2004-06-05 01:42  warnes

	* src/Makefile: Fix typo.

2004-06-05 01:34  warnes

	* src/Makefile: Fix Unix makefile so that it works when invoked
	  directly.

2004-06-05 01:30  warnes

	* src/Makefile: Fixes for Windows

2004-06-05 01:22  warnes

	* man/read.xls.Rd: Minor enhancment to read.xls example.

2004-06-05 00:05  warnes

	* DESCRIPTION, NEWS, src/Makefile, src/Makefile.win, src/iris.xls,
	  src/xls2csv.bat.in, src/xls2csv.in: - Merge Makefile.win into
	  Makefile.  Makefile.win now just redirects   to Makefile.  -
	  Update xls2csv.bat and xls2csv shell script to correctly obtain
	  thier installion path and infer the location of the perl code and
	  libraries.	- The xls2csv.pl script now assumes that the
	  libraries it needs are   installed into the same directory where
	  it is.

2004-06-04 23:16  warnes

	* src/: Makefile.win, xls2csv.bat.in, xls2csv.pl.in: Now things
	  work happily on Windows 2000.

2004-06-04 16:42  warnes

	* src/: Makefile, Makefile.win: More changes, indended to improve
	  installation reliabilty and to make Makefile and Makefile.win as
	  similar as possible.

2004-06-04 09:28  warnes

	* src/Makefile.win: Add initial Makefile for Windows.  With this
	  makefile, and with Microsoft's NMAKE installed into
	  gregmisc/src/NMAKE/, RCMD INSTALL gregmisc succedes.
	  Unfortunately. RCMD build --binary --use-zip gregmisc doesn't
	  proplery include all files

2004-05-27 18:39  warnes

	* src/Makefile: Clean should remove scripts from source directory.

2004-05-27 18:38  warnes

	* src/xls2csv.pl: Moved to xls2csv.pl.in.

2004-05-27 18:36  warnes

	* NEWS: Clarify text describing xls2csv scripts.

2004-05-27 18:30  warnes

	* DESCRIPTION, NEWS: Updated for release.

2004-05-27 18:20  warnes

	* src/: Makefile, xls2csv.pl, xls2csv.pl.in: More fixes.

2004-05-27 18:20  warnes

	* man/elem.Rd: Fix missing brace.

2004-05-27 17:43  warnes

	* man/elem.Rd:
	  Add explicit package name to see also links.

2004-05-27 17:24  warnes

	* src/: Makefile, xls2csv.pl: More xls2csv perl module support
	  changes.

2004-05-27 16:37  warnes

	* src/: Makefile, xls2csv.pl.in: More changes to fix local
	  installation of perl modules.

2004-05-27 11:11  warnes

	* man/plotCI.Rd: Fix spelling error.

2004-05-26 12:21  warnes

	* tests/: env.Ex.Rout.save, fast.prcomp.Ex.R,
	  fast.prcomp.Ex.Rout.save, rtPCR.Ex.Rout.save: Match changes for
	  release 1.11.0.

2004-05-26 11:00  warnes

	* NEWS: Update for 1.11.0 release.

2004-05-26 10:56  warnes

	* R/overplot.R: One more fix to get it right.

2004-05-26 09:50  warnes

	* R/overplot.R: Use triple-colon operator ':::' to access
	  plot.formula from the graphics package.

2004-05-26 09:40  warnes

	* man/: combinations.Rd, read.xls.Rd: Escape underscores in email
	  addresses so Latex is happy.

2004-05-26 09:21  warnes

	* tests/: CrossTable.Rout.save, env.Ex.Rout.save,
	  fast.prcomp.Ex.Rout.save, ll.Ex.Rout.save, overplot.Ex.Rout.save,
	  rename.vars.Ex.Rout.save: Updated to match current output.

2004-05-26 09:20  warnes

	* tests/: CrossTable.Ex.R, aggregate.table.Ex.R, balloonplot.Ex.R,
	  bandplot.Ex.R, barplot2.Ex.R, boxplot.n.Ex.R, capture.Ex.R,
	  ci.Ex.R, colorpanel.Ex.R, combinations.Ex.R, combine.Ex.R,
	  contrast.lm.Ex.R, dirichlet.Ex.R, elem.Ex.R, env.Ex.R,
	  estimable.Ex.R, fast.prcomp.Ex.R, fit.contrast.Ex.R,
	  foldchange.Ex.R, glh.test.Ex.R, heatmap.2.Ex.R, hist2d.Ex.R,
	  interleave.Ex.R, is.what.Ex.R, keep.Ex.R, ll.Ex.R, logit.Ex.R,
	  lowess.Ex.R, make.contrasts.Ex.R, matchcols.Ex.R, mixedsort.Ex.R,
	  nobs.Ex.R, oddeven.Ex.R, ooplot.Ex.R, overplot.Ex.R,
	  permute.Ex.R, plotCI.Ex.R, plotmeans.Ex.R, qqnorm.aov.Ex.R,
	  quantcut.Ex.R, rename.vars.Ex.R, reorder.Ex.R, rtPCR.Ex.R,
	  running.Ex.R, sinkplot.Ex.R, smartlegend.Ex.R, space.Ex.R,
	  textplot.Ex.R, trim.Ex.R, undocumented.Ex.R, wapply.Ex.R: These
	  tests were added some time ago, but were not checked in.

2004-05-26 09:19  warnes

	* man/rich.color.Rd: Replace 'F' by 'FALSE' to pass R CMD check.

2004-05-26 09:18  warnes

	* R/combinations.R: Replace 'T' with 'TRUE' to pass R CMD check.

2004-05-25 14:45  warnes

	* src/: Makefile, xls2csv.in, xls2csv.pl, xls2csv.pl.in: More
	  changes to xls2csv code.

2004-05-25 14:32  warnes

	* R/overplot.R: Work around bug in R 1.9.X due to plot.formula()
	  not having the same arguments as plot().

2004-05-25 13:35  warnes

	* R/Args.R, man/Args.Rd: Add Args() function contributed by Arni
	  Magnusson <arnima@u.washington.edu>.

2004-05-25 13:33  warnes

	* R/rich.color.R, man/rich.color.Rd: Add rich.colors() submitted by
	  Arni Magnusson <arnima@u.washington.edu>.

2004-05-25 13:14  warnes

	* R/read.xls.R:
	  - Change to call perl directly rather than depending on the
	  installed shell script.  This should make the code more portable
	  to MS-Windows systes.

	  - Add additional commants..

2004-05-25 13:11  warnes

	* R/combinations.R: Remove extraneous comments.

2004-05-25 13:08  warnes

	* R/combinations.R: Fix an error in the code when using
	  repeats.allow=T and r>2.  Bug report and fix both due to
	  Elizabeth Purdom <epurdom@stanford.edu>.

2004-05-25 11:18  warnes

	* tests/: CrossTable.Rout.save, env.Ex.Rout.save,
	  rename.vars.Rout.save: Update test output for R-1.9.0-Patched
	  (pre 1.9.1).

2004-05-25 10:53  warnes

	* src/: Makefile, xls2csv.bat.in, xls2csv.in, xls2csv.pl.in:
	  Makefile now modifies xls2csv.bat xls2csv.pl and xls2csv to
	  contain an explicit path to the perl script/libraries.

2004-05-25 07:43  warnes

	* DESCRIPTION: Bump version number to 1.11.0 to reflect the actual
	  'production' status of the package.

2004-05-25 07:41  warnes

	* src/Makefile: R CMD build calls the clean target to purge build
	  files from the source tree when packaging.  To get use this
	  behavior correctly, I've renamed the clean target to cleanup and
	  distclean target to clean.

2004-05-25 07:35  warnes

	* R/read.xls.R, man/read.xls.Rd: Add read.xls(), a function to read
	  Microsoft Excel files by translating them to csv files via the
	  xls2csv.pl script.

2004-05-24 22:58  warnes

	* R/ooplot.R, man/ooplot.Rd: ??

2004-05-24 22:57  warnes

	* R/CrossTable.R, man/CrossTable.Rd: Updates from Mark Schwartz.

2004-05-24 22:46  warnes

	* src/Makefile: More fixes.  Seems to work now.

2004-05-24 22:42  warnes

	* src/xls2csv.in: Needed dirname instead of basename to get
	  installation path.

2004-05-24 19:59  warnes

	* inst/xls/iris.xls: Added iris.xls example file.

2004-05-24 19:46  warnes

	* src/: IO-stringy-2.109.tar.gz, Makefile,
	  OLE-Storage_Lite-0.11.tar.gz,
	  Spreadsheet-ParseExcel-0.2602.tar.gz, iris.csv.save, iris.xls,
	  xls2csv.in, xls2csv.pl: Add files to enable inclusion and
	  installation of xls2csv.pl as part of the package.

2004-05-24 19:43  warnes

	* R/: plotCI.R, plotmeans.R: Modified to use invalid() to check
	  arguments instead of missing().  This fixes some build errors
	  under R-1.9.0-Patched.

2004-05-24 13:36  warnes

	* R/invalid.R: Check if argument is a vector before doing is.na to
	  avoid generating a warning.

2004-05-24 13:17  warnes

	* R/invalid.R, man/invalid.Rd: Add invalid() function for testing
	  if a parameter value is non-missing, non-NA, non-NULL.

2004-04-27 10:33  warnes

	* R/running.R, man/running.Rd: Replaced argument `as.list' with
	  `simplify'.  Updated documentation, and updated examples
	  appropriately.

2004-04-26 12:37  warnes

	* R/running.R, man/running.Rd: Added as.list argument to return one
	  list element per evaluation.

2004-04-22 11:44  warnes

	* R/ooplot.R, man/ooplot.Rd: Integrate changes from Lodewijk
	  Bonebakker <bonebakker@comcast.net>

2004-04-13 22:40  warnes

	* inst/tools/Makefile: Add Makefile for updating/installing R
	  packages from CRAN & BioConductor.

2004-04-13 09:42  warnes

	* R/space.R, man/space.Rd: Add ability to space points along 'y'
	  direction.

2004-04-13 07:48  warnes

	* DESCRIPTION: Update for 0.10.2

2004-04-13 07:46  warnes

	* NEWS: Updated for 0.10.2

2004-04-13 07:41  warnes

	* man/estimable.Rd: Fix latex warning: it doesn't like double
	  subscripts.

2004-04-02 14:06  warnes

	* R/smartlegend.R: Fixed smartlegend() positioning when x and/or y
	  axis are log-scale.

2004-04-01 15:23  warnes

	* R/rename.vars.R, man/rename.vars.Rd: Add function remove.vars().

2004-03-30 14:04  warnes

	* DESCRIPTION, R/textplot.R: - Fix bug in textplot() reported by
	  Wright, Kevin <kevin.d.wright@pioneer.com>.

2004-03-26 17:46  warnes

	* tests/running.R: File removed since running.Ex.R now exists and
	  has newer contents.

2004-03-26 17:45  warnes

	* tests/: CrossTable.Ex.Rout.save, CrossTable.Rout.save,
	  aggregate.table.Ex.Rout.save, aggregate.table.Rout.save,
	  balloonplot.Ex.Rout.save, bandplot.Ex.Rout.save,
	  bandplot.Rout.save, barplot2.Ex.Rout.save, barplot2.Rout.save,
	  boxplot.n.Ex.Rout.save, boxplot.n.Rout.save,
	  capture.Ex.Rout.save, ci.Ex.Rout.save, ci.Rout.save,
	  colorpanel.Ex.Rout.save, combinations.Ex.Rout.save,
	  combinations.Rout.save, combine.Ex.Rout.save, combine.Rout.save,
	  contrast.lm.Ex.Rout.save, dirichlet.Ex.Rout.save,
	  dirichlet.Rout.save, elem.Ex.Rout.save, env.Ex.Rout.save,
	  estimable.Ex.Rout.save, estimable.Rout.save, factorial.Rout.save,
	  fast.prcomp.Ex.Rout.save, fast.prcomp.Rout.save,
	  fit.contrast-2003-11-17-UH.Rout.save, fit.contrast.Ex.Rout.save,
	  fit.contrast.Rout.save, foldchange.Ex.Rout.save,
	  glh.test.Ex.Rout.save, glh.test.Rout.save,
	  heatmap.2.Ex.Rout.save, hist2d.Ex.Rout.save, hist2d.Rout.save,
	  interleave.Ex.Rout.save, interleave.Rout.save,
	  is.what.Ex.Rout.save, keep.Ex.Rout.save, ll.Ex.Rout.save,
	  logit.Ex.Rout.save, lowess.Ex.Rout.save, lowess.Rout.save,
	  make.contrasts.Ex.Rout.save, make.contrasts.Rout.save,
	  matchcols.Ex.Rout.save, mixedsort.Ex.Rout.save,
	  nobs.Ex.Rout.save, nobs.Rout.save, oddeven.Ex.Rout.save,
	  ooplot.Ex.Rout.save, overplot.Ex.Rout.save, permute.Ex.Rout.save,
	  plotCI.Ex.Rout.save, plotCI.Rout.save, plotmeans.Ex.Rout.save,
	  plotmeans.Rout.save, qqnorm.aov.Ex.Rout.save,
	  quantcut.Ex.Rout.save, quantcut.Rout.save,
	  rename.vars.Ex.Rout.save, rename.vars.Rout.save,
	  reorder.Ex.Rout.save, reorder.Rout.save, rtPCR.Ex.Rout.save,
	  running.Ex.Rout.save, running.Rout.save, sinkplot.Ex.Rout.save,
	  smartlegend.Ex.Rout.save, space.Ex.Rout.save, space.Rout.save,
	  textplot.Ex.Rout.save, trim.Ex.Rout.save,
	  undocumented.Ex.Rout.save, wapply.Ex.Rout.save, wapply.Rout.save:
	  Ensure that all of the manual page examples are present in the
	  test directory so we get more complete regression tests .

2004-03-26 17:42  warnes

	* NEWS: Updated for release 0.10.0.

2004-03-26 17:33  warnes

	* TODO: Change proposed names of new packages.

2004-03-26 17:32  warnes

	* DESCRIPTION: - Add  Lodewijk Bonebakker to list of authors -
	  Improve description text - Note dependency on R 1.9.0.

2004-03-26 17:31  warnes

	* man/reorder.Rd: Contents of package 'mva' moveed to 'stats'.

2004-03-26 17:28  warnes

	* man/fast.prcomp.Rd: Reflect movement of code from  'mva' package
	  to 'stats' in R 1.9.0.

2004-03-26 17:27  warnes

	* man/undocumented.Rd: Remove commented-out text.

2004-03-26 17:27  warnes

	* man/textplot.Rd: Update to match changes in textplot() code.

2004-03-26 17:25  warnes

	* man/ooplot.Rd: Remove Windows EOL characters.

2004-03-26 17:21  warnes

	* man/combinations.Rd: Uncomment and fix large 'n' example.

2004-03-26 17:20  warnes

	* man/barplot2.Rd: - Remove some commented-out code.  - Remove cvs
	  log tag.

2004-03-26 17:19  warnes

	* man/running.Rd: - Update to match changes in running() - Add
	  examples to illustrate new arguments.  - Modify running
	  correlation plot example to be more clear.

2004-03-26 17:17  warnes

	* R/zzz.R: Modify to work with R-1.9.0.

2004-03-26 17:16  warnes

	* R/textplot.R: Misc changes.

2004-03-26 17:12  warnes

	* R/running.R: More of the same.

2004-03-26 17:02  warnes

	* R/is.what.R: - Fix is.what() for use under R 1.9.0 - is.what()
	  now uses is.* functions found in any attached frame

2004-03-26 10:34  warnes

	* R/running.R: Fix bug discovered by Sean Davis
	  <sdavis2@mail.nih.gov>.  The running function took an improper
	  shortcut.  When allow.fewer=FALSE it was still passing shorter
	  lists of elements to the called function, and then overwriting
	  the results for the shorter lists with NAs.  The code now skips
	  evaluation of the function on lists shorter than the specified
	  length when allow.fewer=FALSE.

2004-03-25 15:09  warnes

	* R/estimable.R, man/estimable.Rd: - Estimable was reporting
	  sqrt(X^2) rather than X^2 in the output.  - Provide latex math
	  markup for linear algebra expressions in help text.  - Other
	  clarifications in help text

2004-03-25 13:17  warnes

	* R/estimable.R, man/estimable.Rd: Add enhancements to estimable()
	  provided by Sren Hjsgaard \email{sorenh@agrsci.dk}:

	    I have made a modified version of the function [..] which
	    1) also works on geese and gee objects and
	    2) can test hypotheses af the forb L * beta = beta0 both as a
	    single Wald test and row-wise for each row in L.

2004-03-25 11:38  warnes

	* R/factorial.R, man/factorial.Rd: Remove factorial() and
	  lfactorial() code since these are now provided by the base
	  package.

2004-02-17 22:59  warnes

	* TODO: Add need for split into sub-package.

2004-02-17 17:22  warnes

	* man/ooplot.Rd: Minor fix to ooplot documentation.

2004-02-17 17:21  warnes

	* R/ooplot.R, man/ooplot.Rd: Integrate ooplot updates provided by
	  Lodewijk Bonebakker <bonebakker@comcast.net>

2004-02-02 11:26  warnes

	* R/colorpanel.R, man/colorpanel.Rd:
	  - Add colorpanel function, which generates a smoothly varying
	  band of   colors over a three color range (lo, mid, high).

2004-02-02 11:21  warnes

	* DESCRIPTION: Update version number for new release.

2004-01-21 07:10  warnes

	* TODO: Add TODO to contain 'to do' list.

2004-01-21 07:07  warnes

	* man/textplot.Rd: - Correct arguments to halign to match code.

2004-01-21 07:06  warnes

	* R/reorder.R, man/reorder.Rd: - Add ... argument to match generic
	  provided in mva.

2004-01-21 00:17  warnes

	* R/lowess.R: Track R 1.9.0's move of 'lowess' from the base
	  package to the (new) stats package.

2004-01-20 23:48  warnes

	* DESCRIPTION: Updated for 0.8.8 release.

2004-01-20 23:44  warnes

	* man/sinkplot.Rd: - Fix sinkplot() example by replacing 'T' with
	  'TRUE'.

2004-01-20 23:42  warnes

	* man/ooplot.Rd: - Add some more details to the ooplot()
	  documentation.  The	documentation is *not* complete.

2004-01-20 23:31  warnes

	* R/: capture.R, textplot.R: - Mark sprint() as depreciated.  -
	  Replace references to sprint with capture.output() - Use
	  match.arg for halign and valign arguments to textplot.default.  -
	  Fix textplot.character so that a vector of characters is properly
	  displayed. Previouslt, character vectors were plotted on top of
	  each	 other.

2004-01-19 18:43  warnes

	* R/sinkplot.R, man/sinkplot.Rd:
	  New function sinkplot(), as requested on R-devel by Kevin Wright
	  <kwright@eskimo.com> in
	  https://www.stat.math.ethz.ch/pipermail/r-devel/2004-January/028483.html.

2004-01-19 17:45  warnes

	* R/elem.R, R/env.R, R/ll.R, man/keep.Rd, man/ll.Rd: - Integrated
	  (partial) patch submitted by Arni Magnusson to clarify help text.
	  - Modifed code to use match.arg().

2004-01-15 00:14  warnes

	* R/ooplot.R, man/ooplot.Rd:
	  Add initial code and docs for ooplot() function submitted by
	  Lodewijk Bonebakker <bonebakker@comcast.net>.

2003-12-15 16:07  warnes

	* R/env.R:
	  - Applied patch from Arni that fixed a bug that caused env() to
	  crash   if any environment was completely empty

2003-12-02 21:49  warnes

	* DESCRIPTION:
	  - Updated for version 0.8.7

2003-12-02 21:47  warnes

	* tests/: ci.Rout.save, fit.contrast-2003-11-17-UH.R,
	  fit.contrast-2003-11-17-UH.Rout.save:
	  - minor fixes

2003-12-02 21:46  warnes

	* man/: elem.Rd, foldchange.Rd, ll.Rd, lowess.Rd, textplot.Rd,
	  wapply.Rd: - match function argument defaults with 'usage'

2003-12-02 21:42  warnes

	* R/heatmap.2.R, man/heatmap.2.Rd:
	  - Fix buglets in heatmap function - Make a slight enhancement to
	  the example code.

2003-12-02 17:49  warnes

	* R/heatmap.2.R:
	  Integrated some suggestions from Sean Davis
	  <sdavis2@mail.nih.gov>.

2003-12-02 13:22  warnes

	* man/heatmap.2.Rd: - Make final example use 16 colors instead of
	  8.  This looks nicer.

2003-12-02 12:45  warnes

	* tests/fit.contrast-2003-11-17-UH.Rout.save:
	  - Remove no-longer-present warning on loading the gregmisc
	  package.

2003-12-02 12:09  warnes

	* tests/: ci.Rout.save, fit.contrast-2003-11-17-UH.Rout.save:
	  - Updated ci.R test output to match results under R-1.8.  -
	  Corrected fit.contrasts-2003-11.17-UH.R test output.

2003-12-02 12:00  warnes

	* man/ll.Rd:
	  Add one argument, to match code.

2003-12-02 11:58  warnes

	* man/barplot2.Rd:
	  - Remove '%' character from example code to avoid errors.

2003-12-02 11:54  warnes

	* R/plotCI.R:
	  - Add '...' parameter to call to text to allow user to control
	  size/color/etc.

2003-12-01 11:00  warnes

	* man/barplot2.Rd:
	  - updated to match changes to barplot() in base.

2003-12-01 10:59  warnes

	* data/: rtPCR.Rda, rtPCR.rda:
	  - Renamed rtPCR.Rda to rtPCR.rda so that R will properly load the
	  file	 when data(rtPCR) is executed.

2003-12-01 10:56  warnes

	* R/: elem.R, env.R, is.what.R, keep.R, ll.R:
	  - Apply changes submitted by Arni Magnusson

2003-12-01 10:55  warnes

	* R/barplot2.R:
	  - Follow patches applied to barplot() in base.

2003-11-24 16:32  warnes

	* man/heatmap.2.Rd:
	  Fix unbalanced braces.

2003-11-24 10:11  warnes

	* DESCRIPTION:
	  Updated for release.

2003-11-24 10:09  warnes

	* R/overplot.R, man/overplot.Rd:
	  Fix errors reported by R CMD check.

2003-11-21 18:13  warnes

	* man/overplot.Rd:
	  Added missing closing brace.

2003-11-21 18:08  warnes

	* data/rtPCR.Rda, man/rtPCR.Rd:
	  Initial addition of these files.  Used in examples of overplot().

2003-11-21 18:00  warnes

	* man/foldchange.Rd:
	  Removed 'deqn' call that was confusing things.

2003-11-21 17:59  warnes

	* R/heatmap.2.R, man/heatmap.2.Rd:
	  Applied my enhancements to the heatmap() code from R 1.8.0, and
	  added documentation of these changes.

2003-11-21 17:58  warnes

	* R/overplot.R, man/overplot.Rd:
	  - Discovered that axis(N) does the right thing without needing to
	  be   given location for tick marks.  This allowed simplification
	  of the code.

	  - Minor other changes for distribution

	  - Addition of overplot.Rd documentation.

2003-11-21 15:54  warnes

	* man/logit.Rd: Add email address to author field

2003-11-21 15:35  warnes

	* R/foldchange.R, man/foldchange.Rd:
	  - new files

2003-11-21 14:55  warnes

	* tests/fit.contrast-2003-11-17-UH.Rout.save:
	  Updated correct output.

2003-11-21 14:54  warnes

	* R/mixedsort.R, man/mixedsort.Rd:
	  - Change 'T' to 'TRUE' in mixedsort.R - Add missing brace in
	  mixedsort.Rd

2003-11-21 14:50  warnes

	* R/heatmap.2.R, man/heatmap.2.Rd:
	  - Integrated my extensions into the R 1.8.0 version of heatmap.
	  - Add Rd documentation.

2003-11-20 10:56  warnes

	* R/oddeven.R, man/oddeven.Rd:
	  - Move 'odd' and 'even' functions to a separate file & provide
	  documentation

2003-11-19 09:54  warnes

	* man/: env.Rd, is.what.Rd, keep.Rd, ll.Rd:
	  Changes to pass R CMD check.

2003-11-19 09:52  warnes

	* man/bandplot.Rd:
	  Remove extranious NULL that confused R CMD check.

2003-11-18 17:47  warnes

	* R/mixedsort.R, R/smartsort.R, man/mixedsort.Rd:
	  - Renamed smartsort to mixedsort and added documentation.

2003-11-18 13:59  warnes

	* man/barplot2.Rd:
	  - Tiny fix to remove R CMD check error.

2003-11-18 13:58  warnes

	* man/smartlegend.Rd:
	  - Added missing closing brace.

2003-11-18 13:45  warnes

	* R/: elem.R, env.R, is.what.R, keep.R, ll.R, overplot.R:
	  - Convert from MS-Dos to Unix line endings.  - Reformat to 80
	  columns.

2003-11-17 17:09  warnes

	* man/elem.Rd: Replace 'T' with 'TRUE' to remove R CMD check error.

2003-11-17 17:09  warnes

	* man/aggregate.table.Rd: Fix syntax error.

2003-11-17 16:40  warnes

	* R/fit.contrast.R, tests/fit.contrast-2003-11-17-UH.R,
	  tests/fit.contrast-2003-11-17-UH.Rout.save:
	  - Fix incorrect handling of glm objects by fit.contrast, as
	  reported   by Ulrich Halekoh, Phd <ulrich.halekoh@agrsci.dk>.

	  - Add regression test code to for this bug.

2003-11-10 17:11  warnes

	* DESCRIPTION, R/capture.R, R/elem.R, R/env.R, R/heatmap.2.R,
	  R/is.what.R, R/keep.R, R/ll.R, R/overplot.R, R/plotmeans.R,
	  R/smartsort.R, R/space.R, R/wapply.R, R/zzz.R, man/capture.Rd,
	  man/elem.Rd, man/env.Rd, man/is.what.Rd, man/keep.Rd, man/ll.Rd:
	  - Add files contributed by Arni Magnusson
	  <arnima@u.washington.edu>. As well as some of my own.

2003-08-19 10:58  warnes

	* R/heatmap.2.R:
	  - Copy of local changes.

2003-08-19 10:57  warnes

	* R/heatmap.2.R:
	  - Checkin before re-integrating local changes.

2003-08-06 23:49  warnes

	* R/ci.R: - Fixed incorrect denominator in standard error for mean
	  in ci.default.

2003-06-19 17:23  warnes

	* R/heatmap.2.R:
	  - Added enhanced heatmap function.

2003-06-09 11:10  warnes

	* man/smartlegend.Rd:
	  - Add help text for smartlegend.

2003-06-09 10:57  warnes

	* R/smartlegend.R: - New function smartlegend().

2003-06-07 13:58  warnes

	* man/: aggregate.table.Rd, interleave.Rd:
	  - Fixed error in examples.  Had sqrt(var(x)/(n-1)) for the
	  standard   error of the mean instead of sqrt(var(x)/n).

2003-05-28 22:43  warnes

	* R/library.R, man/library.Rd:
	  - Removed library() function.  It is not needed here and will be
	  released properly as part of 1.8.0.

2003-05-23 14:32  warnes

	* R/matchcols.R, man/matchcols.Rd:
	  - Fixed typos

2003-05-23 14:14  warnes

	* R/library.R, R/logit.R, R/matchcols.R, R/zzz.R, man/library.Rd,
	  man/logit.Rd, man/matchcols.Rd, man/undocumented.Rd:
	  - library() backported from 1.7-devel.  This version of the
	  function   adds the "pos=" argument to specify where in the
	  search path the   library should be placed.

	  - updated .First.lib to use library(...pos=3) for MASS to avoid
	  the	'genotype' data set in MASS from masking the genotype
	  funciton in	genetics when it loads gregmisc

	  - Added logit() inv.logit() matchcols() function and
	  corresponding docs

2003-05-20 12:03  warnes

	* R/interleave.R:
	  - Omit NULL variables.

2003-05-20 09:16  warnes

	* DESCRIPTION, R/trim.R, man/trim.Rd:
	  - Added function trim() and assocated docs.

2003-04-22 14:39  warnes

	* tests/fast.prcomp.Rout.save:
	  - One more try.

2003-04-22 14:29  warnes

	* DESCRIPTION:
	  - Update version number.

2003-04-22 14:29  warnes

	* tests/: fast.prcomp.R, fast.prcomp.Rout.save,
	  fit.contrast.Rout.save, plotmeans.Rout.save:
	  - Modified fast.prcomp.R to test data rather than timings.  -
	  Added fast.prcomp.R output to CVS.  - fit.contrast.R to generate
	  a warning message and fail to display one   column.  -
	  plotmeans.R used to generate a warning message.

2003-04-22 13:39  warnes

	* tests/: CrossTable.Rout.save, aggregate.table.Rout.save,
	  bandplot.Rout.save, barplot2.Rout.save, boxplot.n.Rout.save,
	  ci.Rout.save, combinations.Rout.save, combine.Rout.save,
	  dirichlet.Rout.save, estimable.Rout.save, factorial.Rout.save,
	  fit.contrast.Rout.save, glh.test.Rout.save, hist2d.Rout.save,
	  interleave.Rout.save, lowess.Rout.save, make.contrasts.Rout.save,
	  nobs.Rout.save, plotCI.Rout.save, plotmeans.Rout.save,
	  quantcut.Rout.save, rename.vars.Rout.save, reorder.Rout.save,
	  running.Rout.save, space.Rout.save, wapply.Rout.save:
	  - R 1.7.0 changed the default random number generator.  This
	  caused   all examples which used randomly generated data to
	  differ.  This   change the old data with new data generated under
	  1.7.0.

2003-04-22 13:28  warnes

	* R/plotmeans.R:
	  - Fixeed warning messing caused when 'connect' is a vector.

2003-04-22 13:24  warnes

	* R/fit.contrast.R:
	  - the variable 'df' was used within the lme code section
	  overwriting	the argument 'df'.

2003-04-22 12:00  warnes

	* man/combinations.Rd: - Fixed tpyo in example that allowed
	  combinations(500,2) to run when   it should have been ignred for
	  testing..

2003-04-22 11:42  warnes

	* R/reorder.R, man/reorder.Rd:
	  - The mva package (which is part of recommended) now provides a
	  generic 'reorder' function.  Consequently, the 'reorder' function
	    here has been renamed to 'reorder.factor'.

	  - Removed check of whether the argument is a factor object.

2003-04-22 11:34  warnes

	* R/barplot2.R: Update from Marc Schwartz, modified by Gregory
	  Warnes:

	  -  Modified dim() checks for 'ci.l' and 'ci.u' against 'height'
	   to remove R v1.7.0 if() based error msgs for vector conditions.

2003-04-22 11:13  warnes

	* R/zzz.R:
	  - Updated .First.lib() to load mva before MASS, this should
	  correct   problems when library(gregmisc) is in .Rprofile.

2003-04-10 12:22  warnes

	* man/combinations.Rd:
	  - Added note about the need to increase options("expressions") to
	  use	large values for 'n'.  Prompted by bug report from Huan
	  Huang   <huan.huang@bnpparibas.com

2003-04-04 08:59  warnes

	* DESCRIPTION:
	  - Version 0.8.3

2003-04-04 08:58  warnes

	* R/RSCompat.S:
	  - Replace 'T' with 'TRUE'

2003-04-04 08:49  warnes

	* R/balloonplot.R, R/dirichlet.R, man/qqnorm.aov.Rd:
	  - Change occurences of 'T' to 'TRUE'

2003-04-04 08:46  warnes

	* man/capture.Rd:
	  - Allow optional arguments to sprint to be passed to print - Fix
	  R CMD check errors

2003-04-04 08:45  warnes

	* R/capture.R:
	  - Allow optional arguments to sprint to be passed to print

2003-04-04 08:44  warnes

	* man/textplot.Rd:
	  - Updated to match changes in textplot function:   - Added
	  textplot.character   - Renamed arguments "col.margin" and
	  "row.margin" to "cmar", and	  "rmar" so that specifying
	  "col='red'" is possible.  - Fixed R CMD check errors - Improve
	  comments in example - Add textplot.matrix example

2003-04-04 08:41  warnes

	* R/textplot.R:

	  - Added textplot.character to handle character strings.  - Moved
	  test for vector and matrix arguments to textplot.default.  -
	  Renamed arguments "col.margin" and "row.margin" to "cmar", and
	  "rmar" so that specifying "col='red'" is possible.

2003-04-03 08:20  warnes

	* man/capture.Rd:
	  - Had mistyped 'sprint' as 'sprintf'.

2003-04-03 08:18  warnes

	* man/capture.Rd: - Add help file for capture and sprintf.

2003-04-02 17:29  warnes

	* R/textplot.R, man/textplot.Rd:
	  - Added textplot function and friends, as well as documentation.

2003-04-02 17:28  warnes

	* R/capture.R:
	  - Added file 'capture.R' containing capture() and sprint().

2003-03-12 12:58  warnes

	* man/fit.contrast.Rd:
	  - Fixed a typo in the example - Added to lme example

2003-03-08 11:45  warnes

	* tests/: fit.contrast.Rout~, fit.contrast.R~: - Removed trash
	  files from repository.

2003-03-08 11:30  warnes

	* man/balloonplot.Rd:
	  - Forgot to update arglist in \usage section.

2003-03-08 11:26  warnes

	* DESCRIPTION:
	  - Bumped up version number.

2003-03-08 11:22  warnes

	* R/balloonplot.R, man/balloonplot.Rd:
	  - Added parameters for rotation of and amount of space allocated
	  for	the row and column labels.

2003-03-07 10:48  warnes

	* DESCRIPTION, R/RSCompat.S, R/factorial.R, R/fast.prcomp.R,
	  R/hist2d.R, R/qqnorm.aov.R:
	  - Minor changes to code to allow the package to be provided as an
	  S-Plus chapter.

2003-03-07 10:43  warnes

	* R/lowess.R: - Add 'NULL' as the last element of if statement that
	  defines   lowess.default so that when the file is sourced, S-Plus
	  doesn't   display the function definition.

2003-03-07 10:41  warnes

	* R/lowess.R:
	  - Specify where the defualt lowess function should be found.	-
	  Use getFunction in S-Plus instead of 'get'

2003-03-03 12:48  warnes

	* man/reorder.Rd: - Updated to match reorder.Rd which was exetended
	  to handle factor   label names in addition to numeric indices.

2003-03-03 12:24  warnes

	* R/reorder.R:
	  - Added handling of factor level names in addition to numeric
	  indexes.

2003-01-30 17:04  warnes

	* man/contrast.lm.Rd:
	  - fixed typo

2003-01-30 17:00  warnes

	* DESCRIPTION:
	  - New release.

2003-01-30 16:58  warnes

	* tests/contrast.lm.Rout.save:
	  - Renamed to/replaced by fit.contrast.Rout.save.

2003-01-30 16:57  warnes

	* tests/contrast.lm.R: - Renamed to/replaced by fit.contrasts.R

2003-01-30 16:56  warnes

	* man/running.Rd: - Fixed typo in email address.

2003-01-30 16:54  warnes

	* tests/: CrossTable.R, CrossTable.Rout.save, fit.contrast.R,
	  fit.contrast.Rout.save, fit.contrast.Rout~, fit.contrast.R~,
	  make.contrasts.R, make.contrasts.Rout.save:
	  - Updated tests to match changes in contrast.lm() ->
	  fit,contrasts(),   and CrossTable().

2003-01-30 16:53  warnes

	* R/fit.contrast.R, R/contrast.lm.R, man/contrast.lm.Rd,
	  man/fit.contrast.Rd:
	  - Renamed 'contrast.lm' to 'fit.contrast'.  This new name is more
	    descriptive and makes it easier to create and use methods for
	  other   classes, eg lme.

	  - Enabled fit.contrast for lme object now that Doug Bates has
	  provided   the necessary support for contrasts in the nlme
	  package.

	  - New contrast.lm function which generates a 'depreciated'
	  warning and	calls fit.contrast

	  - Updated help text to match changes.

2003-01-30 16:43  warnes

	* R/barplot2.R, man/barplot2.Rd:
	  - Added argument 'add' to allow for the addition of a barplot to
	  an   existing graphic. Default is FALSE

2003-01-30 16:41  warnes

	* R/CrossTable.R, man/CrossTable.Rd:
	  - Removed argument 'correct' and now print separate corrected
	  values   for 2 x 2 tables.  - Added arguments 'prop.r', 'prop.c'
	  and 'prop.t' to toggle printing   of row, col and table
	  percentages. Default is TRUE.  - Added argument 'fisher' to
	  toggle fisher exact test. Default is	 FALSE.  - Added McNemar
	  test to statistics and argument 'mcnemar' to toggle	test.
	  Default is FALSE.  - Added code to generate an invisible return
	  list containing table   counts, proportions and the results of
	  the appropriate statistical tests.

2003-01-30 09:58  warnes

	* R/make.contrasts.R:
	  - Added explicit check to ensure that the number of specified
	  contrasts is less than or equal to the ncol - 1.  Previously,
	  this	 failed with an obtuse error message when the contrast
	  matrix had row   names, and silently dropped contrasts over
	  ncol-1.

2003-01-20 13:35  warnes

	* R/balloonplot.R, man/balloonplot.Rd:
	  - Updated balloonplot help page.

2003-01-20 12:13  warnes

	* R/wapply.R, man/wapply.Rd:
	  - Updated wapply.R to allow specification of evaluation points
	  when	 method is 'width' or 'range' using the 'pts' argument.  -
	  Updated wapply.Rd to add 'pts' argument - Fixed typos, spelling
	  errors, gramatical errors and lack of clarity   in wapply.Rd help
	  text.

2003-01-03 16:34  warnes

	* R/balloonplot.R, man/balloonplot.Rd: - Initial checkin of
	  balloonplot functions and documentation.

2003-01-03 14:23  warnes

	* man/space.Rd: - Added reference to and comparison example of
	  sunflowerplot.  - Added code to put example plots on same plot
	  window using par(mfrow=...).

2003-01-03 14:02  warnes

	* man/contrast.lm.Rd:
	  - Removed duplicate assigment from aov example.

2003-01-02 11:11  warnes

	* DESCRIPTION: Updated version number and added Kjetil to list of
	  contributors.

2003-01-02 11:09  warnes

	* R/barplot2.R:
	  - Changed assignment statements that used "=" to "<-" to avoid
	  syntax   errors in older versions of the S language.

2003-01-02 11:07  warnes

	* R/lowess.R:
	  - Added wrapper code so that R-specific fiddling won't be
	  executed   under S-Plus.

2003-01-02 11:04  warnes

	* R/contrast.lm.R:
	  - Now will run on objects of class aov (but not aovlist!)

2003-01-02 10:42  warnes

	* R/RSCompat.S: - Add nlevels function.

2003-01-02 10:40  warnes

	* R/qqnorm.aov.R, man/qqnorm.aov.Rd: - Renamed first parameter to
	  match qqnorm generic.

2003-01-02 10:14  warnes

	* man/qqnorm.aov.Rd: Added additional help text from Kjeitl.

2002-12-31 14:50  warnes

	* R/qqnorm.aov.R, man/qqnorm.aov.Rd: Initial checkin of qqnorm.aov
	  function and documentation submitted by Kjetil Halvorsen
	  <kjetilh@jupiter.umsanet.edu.bo>.

2002-11-04 09:36  warnes

	* R/zzz.R:
	  - Oops, re-instated 'require(MASS)' in .First.lib() so that MASS
	  gets	 loaded.  (Just stating a dependency in DESCRIPTION doesn't
	  actually   load the library!)

2002-11-04 09:24  warnes

	* DESCRIPTION, R/zzz.R: - Added dependency on R >= 1.6.0 due to
	  code in barplot2() - Since MASS is now a dependency in
	  DESCRIPTION, I removed the now   redundant check for MASS in
	  .First.lib().

2002-11-04 09:21  warnes

	* R/barplot2.R, man/barplot2.Rd: Updates from Marc Schwartz:

	  - Updated underlying code to be based upon the new barplot() in R
	  v1.6.1 - This now uses the 'axis.lty' and 'border' arguments - In
	  R v1.6.0, R Core introduced a new function called axTicks().
	  This is an R equivalent of the C code for CreateAtVector in
	  plot.c.    This now enables me to get the axis tick mark
	  positions consistently    when the 'height' related axis is
	  either linear or log.  Thus, I can	now have consistent tick
	  marks and can plot grid lines in either    situation.  If
	  'plot.grid = TRUE' and 'grid.inc' is specified, then	  I still
	  use pretty() to determine the tick marks and lines.  - This code
	  now depends on R 1.6.0 or later.

2002-11-04 09:13  warnes

	* R/CrossTable.R:
	  - Moved fisher.test() to after table is printed, so that table is
	  still printed in the event that fisher.test() results in
	  errors.

2002-10-30 13:07  warnes

	* tests/: fast.prcomp.R, make.contrasts.R:
	  - Added test code for fast.prcomp, fast.svd, and make.contrasts.

2002-10-29 21:32  warnes

	* DESCRIPTION:
	  Updated version number for 2002-10-29 release.

2002-10-29 21:31  warnes

	* tests/contrast.lm.R:
	  - changes in whitespace

2002-10-29 21:23  warnes

	* man/undocumented.Rd:
	  - Commented out plot.lm documentation - Removed make.contrasts
	  documentation, which is now properly	 documented in
	  man/make.contrasts.Rd

2002-10-29 21:21  warnes

	* R/plot.lm.R:
	  - Commented out plot.lm() code since recent changes in R have
	  broken it.

2002-10-29 18:06  warnes

	* R/fast.prcomp.R, man/fast.prcomp.Rd:
	  - Fixes to fast.svd to make it actually work.  - Updates to man
	  page to fix mistmatches between code and docs and to	 fix
	  warnings.

2002-10-29 18:00  warnes

	* R/contrast.lm.R, R/make.contrasts.R, man/contrast.lm.Rd,
	  man/make.contrasts.Rd:
	  - Moved make.contrasts to a separate file.  - Enhanced make
	  contrasts to better label contrast matrix, to give   how.many a
	  default value, and to coerce vectors into row matrixes.  - Added
	  help page for make.contrasts.  - Added link from contrasts.lm
	  seealso to make.contrasts.

2002-10-29 17:54  warnes

	* tests/: CrossTable.Rout.save, aggregate.table.Rout.save,
	  bandplot.Rout.save, barplot2.Rout.save, boxplot.n.Rout.save,
	  ci.Rout.save, combinations.Rout.save, combine.Rout.save,
	  contrast.lm.Rout.save, dirichlet.Rout.save, estimable.Rout.save,
	  factorial.Rout.save, glh.test.Rout.save, hist2d.Rout.save,
	  interleave.Rout.save, lowess.Rout.save, make.contrasts.Rout.save,
	  nobs.Rout.save, plotCI.Rout.save, plotmeans.Rout.save,
	  quantcut.Rout.save, rename.vars.Rout.save, reorder.Rout.save,
	  running.Rout.save, space.Rout.save, wapply.Rout.save:
	  - Added tests for dirichlet and  make.contrasts.  - Updated
	  everything to match reduced warning message now that plot.lm is
	  not	being overloaded.

2002-10-29 14:55  warnes

	* R/contrast.lm.R, man/contrast.lm.Rd:
	  - Fix bug that prevented contrast.lm() from working on 'aov'
	  objects - Add 'aov' examples to documentation for contrast.lm -
	  Added note about future support for contrast.lme.

2002-10-29 14:29  warnes

	* R/fast.prcomp.R, man/fast.prcomp.Rd: Initial checkin for
	  fast.prcomp() and fast.svd().

2002-10-11 14:38  warnes

	* DESCRIPTION, tests/dirichlet.R:
	  - Updated version number in DESCRIPTION.

2002-10-11 14:22  warnes

	* R/permute.R, man/permute.Rd:
	  - Add permute() function (wraper for sample) and man page

2002-10-11 14:21  warnes

	* man/dirichlet.Rd:
	  - Escaped underscores in my email address that was causing a
	  parse   error in the {r,p}dirichlet man page.

2002-10-11 14:02  warnes

	* R/barplot2.R:
	  - Fixed log scale errors in legend() call

2002-10-01 14:16  warnes

	* man/hist2d.Rd:
	  - Added examples of using 'contour' and 'filled.contour' for
	  display.

2002-09-30 16:45  warnes

	* DESCRIPTION:
	  - Updated version number after adding rdirichlet() and
	  ddirichlet()

2002-09-30 16:43  warnes

	* R/dirichlet.R, man/dirichlet.Rd, tests/dirichlet.R:
	  - Added rdirichlet() and ddirichlet() with accompaning help page
	  and tests.

2002-09-26 08:11  warnes

	* man/glh.test.Rd: - Added note and example code to illustrate how
	  to properly compute	contrasts for the first factor in the
	  model.

2002-09-24 16:20  warnes

	* DESCRIPTION:
	  Update version number after fixing bugs and adding regression
	  tests.

2002-09-24 16:18  warnes

	* tests/: CrossTable.R, CrossTable.Rout.save, aggregate.table.R,
	  aggregate.table.Rout.save, bandplot.R, bandplot.Rout.save,
	  barplot2.R, barplot2.Rout.save, boxplot.n.R, boxplot.n.Rout.save,
	  ci.R, ci.Rout.save, combinations.R, combinations.Rout.save,
	  combine.R, combine.Rout.save, contrast.lm.R,
	  contrast.lm.Rout.save, estimable.R, estimable.Rout.save,
	  factorial.R, factorial.Rout.save, glh.test.R, glh.test.Rout.save,
	  hist2d.R, hist2d.Rout.save, interleave.R, interleave.Rout.save,
	  lowess.R, lowess.Rout.save, nobs.R, nobs.Rout.save, plotCI.R,
	  plotCI.Rout.save, plotmeans.R, plotmeans.Rout.save, quantcut.R,
	  quantcut.Rout.save, rename.vars.R, rename.vars.Rout.save,
	  reorder.R, reorder.Rout.save, running.R, running.Rout.save,
	  space.R, space.Rout.save, wapply.R, wapply.Rout.save:
	  - Added regression test.

2002-09-24 15:12  warnes

	* R/glh.test.R:
	  - Fixed a typo.

2002-09-24 11:55  warnes

	* R/contrast.lm.R:
	  - Add ability to show confidence intervals when showall=TRUE.

2002-09-24 11:01  warnes

	* DESCRIPTION:
	  Updated to version 0.6.1, corresponding to some bug fixes.

2002-09-24 10:57  warnes

	* R/running.R:
	  - Fixed error where running was always calling running2 with
	  'fun=mean', ignoring the specified funtion.

2002-09-24 10:53  warnes

	* R/plotmeans.R:
	  - Changed digits=options("digits") which produces a list of
	  length 1   to digits=getOption("digits") which returns a vector
	  of length one.    The former was causing an error when passed to
	  round().

2002-09-23 10:27  warnes

	* man/: CrossTable.Rd, barplot2.Rd, glh.test.Rd:
	  - Fixed syntax errors in barplot2.Rd and CrossTable.Rd - Fixed
	  incorrect translation of 'F' (distribution) to 'FALSE' in
	  glh.test.Rd

2002-09-23 10:02  warnes

	* inst/doc/: Rnews.dtx, Rnews.sty, gregmisc.pdf, gregmisc.tex:
	  Added inst/doc directory and contents to CVS.

2002-09-23 09:59  warnes

	* R/aggregate.table.R, R/boxplot.n.R, R/ci.R, R/combine.R,
	  R/factorial.R, R/hist2d.R, R/interleave.R, R/lowess.R, R/nobs.R,
	  R/residplot.R, R/zzz.R, man/aggregate.table.Rd, man/bandplot.Rd,
	  man/combinations.Rd, man/combine.Rd, man/contrast.lm.Rd,
	  man/estimable.Rd, man/factorial.Rd, man/glh.test.Rd,
	  man/hist2d.Rd, man/interleave.Rd, man/lowess.Rd, man/nobs.Rd,
	  man/plotCI.Rd, man/quantcut.Rd, man/rename.vars.Rd,
	  man/reorder.Rd, man/space.Rd, man/undocumented.Rd: - Modified all
	  files to include CVS Id and Log tags.

2002-09-23 09:38  warnes

	* DESCRIPTION, R/CrossTable.R, R/barplot2.R, R/combinations.R,
	  man/CrossTable.Rd, man/barplot2.Rd:
	  - Added CrossTable() and barplot2() code and docs contributed by
	  Marc Schwartz.  - Permit combinations() to be used when r>n
	  provided repeat.allowed=TRUE - Bumped up version number

2002-08-01 15:37  warnes

	* DESCRIPTION, R/ci.R, R/contrast.lm.R, R/hist2d.R, R/running.R,
	  R/wapply.R, man/ci.Rd, man/contrast.lm.Rd, man/estimable.Rd,
	  man/glh.test.Rd:
	  - Corrected documentation mismatch for ci, ci.default.

	  - Replaced all occurences of '_' for assignment with '<-'.

	  - Replaced all occurences of 'T' or 'F' for 'TRUE' and 'FALSE'
	  with	 the spelled out version.

	  - Updaded version number and date.

2002-08-01 14:06  warnes

	* R/reorder.R:
	  Added reorder() function to reorder the levels of a factor.

2002-04-15 17:30  warneg

	* man/contrast.lm.Rd: - Separated out, then commented out mention
	  of contrast.lme and lme   objects.  The contrast.lme function
	  will become part of Bates and   Pinhiero's next NLME library.

2002-04-15 17:28  warneg

	* R/contrast.lm.R: - Separated out, then commented out contrast.lme
	  code.  The   contrast.lme function will become part of Bates and
	  Pinhiero's NLME   library.

2002-04-08 20:51  warneg

	* DESCRIPTION, R/bandplot.R, R/boxplot.n.R, R/ci.R,
	  R/combinations.R, R/contrast.lm.R, R/estimable.R, R/glh.test.R,
	  R/hist2d.R, R/plot.lm.R, R/plotCI.R, R/plotmeans.R,
	  R/rename.vars.R, R/residplot.R, R/space.R, R/wapply.R,
	  man/aggregate.table.Rd, man/bandplot.Rd, man/boxplot.n.Rd,
	  man/combinations.Rd, man/glh.test.Rd, man/hist2d.Rd,
	  man/interleave.Rd, man/plotmeans.Rd, man/reorder.Rd,
	  man/running.Rd, man/space.Rd, man/undocumented.Rd, man/wapply.Rd:

	  Checkin for version 0.5.3

2002-04-08 20:46  warneg

	* R/interleave.R: - Properly handle case when some or all arguments
	  are vectors.

2002-04-05 13:27  warneg

	* man/contrast.lm.Rd:
	  - Noted that contrats.lm can be applied to lme objects.  -
	  Clarified return value when conf.int is specified.

2002-04-05 13:23  warneg

	* R/contrast.lm.R:
	  - Updated contrast.lm to handle lme objects - Modified
	  contrast.lm to compute confidence intervals even when   showall
	  is true.  - Added check and warning if conf.int is outside (0,1).
	  This will ensuere   that conf.int=T does not cause nonsense
	  results.

2002-03-27 15:51  warneg

	* man/lowess.Rd:
	  Added "..." argument to lowess.default.

2002-03-27 14:48  warneg

	* R/lowess.R: - Added code to append "..." to the argument list of
	  lowess.default.

	  - Fixed a wrong default for f in lowess.formula.  Was 3, but
	  should   have been 2/3.

2002-03-26 16:22  warneg

	* R/ci.R, R/glh.test.R, R/lowess.R, man/ci.Rd, man/glh.test.Rd,
	  man/lowess.Rd, man/reorder.Rd, man/undocumented.Rd:
	  - Changed methods to include '...' to match the generic.  -
	  Updated for version 0.5.1

2002-03-26 16:21  warneg

	* DESCRIPTION:
	  Updated for version 0.5.1

2002-03-26 16:04  warneg

	* INDEX:
	  Index is now auto-generated. The presence of a file named INDEX
	  prevents that.

2002-03-26 14:29  warneg

	* R/nobs.R:
	  Added ... to methods.

2002-03-26 14:29  warneg

	* man/nobs.Rd:
	  Updated to add ... parameter to function calls.

2002-03-26 14:24  warneg

	* man/hist2d.Rd:
	  Initial checkin.

2002-03-26 10:30  warneg

	* man/glh.test.Rd: Removed incorrect link to 'contrast' from
	  seealso.

2002-03-26 10:27  warneg

	* man/reorder.Rd:
	  Initial checkin.

2002-03-26 09:49  warneg

	* man/quantcut.Rd:
	  Initial Checkin

2002-03-26 09:29  warneg

	* R/quantcut.R:
	  Initial checkin.

2002-03-26 09:28  warneg

	* R/nobs.R: - Added CVS tags

2002-03-19 23:17  warneg

	* R/plotmeans.R: - Changes to add compatibility with S-Plus 2000

2002-03-19 23:16  warneg

	* R/plotCI.R: - Changes to add compatibility with S-Plus 2000.

2002-03-19 22:48  warneg

	* R/boxplot.n.R:
	  - Updated to work in S-Plus 2000 as well as R.

2002-03-19 22:44  warneg

	* R/RSCompat.S: - Added definition of is.R function.

	  - Added boxplot.formula

2002-03-07 18:39  warneg

	* man/running.Rd: - Added documentation and example for running2

2002-03-07 18:38  warneg

	* R/running.R:
	  - Added "running2", which handles both univariate and bivariate
	  cases - Modified "running" to call "running2"

2002-03-05 11:44  warneg

	* R/plotmeans.R: - Replace "T" with "TRUE".  Problems arrive when
	  there is a variable named "T".

2002-02-21 16:45  warneg

	* R/aggregate.table.R:
	  - Fixed bug where row and column labels didn't always correspond
	  to the contents.  This only occured when a factor was used for
	  by1 or by2 and the factors levels weren't in the default sort
	  order.

2002-02-20 17:10  warneg

	* R/aggregate.table.R:
	  New function.

2002-02-20 17:09  warneg

	* man/aggregate.table.Rd:
	  Initial checkin.

2002-02-20 16:41  warneg

	* man/interleave.Rd, R/interleave.R: Initial checkin.

2002-02-20 16:31  warneg

	* man/nobs.Rd:
	  Noted that specialized methods exist.

2002-02-20 16:29  warneg

	* man/nobs.Rd:
	  Incorrectly had contents of nobs.R here instead of help text.
	  Corrected.

2002-02-20 15:09  warneg

	* man/: ci.Rd, estimable.Rd, glh.test.Rd, lowess.Rd, plotCI.Rd,
	  rename.vars.Rd, space.Rd, undocumented.Rd:
	  Minor changes, typo and formatting fixes.

2002-02-20 15:08  warneg

	* INDEX:
	  Updated.

2002-02-20 15:06  warneg

	* R/bandplot.R, man/bandplot.Rd:
	  - Generalized to allow specification of the multiples of the
	  standard deviation levels to be plotted (0=mean, 1=1 sd, ..).  -
	  Now (invisibly) returnes computed smooths.

2002-02-20 15:03  warneg

	* R/nobs.R, man/nobs.Rd: - initial checkin.

2002-02-16 13:16  warneg

	* man/bandplot.Rd:
	  Added bandplot documentation.

2002-02-16 12:58  warneg

	* R/wapply.R:
	  - Fixed Bug: When method=="range", the absolute range of x was
	  being   used to compute the relative width instead of the
	  (correct) relative   range.

2002-02-16 12:23  warneg

	* R/wapply.R:
	  - Corrected problem removing missing values: The missing values
	  of $x   and $y were being removed indepdendently, leaving an
	  uneven number   of points in the result.

2002-02-04 21:20  warneg

	* R/RSCompat.S:
	  - Fix typo that caused code meant to run only under S-Plus to run
	  under R, causing problems.

2002-02-04 21:19  warneg

	* R/zzz.R:
	  - Remove dead code

2002-02-04 18:20  warneg

	* R/space.R:
	  - Add na.rm parameter and make the default TRUE.

2002-02-04 18:19  warneg

	* R/hist2d.R:
	  Initial checkin.

2002-02-04 14:12  warneg

	* R/plotCI.R:
	  - When err="x", 'col' was being used to plot bars, rather than
	  'barcol'.

2002-02-04 14:09  warneg

	* R/plotCI.R:
	  - fixed typo, when err="x", lty was 'slty' causing an error.

2002-01-25 18:00  warneg

	* R/iapply.R:
	  I can't remember what this function was written for, nor can I
	  find any examples of using it. Consequently, I'm deleting it.

2002-01-17 18:51  warneg

	* man/estimable.Rd:
	  - Fixed errror in last example by adding 'conf.int' parameter to
	  'estimable' call.

2002-01-17 18:42  warneg

	* R/glh.test.R:
	  - Fixed typo in code that resulted in an syntax error.

2002-01-17 18:21  warneg

	* man/elementof.Rd:
	  Removed: duplicated built-in %in% operator.

2002-01-17 18:21  warneg

	* R/elementof.R:
	  Removed: duplicates the built-in %in% operator.

2002-01-10 12:35  warneg

	* R/glh.test.R:
	  - print.glh.test() was using cat() to printing the call.  This
	  didn't work and generated an error.

2001-12-19 17:45  warneg

	* R/RSCompat.S: - Added code for %in%.

2001-12-19 15:06  warneg

	* man/glh.test.Rd:
	  - Fixed display of formulae.	- Added description of return value

2001-12-19 15:05  warneg

	* R/glh.test.R:
	  - Removed extra element of return object.

2001-12-18 17:14  warneg

	* man/estimable.Rd:
	  - Updated documentation to reflect change of parameters from
	  'alpha'   to 'conf.int', including the new optional status of the
	  confidence   intervals.

2001-12-18 17:12  warneg

	* R/estimable.R:
	  - Modified to make confidence intervals optional.  Changed
	  'alpha'   parameter giving significance level to 'conf.int'
	  giving confidence   level.

2001-12-18 16:36  warneg

	* man/glh.test.Rd:
	  - Added summary.glh.test to alias, usage, and example sections.

2001-12-18 16:34  warneg

	* R/glh.test.R: - Modified to work correctly when obj is of class
	  'aov' by specifying	summary.lm instead of summary.	This
	  ensures that the summary object   has the fields we need.

	  - Moved detailed reporting of results from 'print' to 'summary'
	  function and added a simpler report to 'print'

2001-12-18 16:27  warneg

	* R/estimable.R:
	  - Modified to work correctly when obj is of class 'aov' by
	  specifying   summary.lm instead of summary.  This ensures that
	  the summary object   has the fields we need.

2001-12-17 19:43  warneg

	* R/glh.test.R, man/glh.test.Rd:
	  Initial checkin.

2001-12-17 14:13  warneg

	* DESCRIPTION, INDEX:
	  Updated to include new functions and thier contributors.

2001-12-17 13:59  warneg

	* man/estimable.Rd:
	  - Fixed spelling errors.

2001-12-17 13:52  warneg

	* man/estimable.Rd:
	  - Fixed the link to contrasts.lm.  - Rephrased title/description
	  to be more clear.

2001-12-11 20:41  warneg

	* man/space.Rd:
	  - Quoted underscore character in my email address.  - Added
	  correct keyword.

2001-12-11 20:39  warneg

	* man/rename.vars.Rd:
	  Added omitted documentaton for 'info' parameter.  Changed example
	  code not to use 'Orthodont' data set so that the nlme package is
	  not required.

2001-12-11 20:37  warneg

	* man/plotmeans.Rd:
	  Added documentation for xaxt parameter.

2001-12-11 20:36  warneg

	* man/undocumented.Rd:
	  Initial checkin.

2001-12-11 20:34  warneg

	* R/lowess.R:
	  Updated to explicitly list control arguments to lowess.formula.

2001-12-11 20:34  warneg

	* man/lowess.Rd:
	  Initial checkin.  Code copied from R source package and extended.

2001-12-10 14:38  warneg

	* man/: contrast.factor.Rd, contrast.lm.Rd: renamed
	  contrast.factor.Rd back to contrast.lm.Rd corresponding to rename
	  of function.

2001-12-10 14:35  warneg

	* man/: estimable.Rd, contrast.coeff.Rd: Renamed
	  'contrsts.coeff.Rd' to 'estimable.Rd' corresponding to function
	  rename.

2001-12-10 14:29  warneg

	* R/contrast.lm.R: incorrectly put contrast.coeff.R (now
	  estimable.R) here.  Now correctly put contrast.factor.R back here

2001-12-10 14:27  warneg

	* R/contrast.factor.R: renamed contrast.factor.R back to
	  contrast.lm.R

2001-12-10 14:26  warneg

	* R/estimable.R: renamed from contrast.coeff.R to estimable.R
	  (incorrectly via contrast.lm.R)

2001-12-10 14:22  warneg

	* R/contrast.coeff.R: Renamed back to 'contrast.lm.R'

2001-12-10 14:20  warneg

	* R/contrast.lm.R: Renamed back to contrast.lm

2001-12-07 20:54  warneg

	* R/rename.vars.R: Changed 'T' to 'TRUE' in parameter list.

2001-12-07 18:53  warneg

	* man/contrast.factor.Rd:
	  Added documentation for 'conf.int' parameter.

2001-12-07 18:34  warneg

	* man/wapply.Rd:
	  Fixed an problem where \code was incorrectly delimited by parens
	  rather than curly brackets.

2001-12-07 18:33  warneg

	* man/rename.vars.Rd: - Fixed see also link.  Mis-typed
	  'data.frame' as 'dataframe'.

2001-12-07 17:56  warneg

	* man/elementof.Rd:
	  Added warning that this function is depreciated.

2001-12-07 17:55  warneg

	* R/rename.vars.R:
	  Added attribution.

2001-12-07 17:49  warneg

	* man/rename.vars.Rd:
	  Added proper attribution to Don MacQueen.

2001-12-07 17:33  warneg

	* R/: iapply.R, lowess.R, plot.lm.R, residplot.R:
	  Initial checkin.

2001-12-07 17:29  warneg

	* man/space.Rd, R/zzz.R:
	  Initial checkin.

2001-12-07 17:24  warneg

	* R/space.R:
	  - Added cvs tags.

2001-12-07 17:23  warneg

	* R/space.R:
	  - Leave first point at center, rather than shifting by s/2 to the
	  left.  This looks better when there are more than 2 'spaced'
	  points.

2001-12-07 16:48  warneg

	* man/rename.vars.Rd:
	  Initial checkin.  Unfortunately, I've lost the email of the
	  person who sent this to me.  I'll credit him/her when I find out
	  who it was!

2001-12-07 16:40  warneg

	* R/rename.vars.R:
	  Initial checkin

2001-12-07 16:06  warneg

	* R/elementof.R:
	  - elementof duplicates '%in%'.  Code now uses '%in%' and issues a
	  warning.

2001-12-07 15:59  warneg

	* man/factorial.Rd, R/factorial.R:
	  Initial checkin.

2001-12-07 15:39  warneg

	* man/contrast.coeff.Rd:
	  - Initial checkin

2001-12-07 15:32  warneg

	* R/contrast.coeff.R: - If cm is not matrix, coerce it into a
	  single-row matrix.

2001-12-07 15:07  warneg

	* R/contrast.coeff.R:
	  Substantial enhancements to initial version:

	   - Added StdErr, t-value, p-value, and DF columns to output.
	   - Modified to use t distribution rather than normal distribution
	  for
	     confidence intervals.

2001-12-07 15:04  warneg

	* R/contrast.coeff.R: Initial checkin.

2001-12-07 14:57  warneg

	* man/contrast.factor.Rd:
	  Renamed 'contrast.lm.Rd' to 'contrast.factor.Rd'.

2001-12-07 14:53  warneg

	* R/contrast.factor.R: Renamed 'contrast.lm.R' to
	  'contrast.factor.R' to highlight that this function only works on
	  individual factors.

2001-12-07 14:50  warneg

	* man/ci.Rd: - Added text noting that lme is now supported.

2001-12-07 14:19  warneg

	* R/ci.R: - Fixed typo:  DF column was being filled in with
	  p-value.

2001-12-07 13:49  warneg

	* R/ci.R: - Added ci.lme method to handle lme objects.

2001-12-05 14:51  warneg

	* R/: combine.R, concat.R:
	  - Renamed 'concat' function to 'combine' to avoid name conflict
	  with	 an existing S-Plus function.

2001-12-05 14:49  warneg

	* R/plotmeans.R: - Added ability to use the t-distribution to
	  compute confidence   intervals.  This is controlled using the
	  'use.t' parameter.

2001-12-05 14:44  warneg

	* man/: combine.Rd, concat.Rd:
	  - Changed function name 'concat' to 'combine' and renamed
	  concat.Rd to	 combine.Rd

2001-12-05 14:41  warneg

	* man/plotmeans.Rd: - Added documentation of use.t parameter.

2001-12-05 14:36  warneg

	* man/wapply.Rd:  - Clarified how the width of the window is
	  computed when method="nobs".

2001-12-05 14:29  warneg

	* R/wapply.R:
	  - Added a better default for "width" when method="nobs".  For
	  this case,   width=max(5, length(x)/10).

	  - Allow omission of x values which result in missing y values via
	    'drop.na' parameter.

2001-11-13 16:19  warneg

	* R/contrast.lm.R: - Fixed error that occured when a factor has 2
	  levels and only one	contrast is specified

2001-10-25 22:48  warneg

	* R/plotmeans.R:
	  Added correct handling of 'xaxt="n"'.

2001-10-16 19:14  warneg

	* man/: ci.Rd, wapply.Rd:
	  Fixed unbalanced brace.

2001-10-16 19:06  warneg

	* man/plotCI.Rd:
	  Added minbar and maxbar parameters.

2001-10-16 19:04  warneg

	* man/plotmeans.Rd:
	  Forgot to add minbar and maxbar to usage section.

2001-10-16 19:03  warneg

	* man/plotmeans.Rd:
	  Added description of minbar and maxbar.

2001-10-16 19:00  warneg

	* R/plotCI.R:
	  - Added minbar and maxbar parameters - Added cvs id and log tags
	  to header

2001-10-16 18:59  warneg

	* R/plotmeans.R:
	  Added cvs id and log tag to file header

2001-10-16 18:57  warneg

	* R/plotmeans.R:
	  Added minbar and maxbar parameters.

2001-10-16 18:35  warneg

	* man/plotmeans.Rd:
	  Added description of minsd parameter.

2001-10-16 18:35  warneg

	* R/plotmeans.R: Added minsd parameter.

2001-09-18 10:15  warneg

	* DESCRIPTION, R/RSCompat.S, R/plotCI.R, R/plotmeans.R:
	  Release 0.3.2

2001-09-18 10:14  warneg

	* R/contrast.lm.R:
	  Fixed bug in make.contrasts.	There was leftover code expecting a
	  parameter 'x' which is no lonber provided.

2001-09-01 15:19  warneg

	* R/RSCompat.S:
	  Initial checkin.

2001-08-31 20:01  warneg

	* DESCRIPTION, INDEX, R/running.R, man/contrast.lm.Rd,
	  man/running.Rd, man/wapply.Rd: Release 0.3.0

2001-08-31 19:45  warneg

	* R/wapply.R: Used wrong character in header (% instead of #).
	  Fixed.

2001-08-31 19:43  warneg

	* R/elementof.R:
	  Used wrong comment character in header (% instead of #). Fixed.

2001-08-31 19:41  warneg

	* R/bandplot.R:
	  Used wrong comment character (% instead of #) in header.  Fixed.

2001-08-31 19:36  warneg

	* R/contrast.lm.R:
	  Added make.contrasts() to allow S-Plus so that the remaining
	  unspecified df for contrats are filled by contrasts orthogonal to
	  the specified ones.  This results in getting the exact same value
	  from computing contrasts in a one-way anova as would be obtained
	  by directly computing the means and performing the approprial
	  linalg.

2001-08-31 16:55  warneg

	* man/contrast.lm.Rd:
	  Updated to match changes in contrast.lm.R version 1.2.

	  Also added more examples.

2001-08-31 16:46  warneg

	* R/contrast.lm.R: Previous version did not actually work.  This
	  version now correctly computes contrasts.  It will also (in
	  conjunction wiht RSCompat.S) work in S-Plus.

2001-08-30 22:25  warneg

	* R/contrast.lm.R: Initial checkin.

2001-08-25 01:54  warneg

	* R/elementof.R: Initial CVS Checkin.

2001-08-25 01:53  warneg

	* R/running.R: Initial CVS checkin.

2001-08-25 01:52  warneg

	* man/ci.Rd: - Added CVS header.  - Added my email address.

2001-08-25 01:50  warneg

	* man/combinations.Rd: Fixed a typo and a syntax error.

2001-08-25 01:48  warneg

	* R/wapply.R: Initial checkin.

2001-08-25 01:46  warneg

	* man/: boxplot.n.Rd, plotmeans.Rd: Added CVS header.

2001-08-25 01:45  warneg

	* man/wapply.Rd: Initial Checkin

2001-08-24 23:59  warneg

	* man/running.Rd: Initial Checkin

2001-08-24 22:16  warneg

	* man/elementof.Rd: Initial checkin.

2001-06-29 09:23  warneg

	* R/combinations.R, man/combinations.Rd:
	  Initial revision.

2001-06-05 14:39  warneg

	* DESCRIPTION, R/.tnatr:fnmap, R/concat.R, man/concat.Rd:
	  Updated with addition of concat.R and concat.Rd.

2001-05-30 09:23  warneg

	* DESCRIPTION, INDEX, R/.tnatr:fnmap, R/boxplot.n.R, R/ci.R,
	  R/plotCI.R, R/plotmeans.R, man/boxplot.n.Rd, man/ci.Rd,
	  man/plotCI.Rd, man/plotmeans.Rd:
	  Initial CVS import

2001-05-30 09:23  warneg

	* DESCRIPTION, INDEX, R/.tnatr:fnmap, R/boxplot.n.R, R/ci.R,
	  R/plotCI.R, R/plotmeans.R, man/boxplot.n.Rd, man/ci.Rd,
	  man/plotCI.Rd, man/plotmeans.Rd: Initial revision

