=TRUE) uses the linked copy of the HTML file in ~/.R if help.start() has been run recently in the session, so the style sheet and hyperlinks should now be found. o dotplot's arguments `color' and `lcolor' are now interpreted correctly if they are vectors of length > 1. (It is not clear from the help that this was ever intended.) o Error messages of e.g. do.call() are now spaced properly. o summary(.matrix | .data.frame) now respects a `digits' argument. o scan() recognises quoted strings by default again. The default for the quote= argument got set wrongly when it was introduced. They are, however, turned off when using sep="\n", since you probably want unprocessed lines of text in that case. o fixed buglet where scan() would double a character following a terminating quote symbol. o kmeans was failing on vector inputs (although not documented to accept such). o fixes in predict.lm (John Maindonald) o NCOL got confused by 1D arrays, which it now reports have 1 column rather than NA. o rep(1:2,c(1,-1)) segfaulted (PR 619) o x[["a"]] <- y rejected some object types for y (e.g. expressions) which were accepted in x$a <- y (PR o data editor froze on empty data frame, and more generally on zero-length cols. o data editor did not handle factors properly in numeric-edit mode. o table() misbehaved on empty (or all-NA) data o data editor now handles empty data frames, allowing data entry to begin with dd<-edit(data.frame()) or dd<-data.frame() ; fix(dd) o plotting math expressions when specified as a LANGSXP or SYMSXP didn't work in several cases: plot(1,main=quote(a)) would segfault and there were problems with title(), text(), and mtext() as well. o optim(): no more segfault for REPORT=0; corrected error msg; .. maxit default is now okay also when "L-*-B" is chosen automatically. Using (abs|rel)tol with that method now gives a warning. o text() did not respect its `xpd' argument, the default of which is still to use par("xpd"); gave a wrong error message in one case. o polygon() had an incorrect documentation and silently disregarded "..." arguments. o predict.loess was giving incorrect results (those for the non-robust fit) in the case of a fit with family = "symmetric" and surface = "direct" and prediction with se = FALSE. The fitted values were missing for such fits. o Better rendering of ^ and ~ in latex in \code{} (and they should not appear outside code and verbatim sections). o Fixed unterminated string problem with lty (PR 584) o Fixed scoping problem with quasi() family (PR 614) -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From guido at hal.stat.unipd.it Wed Aug 16 14:23:06 2000 From: guido at hal.stat.unipd.it (Guido Masarotto) Date: Wed, 16 Aug 2000 13:23:06 +0100 Subject: R 1.1.1 for Windows (NT/9x/2000) Message-ID: <20000816132306.32848@hal.stat.unipd.it> Windows binaries at CRAN (bin/windows/Windows-NT/base) have been updated to R-1.1.1. See below for a list of Windows-specific changes. guido masarotto (for the R-core team) Windows-specific changes to R ============================= New file README.Rterm providing basic documentation on Rterm.exe. undoc() is now available under Windows. There is a new script R_HOME/bin/build.sh, a version of R CMD build. You will need R_HOME set as an environment variable to use it, and you will need the full set of tools from tools.zip (see readme.packages) in your path. The batch wrappers to Perl files Rdconv.bat Rdindex.bat Rd2txt.bat Sd2Rd.bat have been revised to work on more Perl/OS versions. Setting cell widths from the menu in the data editor now works reliably. Having an empty line at the beginning of .Rhistory no longer breaks the history-recall mechanism in Rgui. Characters using the AltGr key now work in interactive use of Rterm. (AltGr used to work like Alt.) Ctrl+V now works as described in a pager (pasting to the console). Other versions of Tcl/Tk may be used by setting TCL_VERSION in MkRules (but only 8.31 has been tested). A file Makevars.win in the src directory of a package will be used in preference to a file Makevars. The Makefiles for packages now allow C++ code (with extension .cc or .cpp or .C) in the src directory. If you use a private library and HTML help, you need to copy R.css from rw1011\library to each private library directory. Function win.version() should give slightly more information (the latest service pack number x.y) on Windows 2000. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From Don.Wingate at intellichem.com Tue Oct 3 18:34:56 2000 From: Don.Wingate at intellichem.com (Don Wingate) Date: Tue, 3 Oct 2000 09:34:56 -0700 Subject: Parse Errors Message-ID: Dear R Development Team, Using Thomas Baier's R Com Server -- or a dll I am building which supports an evaluate function that is based on Baier's function R_Proxy_evaluate contained in proxy_impl.c -- when I issue an invalid command to R such as "plo(x)" the program crashes. There is code in R_Proxy_evaluate to test for a parse error before actually generating code and issuing the command - He calls R_Parse1Buffer(&lBuffer,0,&lStatus) and then tests the value of lStatus for parse error. The trouble is that lStatus == PARSE_OK even though the command is invalid, so the evaluation continues until eval() is called, at which point R terminates and crashes the program. (It does write an error message to the console first, but crashes after that.) Is there a way to handle this? The same command can be issued inside RGui.exe or RTerm.exe with out a problem. Thankyou, Don Wingate. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From mikalzet at libero.it Thu Oct 5 22:20:32 2000 From: mikalzet at libero.it (mikalzet at libero.it) Date: Thu, 5 Oct 2000 22:20:32 +0200 (CEST) Subject: installing R-1.1.1 on Mandrake 7.1 Message-ID: The R-base-1.1.1-1.i586.rpm packaged for Mandrake 7.1 is now available on CRAN. I've installed it on my system and it seems to work all right so far ! Please let me know if there are any problems. -- Dr. Michele Alzetta -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From paradis at isem.univ-montp2.fr Tue Oct 24 14:34:48 2000 From: paradis at isem.univ-montp2.fr (Emmanuel Paradis) Date: Tue, 24 Oct 2000 14:34:48 +0200 Subject: =?iso-8859-1?Q?=22R_pour_les_d=E9butants=22_?= is available in French and in English Message-ID: <3.0.32.20001024143447.009152a0@162.38.183.200> Dear R-users, I have completely revised my tutorial "R pour les d?butants" and translated it in English under the title "R for beginners". The document is now 31 pages-long (the previous version was 15-pages long). It gives a starting point for people with no experience with R (or S). I tried to explain the basics in the simplest way, as well as giving useful details (mostly with tables). Any feed-back would be greatly appreciated. Both versions are on CRAN in the contributed documentation section: http://cran.r-project.org/doc/contrib/Rdebuts_fr.pdf [280 kB] http://cran.r-project.org/doc/contrib/Rdebuts_en.pdf [152 kB] Chers utilisateurs de R, J'ai compl?tement r?vis? mon document "R pour les d?butants" et l'ai traduit en anglais sous le titre "R for beginners". Ce document comporte maintenant 31 pages (la version pr?c?dente en comportait 15). Le but de "R pour les d?butants" est de fournir un point de d?part pour les utilisateurs qui n'ont aucune exp?rience avec R (ou S). J'ai essay? de simplifier les explications, tout en donnant des d?tails utiles (le plus souvent sous forme de tableaux). Tout commentaire ou suggestion serait grandement appr?ci?. Les deux versions sont sur le site du CRAN dans la section "contributed documentation" (cf. liens ci-dessus). Emmanuel Paradis Laboratoire de Pal?ontologie Institut des Sciences de l'?volution Universit? Montpellier II F-34095 Montpellier c?dex 05 France phone: +33 4 67 14 39 64 fax: +33 4 67 14 36 10 mailto:paradis at isem.univ-montp2.fr -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From mjr at stats.mth.uea.ac.uk Mon Nov 13 16:33:46 2000 From: mjr at stats.mth.uea.ac.uk (MJ Ray) Date: 13 Nov 2000 15:33:46 +0000 Subject: Rcgi mailing list Message-ID: Rcgi is a CGI WWW interface to R. Recent versions have the ability to use "embedded code": you can mix user input and code, allowing the HTML author to do anything from load in data sets to enter most of the commands for users without writing CGI scripts. Graphical output is possible in PostScript or GIF formats and the executed code is presented to the user for revision. --[R FAQ, ed. Kurt Hornik] As part of a project, some more development time is to be spent on Rcgi and I'd very much like to do things which will improve its usefulness to statistics teachers. So, a mailing list has been created to gather advice, requests, suggestions and opinions of other users. The list should be relatively low "traffic" and you can subscribe at: http://www.coollist.com/subscribe/subto.cgi?l=rcgi Demo and download of current version are currently available from http://www.mth.uea.ac.uk/~h089/Rcgi/ This will be replaced by a new site in the next week or so. -- MJR (Not an official statement) Please note changes of address -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From Torsten.Hothorn at rzmail.uni-erlangen.de Tue Nov 14 17:48:47 2000 From: Torsten.Hothorn at rzmail.uni-erlangen.de (Torsten Hothorn) Date: Tue, 14 Nov 2000 17:48:47 +0100 (MET) Subject: mvtnorm Message-ID: Announcement: mvtnorm Multivariate Normal and T Distribution mvtnorm implements two R functions for the computation of the multivariate t and normal distribution: pmvt: Computes the the distribution function of the multivariate t distribution for arbitary limits, degrees of freedom and correlation matrices based on algorithms by Genz and Bretz. pmvnorm: Computes the distribution function of the multivariate normal distribution for arbitary limits and correlation matrices based on algorithms by Genz and Bretz. mvtnorm is currently available in CRAN's devel section. Literature: Genz, A. (1992). Numerical computation of multivariate normal probabilities. Journal of Computational and Graphical Statistics, 1, 141-150 Genz, A. (1993). Comparison of methods for the computation of multivariate normal probabilities. Computing Science and Statistics, 25, 400-405 Genz, A. and Bretz, F. (1999), Numerical computation of multivariate t-probabilities with application to power calculation of multiple contrasts. Journal of Statistical Computation and Simulation, 63, 361-378. Genz, A. and Bretz, F. (2001), Methods for the computation of multivariate t-probabilities. (submitted) Bests, Torsten -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From plummer at iarc.fr Fri Nov 17 10:59:58 2000 From: plummer at iarc.fr (Martyn Plummer) Date: Fri, 17 Nov 2000 10:59:58 +0100 (CET) Subject: RPM for Red Hat Linux 7.0 (Intel) available Message-ID: A binary RPM package of R 1.1.1 for Red Hat Linux 7.0 (Intel) is now available on CRAN. Or directly from ftp://ftp-fis.iarc.fr/pub/R/RedHat/7.x/ This package was built with gcc 2.95.2 and passes all the built-in tests. If you are a Red Hat 6.2 user, I do not recommend upgrading to Red Hat 7.0. I shall continue to support version 6.2 at least until version 7.1 comes out. If you want to build R yourself on Red Hat 7.0 then please read ftp://ftp-fis.iarc.fr/pub/R/RedHat/7.x/DIY/ My RPM packages are signed with GPG. For your own security, please verify the signature on the RPM package before installing. You can get a copy of my public key (ID 97D3544E) from any keyserver on pgp.net, and the fingerprint is included at the end of this message. Martyn pub 1024D/97D3544E 2000-11-03 Martyn Plummer Key fingerprint = A218 FA2C 3C55 3681 9447 C4EF FDEB A0F9 97D3 544E sub 1024g/85EA6DD9 2000-11-03 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From p.dalgaard at biostat.ku.dk Fri Dec 15 12:42:57 2000 From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA) Date: 15 Dec 2000 12:42:57 +0100 Subject: R 1.2.0 is released Message-ID: I've rolled up R-1.2.0.tgz a moment ago. This release has major improvements in efficiency and memory handling. You can get it from ftp://cvs.r-project.org/pub/CRAN/src/base/R-1.2.0.tgz or http://cvs.r-project.org/pub/CRAN/src/base/R-1.2.0.tgz or wait for it to be mirrored at a CRAN site near you within a day or two. There's also a version split in three for floppies. For the R Core Team, Peter D. Here's the relevant part of the NEWS file: CHANGES IN R VERSION 1.2.0 NEW FEATURES o There is a new memory management system using a generational garbage collector. This improves performance, sometimes marginally but sometimes by double or more. The workspace is no longer statically sized and both the vector heap and the number of nodes can grow as needed. (They can shrink again, but never below the initially allocated sizes.) See ?Memory for a longer description, including the new command-line options to manage the settings. o values of `--min-nsize' up to 50M (2Gb on 64-bit Solaris) are allowed. o A (preliminary) version of S4-like connections has been added, and most functions which take a "file" argument can now work with a connection as well as a file name. For more details, see the chapter on Connections in the R Data Import/Export manual. o New command-line option `--no-restore-history' implied by `--vanilla'. o Command-line option `--no-restore' is now `--no-restore-data' and `--no-restore' implies `--no-restore-*' (currently `data' and `history'). o The more recent GNU regex from grep-2.4.2 is used. This uses locale-based ordering for ranges on platforms with strcoll. o The print routines now escape " (as \") in a character string only when it is printed as a quoted string. This makes print(, quote=FALSE) and cat() consistent. o The standard methods for add1() and drop1() now attempt to cope with missing values by using a subset of the data that is `cleaned' by na.action for the maximal model under consideration. o anova() for 3 or more lm objects now behaves compatibly with S and anova.glmlist(). The old behaviour is still available by calling anovalist.lm() directly. o anova() for multiple lm and glm objects no longer truncates the formula printed. There is much more extensive documentation for anova() methods. o New method as.data.frame.table() for converting the array-based representation of a contingency table to a data frame containing the classifying factors and the corresponding counts. o New function assocplot() for producing Cohen-Friendly association plots. o autoload() accepts lib.loc and other arguments to library() o bxp() has new argument `frame.plot', as plot.default(). o contour() now has `axes' and `frame.plot' args. o contrasts(, FALSE) now always returns an identity matrix, to make model.matrix compatible with S. This affects models such as lm(y ~ o - 1) where o is an ordered factor. o `where' command added to debug(). o demo(dynload) (which used the superseded call_R interface) has been removed. o Class "dendrogram" in package mva providing general support for tree-like structures (plotting, cutting, ...). o dev.copy2eps() and dev2bitmap() preserve the aspect ratio of the copied device if just one of `width' and `height' is specified. o dump() has new argument append, argument `fileout' has been renamed to `file' (for consistency with all other functions). o edit.default() now checks for an unset `editor' argument, and terminates with an error if the editor cannot be run. o The `mode' argument of exists() and get() is interpreted as mode(x) rather than typeof(x), following S. o New functions file.access() and file.info() for information on files on the user's file systems. o New convenience function file.copy(). o file.show() allows `pager' argument to be an R function, and consequently, the `pager' option can be an R function. o Formatting (and printing) of data.frames with complex objects is improved. toString was added as a new function. o format() has a new argument `justify' controlling the justification of character strings (and factors). o Formula objects now have an environment and code manipulating them needs to take care to preserve it or set an appropriate environment. o New function fourfoldplot() for producing fourfold displays of 2 by 2 by k contingency tables. o gc() now reports the space allocated, not the space free, since the total space is now variable. o New primitive gc.time() to report on time spent in garbage collection. o hclust() takes new argument `members' allowing dissimilarity matrices both for singletons (as until now) and clusters. o help() has an additional `pager' argument which may be passed to file.show() {useful for ESS fans}. o There is now an R `Hershey' list object for Hershey vector font computations and documentation. o hist() now returns a "histogram" object and calls the new function plot.histogram() for plotting. It now also allows character labels. o if(*) now gives a more intelligible error message when "*" cannot be coerced to logical. o inherits() is now an internal function and compatible with S. o New function lag.plot() in package ts. o legend() has a new argument pt.bg. o The commands history can be loaded with loadhistory(), saved with savehistory() and displayed with history(), under Windows and under Unix using the readline or GNOME interfaces. o mad() has new (logical) arguments "low" and "high" (the first giving S compatibility). o New function manova() and summary method. o Function mantelhaen.test() in package ctest now can deal with general I x J x K tables. In addition, in the 2 x 2 x K case, it can also perform an exact conditional test of independence, and gives confidence intervals for the common odds ratio. o model.frame() now uses the environment of its formula argument, rather than the parent environment, to evaluate variables not found in the data argument. See help(formula). o mosaicplot() can now also create extended mosaic plots, which visualize the residuals from a log-linear model using color and outline. o New utility function n2mfrow(). o nlm(check.analyticals = TRUE) now warns if the supplied gradient and/or hessian are of the wrong length. o New function object.size() to give approximate memory allocation. o optim() now checks the length of an analytical gradient at each evaluation. o The L-BFGS-B method of optim() now support tracing, at several levels of detail. o options(check.bounds = TRUE) makes each vector extension by sub-assignment ("x[.] <- .") produce a warning. o options(width) now admits to a limit (previously 200, now 10000) and gives a more informative message if out of range (as it does now for digits and expressions). o Function path.expand() to do tilde-expansion on file paths. This provides an interface to R_ExpandFileName, which is now a documented entry point. o .Platform has new component "endian", useful for binary file manipulations. o plot.function() and curve() now take xlim as default for (from,to) if the former is specified. o plot.hclust() allows arguments main, sub, etc, and has non-empty defaults for these. o plot.ts(x,y) now allows to suppress labels and lines; it is better documented. o The postscript() driver now allows a user-specified family so, for example, one can use the same fonts in diagrams as in running text. o The postscript() driver allows its prolog to be changed (by an expert) via object .ps.prolog. o prop.table() and margin.table() now work with an empty `margin'. o Formerly deprecated function provide() is now defunct. o New functions read.delim() and read.delim2() to make it easier to read delimited files as Windows programs tend to create (usually TAB separated). o New readLines() function to read a file line-by-line. o New functions reshapeLong() and reshapeWide() emulating Stata's reshape command. These are still labeled experimental and might be improved (or removed) in later versions. o row.names() and row.names<-() are now generic functions which call rownames() as their default method and have methods for class "data.frame". o New function Rprof() for profiling R expressions under Unix. Configure with `--enable-R-profiling' (on by default) to make this operational. o save(, oldstyle=TRUE) has been withdrawn. o scan() and read.table() have a new argument `fill' which can be set TRUE to allow reading files with unequal number of fields per line. (Programs like Excel have a habit of creating such files when exporting.) o scan() and read.table() have a new argument `blank.lines.skip' to allow blank lines to be read. o scan() now reads empty character fields as "" not "NA" unless "" is included in na.strings. o smooth() in package eda has a better default (3RS3R instead of 3RSR) and more arguments, e.g. `twiceit' for some S compatibility and kind = "3R" for running medians of 3. o strsplit() has a new argument `extended' controlling whether to use extended (the default) or basic regular expressions for splitting. o Sys.getenv() becomes the preferred name for getenv(), which is now deprecated. o New functions Sys.getlocale() and Sys.setlocale() to query and set aspects of the locale of the R process, and Sys.localeconv() to find the default decimal point, etc. o New function Sys.info() for platform, host and user information. o New function Sys.putenv() to set environment variables. o New function Sys.sleep() to suspend execution for a while. o Date-time support functions with classes "POSIXct" and "POSIXlt" to represent dates/times (resolution 1 second) in the POSIX formats. Functions include Sys.time(), as.POSIXct(), strftime(), strptime(), and methods for format, plot, c, .... There are conversion functions for objects from packages `date' and `chron'; unlike those packages these support functions know about time zones (if the OS does). o tcltk library now has tkpager() which is designed to be used by file.show() and shows help pages etc. in separate text widgets. o tcltk is now more careful about removing the objects representing widgets in the R workspace when the windows are destroyed (e.g. using window manager controls) o tcltk library has had several canvas functions implemented. o tcltk now wraps callbacks to R in a try() construct - the nonlocal return from R's error handling could bring the Tk system into a strange state. o New demos for tcltk: tkfaq, tkfilefind, tkcanvas. o termplot() now has an `ask' argument. o terms() creates objects which now inherit from class "formula", so for example as.formula(terms.object) needs to replaced by formula(terms.object). o traceback() is now printed un-quoted and labelled by the frame number. o New argument `recursive' to unlink(). The default behaviour on Unix is now that of rm -f, not rm -rf. unlink() is now compatible across platforms. o New functions write.ftable() and read.ftable() for writing out and reading in flat contingency tables. o write.table() now quotes factor columns if quote=TRUE, and has a new argument `qmethod' to control the escaping of embedded quotes in character or factor columns. o New function xtabs() providing a formula interface to cross tabulation. o The R Data Import/Export Manual (`R-data.texi') has been added. o The set of valid R names is now described (at last) in R-intro. o The R Language Manual (`R-lang.texi') is now included and built in the same way as the other manuals. o The R manuals (R-intro, R-exts, ...) are converted to HTML format (if the necessary texinfo tools are available) and linked into the top HTML help page. o The header file `R.h' and those included from it are now usable with C++ code. o New header file `R_ext/Boolean.h': Rboolean type with TRUE and FALSE enum constants. o New header file `Rgraphics.h' to allow addons to use graphics structures. o Recommended include file `Rmath.h' replaces `R_ext/Mathlib.h'. o Bessel, beta and gamma functions are now documented as part of the API. Undocumented entry points are no longer in the header files, and some are no longer visible. o Calloc & Realloc failures now give size information. o DESCRIPTION file in installed packages has a new `Built:' field giving build information (R version, platform, date). o Much improved support for C++ code in add-on packages under Unix. New configure/build variables SHLIB_CXXLD and SHLIB_CXXLDFLAGS for specifying the command and flags needed for building shared libraries containing objects from a C++ compiler. Configure tries to get these right in typical cases (GNU tools and/or common platforms). C++ source suffixes `.cpp' and `.C' are now recognized in addition to `.cc'. o Configure/build variables MAINLD and MAINLDFLAGS are renamed to MAIN_LD and MAIN_LDFLAGS for consistency with other MAIN_* vars, similarly for SHLIBLD and SHLIBLDFLAGS. o Configure/build variable FLIBS now only contains the Fortran 77 intrinsic and run-time libraries needed for linking a Fortran 77 program or shared library (as determined by configure). BLAS library detection was extended, with results saved to the Make variable BLAS_LIBS which is also available to add-on packages. o R CMD build and check have been completely re-written in Perl. In addition to running examples, check now also checks the directory structure and control files, makes a temporary installation and runs LaTeX on the help pages. Build has been reduced to cleaning, rewriting indices and creating tar files. The same files of Perl code are now also used under Windows. o Add-ons for utilities like Perl or LaTeX have now a central place in $R_HOME/share. Migration of existing files might take a while, though. o Preliminary support for building R as a shared library (`libR') under Unix. Use configure with option `--enable-R-shlib' or do `make libR' in directory `src/main' to create the shared library. There is also a linker front-end `R CMD LINK' which is useful for creating executable programs linked against the R shared library. BUG FIXES o New "[.AsIs" function fixing PR#665. o Effectively zero-length arrows() are omitted (rather than getting a system- and device-dependent arbitrary angle). o barplot() passes "..." down to plot.window as documented. o bxp(*) now obeys axes, xaxt, yaxt & ylim arguments (again?). o contour(.., labcex = 0.6, .. , vfont = c("sans serif", "plain"), ..) now behaves as it has been documented, PR#740. o D(.) is now more correctly documented, has second argument "name" instead of "namevec" (S compatibility), and gives a warning when name has not length 1. o dbinom() and dpois() now use a the accurate algorithm of C.Loader; e.g., 1 - 2*sum(dbinom(0:999, 1999, 1/2)) is now zero instead of 1e-12. o dbeta(), df(), dt(), dnbinom(), dgeom(), dgamma(), now all use the more accurate algorithms of dbinom() and dpois(); More limits are computed correctly, e.g. dgeom(Inf,*), or dnbinom(*,*,p=0), and integer argument coercion is more consistent. o dbeta(x, a,b) was giving NaN and Inf for large a and b. o The math functions now (again!) return NaN (not NA) when the warning message says so (e.g. gamma(-1)). o Paper sizes for "a4" and "legal" were interchanged in dev.print(). o Improved logic in the re-scaling of plots in dev.print(). o dev.print() and dev.copy2eps() now evaluate arguments as needed, so e.g. dev.print(file="junk.ps", horizontal=F) will work (previously =FALSE was needed). o Now dweibull(0,1) == dexp(0) == 1 for consistency. o Changing column modes from factor/character to numeric in edit.data.frame() (and fix() on data frames) is now allowed. o gctorture() did return a value although documented not to, that of gcinfo. It now returns the previous setting of gctorture. o glm() now follows lm() in dropping unused factor levels when fitting. o hist() now labels y-axis Density rather than Relative Frequency if freq=FALSE. The `intensities' component of the result is now deprecated and `density' should be used instead. o hsv() truncation bug fixed (hopefully correctly this time...) o library.dynam() no longer fails if the library appears more than once in lib.loc. o lm.fit & lm.wfit (and hence lm) now give understandable error messages when there are 0 non-NA cases. o match() does not always use "as.character()" anymore, fixes PR#741. o Trimmed mean() and median() are no longer attempted for complex data. o median() of empty vector is now NA. o model.matrix() can now handle NAs in factors. o model.matrix() now uses ":" not "." in labelling interaction terms, as terms() and the prototype do (PR#701). o old.packages() now sorts version strings correctly by splitting at "." and "-". o optim() has several new precautions against bugs, one of which was an infinite loop in the L-BFGS-B method if the derivatives were inaccurate (or if numerical derivatives were used and the problem was badly scaled). o pairs() now obeys an "cex = " argument, and so does panel.smooth(). o pf() had a bug in the code handling large noncentrality parameters, going all the way back to the original Appl.Stat. algorithm (PR#752). This affected pbeta() as well. o phantom(expr) in plotmath was used to calculate the bounding boxes, but the space was not actually used in typesetting the expression (PR#622). o Problem with subsetting and "..." arguments in plot.formula() (PR#757) o plot.lm() has a better default for its `ask' argument. o plot.new() does *NOT* allow an argument (`ask') anymore. This has not been working (since ~ R 0.49), is low-level and hence should not break anything. o plot.stl() now uses correct time labels for tickmarks of x-axes. o pnorm() is somewhat more accurate (SIXTEN=16; PR#699) and `infinitesimally faster' in some cases, thanks to James M. Rath. o Failure to open a postscript() device now gives diagnostic warnings. o Zero the widths of undefined chars in postscript(). o Make font metrics local to the device in postscript(), so that simultaneous instances of postscript/xfig/bitmap can use different values for `family'. o postscript() no longer uses the initclip operator, which was against the EPSF specifications and broke inclusion of graphics in some documents. o In postscript(), cleaned up the internals to fix some cases where it was unclear whether a variable was meant to set or track device status. o In some cases, emitted postscript violated the PS Document Structuring Conventions since some settings were carried over from one page to the next. (Caused breakage when turning antialiasing on/off in "gv" for instance.) o The DocumentMedia comment in postscript() output was wrong, and the font DSC comments have been changed to the preferred style for DSC 3.0. o pretty(x <- c(2.8,3))[1] - x[1] is now 0; in general, p <- pretty(x) now again fulfills p[1] <= x[] <= p[length(p)]. o print.dist() {mva} now passes "..." to print.default. o print.noquote("ABC") now works. o prompt(fn) uses fn's "source" attribute if it has one. o In prop.test(), the conf.int. now contains the estimate, even when that is 0 or 1 (PR#714). o qnorm(0) and qnorm(1) now give -/+ Inf (again!). o qt(*, log = TRUE) has a somewhat extended working range. o Specifying col.names in read.table() now overrides any header line in the data file. o Bug caused rpois() to generate biased variables in some cases. o scale(scale=TRUE) gave all NAs in any columns containing NAs. o eda's smooth() now computes Tukey's endrule properly. o smooth.spline()'s GCV method now uses a more accurate formula when there are repeated x points. o stars() fix (for 0/NA columns) PR#739. o data(state)'s state.abb has been corrected to use official 2-letter abbrevations. o strsplit() had two memory leaks. o tcltk interface now has better string quoting and no longer breaks on strings with unbalanced braces o tcltk callbacks used to include a "%..." argument on the call if the callback function had a "..." argument. This is no longer the case. o t.test() allows an input vector of length 2. o Method dispatch in primitive functions such as `c' only occurred if they were called by that name, and in particular not if used in lapply or called as .Primitive("c"). It now always occurs. o Method dispatching now forces evaluation of promises, so autoloading works with methods. o c(0.099999994, 0.2) prints as 0.1 0.2 not 0.10 0.20 after correcting the precision calculations. o Internal function fprec was overflowing for numbers around 1e-305. o [internal] .C("strsignif",*) doesn't use fixed size strings anymore (possible overflow). o ff[i] <- r now works for formula (and potentially other non-standard) objects ff. o Errors in argument matching could cause crashes if error handler was used. o NULL == ... now gives logical(0) instead of an error. This fixes a bug with e.g. apply(X,2,median, na.rm = TRUE) and all(NULL == NULL) is now TRUE. o polylines with more than 64K pieces will now work on more X servers with the x11 device. o R CMD Rd2dvi now again works with file names containing "_" or "$". o R CMD Rdconv now handles .rd as input file extension correctly in all cases. o make install could fail if there were no shared libraries to install (e.g. on vanilla Solaris). o Rd's \describe{} constructs are converted better to text output, and \items of >=22 chars now work. o Help aliases "(" and "{" now work, apart from as PDF hyperlinks. o NA || x , NA && y (etc) do not give errors anymore, but work as the "|" and "&" operators and as documented (PR#749). o Coercing lists to functions failed if argument list was empty. (PR#743). Also coercing functions to lists was wrong when the body was a single constant. -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From bates at stat.wisc.edu Fri Dec 15 14:04:42 2000 From: bates at stat.wisc.edu (Douglas Bates) Date: 15 Dec 2000 07:04:42 -0600 Subject: R 1.2.0 is now available via rsync In-Reply-To: Peter Dalgaard BSA's message of "15 Dec 2000 12:42:57 +0100" References: Message-ID: <6r7l51j0np.fsf@franz.stat.wisc.edu> R 1.2.0 is now available via rsync at rsync.r-project.org::r-release -- Douglas Bates bates at stat.wisc.edu Statistics Department 608/262-2598 University of Wisconsin - Madison http://www.stat.wisc.edu/~bates/ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From guido at hal.stat.unipd.it Mon Dec 18 12:09:57 2000 From: guido at hal.stat.unipd.it (Guido Masarotto) Date: Mon, 18 Dec 2000 12:09:57 +0100 Subject: R 1.2.0 for Windows Message-ID: <20001218120957.25753@hal.stat.unipd.it> A binary distribution of R 1.2.0 to run on Windows 95, 98, NT4.0 and 2000 on Intel/clone chips is available. (now at ftp://ftp.stat.unipd.it/users/guido/RWin, from tomorrow, at CRAN) guido masarotto (for the R-core team) Windows-specific changes to R ============================= This version has been compiled against msvcrt.dll not crtdll.dll. This gives small speed increases and generally more accurate results. Packages compiled against crtdll.dll will still work (as far as we are aware), but for best results should be re-compiled. (A few packages need to be re-compiled for 1.2.0 on all platforms, and any that used malloc directly need to be recompiled on this one.) This release has a number of changes to bring its behaviour closer to that of Unix versions of R. - The default font for graphics on windows(), win.printer() and win.metafile() devices is now Arial: the font numbers for the Times New Roman and Arial families have been interchanged. - The history is only saved when the workspace is (to be compatible with Unix versions of R) and whether it is restored is controlled by option --no-restore-history (implied by --no-restore and --vanilla): the default remains to restore. - Environment variables R_HISTFILE and R_HISTSIZE can be set to specify the name of the commands history file (default .Rhistory) and its maximum size (in lines, default 512). - More locale support is now enabled where supported by the version of Windows in use. It means that sorting and comparison of character strings will be locale-specific. You may not want this (the sort order in `English_United Kingdom' is aAbB..., for example) and setting Sys.setlocale("LC_COLLATE", "C") should give the previous behaviour. Further, users of Windows 9x/ME should be able to use their native character set for the names of R objects (as NT/2000 users always have: this is caused by the change to msvcrt.dll). (For the benefit of those used to Unix, LC_ALL can be set in the environment, although this is not usually supported by Windows, and setting individual LC_* such as LC_COLLATE will also work.) - It is possible to make DVI and HTML versions of the manuals: see file INSTALL in the source distribution. - New utility Rcmd.exe to emulate R CMD : see below. - unlink() now works the same way on Windows and Unix. Thus on Windows it no longer deletes empty directories, but has a new argument recursive=TRUE to delete directories (empty or not). - The startup code looks for .Renviron, a file pointed to by environment variable R_ENVIRON and then .Renviron in the home directory. This file can contain lines of the forms NAME=value and NAME=${NAME1-value} to take the value of NAME1 if set (and not empty), otherwise `value'. - make check no longer makes R, just runs the tests (as make test always has). Tests are run in the C locale. Gui changes ----------- - There are new console menu items `Load History' on the File menu and `Clear console' on the Edit menu. (The current line is not cleared.) - The menu items `Load/Save Image' are now called `Load/Save Workspace'. - The Print menu item on the File menu of a console or pager now prints the selection if there is one, and the whole (saved) contents otherwise. - There is a new `Save to File' item on the File menu of a console or pager which saves the selection if there is one, and the whole (saved) contents otherwise. - The Rgui console now uses the same history mechanism as Rterm. The history limit is now just on the number of lines (rather than on the number of lines and the total size). The mechanism has been altered so that Rterm records repeated lines (as Rgui always did). - There are some additional command-line editing commands in Rgui: see the Help | Console information screen. (There is also one addition, ^W, in Rterm: see README.rterm.) - Selection works slightly differently: if the selection extends beyond the last character on the line the (invisible) CRLF is made part of the selection, but not if only up to the last character is selected. - The data editor is no longer modal (which seems not to have worked properly in the GraphApp toolkit) and this allows its popups to be modal. - The size of the console scroll buffer can be set in file Rconsole, and resized (upwards) via the GUI preferences editor. - The GUI console copes much better with receiving output (e.g. from tcltk interactive functions) during input. New utilities for preparing packages ------------------------------------ There are several new utilities in the rw1020sp.zip distribution. The utilities Rd2dvi.sh Rd2txt Rdconv Rdindex Sd2Rd are no longer batch files but accessed through a new front-end Rcmd.exe, so if this is in your path (otherwise use ...\rw1020\bin\Rcmd) you can use Rcmd Rd2dvi.sh [options] files Rcmd Rd2txt file Rcmd Rdconv [options] file Rcmd Rdindex [options] files Rcmd Sd2Rd [options] file There are new utilities INSTALL, REMOVE, SHLIB which can be used to install a source package, remove a package and make a DLL, and implementations of the Unix R utilities BATCH, build and check. Invoke these by Rcmd INSTALL [options] pkgdir(s) Rcmd REMOVE [options] pkg(s) Rcmd SHLIB [options] file(s) Rcmd build [options] pkgdir(s) Rcmd check [options] pkgdir(s) Rcmd BATCH [options] infile [outfile] Use option --help with any of these for fuller details. The default for options("papersize") is set according to the locale, and so might be set to "letter" under US or Canadian versions of Windows. Rterm in interactive use sets the title of the window it is running in, and unsets it when it terminates. The Windows memory manager proved to be (far) too slow to work with the new generational garbage collector, so it has been replaced. The current memory manager rarely releases memory back to Windows (but reuses memory very efficiently) so total memory usage will often grow slowly over the course of a session. Memory used for transient large objects will normally be returned at garbage collection. (Once memory usage has gone over the 256Mb of address space that is initially reserved, it is unlikely to be reduced much, but the allocated memory will be reused.) You can compile R to use the Windows memory manager if you need to. New function memory.size() showing the amount of memory currently in use or the maximum that has been used. New command-line option --max-mem-size to set the maximum memory allocation: it has a minimum allowed value of 10M. This is intended to catch attempts to allocate excessive amounts of memory which may cause other processes to run out of resources. The default is the smaller of the amount of physical RAM in the machine and 256Mb. DLLs for packages (including standard packages supplied with R) automatically gain version information when compiled under this version. (Use the Version tab on the Properties dialog box to see it, or the new function DLL.version() within R.) Windows (.hlp) help files now have hyperlinks to other objects within the same package. The windows() graphics device has a new argument `record' to set the initial state of the recording flag, and this defaults to the setting of the option "graphics.record" (and that defaults to FALSE). The windows() graphics device has new options for what happens when it is resized, which can be set from the command line of from the menu. See ?windows for details. New function bringToTop() to bring a graphics window to the top of the windows stack (useful from menu actions, ...). If the options setting for a pager or editor (or the editor argument to edit.default) is a path containing a space, it is automatically quoted if not already quoted. The range of allowed text sizes in a windows/win.print device has been increased, so smaller values of cex will work. (The smallest allowed text size is 2pt not 8pt.) Interactive use of Rterm.exe on Windows 2000 systems is now possible (including under ESS). Better rendering of wide (lwd > 1) and dashed (lty != "solid") lines on the windows/win.print device. The installer rwinst.exe when first asked to install a package tries to find a current installation of R, first from R_HOME if set in the environment, then from the PATH (it looks for ...\rw1020\bin). make pkgcheck-foo will unzip zipped example files if needed. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From ripley at stats.ox.ac.uk Mon Dec 18 16:39:02 2000 From: ripley at stats.ox.ac.uk (Prof Brian Ripley) Date: Mon, 18 Dec 2000 15:39:02 +0000 (GMT) Subject: Packages for R 1.2.0 for Windows Message-ID: <200012181539.PAA23130@toucan.stats.ox.ac.uk> I have re-built all the compiled packages for R 1.2.0 for Windows, and the set available in CRAN/bin/windows/contrib are now for rw1020. If you are upgrading to rw1020, please replace all the compiled packages you have downloaded by ones from this set. There a few packages available for the first time: RMySQL mlbench netCDF and a few that are not yet running on 1.2.0 on any platform hdf5 locfit wle (crashes with an array overrun). Beware of the following (from the current rw-FAQ) 3.5 Loading a package fails. ============================ Is the package compiled for this version of R? Many of the packages need to be compiled for a fairly recent version, and in particular a substantial minority need to be re-compiled for `rw1020'. You can tell the version the package was compiled for by looking at the `Built:' line in its `DESCRIPTION' file or at the `Version' tab of its DLL (if it has one) in the `libs' directory. (Right-click on the DLL in Windows Explorer, and select `Properties' or use the `DLL.version' function inside R.) If there is no `Built:' line or version tab, the package was compiled too long ago. Packages built with the wrong version may well refuse to load, but they might also load and crash R when in use. They might also run and give incorrect results. Packages for rw1011 and earlier are still available in CRAN/bin/windows/contrib/Old, but will not be updated (and I have taken rw1011 off my machine). -- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From jago at mclink.it Mon Dec 18 18:53:53 2000 From: jago at mclink.it (Stefano Iacus) Date: Mon, 18 Dec 2000 18:53:53 +0100 Subject: Latest/last beta of R 1.1.1 for MacOS (rel Dec 10 2000) Message-ID: Dear R&Mac developers(users), at http://www.eco-dip.unimi.it/R you can find the latest (and last) beat version of R for MacOs corresponding to R vers 1.1.1. Release date is Dec 10 2000. It is no longer a pre-alpha version but a beta one :) In what follows you can find what's new in this version but please remember that it is still a beta version intended mainly for R developers and with the aim to collect as much feedback as possible. Sometimes R application fails to allocate memory and it quits. This is a known bug and it will be fixed in the next release. I think that this is the last porting of R 1.1.1 and next version of R for MacOS will be based on R ver 1.2.0 released on Dec 15 2000. I hope this to be a complete porting and it will come with next year. I would like to thank the R Core Team people for the invaluable help given to me. Stefano p.s. I apologize for this long message. ---- Macintosh porting of R-1.1.1, beta 1, (Dec 10 2000). What's new from R for Mac pre-alpha 2 ====================================== * tempfile() is now supported. Temporary files are stored in a directory "tmp" that it is assumed to be in the main R folder. If it doesn't exist, R create it. All temporary files will be stored there. * unlink() is implemented. It can delete only files and dirs created from the current R session. Wildcards not allowed yet. * Dynamic libraries are fully implemented grace to the code give to me by Luke Tierney. (There is a problem with DLLName. Every function must be searched for global and not for a specific package when calling .C/.Fortran etc) * Most of the packages have been compiled but the tclk one. * tclk demos disabled * Packages. The following packages have been compiled or simply added to the base one: ctest (ex:tested) eda (ex:tested) lqs (ex:tested) modreg (ex:tested) mva (ex:tested) nls (ex:tested, does not work "SSlogis") splines (ex:tested) stepfun (ex:tested) ts (file AnIndex to be built) wavethresh (examples and help files to be built) * Metric Information for graphics device partially working. You can write expressions and symbols in plots but it is not yet perfectly working. * data(women) doesn't load! Can't understand why...yet. * XDR loading/saving has been implemented. I use the code from B. Ripley that (seems) to work fine with very little modifications. * Load and Save of image is now implemented correctly. * Load and Save implemented from menu too. If you save from menu an icon will be added to the file. You can double-click on a R file to start the application or load a file in R if the application is running. You can also drag&drop the file on the R icon to launch R. * Help files are now displayed correctly with colors as under Windows What else still remains to do! ============================== There are lots of things that have to be implemented and fixed. Not all the avalaible packages have been compiled. If you have any particular need please let me know and I will compile and made available the package. There is not an automatic install procedure for building packages under MacOS yet. This current version containes wavethresh and multiv packages but no help files and examples are avalaible yet. If you need them you should only copy the directories "help" and "R-ex" of the Windows distribution in their respectively directory under this distribution. Memory problems =============== There is a strange behaviour of this porting of R with memory that I'm not able to fix yet. As the memory routines will be changed in R 1.2 I decided to fix it in version 1.2 of the MacOS porting. Anyway, the suggested memory parameters are the following: from Finder get Information on the R application and change its assigned memory to 42000k. From within R application preferences set RVSize = 5M and RNSize = 500k. Hystory ======= What was in R for Mac pre-alpha 2 and 1 ======================================= * dir, setcwd, getcwd * macdevice pdated to WasteLib 2.0 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From mikalzet at libero.it Wed Dec 20 14:39:40 2000 From: mikalzet at libero.it (mikalzet at libero.it) Date: Wed, 20 Dec 2000 14:39:40 +0100 (CET) Subject: R 1.2.0 for Mandrake 7.1 and 7.2 Message-ID: The RPM package compiled for Mandrake 7.1 is available on CRAN, the package for Mandrake 7.2 should be available very soon. -- Michele Alzetta -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From chong at stat.purdue.edu Thu Dec 21 21:46:02 2000 From: chong at stat.purdue.edu (Chong Gu) Date: Thu, 21 Dec 2000 15:46:02 -0500 Subject: factor support added in gss Message-ID: <200012212046.PAA100864@odds.stat.purdue.edu> I just uploaded version 0.5-1 of the gss package to CRAN. Factors are now accepted for smoothing. Chong -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From jlindsey at alpha.luc.ac.be Thu Jan 6 08:36:10 2000 From: jlindsey at alpha.luc.ac.be (Jim Lindsey) Date: Thu, 6 Jan 2000 08:36:10 +0100 (MET) Subject: version 0.7 of my libraries Message-ID: <200001060736.IAA24641@alpha.luc.ac.be> Version 0.7 of my libraries for Nonlinear Regression and Repeated Measurements Libraries is now available at www.luc.ac.be/~jlindsey/rcode.html As a reminder the libraries are Event history procedures and models (event) Generalized nonlinear regression models (gnlm) Multivariate normal and elliptically-contoured repeated measurements models (growth) Non-normal repeated measurements models (repeated) Probability functions and generalized regression models for stable distributions (stable) Utilities for nonlinear regression and repeated measurements (rmutil) (required by my other libraries) Some of the major new features since v0.6 include 1. Generalized linear ordinal regression using IWLS (ordglm in gnlm - recall that nordr does nonlinear ordinal regression). 2. Nonlinear stable regression using my symbolic interpreter and data objects (stableglm becomes stablereg in stable). 3. The autoregression coefficient in gar can depend on covariates (gar in repeated). 3. Continuous-time two-state Markov process with random effects (cmcre in repeated) 4. Hidden Markov models for ordinal data thanks to Patrick Lindsey (hidden and chidden in repeated) 5. lm and glm accept repeated my data objects using data=as.data.frame(object) Alpha versions of 0.8 will also soon start appearing in the same place. Jim -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From keitt at nceas.ucsb.edu Sat Jan 8 22:29:24 2000 From: keitt at nceas.ucsb.edu (Timothy H. Keitt) Date: Sat, 08 Jan 2000 13:29:24 -0800 Subject: RPgSQL 0.3 Message-ID: <3877AC34.84AAA18C@nceas.ucsb.edu> A new version of the RPgSQL package is available at http://www.nceas.ucsb.edu/~keitt/R/ (also uploaded to CRAN). I added a configure script. Hopefully this will solve any installation problems. T. -- Timothy H. Keitt National Center for Ecological Analysis and Synthesis 735 State Street, Suite 300, Santa Barbara, CA 93101 Phone: 805-892-2519, FAX: 805-892-2510 http://www.nceas.ucsb.edu/~keitt/ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ From keitt at nceas.ucsb.edu Wed Jan 19 20:51:19 2000 From: keitt at nceas.ucsb.edu (Timothy H. Keitt) Date: Wed, 19 Jan 2000 11:51:19 -0800 Subject: RPgSQL 0.4 Message-ID: <388615B7.84490F20@nceas.ucsb.edu> You can download the latest version from http://www.nceas.ucsb.edu/~keitt/R This version should fix any install problems related to autoconf/make. Cheers, Tim -- Timothy H. Keitt National Center for Ecological Analysis and Synthesis 735 State Street, Suite 300, Santa Barbara, CA 93101 Phone: 805-892-2519, FAX: 805-892-2510 http://www.nceas.ucsb.edu/~keitt/ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-announce-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._