From fharrell at virginia.edu  Wed Jan  1 20:33:05 2003
From: fharrell at virginia.edu (Frank E Harrell Jr)
Date: Wed Jan  1 20:33:05 2003
Subject: Updates to Hmisc and Design Libraries
Message-ID: <20021231231409.316635e3.fharrell@virginia.edu>

The Hmisc and Design libraries have been updated respectively to versions 1.4-2 and 1.1-1.  New versions for Linux/Unix/Windows may be obtained from http://hesweb1.med.virginia.edu/biostat/s/library/r .  Web sites for the libraries are http://hesweb1.med.virginia.edu/biostat/s/Hmisc.html and http://hesweb1.med.virginia.edu/biostat/s/Design.html .

Thanks to Xiao Gang Fan for porting the libraries to Windows once again.

I still have not had time to fix details in the documentation that will allow R CMD check to be passed, which would allow me to submit the libraries to CRAN.

Change logs may be obtained from http://hesweb1.med.virginia.edu/biostat/s/library/common

Several bugs have been fixed, and new features added.  In Hmisc, better use as been made of "units" attributes of variables, and units are incorporated into tables and plots produced by summary.formula.  For plots, plotmath is used, especially for annotating plots with test statistics produced by summary(..., test=TRUE).  A "matrix tapply" function (mApply) has been added.  A new LaTeX table formatting option, ctable, has been added to latex.default.  A new function getHdata makes it easy to download and import datasets and their descriptions from our web site.  latex functions were changed to allow file="" to be specified, for inline inclusion of LaTeX code in Sweave.  Problems with sas.get and [.factor have been fixed.  fit.mult.impute was enhanced to compute Rubin's degrees of freedom for t-statistics for scalar parameter tests, as well as to compute a missing information index.

In Design, glmD works much more reliably.  plotmath is now used by plot.Design. Bill Pikounis' <v_bill_pikounis at merck.com> improvements have been incorporated in bootcov to allow both cluster and group to be specified.   offsets now work in lrm when NAs are present, and predict.Design now works with offsets.  bootcov now works with glmD, and  summary and print work for glmD (thanks: Fredrik Lundgren <fredrik.lundgren at norrkoping.mail.telia.com>).  validate.tree had a bug fix.

Extended documentation for the libraries, and an introduction to the S language have been updated also (http://hesweb1.med.virginia.edu/biostat/s/doc/splus.pdf) and now include more R-specific information.

Thanks to those who have reported bugs and fixes, and Happy New Year to all.
---- 
Frank E Harrell Jr              Prof. of Biostatistics & Statistics
Div. of Biostatistics & Epidem. Dept. of Health Evaluation Sciences
U. Virginia School of Medicine  http://hesweb1.med.virginia.edu/biostat



From rpeng at stat.ucla.edu  Wed Jan  8 17:48:05 2003
From: rpeng at stat.ucla.edu (Roger Peng)
Date: Wed Jan  8 17:48:05 2003
Subject: New package:  gpclib
Message-ID: <Pine.GSO.4.10.10301061914380.11148-100000@fisher.stat.ucla.edu>

I have just uploaded a package to CRAN called `gpclib' for clipping large
and complex polygons.  This package provides an R interface to Alan
Murta's very fast General Polygon Clipper library (written in C), which
has an optimized version of the Vatti algorithm. Not all features of
Murta's library are implemented -- right now you can do intersections,
differences, and unions.  There are also functions for reading/writing
from/to files and coercing between various data types.

For some more details about the package see
http://department.stat.ucla.edu/~rpeng/R/gpclib.

Please send any comments, complaints, and bug reports to
rpeng at stat.ucla.edu.

Here is the DESCRIPTION file for the package:

Package:  gpclib
Version:  1.0
Date:  1/6/2003
Depends:  R (>= 1.6.1)
Title:  General Polygon Clipping Library for R
Author:  R interface by Roger D. Peng <rpeng at stat.ucla.edu>; GPC library
	 by Alan Murta
Maintainer:  Roger D. Peng <rpeng at stat.ucla.edu>
Description:  General polygon clipping routines for R based on Alan
	      Murta's C library
License:  Code written by R. D. Peng is available under the LGPL; the C
	  code for the GPC library is free for non-commercial use (see the
	  files `gpc.c' and `gpc.h' for details)
URL:  http://department.stat.ucla.edu/~rpeng/R/gpclib;
      http://www.cs.man.ac.uk/aig/staff/alan/software

Happy clipping!

-roger
_______________________________
UCLA Department of Statistics
rpeng at stat.ucla.edu
http://www.stat.ucla.edu/~rpeng



From p.dalgaard at biostat.ku.dk  Fri Jan 10 16:53:02 2003
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: Fri Jan 10 16:53:02 2003
Subject: R-1.6.2 is released
Message-ID: <x2adi9rogm.fsf@biostat.ku.dk>

I've rolled up R-1.6.2.tgz a short while ago. This is a minor upgrade,
fixing an assortment of bugs.

You can get it from the developer site at

http://cvs.r-project.org/pub/CRAN/src/base/R-1.6.2.tgz

or wait for it to be mirrored at a CRAN site near you. Binaries for
various platforms will appear in due course.
 
There is also a version split for floppies, but due to the inclusion
of recommended packages as binary .tar.gz files, we are no longer
providing a patch file.

These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:

174e6280aa2f2102388ca9c7930b1843  R-1.6.2.tgz
8d202e80aa52e3fc877994f1a76fc198  R-1.6.2.tgz-split.aa
8153444a5c0bea85ede04e0ced76b7de  R-1.6.2.tgz-split.ab
b1d88962c538ab9fccc81161c2a81a02  R-1.6.2.tgz-split.ac
90fb143e6a3289d472817e5218d2423d  R-1.6.2.tgz-split.ad
0e55aacd637415053f18651ecdc73c3a  R-1.6.2.tgz-split.ae
1c910fa9fe45fd5a15d6b3893c99f7fc  R-1.6.2.tgz-split.af
8706e736541bf60b717e0b56e8a405a0  R-1.6.2.tgz-split.ag

        For the R Core Team,

        Peter D.


Here's the relevant part of the NEWS file:


                CHANGES IN R VERSION 1.6.2


BUG FIXES

    o   plot.stepfun() now obeys a `ylim=.' specification.

    o   removeClass() does a better job of removing inheritance
        information.

    o   setIs() will not allow mismatched representations between two
        classes (without an explicit coerce method).

    o   The code underlying polygon drawing contained a memory leak.
        This showed up in persp, but did not affect other graphics
        functions.  It is now possible to draw big DEMs.

    o   logLik.nls() gave wrong df. (PR#2295)

    o   rbind() with a mixture of data frames and matrices treated the
        matrices as vectors. (PR#2266)

    o   stripchart(method="stack") was not handling missing values. (PR#2018)

    o   Arithmetic functions such as log() lost the object bit from
        classed objects if coercion was needed. (PR#2315)

    o   exp_rand would go into an infinite loop if unif_rand returned 0.

    o   formatC(x, format="fg") could return exponential format if
        rounding pushed x over a positive power of 10. (PR#2299)

    o   attr(x, foo) used partial matching for `foo' (even though not
        documented to do so), and failed to find `foo' if there were
        two or more partial matches before the exact match in the list
        of attributes.

    o   Rdconv now creates direct HTML hyperlinks when linking to
        documentation in the same package.  The code now ensures that
        links which can be resolved within the package are so resolved,
        even when there are possible resolutions in other packages.

    o   If readBin(what=character()) is used incorrectly on a file which
        does not contain C-style character strings, warnings (usually
        many) are now given.

    o   Building libR.so with the zlib in the R sources was not
        finding the local zlib headers.

    o   system(intern=TRUE) has an undocumented line length limit of
        119 chars both on Unix and Windows.  The limit is now 8096 and
        documented.  On Unix (only) every 120th character used to be
        discarded.

    o   plot.POSIX[cl]t were not passing graphics parameters on to
        axis.POSIXct.

    o   On some HP-UX systems, installed scripts were not executable
        when using the BSD-compatible install system program found by
        configure.  We now always use install-sh on HP-UX. (PR#2091)

    o   c() was converting NA names to "NA": now proper NA strings are
        used wherever possible. (PR#2358)

    o   A typo was causing segfaults when using data.entry under SuSE.



-- 
   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



From p.dalgaard at biostat.ku.dk  Fri Jan 10 17:17:02 2003
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: Fri Jan 10 17:17:02 2003
Subject: [R] R-1.6.2 is released
In-Reply-To: <x2adi9rogm.fsf@biostat.ku.dk>
References: <x2adi9rogm.fsf@biostat.ku.dk>
Message-ID: <x2wuldq8rv.fsf@biostat.ku.dk>

Peter Dalgaard BSA <p.dalgaard at biostat.ku.dk> writes:


> Here's the relevant part of the NEWS file:
> 
> 
>                 CHANGES IN R VERSION 1.6.2

Sorry, not quite... This is it:


                CHANGES IN R VERSION 1.6.2


BUG FIXES

    o   plot.stepfun() now obeys a `ylim=.' specification.

    o   removeClass() does a better job of removing inheritance
        information.

    o   setIs() will not allow mismatched representations between two
        classes (without an explicit coerce method).

    o   The code underlying polygon drawing contained a memory leak.
        This showed up in persp, but did not affect other graphics
        functions.  It is now possible to draw big DEMs.

    o   logLik.nls() gave wrong df. (PR#2295)

    o   rbind() with a mixture of data frames and matrices treated the
        matrices as vectors. (PR#2266)

    o   stripchart(method="stack") was not handling missing values. (PR#2018)

    o   Arithmetic functions such as log() lost the object bit from
        classed objects if coercion was needed. (PR#2315)

    o   exp_rand would go into an infinite loop if unif_rand returned 0.

    o   formatC(x, format="fg") could return exponential format if
        rounding pushed x over a positive power of 10. (PR#2299)

    o   attr(x, foo) used partial matching for `foo' (even though not
        documented to do so), and failed to find `foo' if there were
        two or more partial matches before the exact match in the list
        of attributes.

    o   Rdconv now creates direct HTML hyperlinks when linking to
        documentation in the same package.  The code now ensures that
        links which can be resolved within the package are so resolved,
        even when there are possible resolutions in other packages.

    o   If readBin(what=character()) is used incorrectly on a file which
        does not contain C-style character strings, warnings (usually
        many) are now given.

    o   Building libR.so with the zlib in the R sources was not
        finding the local zlib headers.

    o   system(intern=TRUE) has an undocumented line length limit of
        119 chars both on Unix and Windows.  The limit is now 8096 and
        documented.  On Unix (only) every 120th character used to be
        discarded.

    o   plot.POSIX[cl]t were not passing graphics parameters on to
        axis.POSIXct.

    o   On some HP-UX systems, installed scripts were not executable
        when using the BSD-compatible install system program found by
        configure.  We now always use install-sh on HP-UX. (PR#2091)

    o   c() was converting NA names to "NA": now proper NA strings are
        used wherever possible. (PR#2358)

    o   A typo was causing segfaults when using data.entry under SuSE.

    o   mostattributes<-() was failing to copy across dimnames when
        one component was NULL, affecting pmax() and pmin() when the
        first argument was a matrix.  (root cause of PR#2357)

    o   The pdf() device now initialises graphical parameters
        properly.  (PR#2281)

    o   Checks in the C code prevent possible memory faults when
        standardGeneric is called invalidly.

    o   Macros NEW_OBJECT (aka NEW) and MAKE_CLASS added; required by
        the .Call interface to generate arbitrary objects.

    o   Problem that prevented package tcltk from working with Tcl/Tk
        8.4 (crash on initialization) resolved.  (Notice that binaries
        may still require an older Tcl/Tk, for example on Windows).

    o   type.convert() was not getting the levels right if passed a
        character vector containing <NA>s, and `na.strings' did not
        contain "NA".  This affected read.table().

    o   Internal match function did not check for nor handle 0-length
        vectors.  (The R function match() did.)  This could cause
        type.convert() to segfault.

    o   The line length limit in output text connections has been
        raised to 8095 chars.

    o   Sweave now uses anonymous file rather than text connections
        to avoid the limits of the latter (see previous item).

    o   parsing did not work on connections when pushback was used (as
        it had never been implemented).  (PR#2396)

    o   max.col() only found NAs in the first column (typo).

    o   Added a workaround for recent versions of glibc (e.g. RedHat 8.0)
        with inconsistent mktime/localtime functions which caused
        conversion to/from POSIXct times prior to 1970-01-01 to be
        inconsistent.  On such platforms this is a run-time test to
        allow e.g. R compiled on RH7.2 to run on RH8.0.

    o   Clipping was not being reset properly between plots on the gtk()
        device (the default under the GNOME interface). (PR#2366)

    o   axis(*, fg= cc) now works (again) the same as axis(*, col = cc).


-- 
   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



From bates at stat.wisc.edu  Fri Jan 10 17:52:04 2003
From: bates at stat.wisc.edu (Douglas Bates)
Date: Fri Jan 10 17:52:04 2003
Subject: R-1.6.2 is available via rsync
In-Reply-To: <x2adi9rogm.fsf@biostat.ku.dk>
References: <x2adi9rogm.fsf@biostat.ku.dk>
Message-ID: <6rr8blhrro.fsf@bates4.stat.wisc.edu>

Sources for R-1.6.2 are now available via rsync at rsync.r-project.org

$ rsync rsync.r-project.org::
r-release      	R-1.6.2 sources (current released version - approx 30 MB)
r-patched      	R sources (patched released version - approx 30 MB)
r-devel        	R sources (development version)
r-manuals      	Development sources for manuals for R
r-recommended  	Sources for recommended R packages
xlispstat      	xlispstat sources (development version) CVS tree (approx 12 MB)
CRAN           	Complete CRAN ftp area
Bioc-release   	Bioconductor sources (current release version)
Bioc-devel     	Bioconductor sources (development version)
GGobi          	GGobi sources (devel version)
omega-cvs      	Omega Project for Statistical Computing CVS tree
r-project-web  	Web pages for www.r-project.org and mirrors
Omegahat       	Complete ftp archive for Omegahat



From p.dalgaard at biostat.ku.dk  Fri Jan 10 18:13:02 2003
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: Fri Jan 10 18:13:02 2003
Subject: [R] R-1.6.2 is released
In-Reply-To: <3E1EF8A0.F010C41F@bank-banque-canada.ca>
References: <x2adi9rogm.fsf@biostat.ku.dk>
	<3E1EF8A0.F010C41F@bank-banque-canada.ca>
Message-ID: <x2k7hdq670.fsf@biostat.ku.dk>

Paul Gilbert <pgilbert at bank-banque-canada.ca> writes:

> Peter
> 
> When I the URL in your message I am getting:
> 
> <H1>Not Found</H1>
> The requested URL /pub/CRAN/src/base/R-1.6.2.tgz was not found on this
> server.<P>
> <HR>
> <ADDRESS>Apache/1.3.26 Server at franz.stat.wisc.edu Port 80</ADDRESS>
> 

Something got changed, it seems. Try

http://cran.us.r-project.org/src/base/R-1.6.2.tgz

        -p

-- 
   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



From edd at debian.org  Sat Jan 11 11:31:05 2003
From: edd at debian.org (Dirk Eddelbuettel)
Date: Sat Jan 11 11:31:05 2003
Subject: Debian packages for R-1.6.2 released
In-Reply-To: <x2adi9rogm.fsf@biostat.ku.dk>
References: <x2adi9rogm.fsf@biostat.ku.dk>
Message-ID: <20030111040248.GA13518@sonny.eddelbuettel.com>

Debian packages for the Intel i386 platform have been uploaded to Debian's
master archive server. These packages have been built on Debian's 'testing'
release and will install and run on any 'testing' or 'unstable' system.

Debian 'unstable' packages for most of the other eleven hardware platforms
should be built during the night. 

Intel i386 packages for the more recent Debian 3.0 ('stable') release will
be built over the weekend.  

Regards,  Dirk

Files:
 096452016de9240288b2d21bed604012 1048 math optional r-base_1.6.2-1.dsc
 174e6280aa2f2102388ca9c7930b1843 8659106 math optional r-base_1.6.2.orig.tar.gz 
 8055e3bdfa65d531828dcd5f14300af9 6798 math optional r-base_1.6.2-1.diff.gz
 4f5c91a25dc2f17a78c6045921745ce0 4893338 math optional r-base-core_1.6.2-1_i386.deb
 dae9b95d99ab90c70226ea9ba600bbbd 43134 math optional r-gnome_1.6.2-1_i386.deb
 9ea88b758856bf4a1d43e17cdc064031 119940 math optional r-mathlib_1.6.2-1_i386.deb
 be5cb07b6d462240303eb06cffdc119c 3935108 math optional r-recommended_1.6.2-1_i386.deb
 3300604817c35b1fce7bf18e20584d58 14046 math optional r-base_1.6.2-1_all.deb
 2a903d1d11835881bc76b79f38ef8904 1442 devel optional r-base-dev_1.6.2-1_all.deb 
 e3fc89a5f49e5f1288d71edee6c7ad30 779396 math extra r-base-html_1.6.2-1_all.deb
 48a031ba1725ef57c89670ee717316e6 722702 math extra r-base-latex_1.6.2-1_all.deb 
 234c77226c5906253fafd12badc5bedb 4980892 doc optional r-doc-pdf_1.6.2-1_all.deb 
 d29587c5a22993172222f729bafb752f 299764  doc optional r-doc-html_1.6.2-1_all.deb 
 ce0008a4426938064c7bbc471b182415 310398 doc optional r-doc-info_1.6.2-1_all.deb

-- 
Prediction is very difficult, especially about the future. 
				             -- Niels Bohr



From dmurdoch at pair.com  Sat Jan 11 19:55:03 2003
From: dmurdoch at pair.com (Duncan Murdoch)
Date: Sat Jan 11 19:55:03 2003
Subject: Windows build of 1.6.2 uploaded to CRAN
Message-ID: <u5p02vk98pd6ak9c74g9bnalfaksh2g9k3@4ax.com>

I've just uploaded the build of the new R 1.6.2 release to CRAN.  It
will soon be visible there in 

 http://www.cran.r-project.org/bin/windows/base

and by Monday should be available on all the mirrors.

See the CHANGES file for windows-specific news about this release.  A
number of minor bugs have been fixed.

One change should help in debugging external code:  dyn.load now
checks whether or not the DLL it just loaded has messed with the
floating point control word.  This may turn up bugs in old code that
have been hidden for a long time, since the effects of an FPU control
word change are fairly subtle. 

It is also likely to turn up cases where video drivers are messing
with the FPU control word.  

If you see messages like

>Warning message: 
>DLL attempted to change FPU control word from 8001f to 9001f

look at the dyn.load help file, and if you still don't know how to fix
it, feel free to write to me for help.

Duncan Murdoch



From tlumley at u.washington.edu  Sat Jan 25 20:56:03 2003
From: tlumley at u.washington.edu (Thomas Lumley)
Date: Sat Jan 25 20:56:03 2003
Subject: survey package
Message-ID: <Pine.A41.4.44.0301251146060.188130-100000@homer04.u.washington.edu>

A new package `survey' for analysing complex survey samples is on CRAN.
It handles stratification, clustering, and unequal sampling probabilities
in descriptive statistics, glms, and general maximum likelihood fitting.
The package is still under development:
  - it doesn't do the finite population correction to variances
  - it needs some real life worked examples

Most importantly, though, I don't do this sort of analysis routinely, so
it's possible that some part of the interface is completely insane from
the viewpoint of practising survey statisticians. Now would be an
excellent time to complain.

	-thomas


Thomas Lumley			Asst. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle



From fharrell at virginia.edu  Thu Jan 30 13:29:05 2003
From: fharrell at virginia.edu (Frank E Harrell Jr)
Date: Thu Jan 30 13:29:05 2003
Subject: Statistical Tables and Plots using S and LaTeX
Message-ID: <20030129151419.6e90b003.fharrell@virginia.edu>

I am pleased to announce a major revision of the document "Statistical Tables and Plots using S and LaTeX".  It is available at http://hesweb1.med.virginia.edu/biostat/s/doc/summary.pdf (76 pages, 500K).  It should be of interest to those who produce statistical reports or those who use or would be interested in using LaTeX, the greatest productivity tool for document processing in my opinion.

-- 
Frank E Harrell Jr              Prof. of Biostatistics & Statistics
Div. of Biostatistics & Epidem. Dept. of Health Evaluation Sciences
U. Virginia School of Medicine  http://hesweb1.med.virginia.edu/biostat



From chong at stat.purdue.edu  Mon Mar  3 09:52:03 2003
From: chong at stat.purdue.edu (Chong Gu)
Date: Mon Mar  3 09:52:03 2003
Subject: gss_0.8-2
Message-ID: <200303022239.h22MdUP1123098@odds.stat.purdue.edu>

A new version of gss, version 0.8-2, is on CRAN now.  Numerous new
functionalities have been added since my last r-announce post.

An ssanova1 suite has been added since version 0.7-4.  It implements
low-dimensional approximations of the smoothing spline ANOVA models
of the ssanova suite.  ssanova1 scales much better than ssanova with
large sample sizes.

A gssanova1 suite is added for non Gaussian regression.  Similar to
ssanova1, it provides better scalability than gssanova.  Direct
cross-validation is used in gssanova1 instead of the indirect CV of
gssanova.  Currently, only three families are supported: binomial,
poisson, and Gamma; other families of gssanova will be added to
gssanova1 in the (near?) future.

An sshzd suite is added to fit hazard models using right-censored
lifetime data with possible left-truncation and covariates.  It
estimates log hazard as "bivariate" smooth functions of time and
covariates through penalized full likelihood.  It only takes static
covariates but accommodates interactions between time and covariates,
going beyond the proportional hazard models.

Utilities are provided for the calculation of a certain
Kullback-Leibler projection of cross-validated fits to "reduced model"
spaces, for the "testing" of model terms.  Projection code is provide
for ssanova1, gssanova1, ssden, and sshzd fits.

Further details are to be found in the documentations and the examples
therein.  As always, feature suggestions and bug reports will be
sincerely appreciated.

Chong Gu



From adrian.trapletti at lmttrading.com  Tue Mar  4 17:37:20 2003
From: adrian.trapletti at lmttrading.com (Adrian Trapletti)
Date: Tue, 04 Mar 2003 17:37:20 +0100
Subject: tseries contains a class for irregularly spaced time series
Message-ID: <3E64D640.8185C15A@lmttrading.com>

A new version of tseries (0.9-10) has been uploaded to CRAN. The new
version contains the class "irts" for irregularly spaced time series.
Irregular time series are basically time series where each observation
(uni- or multivariate) has a time-stamp represented by an object of
class "POSIXct". It provides some basic functionality such as reading
and writing irregular time series from files, or plotting, printing,
subscripting, and interpolating irregular time series. This is a first
version of the class "irts" and I very much welcome feedback.

best
Adrian

--
Dr. Adrian Trapletti             Phone :             +41 (0) 1 994 5631
Trapletti Statistical Computing  Mobile:             +41 (0)76 370 5631
Wildsbergstrasse 31              Fax   :             +41 (0) 1 994 5631
CH-8610 Uster                    Email :  mailto:a.trapletti at bluewin.ch
Switzerland                      WWW   : http://trapletti.homelinux.com


From gregory_r_warnes at groton.pfizer.com  Thu Mar  6 23:21:37 2003
From: gregory_r_warnes at groton.pfizer.com (Warnes, Gregory R)
Date: Thu, 6 Mar 2003 17:21:37 -0500 
Subject: Initial release of RSessionDA
Message-ID: <D7A3CFD7825BD6119B880002A58F06C202F2C696@groexmb02.pfizer.com>


> Announcing the initial release of RSessionDA.
> 
> RSessionDA provides objects for interacting with R from Zope
> <www.zope.org>, a full-featured web application development system.  These
> objects permit evaluation of functions in the R language using information
> in Zope.  R data objects, graphics files, printed output, script
> transcripts, and data files can be returned to Zope for display. These
> tools make it easy to create web applications that include advanced
> statistical functionality.
> 
> RSessionDA is built on RSOAP package, which provides access to R via the
> SOAP <http://www.w3.org/TR/SOAP/"> communications protocol.  This allows
> Zope to access multiple independent R sessions running (if desired) on a
> separate compute server.
> 
> For more information on or to download RSessionDA see:
> 
> <http://software.biostat.washington.edu/statsoft/snake/RSessionDA> or
> <http://www.zope.org/Members/warnes/RSessionDA/> 
> 
> For more information on or to download RSOAP see:
> 
> <http://software.biostat.washington.edu/statsoft/snake/RSOAP> or 
> 
> For more information on Zope see:
> 
> <http://www.zope.org>
> 
> -Greg


LEGAL NOTICE\ Unless expressly stated otherwise, this message is... [[dropped]]


From e.pebesma at geog.uu.nl  Wed Mar 12 11:46:12 2003
From: e.pebesma at geog.uu.nl (Edzer J. Pebesma)
Date: Wed, 12 Mar 2003 11:46:12 +0100
Subject: Gstat: multivariable geostatistics for S (R and S-Plus)
Message-ID: <3E6F0FF4.CCD7EDC9@geog.uu.nl>

The majority of the functionality present in the gstat stand-alone
program (http://www.gstat.org/) is now available as a package/library for
the S language (R, S-Plus), again called gstat. The package provides
multivariable geostatistical modelling, prediction and simulation, as
well as several visualisation functions.  Gstat was started 10 years
ago and was released under the GPL in 1996; the original stand-alone
program is closely linked to several GIS systems. Gstat was not initially
written for teaching purposes, but for research purposes, emphasizing
flexibility, scalability and portability. It can deal with a large number
of practical issues in geostatistics, including change of support (block
kriging), simple/ordinary/universal (co)kriging, fast local neighbourhood
selection, flexible trend modelling, variables with different sampling
configurations, and efficient simulation of large spatially correlated
random fields, indicator kriging and simulation, and (directional)
variogram and cross variogram modelling. The S formula/models interface
is used to define multivariable geostatistical models.

The source and windows package for R are available from CRAN. The page on
http://www.gstat.org/s.html has links to R and S-Plus (6.x) source code,
as well as examples, graphs, and a longer list of features. (A binary
Win32 S-Plus library is planned later this year.)

On http://www.ci.tuwien.ac.at/Conferences/DSC-2003/ you can find a
draft paper further describing the package.

Any feedback is appreciated.
--
Edzer


From e.pebesma at geog.uu.nl  Wed Mar 12 11:46:12 2003
From: e.pebesma at geog.uu.nl (Edzer J. Pebesma)
Date: Wed, 12 Mar 2003 11:46:12 +0100
Subject: [S] Gstat: multivariable geostatistics for S (R and S-Plus)
Message-ID: <3E6F0FF4.CCD7EDC9@geog.uu.nl>

The majority of the functionality present in the gstat stand-alone
program (http://www.gstat.org/) is now available as a package/library for
the S language (R, S-Plus), again called gstat. The package provides
multivariable geostatistical modelling, prediction and simulation, as
well as several visualisation functions.  Gstat was started 10 years
ago and was released under the GPL in 1996; the original stand-alone
program is closely linked to several GIS systems. Gstat was not initially
written for teaching purposes, but for research purposes, emphasizing
flexibility, scalability and portability. It can deal with a large number
of practical issues in geostatistics, including change of support (block
kriging), simple/ordinary/universal (co)kriging, fast local neighbourhood
selection, flexible trend modelling, variables with different sampling
configurations, and efficient simulation of large spatially correlated
random fields, indicator kriging and simulation, and (directional)
variogram and cross variogram modelling. The S formula/models interface
is used to define multivariable geostatistical models.

The source and windows package for R are available from CRAN. The page on
http://www.gstat.org/s.html has links to R and S-Plus (6.x) source code,
as well as examples, graphs, and a longer list of features. (A binary
Win32 S-Plus library is planned later this year.)

On http://www.ci.tuwien.ac.at/Conferences/DSC-2003/ you can find a
draft paper further describing the package.

Any feedback is appreciated.
--
Edzer
--------------------------------------------------------------------
This message was distributed by s-news at lists.biostat.wustl.edu.  To
...(s-news.. clipped)...

.


From rgentlem at jimmy.harvard.edu  Fri Mar 21 16:01:47 2003
From: rgentlem at jimmy.harvard.edu (Robert Gentleman)
Date: Fri, 21 Mar 2003 10:01:47 -0500
Subject: ArrayAnalyzer and Bioconductor
Message-ID: <20030321100147.B14924@jimmy.harvard.edu>

Today, Insightful Corporation (www.insightful.com) is announcing the
availability of S+ArrayAnalyzer, a new, integrated module for S-PLUS
based on collaboration with the BioConductor Project
(www.bioconductor.org) - an open source and open development software
project for the analysis and comprehension of genomic data.

The collaboration between Insightful and BioConductor delivers
benefits to both commercial and academic researchers analyzing
microarray experiments:

- BioConductor's advanced analytics for genomic data will be available
  to a wider audience via a commercially supported product from
  Insightful, a long-established vendor with fully staffed tech
  support, training, and consulting.

- S+ArrayAnalyzer adds numerous features that can improve productivity
  for many users, such as installation, more data access and import
  options, a guided-workflow interface, interactive graphs with
  hyperlinked annotation, Web deployment of applications.

- Insightful will sponsor a graduate student position in the
  BioConductor project to help drive continued advancements and
  innovation in both the open source and commercial offerings.

- A new differential expression library (lpetest), written by
  Insightful and the University of Virginia, will be ported to R and
  made available on the Comprehensive R Archive Network (CRAN) and
  BioConductor in Summer 2003.

Spokespeople for BioConductor see the collaboration as helping ensure
the distribution and high-level end-user support of key research tools
to the broadest possible population of researchers. These people
include: S.Dudoit, Division of Biostatistics, University of
California, Berkeley; R.A. Irizarry, Department of Biostatistics,
Johns Hopkins University; V.J. Carey, Harvard Medical School;
R. Gentleman, Harvard School of Public Health.

Shawn Javid, Insightful's CEO had this to add, "The collaboration with
BioConductor is a blueprint for how Insightful can work with the open
source community to bring highly innovative data analysis applications
to the widest possible user base.  This cooperation improves the
analytic solutions available to our common base of S programmers and
the non-statisticians who benefit from using applications developed
with S-PLUS and R."

S+ArrayAnalyzer is available now with pricing for commercial and
academic organizations available by calling (800)569-0123 x479, or via
email at pharmasales at insightful.com


From Friedrich.Leisch at ci.tuwien.ac.at  Thu Apr  3 13:08:54 2003
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich.Leisch at ci.tuwien.ac.at)
Date: Thu, 3 Apr 2003 13:08:54 +0200
Subject: R Foundation for Statistical Computing
Message-ID: <16012.5702.313924.464414@galadriel.ci.tuwien.ac.at>


The R Development Core Team would like to formally announce the
creation of the R Foundation for Statistical Computing. The Foundation
is incorporated in Austria and the specific details can be viewed at:

	http://www.r-project.org/foundation/

There are many reasons for this decision on our part, largely it is
based on the belief that R has become a mature and valuable tool and
we would like to ensure its continued development and the development
of future innovations in software for statistical and computational
research.

The R Foundation is a not for profit foundation whose general goals
are to provide support for the R project and other innovations in
statistical computing. The R Foundation will provide a reference point
for individuals, instititutions or commercial enterprises that want to
support or interact with the R development community.

We would like to solicit memberships from interested parties
(individual and institutional) in the R Foundation.  Details regarding
fees and membership categories can be obtained from the web site and
email enquiries can be sent to R-foundation at R-project.org.

Among the goals of the Foundation are the support of continued
development of R, the exploration of new methodology, teaching and
training of statistical computing and the organization of meetings and
conferences with a statistical computing orientation. We hope to
attract sufficient funding to make these goals realities.



For the R Development Core Team:

Robert Gentleman & Ross Ihaka
(Presidents, R Foundation)

Friedrich Leisch
(Secretary General, R Foundation)


From p.dalgaard at biostat.ku.dk  Wed Apr 16 15:42:04 2003
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: 16 Apr 2003 15:42:04 +0200
Subject: R-1.7.0 is released
Message-ID: <x2n0iqa79v.fsf@biostat.ku.dk>


I've rolled up R-1.7.0.tgz a short while ago. This is a new version
with major changes in the methods/class area and with namespaces used
much more widely than before. Several routines now use the faster and
more modern LAPACK library. Also notice that the underscore is now
strongly deprecated as an assignment operator.

There are also a bunch of new functions and an assortment of bugs have
been fixed.

You can get it from

http://cran.us.r-project.org/src/base/R-1.7.0.tgz

or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.
 
There is also a version split for floppies.

These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:

292dbe4dc47e6b492ff72a62471654ca  R-1.7.0.tgz
693d29ea3959f1b862704b59367e4ac1  R-1.7.0.tgz-split.aa
42b3fa5bc17fc3151eaabd2db0f530ca  R-1.7.0.tgz-split.ab
3fa95fa9661b6ff3ff33936ca57bdb89  R-1.7.0.tgz-split.ac
c124f1be4d35676975527bc19efbd579  R-1.7.0.tgz-split.ad
bb3a82202a8f113abf0260b6b585dc92  R-1.7.0.tgz-split.ae
84720f839a564abc8255c9a4b8c2980d  R-1.7.0.tgz-split.af
cfe0314cfc1ceea9ec74d00919e82865  R-1.7.0.tgz-split.ag


        For the R Core Team,

        Peter D.


Here's the relevant part of the NEWS file:


		CHANGES IN R VERSION 1.7.0


USER-VISIBLE CHANGES

    o	solve(), chol(), eigen() and svd() now use LAPACK routines
	unless a new back-compatibility option is turned on.  The
	signs and normalization of eigen/singular vectors may change
	from earlier versions.

    o	The `methods', `modreg', `mva', `nls' and `ts' packages
	are now attached by default at startup (in addition to `ctest').
	The option "defaultPackages" has been added which contains the
	initial list of packages.  See ?Startup and ?options for details.
	Note that .First() is no longer used by R itself.

	class() now always (not just when `methods' is attached) gives
	a non-null class, and UseMethod() always dispatches on the
	class that class() returns.  This means that methods like
	foo.matrix and foo.integer will be used.  Functions oldClass()
	and oldClass<-() get and set the "class" attribute as R
	without `methods' used to.

    o	The default random number generators have been changed to
	`Mersenne-Twister' and `Inversion'.  A new RNGversion()
	function allows you to restore the generators of an earlier R
	version if reproducibility is required.

    o	Namespaces can now be defined for packages other than `base':
	see `Writing R Extensions'.  This hides some internal objects
	and changes the search path from objects in a namespace.  All
	the base packages (except methods and tcltk) have namespaces,
	as well as the recommended packages `KernSmooth', `MASS',
	`boot', `class', `nnet', `rpart' and `spatial'.

    o	Formulae are not longer automatically simplified when terms()
	is called, so the formulae in results may still be in the
	original form rather than the equivalent simplified form
	(which may have reordered the terms): the results are now
	much closer to those of S.

    o	The tables for plotmath, Hershey and Japanese have been moved
	from the help pages (example(plotmath) etc) to demo(plotmath) etc.

    o	Errors and warnings are sent to stderr not stdout on
	command-line versions of R (Unix and Windows).

    o	The R_X11 module is no longer loaded until it is needed, so
	do test that x11() works in a new Unix-alike R installation.


NEW FEATURES

    o	if() and while() give a warning if called with a vector condition.

    o	Installed packages under Unix without compiled code are no
	longer stamped with the platform and can be copied to other
	Unix-alike platforms (but not to other OSes because of
	potential problems with line endings and OS-specific help files).

    o	The internal random number generators will now never return
	values of 0 or 1 for runif.  This might affect simulation
	output in extremely rare cases.	 Note that this is not
	guaranteed for user-supplied random-number generators, nor
	when the standalone Rmath library is used.

    o	When assigning names to a vector, a value that is too short is
	padded by character NAs. (Wishlist part of PR#2358)

    o	It is now recommended to use the 'SystemRequirements:' field in
	the DESCRIPTION file for specifying dependencies external to the
	R system.

    o	Output text connections no longer have a line-length limit.

    o	On platforms where vsnprintf does not return the needed buffer
	size the output line-length limit for fifo(), gzfile() and
	bzfile() has been raised from 10k to 100k chars.

    o	The Math group generic does not check the number of arguments
	supplied before dispatch: it used to if the default method had
	one argument but not if it had two.  This allows trunc.POSIXt()
	to be called via the group generic trunc().

    o	Logical matrix replacement indexing of data frames is now
	implemented (interpreted as if the lhs was a matrix).

    o	Recursive indexing of lists is allowed, so x[[c(4,2)]] is
	shorthand for x[[4]][[2]] etc.	(Wishlist PR#1588)

    o	Most of the time series functions now check explicitly for a
	numeric time series, rather than fail at a later stage.

    o	The postscript output makes use of relative moves, and so is
	somewhat more compact.

    o	%*% and crossprod() for complex arguments make use of BLAS
	routines and so may be much faster on some platforms.

    o	arima() has coef(), logLik() (and hence AIC) and vcov() methods.

    o	New function as.difftime() for time-interval data.

    o	basename() and dirname() are now vectorized.

    o	biplot.default() {mva} allows `xlab' and `ylab' parameters to
	be set (without partially matching to `xlabs' and `ylabs').
	(Thanks to Uwe Ligges.)

    o	New function capture.output() to send printed output from an expression
	to a connection or a text string.

    o	ccf() (pckage ts) now coerces its x and y arguments to class "ts".

    o	chol() and chol2inv() now use LAPACK routines by default.

    o	as.dist(.) is now idempotent, i.e., works for "dist" objects.

    o	Generic function confint() and `lm' method (formerly in
	package MASS, which has `glm' and `nls' methods).

    o	New function constrOptim() for optimisation under linear inequality
	constraints.

    o	Add `difftime' subscript method and methods for the group
	generics. (Thereby fixing PR#2345)

    o	download.file() can now use HTTP proxies which require `basic'
	username/password authentication.

    o	dump() has a new argument `envir'.  The search for named
	objects now starts by default in the environment from which
	dump() is called.

    o	The edit.matrix() and edit.data.frame() editors can now handle
	logical data.

    o	New argument `local' for example() (suggested by Andy Liaw).

    o	New function file.symlink() to create symbolic file links
	where supported by the OS.

    o	New generic function flush() with a method to flush connections.

    o	New function force() to force evaluation of a formal argument.

    o	New functions getFromNamespace(), fixInNamespace() and
	getS3method() to facilitate developing code in packages with
	namespaces.

    o	glm() now accepts `etastart' and `mustart' as alternative ways
	to express starting values.

    o	New function gzcon() which wraps a connection and provides
	(de)compression compatible with gzip.

	load() now uses gzcon(), so can read compressed saves from
	suitable connections.

    o	help.search() can now reliably match individual aliases and
	keywords, provided that all packages searched were installed
	using R 1.7.0 or newer.

    o	hist.default() now returns the nominal break points, not those
	adjusted for numerical tolerances.

	To guard against unthinking use, `include.lowest' in
	hist.default() is now ignored, with a warning, unless `breaks'
	is a vector.  (It either generated an error or had no effect,
	depending how prettification of the range operated.)

    o	New generic functions influence(), hatvalues() and dfbeta()
	with lm and glm methods; the previously normal functions rstudent(),
	rstandard(), cooks.distance() and dfbetas() became generic.
	These have changed behavior for glm objects -- all originating from
	John Fox' car package.

    o	interaction.plot() has several new arguments, and the legend
	is not clipped anymore by default.  It internally uses axis(1,*)
	instead of mtext().
	This also addresses "bugs" PR#820, PR#1305, PR#1899.

    o	New isoreg() function and class for isotonic regression
	(`modreg' package).

    o	La.chol() and La.chol2inv() now give interpretable error
	messages rather than LAPACK error codes.

    o	legend() has a new `plot' argument.  Setting it `FALSE' gives
	size information without plotting (suggested by U.Ligges).

    o	library() was changed so that when the methods package is
	attached it no longer complains about formal generic functions
	not specific to the library.

    o	list.files()/dir() have a new argument `recursive'.

    o	lm.influence() has a new `do.coef' argument allowing *not* to
	compute casewise changed coefficients.	This makes plot.lm() much
	quicker for large data sets.

    o	load() now returns invisibly a character vector of the names
	of the objects which were restored.

    o	New convenience function loadURL() to allow loading data files
	from URLs (requested by Frank Harrell).

    o	New function mapply(), a multivariate lapply().

    o	New function md5sum() in package tools to calculate MD5
	checksums on files (e.g. on parts of the R installation).

    o	medpolish() {package eda} now has an `na.rm' argument (PR#2298).

    o	methods() now looks for registered methods in namespaces, and
	knows about many objects that look like methods but are not.

    o	mosaicplot() has a new default for `main', and supports the
	`las' argument (contributed by Uwe Ligges and Wolfram Fischer).

    o	An attempt to open() an already open connection will be detected
	and ignored with a warning.  This avoids improperly closing
	some types of connections if they are opened repeatedly.

    o	optim(method = "SANN") can now cover combinatorial optimization
	by supplying a move function as the `gr' argument (contributed
	by Adrian Trapletti).

    o	PDF files produced by pdf() have more extensive information
	fields, including the version of R that produced them.

    o	On Unix(-alike) systems the default PDF viewer is now determined
	during configuration, and available as the 'pdfviewer' option.

    o	pie(...) has always accepted graphical pars but only passed
	them on to title().  Now pie(, cex=1.5) works.

    o	plot.dendrogram (`mva' package) now draws leaf labels if present
	by default.

    o	New plot.design() function as in S.

    o	The postscript() and PDF() drivers now allow the title to be set.

    o	New function power.anova.test(), contributed by Claus Ekstr?m.

    o	power.t.test() now behaves correctly for negative delta in the
	two-tailed case.

    o	power.t.test() and power.prop.test() now have a `strict'
	argument that includes rejections in the "wrong tail" in the
	power calculation. (Based in part on code suggested by Ulrich
	Halekoh.)

    o	prcomp() is now fast for n x m inputs with m >> n.

    o	princomp() no longer allows the use of more variables than
	units: use prcomp() instead.

    o	princomp.formula() now has principal argument `formula', so
	update() can be used.

    o	Printing an object with attributes now dispatches on the
	class(es) of the attributes. See ?print.default for the fine
	print. (PR#2506)

    o	print.matrix() and prmatrix() are now separate functions.
	prmatrix() is the old S-compatible function, and
	print.matrix() is a proper print method, currently identical
	to print.default().  prmatrix() and the old print.matrix()
	did not print attributes of a matrix, but the new print.matrix()
	does.

    o	print.summary.{lm,glm} now default to symbolic.cor = FALSE, but
	symbolic.cor can be passed to the print methods from the
	summary methods.  print.summary.{lm,glm} print correlations to
	2 decimal places, and the symbolic printout avoids abbreviating
	labels.

    o	If a prompt() method is called with 'filename' as 'NA', a
	list-style representation of the documentation shell generated
	is returned.  New function promptData() for documenting objects
	as data sets.

    o	qqnorm() and qqline() have an optional logical argument
	`datax' to transpose the plot (S-PLUS compatibility).

    o	qr() now has the option to use LAPACK routines, and the
	results can be used by the helper routines qr.coef(), qr.qy()
	and qr.qty().  The LAPACK-using versions may be much faster
	for large matrices (using an optimized BLAS) but are less
	flexible.

    o	QR objects now have class "qr", and solve.qr() is now just the
	method for solve() for the class.

    o	New function r2dtable() for generating random samples of two-way
	tables with given marginals using Patefield's algorithm.

    o	rchisq() now has a non-centrality parameter `ncp', and there's a
	C API for rnchisq().

    o	New generic function reorder() with a dendrogram method;
	new order.dendrogram() and heatmap().

    o	require() has a new argument, character.only,
	  -- to make it align with library.

    o	New functions rmultinom() and dmultinom(), the first one with
	a C API.

    o	New function runmed() for fast runnning medians (`modreg' package).

    o	New function slice.index() for identifying indexes with respect
	to slices of an array.

    o	solve.default(a) now gives the dimnames one would expect.

    o	stepfun() has a new `right' argument for right-continuous step
	function construction.

    o	str() now shows ordered factors different from unordered ones.
	It also differentiates "NA" and as.character(NA), also for factor
	levels.

    o	symnum() has a new logical argument `abbr.colnames'.

    o	summary(<logical>) now mentions NA's as suggested by
	G?ran Brostr?m.

    o	summaryRprof() now prints times with a precision appropriate
	to the sampling interval, rather than always to 2dp.

    o	New function Sys.getpid() to get the process ID of the R session.

    o	table() now allows exclude= with factor arguments (requested by
	Michael Friendly).

    o	The tempfile() function now takes an optional second argument
	giving the directory name.

    o	The ordering of terms for terms.formula(keep.order=FALSE) is
	now defined on the help page and used consistently, so that
	repeated calls will not alter the ordering (which is why
	delete.response() was failing: see the bug fixes).  The
	formula is not simplified unless the new argument `simplify'
	is true.

    o	added "[" method for terms objects.

    o	New argument `silent' to try().

    o	ts() now allows arbitrary values for y in start/end = c(x, y):
	it always allowed y < 1 but objected to y > frequency.

    o	unique.default() now works for POSIXct objects, and hence so
	does factor().


    o	Package tcltk now allows return values from the R side to the
	Tcl side in callbacks and the R_eval command. If the return
	value from the R function or expression is of class "tclObj"
	then it will be returned to Tcl.

    o	A new HIGHLY EXPERIMENTAL graphical user interface using the tcltk
	package is provided. Currently, little more than a proof of concept.
	It can be started by calling "R -g Tk" (this may change in later
	versions) or by evaluating tkStartGUI(). Only Unix-like systems
	for now. It is not too stable at this point; in particular, signal
	handling is not working properly.


    o	Changes to support name spaces:

	- Placing base in a name space can no longer be disabled by
	  defining the environment variable R_NO_BASE_NAMESPACE.

	- New function topenv() to determine the nearest top level
	  environment (usually .GlobalEnv or a name space environment).

	- Added name space support for packages that do not use methods.

    o	Formal classes and methods can be `sealed', by using the
	corresponding argument to setClass or setMethod.  New
	functions isSealedClass() and isSealedMethod() test sealing.

    o	packages can now be loaded with version numbers. This allows
	for multiple versions of files to be installed (and potentially
	loaded). Some serious testing will be going on, but it should
	have no effect unless specifically asked for.


INSTALLATION CHANGES

    o	TITLE files in packages are no longer used, the Title field
	in the DESCRIPTION file being preferred.  TITLE files will be
	ignored in both installed packages and source packages.

    o	When searching for a Fortran 77 compiler, configure by default
	now also looks for Fujitsu's frt and Compaq's fort, but no
	longer for cf77 and cft77.

    o	Configure checks that mixed C/Fortran code can be run before
	checking compatibility on ints and doubles: the latter test
	was sometimes failing because the Fortran libraries were not
	found.

    o	PCRE and bzip2 are built from versions in the R sources if the
	appropriate library is not found.

    o	New configure option --with-lapack to allow high-performance
	LAPACK libraries to be used: a generic LAPACK library will be
	used if found.	This option is not the default.

    o	New configure options --with-libpng, --with-jpeglib, --with-zlib,
	--with-bzlib and --with-pcre, principally to allow these
	libraries to be avoided if they are unsuitable.

    o	If the precious variable R_BROWSER is set at configure time
	it overrides the automatic selection of the default browser.
	It should be set to the full path unless the browser appears
	at different locations on different client machines.

    o	Perl requirements are down again to 5.004 or newer.

    o	Autoconf 2.57 or later is required to build the configure
	script.

    o	Configure provides a more comprehensive summary of its results.

    o	Index generation now happens when installing source packages
	using R code in package tools.	An existing 'INDEX' file is used
	as is; otherwise, it is automatically generated from the \name
	and \title entries in the Rd files.  Data, demo and vignette
	indices are computed from all available files of the respective
	kind, and the corresponding index information (in the Rd files,
	the 'demo/00Index' file, and the \VignetteIndexEntry{} entries,
	respectively).	These index files, as well as the package Rd
	contents data base, are serialized as R objects in the 'Meta'
	subdirectory of the top-level package directory, allowing for
	faster and more reliable index-based computations (e.g., in
	help.search()).

    o	The Rd contents data base is now computed when installing source
	packages using R code in package tools.	 The information is
	represented as a data frame without collapsing the aliases and
	keywords, and serialized as an R object.  (The 'CONTENTS' file
	in Debian Control Format is still written, as it is used by the
	HTML search engine.)

    o	A NAMESPACE file in root directory of a source package is copied
	to the root of the package installation directory.  Attempting to
	install a package with a NAMESPACE file using --save signals an
	error; this is a temporary measure.


DEPRECATED & DEFUNCT

    o	The assignment operator `_' will be removed in the next
	release and users are now warned on every usage: you may even see
	multiple warnings for each usage.

	If environment variable R_NO_UNDERLINE is set to anything of
	positive length then use of `_' becomes a syntax error.

    o	machine(), Machine() and Platform() are defunct.

    o	restart() is defunct.  Use try(), as has long been recommended.

    o	The deprecated arguments `pkg' and `lib' of system.file() have
	been removed.

    o	printNoClass() {methods} is deprecated (and moved to base,
	since it was a copy of a base function).

    o	Primitives dataClass() and objWithClass() have been replaced
	by class() and class<-(); they were internal support functions
	for use by package methods.

    o	The use of SIGUSR2 to quit a running R process under Unix is
	deprecated, the signal may need to be reclaimed for other
	purposes.


UTILITIES

    o	R CMD check more compactly displays the tests of DESCRIPTION
	meta-information.  It now reports demos and vignettes without
	available index information.  Unless installation tests are
	skipped, checking is aborted if the package dependencies cannot
	be resolved at run time.  Rd files are now also explicitly
	checked for empty \name and \title entries.  The examples are
	always run with T and F redefined to give an error if used
	instead of TRUE and FALSE.

    o	The Perl code to build help now removes an existing example
	file if there are no examples in the current help file.

    o	R CMD Rdindex is now deprecated in favor of function Rdindex()
	in package tools.

    o	Sweave() now encloses the Sinput and Soutput environments of
	each chunk in an Schunk environment. This allows to fix some
	vertical spacing problems when using the latex class slides.


C-LEVEL FACILITIES

    o	A full double-precision LAPACK shared library is made
	available as -lRlapack.	 To use this include
	$(LAPACK_LIBS) $(BLAS_LIBS) in PKG_LIBS.

    o	Header file R_ext/Lapack.h added.  C declarations of BLAS
	routines moved to R_ext/BLAS.h and included in R_ext/Applic.h
	and R_ext/Linpack.h for backward compatibility.

    o	R will automatically call initialization and unload routines, if
	present, in shared libraries/DLLs during dyn.load() and
	dyn.unload() calls. The routines are named R_init_<dll name>
	and R_unload_<dll name>, respectively.	See the Writing R
	Extensions Manual for more information.

    o	Routines exported directly from the R executable for use with
	.C(), .Call(), .Fortran() and .External() are now accessed via
	the registration mechanism (optionally) used by packages.  The
	ROUTINES file (in src/appl/) and associated scripts to
	generate FFTab.h and FFDecl.h are no longer used.

    o	Entry point Rf_append is no longer in the installed headers
	(but is still available).  It is apparently unused.

    o	Many conflicts between other headers and R's can be avoided by
	defining STRICT_R_HEADERS and/or R_NO_REMAP -- see `Writing R
	Extensions' for details.

    o	New entry point R_GetX11Image and formerly undocumented
	ptr_R_GetX11Image are in new header R_ext/GetX11Image.	These
	are used by package tkrplot.


BUG FIXES

    o	Sys.sleep() on Unix was having trouble with waits of less than 0.5s

    o	The fix to PR#2396 broke read.table() on files with CR line
	endings. (PR#2469)   Separate problem with this on Carbon MacOS
	build fixed as well.

    o	Converting Sweave files to noweb syntax using SweaveSyntConv()
	was broken.

    o	Printing numbers near the minimum could get the number of
	significant figures wrong due to underflow: for example 4e-308
	might print as 4.00000e-308.  (Seen on some Windows builds,
	and also on numbers around 1e-317 on Linux.)

    o	wilcox.test() could give integer overflow warnings on very long
	vectors.  Also added tests for numeric inputs, as per the help
	page.  (PR#2453)

    o	Printing unquoted character vectors containing escape
	characters was computing the wrong length and hence
	misaligning names.  This was due to a bug in Rstrlen which
	might have had other effects.

    o	if(logical(0)) and while(logical(0)) now report zero length,
	not `missing value where logical is needed'.

    o	The gaussian() and inverse.gaussian() families were documented
	to allow only one link, which has not been true in R for at
	least four years.

    o	prmatrix() forced conversion to character if `na.print' was
	used, and that conversion neither respected `digits' nor
	`quote'.

    o	Rprof() might give misleading results for too small values of
	`interval' and in practice the default 20ms was about as small
	as is advisable on Linux.  Now the interval is forced to be at
	least one clock tick.

    o	summary.data.frame() was not giving interpretable results when
	the data frame contained a data frame as a column. (PR#1891)

    o	delete.response() might re-order the rhs terms so prediction
	might fail or even give incorrect results. (PR#2206)

    o	StructTS() now accepts numeric time series of integer storage mode.

    o	all(), any() now handle NAs as documented.

    o	Subsetting arrays to a result with 0 dimension(s) failed if
	the array had dimnames. (PR#2507)

    o	If the call to data.frame() included 0-row arguments, it tried
	to replicate them to the maximum number of rows, and failed if
	this was 1 or more.

    o	replicate() now understands data frames to which na.omit() has
	been applied.

    o	is.ts() was too liberal: a time series must have at least one point.

    o	methods() was sorting by package, not by name.

    o	symbols(thermometers=) was often giving a spurious warning about
	the range.

    o	tcltk was using deprecated internals of the Tcl library when
	accessing error messages.  Not likely to be a user-visible
	change.

    o	The automatic search for BLAS libs now tries Sun's libsunperf
	the way the latest versions require. (PR#2530)

    o	str(array(1)) now does show the array.
	str(Surv(...)) now works again.

    o	step(), add1.default() and drop1.default() now work somewhat
	better if called from a function.

    o	page() was searching from the wrong environment, and so
	searching base before the workspace.

    o	crossprod(Z) for complex Z was returning nonsense.

    o	La.chol2inv() gave incorrect results unless the matrix was square.

    o	When the POSIXt date functions were required to guess DST,
	they sometimes guessed correctly that DST was in force but
	converted a POSIXlt time as if standard time was given.

    o	c/rbind were not handling zero col/row matrices correctly.
	(PR#2541 was one symptom.)

    o	approx() and approxfun() now work with 1 knot if
	method = "constant".  stepfun(), ecdf() and plot.stepfun() do so
	as well.

    o	AIC.lm/default was failing if multiple objects and k were
	specified.  (PR#2518)

    o	removeMethods{methods} was broken. (PR#2519)

    o	summary.glm() had two `aic' components in the returned object.

    o	autoload() was returning the value of its last command, a
	promise, even though it was documented to have no value.
	As a result some packages (e.g. nlme) were loading packages
	they meant to autoload.

    o	Fixes to methods and classes:
	   - show() is consistent with using setOldClass for S3 classes.
	   - several problems with the coerce and replace methods
	     generated by setIs have been fixed.
	   - more thorough tests & informative messages for invalid
	     `def' arguments to setGeneric
	   - setGeneric will now create the generic function even when
	     a generic of the same name already exists (it does issue
	     a warning).

    o	unz() connections could no longer be opened. (PR#2579)

    o	unique(ordered factor) returned an unordered factor. (PR#2591)

    o	x[] <- value coerced x to the mode of value if and only if x
	had length 0!  (Should only happen if x is null: PR#2590)

    o	lm() mislabelled the cols of the qr decomposition. (cause of PR#2586)

    o	data() looks for file extensions in an order prescribed in the
	help file: previously whether foo.R or foo.csv was used was
	locale-dependent.

    o	sys.function() now returns the actual function being evaluated in
	the specified frame rather than one inferred from the call.

    o	match.call() now uses the definition of the actual function being
	evaluated rather than one inferred from the call.

    o	abbreviate(*, dot = TRUE) now only adds a "." where abbreviations
	did happen.

    o	Changing timezones in the POSIXt functions was not working on
	some Linux systems, and this has been corrected.

    o	ks.test() in package ctest had numerical problems in the lower
	tail of the asymptotic distribution (PR#2571).

    o	Sweave() now handles empty chunks at the end of files correctly.

    o	[<-() lost the object bit if coercion was involved.

    o	package::object wasn't being deparsed properly.

    o	seq.POSIXt() with `by' an object of class "difftime" ignored
	the units.

    o	rank(c("B", NA)) no longer returns character.

    o	reference to by() added in ?tapply

    o	?lm describes what happens with matrix response

    o	The X11 device has improved event handling. In particular it
	used to often miss the last of a series of resize events.

    o	lm.influence() and related functions now work again for the
	multivariate case and when there are zero weights.

    o	format( <character> ) now always keeps names and dimnames.

    o	table(factor(c(2,NA), exclude=NULL)) prints better now.

    o	predict(foo, type = "terms") and hence
	residuals(foo, type = "partial") now work for lm and glm objects
	with weights zero.  Further, model.matrix() is now only called once.

    o	R CMD config now works correctly when called from a Makefile
	using GNU make.

    o	The data.frame method for rbind() was
	- converting character columns to factors,
	- converting ordered factor columns to unordered factors,
	- failing to append correctly a factor to a character column
	  and vice versa.

    o	as.hclust.twins() now does provide proper `labels', `method' and
	`call' components.

    o	cycle() sometimes failed on a time series which started at a cycle
	other than 1.

    o	read.dcf() read incorrectly files which did not end in a new line.

    o   read.socket() dropped certain non-alphanumeric characters. (PR#2639)

    o   termplot() handles missing data better (PR#2687, 
         <Mark.Bravington at csiro.au>)

    o	Corrected MacRoman encoding for Icircumflex etc.


-- 
   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


From bates at stat.wisc.edu  Wed Apr 16 17:23:22 2003
From: bates at stat.wisc.edu (Douglas Bates)
Date: 16 Apr 2003 10:23:22 -0500
Subject: R-1.7.0 sources now available through rsync
Message-ID: <6rn0iqpitx.fsf@bates4.stat.wisc.edu>

Sources for R-1.7.0 are now available through rsync to
rsync.r-project.org.

$ rsync rsync.r-project.org::
r-release      	R-1.7.0 sources (current released version - approx 30 MB)
r-patched      	R sources (patched released version - approx 30 MB)
r-devel        	R sources (development version)
r-manuals      	Development sources for manuals for R
r-recommended  	Sources for recommended R packages
xlispstat      	xlispstat sources (development version) CVS tree (approx 12 MB)
CRAN           	Complete CRAN ftp area
Bioc-release   	Bioconductor sources (current release version)
Bioc-devel     	Bioconductor sources (development version)
GGobi          	GGobi sources (devel version)
omega-cvs      	Omega Project for Statistical Computing CVS tree
r-project-web  	Web pages for www.r-project.org and mirrors
Omegahat       	Complete ftp archive for Omegahat


From edd at debian.org  Thu Apr 17 04:36:16 2003
From: edd at debian.org (Dirk Eddelbuettel)
Date: Wed, 16 Apr 2003 21:36:16 -0500
Subject: Debian packages for R-1.7.0 available
In-Reply-To: <x2n0iqa79v.fsf@biostat.ku.dk>
References: <x2n0iqa79v.fsf@biostat.ku.dk>
Message-ID: <20030417023616.GA30170@sonny.eddelbuettel.com>


Earlier today Doug Bates uploaded R 1.7.0 packages for Debian, which will be
installed into the master Debian archive, and which should be available on
mirrors soon afterwards. Doug also prepared versions for testing and stable
which are available via the Debian section of CRAN rather than the Debian
mirrors.

All these 1.7.0 versions builds upon the 7 pre-releases we made of R 1.7.0.
One noteworthy change is that the R_LIBS variable is now set. Its default
value, set via /etc/R/Renviron (to which /usr/lib/R/etc/Renviron links) sets
up three directories such that /usr/local/lib/R/site-library will
automatically be used for user-installed R packages, /usr/lib/R/site-library
is available for use by Debian R packages (such as, e.g., r-cran-tseries)
and /usr/lib/R/library will be used by packages contained in a main R
release such as 1.7.0.  We also improved upon our support for Atlas versions
of Lapack and Blas, and made some other smaller changes.

Regards,  Dirk

-- 
Better to have an approximate answer to the right question than a precise 
answer to the wrong question.  --  John Tukey as quoted by John Chambers


From dmurdoch at pair.com  Fri Apr 18 03:29:05 2003
From: dmurdoch at pair.com (Duncan Murdoch)
Date: Thu, 17 Apr 2003 21:29:05 -0400
Subject: R 1.7.0 Windows binary build released
Message-ID: <hrku9vgk9eet6g3nub6t9h4bdp0kdbei3i@4ax.com>

I've just finished uploading the Windows binary of R 1.7.0 to CRAN.
It should move to the public areas and the mirrors in a day or two.

It will appear in <http://cran.r-project.org/bin/windows/base> and the
corresponding directory on a mirror near you.

Duncan Murdoch


From erich.neuwirth at univie.ac.at  Thu Apr 24 00:38:36 2003
From: erich.neuwirth at univie.ac.at (Erich Neuwirth)
Date: Thu, 24 Apr 2003 00:38:36 +0200
Subject: R (D)COM server 1.2 and RExcel 1.0 available
Message-ID: <3EA715EC.6020404@univie.ac.at>

We have uploaded a major upgrade of our packages

R (D)COM Server V1.2
and
RExcel 1.0

The combined package is available in the
Software->Other
section of CRAN

 From the documentation:
This package contains a COM server used to connect a client application 
(e.g. Microsoft Excel) with R.
An Add-In for Microsoft Excel is provided as well as Active X controls 
to  be included in your applications.

Thomas Baier
Erich Neuwirth


From jfox at mcmaster.ca  Sat Apr 26 21:53:53 2003
From: jfox at mcmaster.ca (John Fox)
Date: Sat, 26 Apr 2003 15:53:53 -0400
Subject: new package: effects
Message-ID: <5.1.0.14.2.20030426155142.01e2de28@mcmail.cis.mcmaster.ca>

I've uploaded to CRAN a new package called effects. The package contains 
functions for tabular or graphical display of terms in a linear or 
generalized linear model, and is particularly suitable for models that 
contain terms -- such as main effects and interactions, or polynomial 
regressors -- related by marginality (hierarchy). A draft paper describing 
the package is located at 
<http://www.socsci.mcmaster.ca/jfox/Papers/effect-displays.pdf>.

John
-----------------------------------------------------
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario, Canada L8S 4M4
email: jfox at mcmaster.ca
phone: 905-525-9140x23604
web: www.socsci.mcmaster.ca/jfox


From hastie at stanford.edu  Wed Apr 30 20:19:29 2003
From: hastie at stanford.edu (Trevor Hastie)
Date: Wed, 30 Apr 2003 11:19:29 -0700
Subject: Least Angle Regression  packages for R
Message-ID: <00d601c30f45$0b30bf50$1b6640ab@stanford.edu>

Least Angle Regression software: LARS

"Least Angle Regression" ("LAR") is a new model selection
algorithm; a useful and less greedy version of traditional
forward selection methods. LAR is described in detail in a paper 
by Brad Efron, Trevor Hastie, Iain Johnstone and Rob Tibshirani,
soon to appear in the Annals of Statistics. 

The paper, as well as R and Splus packages, are available at
http://www-stat.stanford.edu/~hastie/Papers#LARS

A simple modification of the LAR algorithm implements Tibshirani's
Lasso, an attractive version of OLS that constrains the sum of the
absolute regression coefficients; the Lasso modification of the LARS
software calculates the entire Lasso path of coefficients for a given
problem at the cost of a single least squares fit.

A different LARS modification efficiently implements epsilon Forward
Stagewise linear regression, another promising new model selection
method closely related to Boosting.

The packages for R have also been submitted to CRAN

--------------------------------------------------------------------
  Trevor Hastie             hastie at stanford.edu  
  Professor, Department of Statistics, Stanford University
  Phone: (650) 725-2231 (Statistics)          Fax: (650) 725-8977  
  (650) 498-5233 (Biostatistics)   Fax: (650) 725-6951
  URL: http://www-stat.stanford.edu/~hastie  
  address: room 104, Department of Statistics, Sequoia Hall
           390 Serra Mall, Stanford University, CA 94305-4065  
--------------------------------------------------------------------

	[[alternate HTML version deleted]]


From jfox at mcmaster.ca  Mon May 26 16:27:53 2003
From: jfox at mcmaster.ca (John Fox)
Date: Mon, 26 May 2003 10:27:53 -0400
Subject: new cross-platform basic-statistics GUI
Message-ID: <5.1.0.14.2.20030526102510.01ea68e0@mcmail.cis.mcmaster.ca>

Dear R-announce list members,

I've submitted a new package to CRAN, Rcmdr, which provides a 
cross-platform basic-statistics GUI for R. Rcmdr is based on the tcltk 
package and uses only standard Tk widgets. It therefore runs under Windows 
if Tcl/Tk support is installed with R, although it requires the 
single-document interface (SDI). I've tested Rcmdr with Windows and Red Hat 
Linux; others have reported that it works on other Linux/Unix and Macintosh 
systems (the latter under X11).

The R-Commander GUI consists of a window containing several menus, buttons, 
and information fields. The Commander window also contains a log/script 
box. The R-Commander menus are easily configurable through a text file. The 
menu tree and additional information are available at 
<http://www.socsci.mcmaster.ca/jfox/Misc/Rcmdr/>.

The menus lead to simple dialog boxes, the general contents of which are 
more or less obvious from the names of the menu items. These boxes have a 
common structure, including a help button leading to the help page for a 
relevant function.

Commands generated via dialogs are posted to the R session window, along 
with printed output, and to the log window. Lines in the log window may be 
edited and (re)submitted for execution. Logs can be saved and reloaded.

My object in designing and implementing this GUI was to cover the content 
of a basic-statistics course. The target text was Moore's The Basic 
Practice of Statistics, Second Edition (Freeman, 2000), which is the text 
that I currently use for a two-semester introduction to statistics for 
undergraduate sociology majors. The R Commander implements the content of 
this text plus some additional material (e.g., linear and generalized 
linear models). As a result of several suggestions that I received, the 
coverage is now larger than originally envisaged, and I'm happy to 
entertain suggestions for further additions -- keeping in mind, however, 
the intended limited scope of the project.

Until the package appears on CRAN, you can download the package source and 
a Windows binary from my web site. The Rcmdr package mostly uses functions 
in the base and recommended packages; it also uses some functions in my car 
package.

John

-----------------------------------------------------
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario, Canada L8S 4M4
email: jfox at mcmaster.ca
phone: 905-525-9140x23604
web: www.socsci.mcmaster.ca/jfox



From Friedrich.Leisch at ci.tuwien.ac.at  Thu Jun  5 14:32:52 2003
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich.Leisch at ci.tuwien.ac.at)
Date: Thu, 5 Jun 2003 14:32:52 +0200
Subject: R News Volume 3/1
Message-ID: <16095.14452.682830.688153@galadriel.ci.tuwien.ac.at>

We have published the 2003/1 issue of R News on

        http://cran.R-project.org/doc/Rnews

where you can download the newsletter as PDF or Postscript file. It
will propagate to the CRAN mirrors within a day or two.


Contents of this issue:

Name Space Management for R
Converting Packages to S4
The genetics Package
Variance Inflation Factors    13
Building Microsoft Windows Versions of R and R packages under Intel Linux
Analysing Survey Data in R
Computational Gains Using RPVM on a Beowulf Cluster
R Help Desk  
Book Reviews   
Changes in R 1.7.0 
Changes on CRAN 
Crossword 
Recent Events


For the editorial board,
Fritz Leisch



From gb at stat.umu.se  Mon Jun 16 11:20:07 2003
From: gb at stat.umu.se (=?ISO-8859-1?Q?G=F6ran_Brostr=F6m?=)
Date: Mon, 16 Jun 2003 11:20:07 +0200 (CEST)
Subject: new package: eha
Message-ID: <Pine.LNX.4.44.0306161115420.8790-100000@tal.stat.umu.se>

A few days ago I uploaded to CRAN a new package called 'eha', which 
stands for 'Event History Analysis'. Its main focus is on proportional 
hazards modeling in survival analysis, and in that respect  eha  can
be regarded as a complement and an extension to the 'survival'
package. In fact  eha  requires  survival. Eha contains three functions
for proportional hazards analysis:

1. 'coxreg': Performs Cox regression, almost as 'coxph' in survival. 
There are two methods, 'efron' (default) and 'breslow', exactly as in
coxph. There are two extensions, compared to  coxph: (i) Sampling of 
survivors in risk sets (at event times), which can be useful with 
huge data sets and few events. (ii) The so-called 'weird bootstrap':
For the fitted model, new events are drawn in each risk set with 
probabilities given by the fitted model, independently between 
risk sets (that's the 'weird' part). This is repeated  R  times
and the output is two Rxp matrices, one with the bootstrap estimates 
of the regression coefficients, and one with the corresponding 
standard errors. The analysis is up to the user for now.
The 'boot' package?

2. 'mlreg': A discrete time proportional hazards model is fitted along 
the lines of Kalbfleisch & Prentice (1980, pp. 98--103). See also 
Brostr?m (2002): "Cox regression; Ties withot tears", Communications 
in Statistics, Theory & Methods 31, 285--297. This function has two methods;
"ML", the purely discrete model with one parameter per observed distinct 
event time, and "MPPL", which is a hybrid between Cox regression and 
the discrete model: Only tied event times are associated to a unique
parameter; the untied event times contributes a "Cox regression term".
For completely untied data this results in ordinary Cox regression.
"MPPL" can be regarded as an attempt to handle tied data in Cox regression, 
comparable to the 'efron' method. This method does not break down because 
of too heavily tied data, which the  efron  method might do.    
 
3. 'weibreg': Weibull regression for left truncated and right censored 
data. Allows for stratification with different shape and scale parameters 
in the strata. 

Moreover, there are functions for extracting subsamples as 'rectangles'
in the Lexis diagram, including external ('communal') covariates in a
'survival data frame', extracting information from risk sets, summary 
statistics from the Lexis diagram, etc, etc.

G?ran
---
 G?ran Brostr?m                    tel: +46 90 786 5223
 Department of Statistics          fax: +46 90 786 6614
 Ume? University                   http://www.stat.umu.se/egna/gb/
 SE-90187 Ume?, Sweden             e-mail: gb at stat.umu.se



From p.dalgaard at biostat.ku.dk  Mon Jun 16 12:48:33 2003
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: Mon, 16 Jun 2003 10:48:33 -0000
Subject: R 1.7.1 is released
Message-ID: <x2n0gil26b.fsf@biostat.ku.dk>

I've rolled up R-1.7.1.tgz a short while ago. This is a patch version
mainly fixing up an assortment of issues (see below). Note also that
it comes with an updated set of recommended packages, fixing a couple
of nasty issues in at least foreign and nlme.

You can get it from

http://cran.us.r-project.org/src/base/R-1.7.1.tgz

or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.
 
There is also a version split for floppies. 

These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:

833c2a9a62818211f2f9f0353ecd9bbd  R-1.7.1.tgz
0c3029b42f8eba12cc9acab6f28196dc  R-1.7.1.tgz-split.aa
3aafef440adfa65d1dd34b50399736d2  R-1.7.1.tgz-split.ab
388544d79c50b294783838ff8d3646e2  R-1.7.1.tgz-split.ac
f1f6e913030568b3416b9fe09d486aa6  R-1.7.1.tgz-split.ad
191cfeb78a2f98f084def26b4716e3ed  R-1.7.1.tgz-split.ae
73cf3ede9066716568219a8b13765fcf  R-1.7.1.tgz-split.af
65dc2729eaa13e91e867b2624cb80e11  R-1.7.1.tgz-split.ag


        For the R Core Team,

        Peter D.


Here's the relevant part of the NEWS file:

                CHANGES IN R VERSION 1.7.1


NEW FEATURES

    o   The help pages give appropriate references to the Blue,
        White or Green books for functions based on the descriptions
        of S functions given there. (E&OE)

    o   Function getAnywhere() can find non-exported objects, for
        namespaces or registered methods.


DEPRECATED & DEFUNCT

    o   The (unimplemented) argument 'white' of parse() is deprecated.

    o   The tkfilefind demo in the tcltk library is deprecated, since
        it never worked well, and apparently not at all with Tcl/Tk 8.4.


BUG FIXES

    o   print.table() used too much white space in some cases in 1.7.0.

    o   selectMethod() failed if `f' was a non-generic and
        optional=TRUE, and gave a confusing error message if
        optional=FALSE.

    o   pchisq(*, ncp) and qchisq(*, ncp) work in more cases for large ncp
        or quantile and give warning or error messages otherwise.

    o   str(x) now also works when x is an "externalptr" (or "weakref").

    o   rbeta(), rf(), and rt() now support infinite parameter values;
        other distributions return NaN instead of NA for such.

    o   Redefining a class is now safer if the new definition
        generates an error (previously some invalid metadata could be
        left behind).

    o   A number of errors are now caught in setClass() that
        previously either went unchecked or waited until new() to
        appear:
        - classes may not contain themselves, directly or indirectly;
        - classes appearing either as slots or as superclasses must
          themselves be defined;
        - slot names (direct or inherited) must be unique.
        In related changes, prototype() now works as documented, and is the
        recommended way to provide prototype objects.

    o   Sorting an ordered factor would return an unordered one.
        This caused some trouble with panel.superpose (PR#974).

    o   methods() could return duplicates if a method in a namespace
        was both exported and registered.

    o   The internal zip.unpack() could crash if more than 500 files
        were to be extracted. (PR#2818)

    o   The "r+" and "r+b" modes of opening file connections disallowed
        writing.

    o   library() now warns the user if the chosen package name
        doesn't match the internal package name, and corrects the
        error. (PR#2816)

    o   qr(LAPACK=TRUE) (and qr for complex arguments) might have failed
        to pivot for rank-deficient inputs. (PR#2867)

    o   Only re-mapped symbols are exported by regex.o, to avoid
        problems with embedded R on RedHat 9.

    o   arima() did not set transform.pars to FALSE if AR parameters
        were fixed, although it claimed to.

    o   pnorm() was slower than necessary in the outer tails in some
        cases due to a typo in the improvements from PR#699.  (PR#2883)

    o   setGeneric() and setMethod() now catch some examples where the
        generic and the method have different argument lists; the
        evaluator checks for internal consistency of these argument lists.

    o   expand.grid(x) {the rare case of one argument} now treats factor
        levels as in the typical case of two or more arguments.

    o   Some implicit coercions to lists could cause segfaults, e.g.
          x <- matrix(nrow=20000, ncol=20); x$any <- numeric(0)
        due to a PROTECT bug. (PR#2923)

    o   The replacement functions for colnames() and rownames() did not
        work for arrays with more than two dimensions.  They could
        create dimnames of the form list(NULL, NULL) rather than
        remove the dimnames attribute.

    o   termplot() gave incorrect answers with rug=TRUE or
        partial=TRUE for factors whose levels were not in
        lexicographical order.

    o   A serious performance flaw in as() computations was fixed (the
        methods were not being cached properly.)

    o   model.frame(~1, data) always returned 1 row. (PR#2958)

    o   The data editor was truncating objects to 65535 rows.  Pro
        tem, editing objects with more than 65535 rows is an error,
        and objects cannot be extended beyond that row. This restriction
        will be removed in 1.8.0.  (PR#2962)

    o   A bug could produce apparent loops in formal method selection
        when inheritance was restricted (used for the as() function).
        A related problem sometimes broke attaching a package that had
        methods for basic functions, such as names(), used in method
        selection.

    o   Empty expressions as in return(x,) could generate subsequent
        segfaults: they are now errors.  (PR#2880)

    o   The Kinderman-Ramage Normal Random Generator had several
        problems leading to not-quite normally distributed variates
        (PR#2846).  One problem was traced to an error in the original
        1976 JASA paper!  Thanks to Josef Leydold and his team for
        investigating this. The old generator has been retained for
        reproducibility of older results, under the name
        "Buggy Kinderman-Ramage".  A warning is issued if you select it
        (also indirectly via RNGversion()).

    o   promptMethods() now puts the \alias lines for methods in the
        normal place, near the top of the file, and quotes class
         names in signatures.

    o   getS3method() and methods() were not finding methods for
        coefficients() and fitted.values() (which dispatch on "coef"
        and "fitted" respectively).

    o   scan() (and hence read.table) was not finding matches for
        separator chars with the upper bit set.  (PR#3035)

    o   lm.(w)fit failed if the fit had rank 0.

    o   lqs() did not report explicitly that it had failed if all
        samples gave singular fits.

    o   predict.lm(*, se=TRUE) {w/ weights, w/o newdata} now gives correct
        SE's.  (PR#3043)

    o   cor.test(x, y, method="spearman") now also works for
        length(x) > 1290.

    o   Matrices were printed mis-aligned if right=TRUE and na.print
        was specified.  (PR#3058)

    o   R CMD check gives now a clearer message when latex produces
        errors on the package manual.  (PR#3070)

    o   isSeekable() was incorrectly returning FALSE on all file connections.

    o   tkpager() wasn't quite using its title and header arguments in
        the way prescribed by file.show()

    o   legend(*, pch=p, lty=l) now works better when `p' or `l' have
        NAs.

    o   All braces in regular expressions used by Sweave() are now
        escaped by a backslash.

    o   unloadNamespace() failed because getNamespaceImports() now coerces a
        string argument to a name space.

    o   deriv3 gave incorrect Hessians for some very simple
        expressions such as expression(x*y) (since the comments in the
        C code were incorrect).  (PR#2577)

    o   power.t.test(..., delta=NULL,alternative='two.sided') failed. (PR#2993)

    o   Lines on postscript() plots with thousands of segments might
        have been plotted inaccurately in 1.7.0. (PR#3132)

        Solid lines in postscript() output are split into groups of 1000
        segments to help some PostScript interpreters (typically old
        level-1 interpreters).

    o   cut.POSIXt failed when the breaks were date/time objects. (PR#3181)

    o   Usage of methods in dist.Rd is now correctly documented
        (as.matrix.dist() is not an exported symbol).

    o   The predict() method for ar fits was not retrieving the series
        from the parent environment.

    o   eigen() and La.eigen() were not returning a matrix of
        eigenvectors for a 1x1 input.

    o   hsv() and rgb() now return character(0) when one of their args has
        length 0.  This also fixes terrain.color(1). (PR#3233)

    o   [[<-.data.frame checked if a replacment was too short, but not
        if it was too long.  (related to PR#3229)

    o   qt(x, df) was quite inaccurate for df=1+epsilon; it is now much more
        accurate for df in (1,2) and more precise for other df. (PR#2991)

    o   qbeta() now has slightly improved C code in two places, as suggested
        in the 2nd followup to PR#2894.





-- 
   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



From dmurdoch at pair.com  Tue Jun 17 01:04:45 2003
From: dmurdoch at pair.com (Duncan Murdoch)
Date: Mon, 16 Jun 2003 19:04:45 -0400
Subject: Windows binary for 1.7.1 uploaded to CRAN
Message-ID: <36jsevkatmrbr6lrrgv6opv8t1jl98tpqg@4ax.com>

I've built the Windows binary for 1.7.1, and sent it to CRAN.  It
should be visible within a few hours, and will soon propagate to the
mirrors.

Duncan Murdoch



From stefano.iacus at unimi.it  Tue Jun 17 01:21:18 2003
From: stefano.iacus at unimi.it (Stefano Iacus)
Date: Tue, 17 Jun 2003 01:21:18 +0200
Subject: Carbon R 1.7.1 on CRAN
Message-ID: <3BA35499-A051-11D7-B5A3-003065CC4CB8@unimi.it>

I have just uploaded Carbon R 1.7.1 on CRAN.
It will be available to you with the usual timing of mirroring.

Contributed packages and the BioConductore bunble will follow shortly.

stefano iacus


-----------------------------------

Stefano M. Iacus
Department of Economics
University of Milan
Via Mercalli, 23
I-20123 Milan - Italy
Ph.: +39 02 50321 461
Fax: +39 02 50321 505
------------------------------------------------------------------------ 
------------
Please don't send me Word or PowerPoint attachments if not
absolutely necessary. See:
http://www.gnu.org/philosophy/no-word-attachments.html



From gregr at rand.org  Tue Jul 15 01:08:11 2003
From: gregr at rand.org (Greg Ridgeway)
Date: Mon, 14 Jul 2003 16:08:11 -0700
Subject: package announcement: Generalized Boosted Models (gbm)
Message-ID: <056e01c34a5c$cbe699c0$3f039a82@rand.org>

Generalized Boosted Models (gbm)

This package implements extensions to Y. Freund and R. Schapire's AdaBoost
algorithm and J. Friedman's gradient boosting machine (aka multivariate
adaptive regression trees, MART). It includes regression methods for least
squares, absolute loss, logistic, Poisson, Cox proportional hazards/partial
likelihood, and the AdaBoost exponential loss. It handles continuous,
nominal, ordinal covariates as well as those containing missing values. This
package also includes a preliminary out-of-bag estimator for the optimal
number of iterations, graphical tools for lower dimensional projections of
the fitted surface, and a few demos of example gbm sessions.

gbm 1.0 will soon appear on CRAN. Earlier versions have been up for a few
months and the latest includes many of the suggestions and fixes sent to me
by the early adopters.

Enjoy!

Greg

_______________________________________________________________
Greg Ridgeway, Ph.D.
Statistician
RAND
http://www.rand.org/methodology/stat/



From Friedrich.Leisch at ci.tuwien.ac.at  Wed Jul 16 11:13:46 2003
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich.Leisch at ci.tuwien.ac.at)
Date: Wed, 16 Jul 2003 11:13:46 +0200
Subject: CRAN package orphanizing process
Message-ID: <16149.5962.212995.750145@galadriel.ci.tuwien.ac.at>


As the list of packages on CRAN becomes longer almost on a weekly
basis, we need a formal mechanism to handle the case when somebody
wants to resign from maintaining a package.


Possible reasons for orphanizing a package:

1) The current maintainer actively wants to orphanize the package,
   e.g., because he has no longer the time or interest to act as
   package maintainer.

2) The current maintainer does not answer to emails by the CRAN admins
   for longer periods of time.


The orphanizing process:

1) The package gets the special keyword "ORPHANED" as maintainer in
   the DESCRIPTION file, the patch level of the version number is
   increased.

2) The package is moved from $CRAN/src/contrib to
   $CRAN/src/contrin/Orphaned.

3) As long as the package passes "R CMD check" for the current release
   version of R, it additionally remains in $CRAN/src/contrib/.


Everybody is more than welcome to take over as maintainer of an
orphaned package. Simply download the package sources, make changes if
necessary (respecting original author and license!) and resubmit the
package to CRAN with your name as maintainer in the DESCRIPTION file
of the package.

For the CRAN admins,
Fritz Leisch



From tlumley at u.washington.edu  Mon Jul 28 02:16:50 2003
From: tlumley at u.washington.edu (Thomas Lumley)
Date: Sun, 27 Jul 2003 17:16:50 -0700 (PDT)
Subject: survey package
Message-ID: <Pine.A41.4.44.0307271703170.159126-100000@homer06.u.washington.edu>


Version 1.9 of the survey package, now percolating through CRAN, adds a
beta implementation of replication weights.  These can either be created
from a survey design (using BRR, JK1, or JKn schemes) or provided by the
user.  These have been tested on only a few examples so far: there seem to
be relatively few published datasets with suitable analyses.

As with earlier versions of the package, I particularly welcome feedback
on the user interface from practising survey statisticians.


	-thomas

Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle



From fharrell at virginia.edu  Fri Jul 18 18:39:59 2003
From: fharrell at virginia.edu (Frank E Harrell Jr)
Date: Fri, 18 Jul 2003 16:39:59 -0000
Subject: Hmisc on CRAN
Message-ID: <20030718072911.0a9d38af.fharrell@virginia.edu>

I am pleased to announce that a new version of the Hmisc package, 2.0-0, is on CRAN.  Thanks to Kurt Hornik and Uwe Ligges and others for making this possible.  Thanks also to Xiao Gang Fan who has generously ported Hmisc and Design to Windows multiple times until now.  The Design package will soon be on CRAN too.

---
Frank E Harrell Jr              Prof. of Biostatistics & Statistics
Div. of Biostatistics & Epidem. Dept. of Health Evaluation Sciences
U. Virginia School of Medicine  http://hesweb1.med.virginia.edu/biostat



From Giles.Heywood at CommerzbankIB.com  Mon Aug 11 08:27:03 2003
From: Giles.Heywood at CommerzbankIB.com (Heywood, Giles)
Date: Mon, 11 Aug 2003 07:27:03 +0100
Subject: New package: irregular time-series (its)
Message-ID: <8CBAA121CEB4D5118CB200508BB2BBEF54043E@xmx8lonib.lonib.commerzbank.com>

I have uploaded to CRAN a new package named 'its' (Irregular Time-Series).
It
implements irregular time-series as an S4 class, extending the matrix class,
and records the time-stamp of each row in the matrix using POSIX.  Print,
plot,
extraction, append, and related functionality are available.

Feedback and suggestions are welcome.

Giles Heywood


********************************************************************** 
This is a commercial communication from Commerzbank AG.\ \ T...{{dropped}}



From ligges at statistik.uni-dortmund.de  Fri Aug 29 20:15:09 2003
From: ligges at statistik.uni-dortmund.de (Uwe Ligges)
Date: Fri, 29 Aug 2003 20:15:09 +0200
Subject: Notes on Windows binaries of contributed  packages
Message-ID: <3F4F982D.3030300@statistik.uni-dortmund.de>

Announcement for Windows users of R < 1.7.0
  and maintainers of contributed packages


[Please do not reply to r-announce!]


Windows users of R < 1.7.0
==========================
[Users of R-1.7.x are not affected.]

In order to clean up the directory structure on CRAN, the Windows binary
version of contributed packages for R < 1.7.0 will be moved from
   Your-CRAN-Mirror/bin/windows/contrib
to a subdirectory ./1.6 shortly.
Therefore, install.packages() and friends of R < 1.7.0 won't work
without specifying argument "contriburl" explicitly. Of course, manual
download and installation is possible as well. Note that these packages
are no longer being updated (last update was: 11-Apr-2003).
ReadMe files will be available in the corresponding directories.

It is highly recommended to upgrade to a recent version of R!


Maintainers of contributed packages
===================================
Starting with the first alpha releases of R-1.8.0 (in development), I am
going to make Windows binary versions of contributed packages available
(around September 13) at Your-CRAN-Mirror/bin/windows/contrib/1.8
(currently still linked to the ./1.7 directory).
Packages that do not compile out of the box or do not pass "Rcmd check"
with "OK" or "WARNING" will *not* be published. This "Status", i.e.
result of "Rcmd check" ("OK", "WARNING", "ERROR"), will be listed in a
file "./1.8/Status". Corresponding check.log will be available in
subdirectory ./1.8/check.
For details, please read the ReadMe (to appear).


Best regards,
Uwe Ligges



From Friedrich.Leisch at ci.tuwien.ac.at  Tue Sep  2 08:37:42 2003
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich.Leisch at ci.tuwien.ac.at)
Date: Tue, 2 Sep 2003 08:37:42 +0200
Subject: R News: Call for Papers
Message-ID: <16212.15030.153585.393504@celeborn.leisch.at>


R News (see http://CRAN.R-project.org/doc/Rnews/) is running low on
submissions lately. If you are the author of a package on CRAN or
Bioconductor and want to attract a larger audience to your software,
you should consider writing a short article introducing the
package. Another "typical" kind of R News article is to describe a
data analysis application using R (not necessarily using software you
have written).

We are looking forward to all contributions!

For the editorial board,
Fritz Leisch

-- 
-------------------------------------------------------------------
                        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



From maechler at stat.math.ethz.ch  Mon Sep 15 17:07:09 2003
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Mon, 15 Sep 2003 17:07:09 +0200
Subject: Fourth R Mailing List : "R-packages"
Message-ID: <16229.54685.100766.810816@gargle.gargle.HOWL>

We (mainly the R core team) have been discussing the creation of another
R mailing list, with the goal to fill the gap between

   R-help	 very high volume, with its great merits, but....

and 

   R-announce	 only for R important announcements (mostly R-core)
		 hence __MODERATED__ and *very* low volume, and hence 
		 highly recommended for almost all users of R.
		 *** all messages are forwarded to R-help ***

In the past, several CRAN package authors have rightly felt that
they would like the announcement of a major update of a package
be a bit more prominent than the flood of messages on R-help but
(most of the time) they still weren't supposed nor granted to
use R-announce for this. This has been one main motivation for
this new mailing list:

  R-packages  	o  all messages forwarded to R-help
  	        o  moderated (i.e. not accepting posts by anyone),
                   but CRAN package authors (and others,
		   similarly qualified) can freely post without
		   moderator interaction {unless there's abuse}.

The corresponding (new) web page,
    http://www.stat.math.ethz.ch/mailman/listinfo/r-packages/
now has

  TITLE:	     R Packages & Extensions Announcements

  DESCRIPTION :

     A moderated board for announcements about contributed R packages
     and similar R project extensions.

     All messages are forwarded to R-help automatically, so please do
     not subscribe to this list if you are subscribed to R-help.

     For major announcements on the R project, see the R-announce
     mailing list, instead.

And R-project.org's "Mailing Lists" web page will describe it
from tomorrow as

>> R-packages
>> 
>>     This list is for announcements as well, usually on the
>>     availability of new or enhanced contributed packages (on CRAN, typically).
>> 
>>     Note that the list is moderated. However, CRAN package
>>     authors (and others, similarly qualified) can freely post.
>> 
>>     As with R-announce, all messages to R-packages are
>>     automatically forwarded to the main R-help mailing list;
>>     hence you should only subscribe to R-packages if you do not
>>     to R-help.
>> 
>>     Use the web interface for information, subscription, archives, etc.

Amount of mail to expect:  Of course, we don't know yet, but
       I'd expect to see only a few messages per week.

Finally, just re-iterating the obvious: 

 o	This is *NOT* a list for discussion, just announcements of extensions to R.

 o	Do only subscribe if you are *NOT* subscribed to R-help,
	(but then, strongly consider doing it)!
 
For more info, subscription, etc, please use the URL above

Your R mailing list maintainer,
Martin Maechler <maechler at stat.math.ethz.ch>	http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum  LEO C16	Leonhardstr. 27
ETH (Federal Inst. Technology)	8092 Zurich	SWITZERLAND
phone: x-41-1-632-3408		fax: ...-1228			<><



From p.dalgaard at biostat.ku.dk  Wed Oct  8 14:06:39 2003
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard BSA)
Date: Wed, 08 Oct 2003 12:06:39 -0000
Subject: R-1.8.0 is released
Message-ID: <x23ce4gcd6.fsf@biostat.ku.dk>

I've rolled up R-1.8.0.tgz a short while ago. This is a new version
with major changes (see below). Notably, the Macintosh version for OS
X has been substantially improved; the old Carbon interface is no
longer being supported.

Also notice that the underscore will no longer work as an assignment
operator.

There is also a bunch of new functions and an assortment of bugs have
been fixed.

You can get it from

http://cran.us.r-project.org/src/base/R-1.8.0.tgz

or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.
 
There is also a version split for floppies.

These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:

bb019d7e12e38ac8a8bc247f06cc6b42  R-1.8.0.tgz
80fd20fdd2b995ab69cfd8cde80267cf  R-1.8.0.tgz-split.aa
074140872c9c015089543c9497a3be87  R-1.8.0.tgz-split.ab
f0e6005491839dd27636020f6475f4e2  R-1.8.0.tgz-split.ac
e7e817911d57e3c88959d6b86c061dd5  R-1.8.0.tgz-split.ad
52e9aff83357b65926f422abececba92  R-1.8.0.tgz-split.ae
6c6965e7f97b627280326ec6c436ab48  R-1.8.0.tgz-split.af
00ce1b1384f403ba76d8de302e92da1d  R-1.8.0.tgz-split.ag

On behalf of the R Core Team,

        Peter Dalgaard


Here's the relevant part of the NEWS file


		CHANGES IN R VERSION 1.8.0


MACOS CHANGES

    o	As from this release there is only one R port for the
	Macintosh, which runs only on MacOS X.	(The `Carbon' port has
	been discontinued, and the `Darwin' port is part of the new
	version.)   The current version can be run either as a
	command-line application or as an `Aqua' console.  There is a
	`Quartz' device quartz(), and the download and installation of
	both source and binary packages is supported from the Aqua
	console.  Those CRAN and BioC packages which build under MacOS
	X have binary versions updated daily.


USER-VISIBLE CHANGES

    o	The defaults for glm.control(epsilon=1e-8, maxit=25) have been
	tightened: this will produce more accurate results, slightly
	slower.

    o	sub, gsub, grep, regexpr, chartr, tolower, toupper, substr,
	substring, abbreviate and strsplit now handle missing values
	differently from "NA".

    o	Saving data containing name space references no longer warns
	about name spaces possibly being unavailable on load.

    o	On Unix-like systems interrupt signals now set a flag that is
	checked periodically rather than calling longjmp from the
	signal handler.	 This is analogous to the behavior on Windows.
	This reduces responsiveness to interrupts but prevents bugs
	caused by interrupting computations in a way that leaves the
	system in an inconsistent state.  It also reduces the number
	of system calls, which can speed up computations on some
	platforms and make R more usable with systems like Mosix.


CHANGES TO THE LANGUAGE

    o	Error and warning handling has been modified to incorporate a
	flexible condition handling mechanism.	See the online
	documentation of 'tryCatch' and 'signalCondition'.  Code that
	does not use these new facilities should remain unaffected.

    o	A triple colon operator can be used to access values of internal
	variables in a name space (i.e. a:::b is the value of the internal
	variable b in name space a).

    o	Non-syntactic variable names can now be specified by inclusion
	between backticks `Like This`.	The deparse() code has been
	changed to output non-syntactical names with this convention,
	when they occur as operands in expressions.  This is controlled
	by a `backtick' argument, which is by default TRUE for
	composite expressions and FALSE for single symbols.  This
	should give minimal interference with existing code.

    o	Variables in formulae can be quoted by backticks, and such
	formulae can be used in the common model-fitting functions.
	terms.formula() will quote (by backticks) non-syntactic names
	in its "term.labels" attribute.	 [Note that other code using
	terms objects may expect syntactic names and/or not accept
	quoted names: such code will still work if the new feature is
	not used.]


NEW FEATURES

    o	New function bquote() does partial substitution like LISP backquote.

    o	capture.output() takes arbitrary connections for `file' argument.

    o	contr.poly() has a new `scores' argument to use as the base set
	for the polynomials.

    o	cor() has a new argument `method = c("pearson","spearman","kendall")'
	as cor.test() did forever. The two rank based measures do work with
	all three missing value strategies.

    o	New utility function cov2cor() {Cov -> Corr matrix}.

    o	cut.POSIXt() now allows `breaks' to be more general intervals
	as allowed for the `by' argument to seq.POSIXt().

    o	data() now has an 'envir' argument.

    o	det() uses an LU decomposition and LAPACK.  The `method'
	argument to det() no longer has any effect.

    o	dev.control() now accepts "enable" as well as "inhibit".
	(Wishlist PR#3424)

    o	*, - and / work more generally on "difftime" objects, which now
	have a diff() method.

    o	dt(*, ncp = V)	is now implemented, thanks to Claus Ekstroem.

    o	dump() only quotes object names in the file where necessary.

    o	eval() of a promise forces the promise

    o	file.path() now returns an empty character vector if given at
	least one zero-length argument.

    o	format() and hence print() make an effort to handle corrupt
	data frames, with a warning.

    o	format.info() now also works with `nsmall' in analogy with
	format.default().

    o	gamma(n) is very slightly more precise for integer n in 11:50.

    o	? and help() will accept more un-quoted arguments, e.g. NULL.

    o	The "?" operator has new forms for querying documentation on
	S4 methods.  See the online documentation.

    o	New argument frame.plot = axes (== TRUE)  for filled.contour().

    o	New argument fixed = TRUE for grep() and regexpr() to avoid the
	need to escape strings to match.

    o	grep(x, ..., value = TRUE) preserves names of x.

    o	hist.POSIXt() can now pass arguments to hist.default()

    o	legend() and symbols() now make use of xy.coords() and accept
	a wider range of coordinate specifications.

    o	Added function library.dynam.unload() to call dyn.unload() on
	a loaded DLL and tidy up.  This is called for all the standard
	packages in namespaces with DLLs if their namespaces are unloaded.

    o	lm(singular.ok = FALSE) is now implemented.

    o	Empty lm() and glm() fits are now handled by the normal
	code: there are no methods for classes "lm.null" and
	"glm.null".  Zero-rank fits are handled consistently.

    o	make.names() has improvements, and there is a new auxiliary
	function make.unique().	 (Based on code contributed by Tom
	Minka, since converted to a .Internal function.)  In
	particular make.names() now recognises that names beginning
	with a dot are valid and that reserved words are not.

    o	methods() has a print method which asterisks functions which
	are not user-visible.  methods(class = "foo") now lists
	non-visible functions, and checks that there is a matching generic.

    o	model.matrix() now warns when it removes the response from the
	rhs of the formula: that this happens is now documented on its
	help page.

    o	New option `locatorBell' to control the confirmation beep
	during the use of locator() and identify().

    o	New option("scipen") provides some user control over the
	printing of numbers in fixed-point or exponential notation.
	(Contributed by David Brahm.)

    o	plot.formula() now accepts horizontal=TRUE and works correctly
	when boxplots are produced.  (Wishlist PR#1207)	 The code has
	been much simplified and corrected.

    o	polygon() and rect() now interpret density < 0 or NA to mean
	filling (by colour) is desired: this allows filling and
	shading to be mixed in one call, e.g. from legend().

    o	The predict() methods for classes lm, glm, mlm and lqs take a
	`na.action' argument that controls how missing values in
	`newdata' are handled (and defaults to predicting NA).
	[Previously the value of getOption("na.action") was used and
	this by default omitted cases with missing values, even if set
	to `na.exclude'.]

    o	print.summary.glm() now reports omitted coefficients in the
	same way as print.summary.lm(), and both show them as NAs in
	the table of coefficients.

    o	print.table() has a new argument `zero.print' and is now
	documented.

    o	rank(x, na.last = "keep") now preserves NAs in `x', and the
	argument `ties.method' allows to use non-averaging ranks in the
	presence of ties.

    o	read.table()'s 'as.is' argument can be character, naming columns
	not to be converted.

    o	rep() is now a generic function, with default, POSIXct and
	POSIXlt methods.  For efficiency, the base code uses rep.int()
	rather than rep() where possible.

    o	New function replicate() for repeated evaluation of expression
	and collection of results, wrapping a common use of sapply()
	for simulation purposes.

    o	rev() is now a generic function, with default and dendrogram
	methods.

    o	serialize() and unserialize() functions are available for
	low-level serialization to connections.

    o	socketSelect() allows waiting on multiple sockets.

    o	sort(method = "quick", decreasing = TRUE) is now implemented.

    o	sort.list() has methods "quick" (a wrapper for sort(method =
	"quick", index.return = TRUE) and "radix" (a very fast method
	for small integers).  The default "shell" method works faster
	on long vectors with many ties.

    o	stripchart() now has `log', `add' and `at' arguments.

    o	strsplit(x, *) now preserves names() but won't work for
	non-character `x' anymore {formerly used as.character(x),
	destroying names(x)}.

    o	textConnection() now has a local argument for use with output
	connections.  local = TRUE means the variable containing the
	output is assigned in the frame of the caller.

    o	Using UseMethod() with more than two arguments now gives a
	warning (as R-lang.texi has long claimed it did).

    o	New function vignette() for viewing or listing vignettes.

    o	which.min(x) and which.max(x) now preserve names.

    o	xy.coords() coerces "POSIXt" objects to "POSIXct", allowing
	lines etc to added to plot.POSIXlt() plots.

    o	.Machine has a new entry, sizeof.pointer.

    o	.Random.seed is only looked for and stored in the user's
	workspace.  Previously the first place a variable of that name
	was found on the search path was used.

    o	Subscripting for data.frames has been rationalized:

	- Using a single argument now ignores any `drop' argument
	  (with a warning).  Previously using `drop' inhibited list-like
	  subscripting.

	- adf$name <- value now checks for the correct length of
	  `value', replicating a whole number of times if needed.

	- adf[j] <- value and adf[[j]] <- value did not convert
	  character vectors to factors, but adf[,j] <- value did.
	  Now none do.	Nor is a list `value' coerced to a data frame
	  (thereby coercing character elements to factors).

	- Where replicating the replacement value a whole number of
	  times will produce the right number of values, this is
	  always done (rather than some times but not others).

	- Replacement list values can include NULL elements.

	- Subsetting a data frame can no longer produce duplicate
	  column names.

	- Subsetting with drop=TRUE no longer sometimes drops
	  dimensions on matrix or data frame columns of the data frame.

	- Attributes are no longer stripped when replacing part of a column.

	- Columns added in replacement operations will always be
	  named, using the names of a list value if appropriate.

	- as.data.frame.list() did not cope with list names such as
	  `check.rows',	 and formatting/printing data frames with such
	  column names now works.

	- Row names in extraction are still made unique, but without
	  forcing them to be syntactic names.

	- adf[x] <- list() failed if x was of length zero.


    o	Setting dimnames to a factor now coerces to character, as S
	does.  (Earlier versions of R used the internal codes.)

    o	When coercion of a list fails, a meaningful error message is given.

    o	Adding to NULL with [[ ]] generates a list if more than one
	element is added (as S does).

    o	There is a new command-line flag --args that causes the rest of
	the command line to be skipped (but recorded in commandArgs()
	for further processing).

    o	S4 generic functions and method dispatch have been modified to
	make the generic functions more self-contained (e.g., usable
	in apply-type operations) and potentially to speed dispatch.

    o	The data editor is no longer limited to 65535 rows, and will
	be substantially faster for large numbers of columns.

    o	Standalone Rmath now has a get_seed function as requested (PR#3160).

    o	GC timing is not enabled until the first call to gc.time(); it
	can be disabled by calling gc.time(FALSE).  This can speed up
	the garbage collector and reduce system calls on some
	platforms.

    o	textConnection() now has a local argument for use with output
	connections. local = TRUE means the variable containing the output
	is assigned in the frame of the caller.


STANDARD PACKAGES

    o	New package 'mle'. This is a simple package to find maximum
	likelihood estimates, and perform likelihood profiling and
	approximate confidence limits based upon it.  A well-behaved
	likelihood function is assumed, and it is the responsibility
	of the user to gauge the applicability of the asymptotic
	theory.  This package is based on S4 methods and classes.

    o	Changes in package 'mva':

	- factanal() now returns the test statistic and P-value formerly
	  computed in the print method.

	- heatmap() has many more arguments, partly thanks to Wolfgang
	  Huber and Andy Liaw.

	- Arguments `unit' and `hmin' of plclust() are now implemented.

	- prcomp() now accepts complex matrices, and there is biplot()
	  method for its output (in the real case).

	- dendrograms are slightly better documented, methods working with
	  "label", not "text" attribute.  New rev() method for dendrograms.

	- plot.dendrogram() has an explicit `frame.plot' argument
	  defaulting to FALSE (instead of an implicit one defaulting to TRUE).

    o	Changes in package 'tcltk':

	- The package is now in a namespace.  To remove it you will
	  now need to use unloadNamespace("tcltk").

	- The interface to Tcl has been made much more efficient by
	  evaluating Tcl commands via a vector of Tcl objects rather
	  than by constructing the string representation.

	- An interface to Tcl arrays has been introduced.

	- as.tclObj() has gained a `drop' argument to resolve an
	  ambiguity for vectors of length one.

    o	Changes in package 'tools':

	- Utilities for testing and listing files, manipulating file
	  paths, and delimited pattern matching are now exported.

	- Functions checkAssignFuns(), checkDocArgs() and checkMethods()
	  have been renamed to checkReplaceFuns(), checkDocFiles(), and
	  checkS3methods, to given better descriptions of what they do.

	- R itself is now used for analyzing the markup in the \usage
	  sections.  Hence in particular, replacement functions or S3
	  replacement methods are no longer ignored.

	- checkDocFiles() now also determines 'over-documented' arguments
	  which are given in the \arguments section but not in \usage.

	- checkDocStyle() and checkS3Methods() now know about internal S3
	  generics and S3 group generics.

	- S4 classes and methods are included in the QC tests.
	  Warnings will be issued from undoc() for classes  and
	  methods defined but not documented.  Default methods
	  automatically generated from nongeneric functions do not
	  need to be documented.

	- New (experimental) functions codocClasses() and codocData()
	  for code/documentation consistency checking for S4 classes and
	  data sets.

    o	Changes in package 'ts':

	- arima.sim() now checks for inconsistent order specification
	  (as requested in PR#3495: it was previously documented not to).

	- decompose() has a new argument `filter'.

	- HoltWinters() has new arguments `optim.start' and
	  `optim.control', and returns more components in the fitted
	  values.  The plot method allows `ylim' to be set.

	- plot.ts() has a new argument `nc' controlling the number of
	  columns (with default the old behaviour for plot.mts).

	- StructTS() now allows the first value of the series to be
	  missing (although it is better to omit leading NAs). (PR#3990)


USING PACKAGES

    o	library() has a pos argument, controlling where the package is
	attached (defaulting to pos=2 as before).

    o	require() now maintains a list of required packages in the
	toplevel environment (typically, .GlobalEnv).  Two features
	use this:  detach() now warns if a package is detached that is
	required by an attached package, and packages that install
	with saved images no longer need to use require() in the
	.First as well as in the main source.

    o	Packages with name spaces can now be installed using --save.

    o	Packages that use S4 classes and methods should now work with
	or without saved images (saved images are still recommended
	for efficiency), writing setMethod(), etc. calls with the
	default for argument `where'.  The topenv() function and
	sys.source() have been changed correspondingly.	 See the
	online help.

    o	Users can specify in the DESCRIPTION file the collation order
	for files in the R source directory of a package.


DOCUMENTATION CHANGES

    o	Changes in R documentation format:

	- New logical markup commands for emphasizing (\strong) and
	  quoting (\sQuote and \dQuote) text, for indicating the usage
	  of an S4 method (\S4method), and for indicating specific kinds
	  of text (\acronym, \cite, \command, \dfn, \env, \kbd, \option,
	  \pkg, \samp, \var).

	- New markup \preformatted for pre-formatted blocks of text
	  (like \example but within another section).  (Based on a
	  contribution by Greg Warnes.)

	- New markup \concept for concept index entries for use by
	  help.search().

    o	Rdconv now produces more informative output from the special
	\method{GENERIC}{CLASS} markup for indicating the usage of S3
	methods, providing the CLASS info in a comment.

    o	\dontrun sections are now marked within comments in the
	user-readable versions of the converted help pages.

    o	\dontshow is now the preferred name for \testonly.


INSTALLATION CHANGES

    o	The zlib code in the sources is used unless the external
	version found is at least version 1.1.4 (up from 1.1.3).

    o	The regression checks now have to be passed exactly, except
	those depending on recommended packages (which cannot be
	assumed to be present).

    o	The target make check-all now runs R CMD check on all the
	recommended packages (and not just runs their examples).

    o	There are new macros DYLIB_* for building dynamic libraries,
	and these are used for the dynamic Rmath library (which was
	previously built as a shared object).

    o	If a system function log1p is found, it is tested for accuracy
	and if inadequate the substitute function in src/nmath is
	used, with name remapped to Rlog1p.  (Apparently needed on
	OpenBSD/NetBSD.)


C-LEVEL FACILITIES

    o	There is a new installed header file R_ext/Parse.h which
	allows R_ParseVector to be called by those writing extensions.
	(Note that the interface is changed from that used in the
	unexported header Parse.h in earlier versions, and is not
	guaranteed to remain unchanged.)

    o	The header R_ext/Mathlib.h has been removed.  It was replaced by
	Rmath.h in R 1.2.0.

    o	PREXPR has been replaced by two macros, PREXPR for obtaining the
	expression and PRCODE for obtaining the code for use in eval.
	The macro BODY_EXPR has been added for use with closures.
	For a closure with a byte compiled body, the macro BODY_EXPR
	returns the expression that was compiled; if the body is not
	compiled then the body is returned.  This is to support byte
	compilation.

    o	Internal support for executing byte compiled code has been added.
	A compiler for producing byte compiled code will be made available
	separately and should become part of a future R release.

    o	On Unix-like systems calls to the popen() and system() C library
	functions now go through R_popen and R_system.	On Mac OS X these
	suspend SIGALRM interrupts around the library call.  (Related to
	PR#1140.)


UTILITIES

    o	R CMD check accepts "ORPHANED" as package maintainer. Package
	maintainers can now officially orphan a package, i.e., resign
	from maintaining a package.

    o	R CMD INSTALL (Unix only) is now 'safe': if the attempt to
	install a package fails, leftovers are removed.	 If the package
	was already installed, the old version is restored.

    o	R CMD build excludes possible (obsolete) data and vignette
	indices in DCF format (and hence also no longer rebuilds them).

    o	R CMD check now tests whether file names are valid across file
	systems and supported operating system platforms.  There is some
	support for code/documentation consistency checking for data
	sets and S4 classes.  Replacement functions and S3 methods in
	\usage sections are no longer ignored.

    o	R CMD Rdindex has been removed.


DEPRECATED & DEFUNCT

    o	The assignment operator `_' has been removed.

    o	printNoClass() is defunct.

    o	The classic MacOS port is no longer supported, and its files
	have been removed from the sources.

    o	The deprecated argument 'white' of parse() has been removed.

    o	Methods pacf/plot.mts() have been removed and their functionality
	incorporated into pacf.default/plot.ts().

    o	print.coefmat() is deprecated in favour of printCoefmat()
	(which is identical apart from the default for na.print which
	is changed from "" to "NA", and better handling of the 0-rank
	case where all coefficients are missing).

    o	codes() and codes<-() are deprecated, as almost all uses
	misunderstood what they actually do.

    o	The use of multi-argument return() calls is deprecated: use a
	(named) list instead.

    o	anovalist.lm (replaced in 1.2.0) is now deprecated.

    o	- and Ops methods for POSIX[cl]t objects are removed: the
	POSIXt methods have been used since 1.3.0.

    o	glm.fit.null(), lm.fit.null() and lm.wfit.null() are deprecated.

    o	Classes "lm.null" and "glm.null" are deprecated and all of their
	methods have been removed.

    o	Method weights.lm(), a copy of weights.default(), has been removed.

    o	print.atomic() is now deprecated.

    o	The back-compatibility entry point Rf_log1p in standalone
	Rmath has been removed.


BUG FIXES

    o	ARMAacf() sometimes gave too many results or failed if `lag.max'
	was used.

    o	Functions anova.glm(), contrasts(), getS3method(), glm() and
	make.tables() were applying get() without asking for a
	function and/or not starting the search in the environment of
	the caller.

    o	as.data.frame.matrix() ignored the `row.names' argument.

    o	as.data.frame.list(optional = TRUE) was converting names, and
	hence data.frame(list(...), check.names = FALSE) was.  (PR#3280)

    o	as.dist(m) {mva} now obeys `diag=TRUE' or `upper=TRUE' in all cases.

    o	as.double(list()) etc was regarded as an error, because of a
	bug in isVectorizable.

    o	On some platforms the wday component of the result of
	as.POSIXlt() was corrupted when trying to guess the DST offset
	at dates the OS was unable to handle.

    o	ave(x, g) didn't work when `g' had unused levels.

    o	biplot.default() allows xlim and ylim to be set.  (PR#3168)

    o	bgroup with a null (.) delimiter was setting font to Greek.  (PR#3099)

    o	body() and formals() were looking for named functions in
	different places: they now both look starting at the
	environment in which they are called.  Several documentation
	errors for these functions have been corrected.

    o	boxplot() was ignoring cex.axis.  (PR#2628)

    o	cut.POSIXt() now passes on ... to cut.default(), as documented.

    o	crossprod() now works for 1d arrays with unnamed dimnames (PR#4092).

    o	data() sometimes failed with multiple files, as the paths
	variable got corrupted.

    o	data.frame() failed with a nonsensical error message if it
	grabbed row names from an argument that was subsequently
	recycled.  Now they are discarded, with a warning.

    o	data.matrix() was documented to replace factors by their
	codes, but in fact re-coded into the alphabetical ordering of
	the levels.

    o	decompose() with even frequency used an asymmetric moving
	average window.

    o	demo() was using `topic' as a regexp rather than an exact match.

    o	dotchart() now does recycle the `color' argument and better
	documents the `bg' one (PR#4343).

    o	getAnywhere() didn't not correctly check for S3 methods, when
	the generic or the class name contains a "." (PR#4275).

    o	file.copy() ignored the overwrite argument.  (PR#3529)

    o	filter(method="recursive") was unnecessarily requiring the
	time series to be longer than the filter.

    o	format(*, nsmall = m) with m > 0 now returns exponential format
	less often.

    o	get() and exists() were ignoring the `mode' argument for
	variables in base.  The error message for get() now mentions
	the mode requested if not "any".  A bug in setting the NAMED
	field in do_get was fixed.

    o	getS3method(f, cl, optional=TRUE) now returns NULL if `f' does
	not exist.

    o	HoltWinters() would segfault if only gamma was optimized, and
	not converge if gamma=0 and seasonal="mult".

    o	hyperref.cfg now contains definitions for colors it uses.

    o	identify.default() detects zero-length arguments.  (PR#4057)

    o	legend() allows shading without filling again.

    o	legend(x, y, leg) doesn't triple `leg' anymore when it is a call.

    o	Corrected many problems with 0-rank (but not necessarily empty
	model) lm() and glm() fits.

    o	lm.influence() now handles 0-rank models, and names its output
	appropriately.	It also ensures that hat values are not greater
	than one, and rounds values within rounding error of one.

    o	The `method' argument to loess() did not work.	(PR#3332)

    o	lsfit() was returning incorrect residuals for 0-rank fits.

    o	methods("$") and methods("$<-") were failing to find methods.

    o	methods() and getS3method() find methods if the generic
	dispatches on a name other than its own.  (The cases of
	coefficients() and fitted.values() were fixed in 1.7.1.)

    o	model.matrix.default() was throwing an error on 0-term models,
	but now handles them correctly.

    o	Printing `nls' objects misbehaved when `data' was a composite
	expression.

    o	.NotYetImplemented() gave "Error in .NotYet...(): .."

    o	numericDeriv() was failing if the first argument was a name
	rather than a call.  (PR#3746)

    o	pacf() was failing if called on a one-column matrix.

    o	paste() applied to 0-length vectors gave "" not a 0-length vector.

    o	The length of a string specification of par(lty=) is now checked: it
	should be 2, 4, 6 or 8.

    o	Using lty=as.integer(NA) and as.double(NA) were being accepted
	but giving nonsensical results.	 Those are not documented
	valid values for lty.  (PR#3217)

    o	Erroneously calling par(new=TRUE) with no plot was not caught
	and so could result in invalid graphics files.	(PR#4037)

    o	par(tck=) was being interpreted incorrectly.  It is now
	documented in the same way as S, and now behaves as
	documented.  (PR#3504)

    o	plclust() [and hence plot.hclust()] sometimes now uses correct `ylim's
	also in unusual cases.	(PR#4197)

    o	plot.POSIX[cl]t no longer passes col, lty, lwd to axis.POSIXt.

    o	The png(), jpeg(), png() and win.metafile() devices now
	enforce the length limit on the filename.  (PR#3466)

    o	pnorm(x, 1, 0) does not give NaN anymore;
	also, pnorm(x, m, s=Inf) == lim{s -> Inf} pnorm(x,m,s).
	Similar changes for dnorm(), cf PR#1218.

    o	On some machines the internal rounding used in postscript() was
	imperfect, causing unnecessarily verbose output (-0.00 instead of
	0) and problems with make check.

    o	qqnorm()'s result now keeps NAs from its input. (PR#3750)

    o	rank() sometimes preserved and sometimes dropped names.

    o	readBin(what = "foo") didn't convert `what' to its type.  (PR#4043)

    o	reorder.dendrogram() now properly resets the "midpoint" attributes
	such that reorder()ed dendrograms now plot properly.

    o	rmultinom(1,100, c(3, 4, 2, 0,0))[3] was NA. (PR#4431)

    o	sapply() for matrix result does not return list(NULL,NULL) dimnames
	anymore.

    o	scan() now interprets quoting in fields to be skipped.	(PR#4128)

    o	seq.POSIXt(from, to, by="DSTday") was failing or calculating
	the length incorrectly.

    o	sort() and unique.default() were failing on 0-level factors.

    o	step() adds a fuzz for reduction in AIC for 0-df terms.	 (PR#3491)

    o	str(x) gives better output when x is of mode "(".  Its "dendrogram"
	method obeys the `give.attr' argument which now defaults to FALSE.

    o	strwidth(f) and strheight(f) could seg.fault when `f' was a
	function.  The fix [to C-level coerceVector()] now gives an error
	instead of passing through.  This may catch other potential
	problems.

    o	Sweave() reports the chunk number rather than the driver call when
	a try error gets caught.

    o	trunc.POSIXt(x) for 0-length x does not return invalid structures
	anymore.  (PR#3763).

    o	warnings() now returns NULL instead of an error when no warnings
	have occured yet.  (PR#4389)

    o	Using write.table() setting the `dec' argument and with no
	numeric columns failed.	 (PR#3532)

    o	$<- did not duplicate when it needed to.

    o	Recursive indexing of lists had too little error-checking.
	(related to PR#3324)

    o	Removed warning about names in persistent strings when a
	namespace is saved.

    o	Fixed some malformed error messages in the methods package.

    o	pipes were not opening properly when profiling on a Mac. (PR#1140)

    o	Lapack error messages (PR#3494) and call to DGEQP3 (PR#2867) are
	corrected.

    o	Rd conversion was limiting a file to 1000 pairs of braces,
	without any warning.  Now the limit is 10000, with a warning.
	(PR#3400)

    o	In the tcltk package, the tkimage.*() commands were defined
	nonsensically as widget commands. They have been redefined to be
	more useful now.

    o	Registered group generics were not being used. (PR#3536)

    o	Subsetting data frames did not always correctly detect that
	non-existent columns were specified.

    o	There are many more checks for over-running internal buffers,
	almost always reporting errors.

    o	Added some buffer overflow checking in gram.y.

    o	Internals for complex assignment did not check that function name
	was a symbol, which could cause a segfault.

    o	Fixed bug in S4 methods dispatch that made local variables in the
	generic visible when executing the body of a method, thus violating
	lexical scope.



-- 
   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



From bates at stat.wisc.edu  Wed Oct  8 17:29:25 2003
From: bates at stat.wisc.edu (Douglas Bates)
Date: Wed, 08 Oct 2003 15:29:25 -0000
Subject: R-1.8.0 sources available via rsync
Message-ID: <6r7k3fbvcj.fsf@bates4.stat.wisc.edu>

The sources for R-1.8.0 are now available via rsync to the host
rsync.r-project.org

Use

 rsync rsync.r-project.org::

to get the listing of possible versions.



From bates at stat.wisc.edu  Thu Oct  9 15:07:30 2003
From: bates at stat.wisc.edu (Douglas Bates)
Date: Thu, 09 Oct 2003 13:07:30 -0000
Subject: anonymous access to the R CVS archive
Message-ID: <6rwubed0dx.fsf@bates4.stat.wisc.edu>

Thanks to John Eaton of the Octave project we now have anonymous CVS
access to (a copy of) the R archive.  See http://anoncvs.r-project.org/



From dmurdoch at pair.com  Fri Oct 10 03:23:12 2003
From: dmurdoch at pair.com (Duncan Murdoch)
Date: Thu, 09 Oct 2003 21:23:12 -0400
Subject: R 1.8.0 Windows binaries uploaded
Message-ID: <md2covk1vhb9gqi2aqt8sapul1gb6e9u0u@4ax.com>

I've just uploaded the 1.8.0 binary build for Windows.  It should be
available on CRAN and the mirrors tomorrow.

Duncan Murdoch



From bates at stat.wisc.edu  Fri Oct 10 14:59:40 2003
From: bates at stat.wisc.edu (Douglas Bates)
Date: 10 Oct 2003 07:59:40 -0500
Subject: R 1.8.0 Windows binaries available on U.S. mirror
In-Reply-To: <md2covk1vhb9gqi2aqt8sapul1gb6e9u0u@4ax.com>
References: <md2covk1vhb9gqi2aqt8sapul1gb6e9u0u@4ax.com>
Message-ID: <6r4qyhtfib.fsf@bates4.stat.wisc.edu>

The Windows binaries are now available on the cran.us.r-project.org
mirror, the recommended download site for those in the U.S.A.

Duncan Murdoch <dmurdoch at pair.com> writes:

> I've just uploaded the 1.8.0 binary build for Windows.  It should be
> available on CRAN and the mirrors tomorrow.



From bates at stat.wisc.edu  Fri Oct 10 19:03:09 2003
From: bates at stat.wisc.edu (Douglas Bates)
Date: 10 Oct 2003 12:03:09 -0500
Subject: Debian (testing) packages for R-1.8.0
Message-ID: <6rd6d5rpo2.fsf@bates4.stat.wisc.edu>

Packages of R-1.8.0 for the Debian testing (or sarge) distribution are
now available on http://cran.us.r-project.org/bin/linux/debian and
should appear on other mirrors in a day or two.



From Friedrich.Leisch at ci.tuwien.ac.at  Fri Oct 24 14:17:34 2003
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich.Leisch at ci.tuwien.ac.at)
Date: Fri, 24 Oct 2003 14:17:34 +0200
Subject: CRAN down on Sunday, 26.10.2003
Message-ID: <16281.6238.405333.480843@galadriel.ci.tuwien.ac.at>


Due to construction work in a neighboring building there will be a
power outage in our offices for the complete day of

	Sunday, 26.10.2003

which means we will shut down all our computers some time tomorrow and
reboot them Monday morning (central European time).

This includes the server for

	www.R-project.org
	cran.R-project.org
	cran.at.R-project.org

Please a mirror site on this day (and do not flood us with "bug"
reports stating that CRAN is down :-).

Best,

-- 
-------------------------------------------------------------------
                        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



From Friedrich.Leisch at ci.tuwien.ac.at  Thu Oct 30 09:35:32 2003
From: Friedrich.Leisch at ci.tuwien.ac.at (Friedrich.Leisch at ci.tuwien.ac.at)
Date: Thu, 30 Oct 2003 09:35:32 +0100
Subject: R News Volume 3/2
Message-ID: <16288.52564.960646.249967@celeborn.leisch.at>


We have published the 2003/2 issue of R News on

	http://cran.R-project.org/doc/Rnews

where you can download the newsletter as PDF or Postscript file. It
will propagate to the CRAN mirrors within a day or two.

Contents of this issue:
                                                                      
R Help Desk
Integrating grid Graphics Output with Base Graphics Output
A New Package for the General Error Distribution
Web-based Microarray Analysis using Bioconductor
Sweave, Part II: Package Vignettes
R Foundation News
Recent Events
Book Reviews
Changes in R 1.8.0
Changes on CRAN
Crossword Solution
Correction to ``Building Microsoft Windows Versions of R and R
	packages under Intel Linux''


For the editorial board,
Fritz Leisch

-- 
-------------------------------------------------------------------
                        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



From Torsten.Hothorn at rzmail.uni-erlangen.de  Tue Nov 11 08:49:05 2003
From: Torsten.Hothorn at rzmail.uni-erlangen.de (Torsten Hothorn)
Date: Tue, 11 Nov 2003 08:49:05 +0100 (CET)
Subject: useR! 2004
Message-ID: <Pine.LNX.4.51.0311110847230.2239@artemis.imbe.med.uni-erlangen.de>



We are happy to announce that the first R user conference

  useR! 2004

is scheduled for May 20-22 2004 and will take place at the Vienna
University of Technology.

The conference will focus on
  - giving an overview of the new features of the rapidly evolving R project,
  - providing a platform for R users to discuss and exchange ideas how R can
    be used to do statistical computations, data analysis, visualization and
    exciting applications in various fields.


KEYNOTE LECTURES
A huge amount of exciting features and innovations came up in the last
releases of R. How these features can be used efficiently will be presented in
keynote lectures given by R core team members, addressing hot topics such as
  - grid Graphics
  - Good Programming Practice
  - Dynamic Documents
  - Language Interfaces
  - Packaging and Quality Assurance
  - Datamining and Large Databases

Speakers will include Peter Dalgaard, Kurt Hornik, Fritz Leisch, Paul Murrell
and Brian D. Ripley.

USER-CONTRIBUTED SESSIONS
Oral and poster presentations will be a platform to bring together R users,
contributers, package maintainers and developers in the S spirit that
`users are developers'. People from different fields will show us how they solve
problems with R in fascinating applications. The sessions are organized by
members of the program committee, including Axel Benner, Roger Bivand, Dirk
Eddelbuettel, John Fox, Kurt Hornik, Stefano Iacus, Steffen L. Lauritzen,
Friedrich Leisch, Uwe Ligges and Martin Theus, and will cover topics such as
  - Finance & Econometrics
  - Visualization & Graphics
  - Spatial Statistics
  - Biostatistics
  - Graphical Models
  - and many more.

After the official presentations, Vienna's famous wine and beer pubs, cafes
and restaurants proofed to be a very stimulating environment for fruitful
discussions at previous meetings of the R community like this year's DSC 2003.

We invite all R users to submit abstracts on topics presenting innovations or
exciting applications of R. A web page offering more information on the `useR!'
conference, abstract submission, registration and Vienna is available at

  http://www.ci.tuwien.ac.at/Conferences/useR-2004/

We hope to meet you in Vienna!

For the organizing committee:

Torsten Hothorn, Achim Zeileis and David Meyer.



From p.dalgaard at biostat.ku.dk  Fri Nov 21 13:45:53 2003
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: 21 Nov 2003 13:45:53 +0100
Subject: R-1.8.1 is released 
Message-ID: <x2oev5x532.fsf@biostat.ku.dk>

I've rolled up R-1.8.1.tgz a short while ago. This is a patch version
mostly fixing a number of issues in 1.8.0, some of which were quite
serious. As usual, a few new features have crept in as well. (See below
for details.)

You can get it from

http://cran.us.r-project.org/src/base/R-1.8.1.tgz

or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.
 
There is also a version split for floppies.

These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:

cd81fdeaf22f93dfc28979e8132722ec  R-1.8.1.tgz
5690ed4e1f453115551122facb4b34b0  R-1.8.1.tgz-split.aa
cd2fd749085c1e63fce22e3e09f70cdb  R-1.8.1.tgz-split.ab
ab0b08746d1f5bd56a736a8b1f5bfee6  R-1.8.1.tgz-split.ac
41332e09272598bfb64c25ac84274404  R-1.8.1.tgz-split.ad
51d3f4e376efdee4ae069b135f909621  R-1.8.1.tgz-split.ae
c50f27fdf41c44c71c5b4f285a2dd98f  R-1.8.1.tgz-split.af
2eb71e8a54e41b3e30e3e40f35151aa0  R-1.8.1.tgz-split.ag

On behalf of the R Core Team,

        Peter Dalgaard


Here's the relevant part of the NEWS file


		CHANGES IN R VERSION 1.8.1


NEW FEATURES

    o	There is now a "Complex" S3 group generic (a side-effect of
	fixing up the corresponding S4 group generic).

    o	help("regex") now gives a description of the regular expressions
	used in R.

    o	The startup message now shows the R Foundation as copyright
	holder, and includes the R ISBN number and a pointer to the new
	citation() function.

    o	The solve() function now uses the `tol' argument for all
	non-complex cases.  The default tolerance for LINPACK is 1e-7,
	as before.  For LAPACK it currently is .Machine$double.eps but
	may be changed in later versions of R.

    o	help.search() now defaults to agrep = FALSE when keyword= is
	specified, since no one wants fuzzy matching of categories.

    o	Function texi2dvi() in package tools can be used to compile
	latex files from within R.

    o	Objects with formal S4 classes saved in pre-1.8 versions and
	loaded into the current version have incompatible class
	attributes (no package information).  A new function,
	fixPre1.8() in package methods, will fix the class attributes.
	See the help for this function.

    o	heatmap() allows Rowv/Colv = NA, suppressing the corresponding
	dendrogram.

    o   An "antifeature": Tcl 8.0 is now officially unsupported. In 1.8.0
	it just didn't work. This very old version lacks several features
        that are needed for the new version of the tcltk package. R will
	still build the tcltk package against Tcl 8.0 but the resulting
	package will not load.


BUG FIXES

    o	symnum(x) now behaves as documented when length(x) == 0 and uses
	lower.triangular = FALSE for logical arrays.

    o	c() now has a method for "noquote" objects and hence works as
	expected.

    o	split(1:10, c(1,2)) no longer gives a spurious warning.

    o	The "Complex" S4 group generic now works.

    o	abbreviate() doesn't get into infinite loops on input that differs
	only by leading/trailing space

    o	Added check for user interrupt in Rvprintf to allow printing to be
	interrupted.

    o	Fixed bug that would cause segfault on protect stack overflow.

    o	crossprod() on matrices with zero extents would return an
	uninitialized matrix (rather than one filled with zeros).

    o	DF[[i,j]] for a data frame used row j and col i, not as intended
	row i and col j.

    o	Even more user errors in recursive indexing of lists are now
	caught.	 (PR#4486)

    o	cor(<matrix>, use = "pairwise") gave wrong result in 1.8.0 (only).
	(PR#4646)

    o	merge.data.frame() could give incorrect names when one of the
	arguments had only one column.	(PR#4299)

    o	Subsetting a one-dimensional array dropped dimensions even when
	they were not of length one.  (Related to PR#4110)

    o	The plot() method for `ecdf' objects, plot.ecdf(), now allows to
	set a `ylab' argument (different from the default).

    o	cor.test(*, method="spearman") gave wrong results `randomly'
	(because of a wrong type passed to C; PR#4718).

    o	dist() objects with NA's didn't print these, now do. (PR#4866).

    o	regexpr(fixed = TRUE) returned 0-based indices.

    o	df[, length_1_index] <- value did not recycle short rhs. (PR#4820)

    o	median() no longer `works' for odd-length factor variables.

    o	packageStatus() is more robust to failing to contact a
	repository, and contacts the correct paths in the repositories
	under Windows.

    o	.setOldIs (methods) contained a typo stopping POSIXct objects (etc)
	being included in formal classes.

    o	terms() sometimes removed offset() terms incorrectly, since it
	counted by variables and not terms.  Its "offset" attribute
	was incorrectly documented as referring to terms not
	variables. (Related to PR#4941)

    o	buildVignettes() and pkgVignettes() in package tools are now
	documented.  The call to texi2dvi is wrapped in the new
	function texi2dvi() which also works on Windows.

    o   hclust() was sometimes not finding the correct inter-cluster
	distances with non-monotone methods.  (PR#4195)

    o   plot.hclust() now tolerates mode changes on dumped objects. (PR#4361)

    o   prompt() no longer insists files are in the current directory.
	(PR#4978)

    o   filter() did not use init in reverse order as documented. (PR#5017)

    o	contrasts<-() and model.matrix() now have sanity checks that
	factors having at least 2 levels (or one level and a contrast
	matrix): model.matrix() gave nonsensical results for 0-level
	factors.

    o   writeChar() could segfault if more characters were requested
	than exist. (PR#5090)

    o	round() and signif() dropped attributes with 0-length inputs,
	only. (PR#4710)

    o	The default graphics device in the GNOME interface was gtk,
	which is no longer in the base package. It is now X11.

    o	The print button on the toolbar of the GNOME graphics device
	did not work.

    o	The example code on the man page for TkWidgetcmds had not been
	updated after the change that made tkget (et al.) return
	tclObj objects, so the "Submit" button didn't work.

    o	Rd conversion to latex did not add a new line before
	\end{Section} for the section environments, which caused
	problems if the last thing in a section was \preformatted{}
	(and potentially elsewhere).

    o	Under some circumstances mosaicplot() failed if main was
	supplied as it was passed on to model.frame.default().

    o	Conversion to POSIXlt (including printing) of POSIXct dates
	before 1902 and after 2038 computed which were leap years from
	(year-1900) so got some xx00 years wrong.


-- 
   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



From dmurdoch at pair.com  Sat Nov 22 15:07:12 2003
From: dmurdoch at pair.com (Duncan Murdoch)
Date: Sat, 22 Nov 2003 09:07:12 -0500
Subject: [R] R-1.8.1 is released 
In-Reply-To: <x2oev5x532.fsf@biostat.ku.dk>
References: <x2oev5x532.fsf@biostat.ku.dk>
Message-ID: <84rurv0ltq4kcl6hse170od1sgkhn7fpr6@4ax.com>

On 21 Nov 2003 13:45:53 +0100, you wrote:

>I've rolled up R-1.8.1.tgz a short while ago. This is a patch version
>mostly fixing a number of issues in 1.8.0, some of which were quite
>serious. As usual, a few new features have crept in as well. (See below
>for details.)
>
>You can get it from
>
>http://cran.us.r-project.org/src/base/R-1.8.1.tgz

The Windows build of 1.8.1 is now on CRAN and the mirrors.  Get it at

<http://cran.us.r-project.org/bin/windows/base>.

See the CHANGES file in that directory for Windows-specific news.


Duncan Murdoch



From Torsten.Hothorn at rzmail.uni-erlangen.de  Fri Dec 19 18:04:36 2003
From: Torsten.Hothorn at rzmail.uni-erlangen.de (Torsten Hothorn)
Date: Fri, 19 Dec 2003 18:04:36 +0100 (CET)
Subject: `useR! 2004': Submission & Registration started
Message-ID: <Pine.LNX.4.51.0312191802400.16585@artemis.imbe.med.uni-erlangen.de>


We are happy to inform you that the topics of the keynote lectures to be
presented at the first R user conference `useR! 2004' in Vienna (May
20-22th) are now available from the conference web page at

        http://www.ci.tuwien.ac.at/Conferences/useR-2004/

The submission process for oral and poster presentations started this
month and a web form for registration is available since last week.

The Xmas days are a perfect time to write and submit an abstract, the
final deadline for the submission of oral or poster presentations is
February 15th, 2004. Authors will be notified about the acceptance of
their contribution until March 15th. For poster presentations only, an
extended final deadline ends April 15th.

A poster highlighting the most important informations about the conference
is available from the conference web page. It would be great if you could
put up a poster in your department if only to demonstrate that using R is
serious research and not only a hobby for computer geeks.

We wish you a Merry Xmas, a Happy New Year and hope to see you in Vienna!

Torsten, Achim, David.