r-cran-gplots 2.11.3-1 / usr / lib / R / site-library / gplots / ChangeLog

2013-06-27  warnes

	* [r1678] DESCRIPTION: Update for release 2.11.3
	* [r1677] tests/heatmap2Test.Rout.save: Update with tests for only
	  1 row/column separator
	* [r1676] man/plotmeans.Rd: Fix typo
	* [r1675] tests/heatmap2Test.R: Add test for one row/column
	  separator
	* [r1674] R/baseOf.R: Add more in-line comments
	* [r1673] R/sinkplot.R, man/sinkplot.Rd: Modify sinkplot to use a
	  local environement to store its information instead of the global
	  environment.

2013-03-24  warnes

	* [r1647] inst/NEWS: Update news for release 2.11.2
	* [r1646] R/barplot2.R, man/barplot2.Rd: Add ci.width argument to
	  barplot2() to allow varying the length of the 't' at the end of
	  confidence interval bars.
	* [r1642] DESCRIPTION: Update for release 2.11.2
	* [r1641] man/lowess.Rd: Update manual page for lowess.default() to
	  match changed argument list for lowess() in R 3.0.0

2012-12-14  warnes

	* [r1631] R/plot.venn.R: Fix typo: warn() instead of warning().
	* [r1630] vignettes/venn.Rnw: Fix syntax of VignetteIndexEntry in
	  venn.Rnw.
	* [r1629] vignettes/venn.Rnw, vignettes/venn.pdf: Add generated
	  vignette pdf.
	* [r1628] vignettes/venn.Rnw: Add required VignetteIndexEntry
	  metadata to venn vignette code.
	* [r1627] DESCRIPTION, inst/NEWS: Update DESCRIPTION and NEWS for
	  release 2.11.1.
	* [r1626] R/baseOf.R, R/plot.venn.R, R/venn.R, vignettes,
	  vignettes/venn.Rnw: Improve venn() to work with PDF and
	  Sweave/pdflatex. Provide a vignette for venn().
	* [r1625] R/heatmap.2.R: Fix error in processing the colsep
	  argument to heatmap.2.
	* [r1624] man/plotmeans.Rd: Clarify that plotmeans is intended for
	  a *continuous* outcome based on
	  a *factor* grouping level.
	* [r1623] inst/doc/BalloonPlot.pdf: Replace corrupted
	  BalloonPlot.pdf file and remove svn properties that were causing
	  it to be corrupted.

2012-06-08  warnes

	* [r1558] inst/NEWS: Update NEWS for 2.11.0 release.
	* [r1557] DESCRIPTION, R/barplot2.R, R/ooplot.R, R/plotCI.R,
	  R/sinkplot.R, man/qqnorm.aov.Rd, tests/heatmap2Test.Rout.save:
	  Fix R CMD check warnings.
	* [r1556] man/hist2d.Rd: Move incorrectly placed closing brace.

2012-06-07  warnes

	* [r1555] R/ci2d.R, R/hist2d.R, R/print.hist2d.R, man/hist2d.Rd:
	  Object returned by hist2d() has been changed:
	  - $x and $y now contain the n midpoints of the bins in each
	  direction
	  - $x.breaks, $y.breaks now contain the n+1 limits of the bins in
	  each direction
	  The function print.hist2d() has been updated appropriately.
	* [r1554] R/hist2d.R: Correct error in handling binning:
	  (N+1)x(N+1) bins were being created
	  instead of NxN bins, and the highest row/column in each direction
	  was
	  being omitted from the results and plot.
	* [r1553] R/plotmeans.R, man/plotmeans.Rd: Add default value for
	  lwd argument to plotmeans()

2012-05-31  warnes

	* [r1533] man/qqnorm.aov.Rd: Properly mark up S3 method.

2011-12-09  warnes

	* [r1519] R/plotmeans.R, man/plotmeans.Rd: Add 'lwd' (linewidth) to
	  arguments handled by plotmeans.

2011-09-02  warnes

	* [r1505] inst/NEWS: Update NEWS for release 2.10.1.
	* [r1504] DESCRIPTION: Increment version counter.
	* [r1503] man/ci2d.Rd, man/hist2d.Rd: Add necessary alias statment
	  to man files for for 'hist2d' and 'ci2d'
	  print methods.
	* [r1502] R/print.hist2d, R/print.hist2d.R: Fix naming error
	* [r1501] NAMESPACE, R/ci2d.R, R/hist2d.R, R/print.ci2d.R,
	  R/print.hist2d, man/ci2d.Rd, man/hist2d.Rd: Provide print()
	  methods for 'hist2d' and 'ci2d' objects.
	* [r1498] DESCRIPTION: Correct dependence on R >= 2.10

2011-09-01  warnes

	* [r1491] NAMESPACE, man/ci2d.Rd: - Correct issues in ci2d() man
	  page.
	* [r1490] DESCRIPTION, NAMESPACE, tests/heatmap2Test.Rout.save: -
	  Comment out import from KernSmooth in NAMESPACES, since
	  KernSmooth
	  doesn't provide a namespace.
	  - Update a test output.
	* [r1489] DESCRIPTION, inst/NEWS: - Update NEWS file and correct
	  version number
	* [r1488] DESCRIPTION: - Depend on KernSmooth package. Increment
	  version number.
	* [r1487] NAMESPACE: - Depend on KernSmooth package and import
	  'bkdeD2' and 'dpik'.
	* [r1486] R/ci2d.R, man/ci2d.Rd: Improvements to ci2d():
	  
	  - Add option to utilize KernDensity::bkde2D to estimate the 2-d
	  density (now the default).
	  
	  - Add option to display points for original data on generated
	  plots
	  
	  - Name elements of returned contour list according to the
	  significance
	  level to make it easier to select desired contours.
	  
	  - Improve handling of x and y labels
	* [r1485] man/hist2d.Rd: Remove log tag and comments from top of
	  the file.

2011-08-26  warnes

	* [r1478] inst/NEWS: Update NEWS for 2.10.0 release
	* [r1477] DESCRIPTION: Add dependency on R>= 2.10 to handle
	  compressed Rda data file.
	* [r1476] data/rtPCR.rda: Compress rtPCR example data set to make
	  distributed package smaller.
	* [r1475] R/ci2d.R: Remove '1.0' confidence line from
	  ci2d(..,show="contour").

2011-08-25  warnes

	* [r1474] DESCRIPTION, NAMESPACE, R/ci2d.R, man/ci2d.Rd,
	  man/rich.colors.Rd: - Add 'ci2d()' to compute 2-dimensional
	  emipirical confidence interval.
	  - Fix parse error in help page for 'rich.colors()'.

2011-08-16  warnes

	* [r1473] DESCRIPTION: Update DESCRIPTION file for 2.8.1.
	* [r1472] R/rich.colors.R, man/rich.colors.Rd: Add 'alpha' argument
	  to rich.colors() to control transparency.
	* [r1471] R/hist2d.R, man/hist2d.Rd: Accellerate hist2d by
	  replacing for() loop with tapply(), and allow user to specify
	  summary function applied, per suggestion by Peter Hagedorn (PHA
	  -at- santaris -dot- com).

2011-05-02  arnima

	* [r1470] R/rich.colors.R, man/rich.colors.Rd: Added argument
	  'alpha' and removed argument 'rgb' in rich.colors()

2010-12-13  warnes

	* [r1463] R/heatmap.2.R: Correct error that arises when data
	  includes NA values, identified by Melissa Key

2010-06-11  warnes

	* [r1446] man/venn.Rd: Fix errors detected by R CMD check
	* [r1445] man/venn.Rd: Fix errors detected by R CMD check
	* [r1444] man/venn.Rd: Use 'TRUE' instead of 'T' for true in venn
	  man page
	* [r1443] DESCRIPTION, NAMESPACE, inst/NEWS: Update for gplots
	  2.8.0
	* [r1442] R/baseOf.R: Moved baseOf() into a separate file
	* [r1441] man/balloonplot.Rd, man/bandplot.Rd, man/boxplot.n.Rd,
	  man/colorpanel.Rd, man/hist2d.Rd, man/ooplot.Rd, man/overplot.Rd,
	  man/plot.lm2.Rd, man/plotCI.Rd, man/plotmeans.Rd,
	  man/residplot.Rd, man/sinkplot.Rd, man/smartlegend.Rd,
	  man/space.Rd, man/textplot.Rd, man/wapply.Rd: Update Greg's email
	  address
	* [r1440] R/plot.venn.R, R/venn.R, man/venn.Rd: - venn() now
	  returns an object of class venn() and a plot method for
	  this class is provided.
	  
	  - Manual page for venn has been improved, based on contributions
	  by
	  Steffen Moeller

2010-02-17  warnes

	* [r1420] DESCRIPTION, R/hist2d.R, inst/NEWS: Improve performance
	  of hist2d thanks to suggestion by Joerg van den Hoff.

2010-01-22  arnima

	* [r1372] R/rich.color.R, R/rich.colors.R, man/rich.color.Rd,
	  man/rich.colors.Rd: Renamed files rich.color.* to rich.colors.*
	  and renamed rich.colors args

2009-11-16  arnima

	* [r1367] R/rich.color.R: Minor reformatting only.

2009-11-12  warnes

	* [r1365] DESCRIPTION, R/plotmeans.R, inst/NEWS,
	  tests/plotmeans_nobars.R: Correct bug reported by Alan Yong:
	  plotmeans() crashed when 'bars=FALSE'.

2009-10-22  warnes

	* [r1364] R/heatmap.2.R: Fixed typo in bug fix.
	* [r1363] DESCRIPTION, inst/NEWS: Update NEWS and DESCRIPTION for
	  gplots 2.7.3
	* [r1362] R/heatmap.2.R: Fix transposed display of data (but not
	  labels) in heatmap.2 when symm=TRUE

2009-10-12  warnes

	* [r1361] DESCRIPTION, inst/NEWS: Update version number to 2.7.2,
	  2.7.1 was already up but apparently DESCRIPTION wasn't commited
	  with change.

2009-10-10  warnes

	* [r1360] R/col2hex.R, man/colorpanel.Rd, man/lowess.Rd,
	  man/ooplot.Rd, man/overplot.Rd, man/smartlegend.Rd, man/space.Rd,
	  tests/heatmap2Test.Rout.save: Various minor changes to remove new
	  R CMD CHECK warnings.
	* [r1359] DESCRIPTION, inst/NEWS: Update DESCRIPTION and NEWS file
	  for 2.7.1
	* [r1358] R/col2hex.R: Fix bug reported by Ken Lo: col2hex had blue
	  and green components swapped.

2009-05-08  warnes

	* [r1324] tests/heatmap_to_heatmap.2_test.R: Add test of using a
	  dendrogram created by heatmap() with heatmap.2()
	* [r1323] R/heatmap.2.R: heatmap.2: handle NA for RowV or ColV the
	  same way as NULL
	* [r1322] man/plotCI.Rd: Fix typo
	* [r1321] inst/NEWS: Update NEWS for release 2.7.0
	* [r1320] inst/ChangeLog: We don't want the Changelog in svn, since
	  it is autogenerated from svn logs!
	* [r1319] man/balloonplot.Rd, man/bandplot.Rd, man/boxplot.n.Rd,
	  man/colorpanel.Rd, man/hist2d.Rd, man/ooplot.Rd, man/overplot.Rd,
	  man/plot.lm2.Rd, man/plotCI.Rd, man/plotmeans.Rd,
	  man/residplot.Rd, man/sinkplot.Rd, man/smartlegend.Rd,
	  man/space.Rd, man/textplot.Rd, man/wapply.Rd: Update Greg's email
	  address to 'greg@random-technologies-llc.com'
	* [r1318] R/plotCI.R, man/plotCI.Rd: plotCI now properly handles
	  'NULL' and 'NA' values for ui, li, uiw, and liw.
	* [r1317] R/heatmap.2.R, man/heatmap.2.Rd,
	  tests/heatmap2Test.Rout.save: heatmap.2: Add option to create
	  breakpoints symmetric around 0, provide additional information in
	  the return value
	* [r1316] man/space.Rd: Fix Rd syntax error

2009-04-22  warnes

	* [r1315] man/barplot2.Rd, man/ooplot.Rd: VADeaths data set has
	  move to dataset package

2008-08-14  warnes

	* [r1302] R/balloonplot.R: balloonpot() was incorrectly displaying
	  warning about z values below 0 when scale.method="relative".
	  Fixed.

2008-08-07  warnes

	* [r1301] DESCRIPTION, NAMESPACE, inst/ChangeLog, inst/NEWS: Update
	  DESCRIPTION NAMESPACE and NEWS for 2.7.0 release

2008-06-16  warnes

	* [r1296] TODO, inst/TODO: Add TODO list to gplots

2008-05-20  warnes

	* [r1274] DESCRIPTION, man/plot.lm2.Rd: Update man page to match
	  recent changes to plot.lm2()
	* [r1273] man/venn.Rd: More work on documentation for venn()
	* [r1272] R/bandplot.R, man/bandplot.Rd: Fix code/doc mismatch due
	  to recent changes to bandplot()
	* [r1271] DESCRIPTION, NAMESPACE, R/venn.R, man/venn.Rd: Add Venn
	  Diagram plot submitted by Steffen Moeller

2008-05-07  warnes

	* [r1264] DESCRIPTION, R/bandplot.R: Improve performance of
	  bandplot by calculating running standard deviation using
	  caTools::runsd() instead of (ver slow) window() call. In addtion,
	  the standard deviations are now only calculated once, rather than
	  once for each band.
	* [r1263] R/plot.lm.R: Improve performance of plot.lm for large lm
	  objects by using fitted() instead of predict() to get y-hat

2008-05-05  warnes

	* [r1262] DESCRIPTION, R/bandplot.R: Use caTools's runsd in
	  bandplot for a dramatic speedup for large data
	* [r1261] NAMESPACE: Add import of gtools::reorder.factor for
	  ballonplot man page
	* [r1260] R/balloonplot.R, man/balloonplot.Rd: balloonplot: Add
	  option to scale balloons so [min,max]->[0,1] (relative) or so
	  [0,max] <- [0,1] (absolute)

2008-04-07  warnes

	* [r1254] man/barplot2.Rd: Fix typo in barplot2() man page
	* [r1253] DESCRIPTION, inst/ChangeLog, inst/NEWS: Updates for
	  gplots 2.6.0
	* [r1252] R/heatmap.2.R, man/heatmap.2.Rd: Add ability to control
	  location of individual heatmap.2 components

2008-03-27  warnes

	* [r1251] R/heatmap.2.R: Fix bug in handling rowsep, per suggestion
	  by Steven Paugh

2008-01-04  warnes

	* [r1238] man/overplot.Rd: Fix examples for overplot()

2008-01-02  warnes

	* [r1237] man/barplot2.Rd: Update Marc's email address

2007-12-20  warnes

	* [r1235] man/heatmap.2.Rd: Two letter clarification of help text
	  for heatmap.2()
	* [r1234] man/ooplot.Rd: Restore plot layout at end of ooplot()
	  example

2007-11-06  warnes

	* [r1222] man/hist2d.Rd: Remove extraneous closing brace in the
	  hist2d documentation file

2007-11-05  warnes

	* [r1221] inst/NEWS: Fix typo in NEWS: col2hex() is the new
	  function, not col2rgb() which is part of grDevices

2007-11-02  warnes

	* [r1219] DESCRIPTION, NAMESPACE, inst/ChangeLog, inst/NEWS:
	  Updates for gplots 2.5.0
	* [r1218] tests/heatmap2Test.Rout.save: Update saved test output
	  due to changes in how R reports warnings
	* [r1217] ChangeLog, NEWS: Create soft links of gmodels/ChangeLog
	  -> gmodels/inst/ChangeLog, and gmodels/NEWS -> gmodels/inst/NEWS
	  for my convenience
	* [r1216] ChangeLog, NEWS, inst/ChangeLog, inst/NEWS: Move actual
	  ChangeLog and NEWS files to gmodels/inst so they will be copied
	  into the installed R package area
	* [r1215] man/bandplot.Rd, man/textplot.Rd: Fix code/doc mismatches
	* [r1214] R/plot.lm.R: Update plot.lm2 to match changes made to
	  bandplot

2007-11-01  warnes

	* [r1213] ChangeLog, DESCRIPTION, R/replaceTabs.R, R/textplot.R: in
	  textplot(), convert tab characters to spaces before processing to
	  avoid problems with computing height and width of text including
	  tabs when using pdf()
	* [r1212] R/overplot.R, man/overplot.Rd: Minor reformatting of
	  overplot code and docs

2007-10-22  warnes

	* [r1196] DESCRIPTION: Clarify GPL version

2007-08-14  warnes

	* [r1141] R/balloonplot.R: Correct error in balloonplot when z
	  contains NA values.
	* [r1140] R/balloonplot.R, man/balloonplot.Rd: Augment
	  balloonplot() with control of character size and color for text
	  and label items
	* [r1139] R/balloonplot.R: Correct balloonplot.default to properly
	  show specified x and y axis labels when explicitly provided

2007-03-09  ggorjan

	* [r1073] man/ooplot.Rd: use of \method in Rd markup - issues a
	  warning with _R_CHECK_RD_STYLE_=TRUE env. variable with R 2.5.0

2007-02-08  warnes

	* [r1052] DESCRIPTION: Bump version number
	* [r1051] man/textplot.Rd: Update documentation for textplot()
	* [r1050] R/col2hex.R, man/col2hex.Rd: Add col2rgb() function to
	  convert color names to rgb hex codes
	* [r1049] R/textplot.R: Add paramaeters 'col.data', 'col.rows', and
	  'col.columns' to
	  textplot.matrix to allow specification of the color of the matrix
	  data, rows, and columns.
	* [r1048] R/bandplot.R: Add parameters to control line width and
	  line type.

2006-11-14  ggorjan

	* [r1012] R/bandplot.R, R/boxplot.n.R, R/lowess.R, R/plot.lm.R,
	  R/plotCI.R, R/plotmeans.R, R/residplot.R, R/wapply.R,
	  man/boxplot.n.Rd, man/plotCI.Rd, man/plotmeans.Rd: Removed
	  executable property

2006-11-14  warnes

	* [r1010] tests/heatmap2Test.Rout.save: Update output file to match
	  (trivial) changes in the test code.
	* [r1008] ChangeLog, NEWS: Update ChangeLog and NEWS files for
	  release 2.3.2.
	* [r1007] DESCRIPTION: Update version number
	* [r1006] DESCRIPTION: Update version number and maintainer
	* [r1005] man/heatmap.2.Rd: Correct problem with labeled
	  correlation matrix example. Thanks to Jean Vidal for reporting
	  the error..

2006-08-02  warnes

	* [r977] inst/doc/BalloonPlot.pdf, man/balloonplot.Rd,
	  man/bandplot.Rd, man/boxplot.n.Rd, man/colorpanel.Rd,
	  man/hist2d.Rd, man/ooplot.Rd, man/overplot.Rd, man/plot.lm2.Rd,
	  man/plotCI.Rd, man/plotmeans.Rd, man/residplot.Rd,
	  man/sinkplot.Rd, man/smartlegend.Rd, man/space.Rd,
	  man/textplot.Rd, man/wapply.Rd: Update my email address

2006-06-26  nj7w

	* [r967] R/heatmap.2.R: Fixed a bug which displayed warnings when
	  Rowv and Colv were specified as dendrograms

2006-03-10  warnes

	* [r937] tests/heatmap2Test.R: Remove code that added a local path

2006-03-09  nj7w

	* [r935] tests/heatmap2Test.R, tests/heatmap2Test.Rout.save: Added
	  the correct library path where gplots is installed locally and
	  corresponding .save file
	* [r934] tests/heatmap2Test.R: Updated the tests file
	* [r933] R/heatmap.2.R: Removed the condition Colv != Rowv as it
	  has already been taken care of
	* [r932] rtPCR.rda: Deleted rtPCR.rda from the main directory
	* [r931] ChangeLog: Added ChangeLog

2006-03-07  nj7w

	* [r919] DESCRIPTION, NEWS: Updated ChangeLog and NEWS
	* [r918] tests, tests/heatmap2Test.R, tests/heatmap2Test.Rout.save:
	  Added the tests and fixed corrupted files
	* [r917] data/rtPCR.rda: Replaced the corrupted rtPCR.rda file in
	  data directory
	* [r916] tests: Removed the corrputed tests directory
	* [r915] data/rtPCR.rda, rtPCR.rda: Replaced the corrupted
	  rtPCR.rda file in data directory

2006-03-03  nj7w

	* [r914] R/heatmap.2.R, man/heatmap.2.Rd: Updated the code and man
	  page to make sure the Rowv and Colv values are properly handled

2006-03-02  warnes

	* [r908] R/balloonplot.R: Adjust row total placement to adjust for
	  width of the totals
	* [r907] DESCRIPTION, R/balloonplot.R, man/1: Row totals in
	  ballonplot were in reverse order. Fixed.

2006-02-23  nj7w

	* [r899] R/heatmap.2.R, tests/heatmap2Test.R: Add ability to scale
	  the color key using the new 'keysize' argument.
	* [r898] tests, tests/heatmap2Test.R, tests/heatmap2Test.Rout.save:
	  Add tests for heatmap.2
	* [r897] inst/doc/Figure1.eps, inst/doc/Table.eps,
	  inst/doc/bka.bst, inst/doc/heatmap2.R, inst/doc/heatmap2.tex,
	  inst/doc/regression_rank_image.Rda,
	  inst/doc/regression_rank_image_II.Rda: Move heatmap and
	  ballonplot paper source materials to their respective cvs modules
	* [r896] inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex,
	  inst/doc/Figure1.pdf, inst/doc/Figure2.pdf, inst/doc/Figure3.pdf,
	  inst/doc/Figure4.pdf, inst/doc/Rnews.sty,
	  inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
	  inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Moved
	  balloonplot paper materials to BallonPlotPaper cvs module
	* [r891] inst/doc/colSeparator.pdf, inst/doc/logData.pdf,
	  inst/doc/logDataColDendrogram.pdf, inst/doc/logDataColOrd.pdf,
	  inst/doc/logDataColOrdNo.pdf, inst/doc/logDataRowDendrogram.pdf,
	  inst/doc/origScale.pdf, inst/doc/rowSeparator.pdf,
	  inst/doc/scaled.pdf: Remove heatmap paper files and move them to
	  the HeatmapPaper cvs module.
	* [r888] inst/doc/colSeparator.pdf, inst/doc/logData.pdf,
	  inst/doc/logDataColDendrogram.pdf, inst/doc/logDataColOrd.pdf,
	  inst/doc/logDataColOrdNo.pdf, inst/doc/logDataRowDendrogram.pdf,
	  inst/doc/origScale.pdf, inst/doc/rowSeparator.pdf,
	  inst/doc/scaled.pdf: Added figures for heatmap2 paper
	* [r887] inst/doc/regression_rank_image.Rda,
	  inst/doc/regression_rank_image_II.Rda: Added the .Rda files for
	  the heatmap2 paper
	* [r886] inst/doc/heatmap2.tex: Added the source - (tex file) of
	  the heatmap paper
	* [r885] inst/doc/heatmap2.R: Added the code for the figures of
	  heatmap paper

2006-02-21  nj7w

	* [r884] R/heatmap.2.R, man/heatmap.2.Rd: Minor updates to
	  heatmap.2 - fixed Rowv, Colv and dendrogram behaviour. Now
	  Rowv=NULL or FALSE both imply no dendrogram computation.

2006-01-12  warnes

	* [r844] inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.pdf,
	  inst/doc/BalloonPlot.tex, inst/doc/Figure1.pdf,
	  inst/doc/Figure2.pdf, inst/doc/Figure3.pdf, inst/doc/Figure4.pdf:
	  more updates
	* [r843] inst/doc/bka.bst: Add Biometrica bibliography style file
	* [r842] inst/doc/BalloonPlot.tex: A little more.
	* [r841] inst/doc/BalloonPlot.tex: Updates to respond to referee.

2006-01-12  nj7w

	* [r840] inst/doc/BalloonPlot.tex: Added references

2005-12-13  nj7w

	* [r811] inst/doc/BalloonPlot.tex: Fixed Nitin's company name
	* [r809] ChangeLog, NEWS: Updated NEWS and removed ChangeLog

2005-12-12  nj7w

	* [r802] R/plotmeans.R: Fixed bug in plotmeans - based on Stefano
	  Calza's suggestion

2005-12-07  nj7w

	* [r787] DESCRIPTION: Updated version number
	* [r786] NAMESPACE, R/plot.lm.R, man/plot.lm2.Rd: Added plot.lm
	* [r785] man/barplot2.Rd: Changed the default grey colors to heat
	  colors, if height is matrix
	* [r784] R/barplot2.R: Changed the default greay colors to heat
	  colors, if height is matrix

2005-12-06  nj7w

	* [r783] man/barplot2.Rd: Fixed minor error in documentation of
	  barplot2

2005-12-02  warnes

	* [r777] R/plot.lm.R: Remove .Alias calls, since .Alias is defunct.

2005-12-01  nj7w

	* [r776] man/balloonplot.Rd, man/bandplot.Rd, man/boxplot.n.Rd,
	  man/colorpanel.Rd, man/overplot.Rd, man/plotmeans.Rd,
	  man/textplot.Rd, man/wapply.Rd: Updated Greg's email address

2005-11-23  nj7w

	* [r764] inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.pdf,
	  inst/doc/BalloonPlot.tex, inst/doc/Figure2.pdf: Updated Figure 2
	  colors

2005-11-18  warnes

	* [r743] inst/doc/BalloonPlot.pdf, inst/doc/Figure1.pdf,
	  inst/doc/Figure2.pdf, inst/doc/Figure3.pdf, inst/doc/Figure4.pdf:
	  Latest version of the pdf files
	* [r742] inst/doc/BalloonPlot.tex: Nitin works for the Cambrige
	  Group, not Pfizer.
	* [r741] inst/doc/BalloonPlot.tex: Minor text rewording.
	* [r740] inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex: More
	  edits.
	* [r739] R/balloonplot.R: Recent changes to align row totals with
	  the overall total broke how
	  the marginal cumulative fractions were displayed. This patch
	  fixes
	  the problem.
	* [r737] DESCRIPTION, R/balloonplot.R, R/plot.lm.R,
	  inst/doc/BalloonPlot.pdf, man/balloonplot.Rd: - Update
	  documentation for balloonplot to match the latest code.
	  - Correct spelling of 'show.zeroes' to 'show.zeros'
	* [r736] R/colorpanel.R: More changes: colorpanel now allows only 2
	  colors to be specified if
	  no 'middle' color is desired.

2005-11-17  warnes

	* [r735] R/balloonplot.R: Allow user to control removal of
	  duplicate entries in balloonplot.
	* [r734] R/colorpanel.R, man/colorpanel.Rd: Extend colorpanel to
	  handle just two-colors in addition to three.

2005-11-09  nj7w

	* [r733] inst/doc/BalloonPlot.pdf: Updated the pdf file
	* [r732] inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex: Updated
	  the changes
	* [r731] inst/doc/Figure4.pdf: Modified figure 4
	* [r730] inst/doc/BalloonPlot.R: Updated code
	* [r729] inst/doc/Figure3.pdf: Modified figure 3
	* [r728] inst/doc/Figure2.pdf: Modified figure 2
	* [r727] inst/doc/Figure1.pdf: Modified figure 1

2005-11-08  nj7w

	* [r726] man/plotCI.Rd: Updated Greg's email

2005-11-07  nj7w

	* [r725] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Minor
	  modifications to fit the code properly on pdf

2005-11-07  warnes

	* [r724] inst/doc/BalloonPlot.R: Add R code that generates plots
	* [r723] inst/doc/Figure2.pdf, inst/doc/Figure3.pdf,
	  inst/doc/Figure4.pdf: Add figures to CVS
	* [r722] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex,
	  inst/doc/Figure1.pdf: Text changes

2005-11-04  warnes

	* [r721] R/balloonplot.R: Fix some alignment issues.
	* [r720] inst/doc/BalloonPlot.pdf, inst/doc/Table.pdf: Remove
	  Table.pdf since it is no longer needed
	* [r719] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex,
	  inst/doc/Figure1.pdf: Nitin's Changes
	* [r718] inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
	  inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Add figure
	  plots
	* [r717] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Fix
	  paths

2005-10-20  nj7w

	* [r705] inst/doc/Figure1.eps, inst/doc/Table.eps: added the eps
	  version of figures
	* [r704] inst/doc/BalloonPlot.pdf: Updated BallonPlot.pdf
	* [r703] inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
	  inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Removed Old
	  Figure
	* [r702] inst/doc/Figure1.pdf, inst/doc/Table.pdf: Added the new
	  figure - for total popluation - Balloonplot
	* [r701] inst/doc/BalloonPlot.tex: Modified the BallonPlot article
	* [r700] inst/doc/BalloonPlot.tex: Added references

2005-10-19  arnima

	* [r697] man/rich.color.Rd: The last example now displays the
	  correct heat.colors.
	  Default 'palette' argument is now a single string, not a vector.
	* [r696] R/rich.color.R: Default 'palette' argument is now a single
	  string, not a vector.

2005-10-14  warnes

	* [r694] DESCRIPTION, R/balloonplot.R, man/balloonplot.Rd:
	  Formatting fixes:
	  - Handle multiple row or column category variables
	  - Separate rows/columns of category labels by lines
	  - Fix handling of 'cumsum' plots on row/column labels
	  - Improve display of row/column sums

2005-10-13  warnes

	* [r693] man/balloonplot.Rd: Add example using Titanic data that
	  exercises the multi-factor
	  display.

2005-10-11  warnes

	* [r692] R/balloonplot.R: Initial changes to allow multiple x and y
	  factor variables. Yet to
	  be done: 1) remove extra 'boxes'. 2) omit duplicated values

2005-10-04  warnes

	* [r691] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: more
	  minor fixes
	* [r690] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: fix
	  spacing
	* [r689] inst/doc/Rnews.sty: Inlcude Rnews.sty
	* [r688] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Some
	  textual edits.

2005-10-03  nj7w

	* [r687] inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
	  inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Added figures
	  for the R-News Article

2005-09-29  nj7w

	* [r680] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex:
	  Updated the documentation - added the name of the person who
	  asked the question
	* [r679] inst, inst/doc, inst/doc/BalloonPlot.pdf,
	  inst/doc/BalloonPlot.tex: Added R-news article

2005-09-12  nj7w

	* [r671] man/hist2d.Rd, man/ooplot.Rd, man/residplot.Rd,
	  man/sinkplot.Rd, man/smartlegend.Rd, man/space.Rd: Updated Greg's
	  email
	* [r670] R/balloonplot.R: Updated version of balloonplot - by
	  Romain Francois <francoisromain@free.fr>

2005-09-09  nj7w

	* [r669] ChangeLog, DESCRIPTION: Updated the version and ChangeLog
	* [r668] R/balloonplot.R, man/balloonplot.Rd: Changes in ballon
	  plot based on Romain Francois (francoisromain@free.fr)
	  suggestions

2005-09-06  nj7w

	* [r666] DESCRIPTION: Updated package dependencies
	* [r665] NEWS: Added NEWS

2005-09-02  nj7w

	* [r655] ChangeLog: Added ChangeLog

2005-08-31  nj7w

	* [r644] DESCRIPTION: Added DESCRIPTION file
	* [r643] DESCRIPTION.in: removed DESCRIPTION.in

2005-06-09  nj7w

	* [r625] R/balloonplot.R, R/bandplot.R, R/boxplot.n.R,
	  R/colorpanel.R, R/heatmap.2.R, R/hist2d.R, R/lowess.R,
	  R/ooplot.R, R/overplot.R, R/plotCI.R, R/plotmeans.R,
	  R/qqnorm.aov.R, R/residplot.R, R/rich.color.R, R/sinkplot.R,
	  R/smartlegend.R, R/space.R, R/textplot.R, R/wapply.R, man/1,
	  man/bandplot.Rd, man/barplot2.Rd, man/boxplot.n.Rd,
	  man/hist2d.Rd, man/lowess.Rd, man/plotCI.Rd, man/plotmeans.Rd,
	  man/residplot.Rd, man/space.Rd, man/wapply.Rd: Updating the
	  version number, and various help files to synchronize splitting
	  of gregmisc bundle in 4 individual components.
	* [r624] R/barplot2.R: Changes based on Marc Schwartz's suggestions
	  to handel 0's and NA's appropriately.

2005-05-13  nj7w

	* [r621] man/heatmap.2.Rd: 1) Using dQuote.ascii function in
	  read.xls as the new version of dQuote doesn't work proprly with
	  UTF-8 locale.
	  2) Modified CrossTable.Rd usage in gmodels
	  3) Modified heatmap.2 usage in gplots.

2005-04-04  warnes

	* [r603] R/overplot.R: Explicitly reference package containing
	  lowess.formula in
	  panel.overplot(). This should fix the error reported by Troels
	  Ring
	  <tring@gvdnet.dk>.

2005-02-26  nj7w

	* [r565] R/heatmap.2.R, man/heatmap.2.Rd, man/rich.color.Rd,
	  man/sinkplot.Rd, man/textplot.Rd: *** empty log message ***

2005-02-25  warnes

	* [r563] man/rich.color.Rd: Integrate changes submitted by Arni
	  Magnusson
	* [r559] NAMESPACE: Add dependency imports from 'stats' package.

2005-02-22  warnes

	* [r555] R/bandplot.R: Fix problem in passing graphical parameters
	  (xlim,etc).@

2005-02-08  warnes

	* [r541] DESCRIPTION.in: Improve package title.
	* [r540] R/heatmap.2.R: Ignore missing values when computing
	  symmetric range.

2005-02-02  warnes

	* [r530] man/plotmeans.Rd: Add more extensive example.

2005-01-14  warnes

	* [r516] R/textplot.R: Code can be simplified because R now
	  supports selecting a fixed width font.

2005-01-12  warnes

	* [r515] DESCRIPTION.in: Add dependency on R 1.9.0+ to prevent
	  poeple from installing on old
	  versions of R which don't support namespaces.

2004-11-30  warnes

	* [r495] R/heatmap.2.R, man/heatmap.2.Rd: 1. Add new parameters for
	  controlling color key:
	  - If `symkey==TRUE', the color key will be made symmetric about
	  0.
	  - The `densadj' parameter can be used to modify the smoother
	  width
	  (see the `adjust' parameter under `help(density)') for the
	  density
	  plotted in the key.
	  
	  2. Fix handling of rowsep/colsep.
	  
	  3. Vector of length 2 giving the width (colsep) or height
	  (rowsep) the separator box
	  drawn by colsep and rowsep as a function of the width (colsep) or
	  height (rowsep) of a cell.
	  
	  4. Appropriate changes to the corresponding help page, plus some
	  minor formatting changes.

2004-11-03  warnes

	* [r474] R/heatmap.2.R: Fix bugs in layout of cell notes. They were
	  being plotted top down
	  rather than bottom up. Further reordering of the x matrix didn't
	  also reorder the notes. Both issues should now be resolved.

2004-09-27  warneg

	* [r461] DESCRIPTION, DESCRIPTION.in, man/sinkplot.Rd,
	  man/textplot.Rd: Updated to pass R CMD check.

2004-09-03  warneg

	* [r453] man/textplot.Rd: Provide explicit package for call to
	  nobs.
	* [r452] man/heatmap.2.Rd: Fix typos.
	* [r446] DESCRIPTION, NAMESPACE, R/balloonplot.R, R/bandplot.R,
	  R/barplot2.R, R/boxplot.n.R, R/colorpanel.R, R/heatmap.2.R,
	  R/hist2d.R, R/lowess.R, R/ooplot.R, R/overplot.R, R/plotCI.R,
	  R/plotmeans.R, R/qqnorm.aov.R, R/residplot.R, R/rich.color.R,
	  R/sinkplot.R, R/smartlegend.R, R/space.R, R/textplot.R,
	  R/wapply.R: initial bundle checkin

2004-09-02  warneg

	* [r442] DESCRIPTION, DESCRIPTION.in, NAMESPACE, man/1,
	  man/residplot.Rd: Initial revision

2004-07-29  warnes

	* [r426] R/plotCI.R, man/plotCI.Rd: Integrate changes from the
	  version of plotCI maintained by Martin Maechler.

2004-06-30  warnes

	* [r393] R/textplot.R: Remove commented-out code.
	* [r392] R/textplot.R: Fixed text size calculations

2004-06-28  warnes

	* [r391] R/barplot2.R, man/barplot2.Rd: - Default 2-d color set to
	  grey as in (v2.0.0) r-devel
	  - The default (v1.9.1) barplot method now handles vectors and 1-d
	  arrays
	  (e.g., obtained by table()) the same, and uses grey instead of
	  heat color palettes in these cases. (Also fixes PR#6776.)
	  - Updated to reflect the addition of 'offset' argument in base
	  - Fix bug in stacked barplots, which would not be plotted
	  properly

2004-06-24  warnes

	* [r385] R/heatmap.2.R, man/heatmap.2.Rd: Add ability to specify
	  color of NA cells.

2004-05-27  warnes

	* [r349] man/plotCI.Rd: Fix spelling error.

2004-05-26  warnes

	* [r347] R/overplot.R: One more fix to get it right.
	* [r346] R/overplot.R: Use triple-colon operator ':::' to access
	  plot.formula from the graphics package.
	* [r344] man/rich.color.Rd: Replace 'F' by 'FALSE' to pass R CMD
	  check.

2004-05-25  warnes

	* [r338] R/overplot.R: Work around bug in R 1.9.X due to
	  plot.formula() not having the same
	  arguments as plot().
	* [r336] R/rich.color.R, man/rich.color.Rd: Add rich.colors()
	  submitted by Arni Magnusson <arnima@u.washington.edu>.
	* [r328] R/ooplot.R, man/ooplot.Rd: ??

2004-05-24  warnes

	* [r324] R/plotCI.R, R/plotmeans.R: Modified to use invalid() to
	  check arguments instead of missing().
	  This fixes some build errors under R-1.9.0-Patched.

2004-04-22  warnes

	* [r319] R/ooplot.R, man/ooplot.Rd: Integrate changes from Lodewijk
	  Bonebakker <bonebakker@comcast.net>

2004-04-13  warnes

	* [r318] R/space.R, man/space.Rd: Add ability to space points along
	  'y' direction.

2004-04-02  warnes

	* [r313] R/smartlegend.R: Fixed smartlegend() positioning when x
	  and/or y axis are log-scale.

2004-03-30  warnes

	* [r311] R/textplot.R: - Fix bug in textplot() reported by Wright,
	  Kevin <kevin.d.wright@pioneer.com>.

2004-03-26  warnes

	* [r305] man/textplot.Rd: Update to match changes in textplot()
	  code.
	* [r304] man/ooplot.Rd: Remove Windows EOL characters.
	* [r302] man/barplot2.Rd: - Remove some commented-out code.
	  - Remove cvs log tag.
	* [r300] R/textplot.R: Misc changes.

2004-02-17  warnes

	* [r290] man/ooplot.Rd: Minor fix to ooplot documentation.
	* [r289] R/ooplot.R, man/ooplot.Rd: Integrate ooplot updates
	  provided by Lodewijk Bonebakker
	  <bonebakker@comcast.net>

2004-02-02  warnes

	* [r287] 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).

2004-01-21  warnes

	* [r283] man/textplot.Rd: - Correct arguments to halign to match
	  code.
	* [r281] R/lowess.R: Track R 1.9.0's move of 'lowess' from the base
	  package to the (new)
	  stats package.
	* [r279] man/sinkplot.Rd: - Fix sinkplot() example by replacing 'T'
	  with 'TRUE'.
	* [r278] man/ooplot.Rd: - Add some more details to the ooplot()
	  documentation. The
	  documentation is *not* complete.
	* [r277] 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  warnes

	* [r276] 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.

2004-01-15  warnes

	* [r274] R/ooplot.R, man/ooplot.Rd: Add initial code and docs for
	  ooplot() function submitted by Lodewijk
	  Bonebakker <bonebakker@comcast.net>.

2003-12-03  warnes

	* [r253] man/lowess.Rd, man/textplot.Rd, man/wapply.Rd: - match
	  function argument defaults with 'usage'
	* [r252] R/heatmap.2.R, man/heatmap.2.Rd: - Fix buglets in heatmap
	  function
	  - Make a slight enhancement to the example code.

2003-12-02  warnes

	* [r251] R/heatmap.2.R: Integrated some suggestions from Sean Davis
	  <sdavis2@mail.nih.gov>.
	* [r250] man/heatmap.2.Rd: - Make final example use 16 colors
	  instead of 8. This looks nicer.
	* [r248] man/barplot2.Rd: - Remove '%' character from example code
	  to avoid errors.
	* [r247] R/plotCI.R: - Add '...' parameter to call to text to allow
	  user to control size/color/etc.

2003-12-01  warnes

	* [r246] man/barplot2.Rd: - updated to match changes to barplot()
	  in base.
	* [r245] data, data/rtPCR.rda: - Renamed rtPCR.Rda to rtPCR.rda so
	  that R will properly load the file
	  when data(rtPCR) is executed.
	* [r243] R/barplot2.R: - Follow patches applied to barplot() in
	  base.

2003-11-24  warnes

	* [r242] man/heatmap.2.Rd: Fix unbalanced braces.
	* [r240] R/overplot.R, man/overplot.Rd: Fix errors reported by R
	  CMD check.

2003-11-21  warnes

	* [r239] man/overplot.Rd: Added missing closing brace.
	* [r238] man/rtPCR.Rd: Initial addition of these files. Used in
	  examples of overplot().
	* [r236] 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.
	* [r235] 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.
	* [r231] R/heatmap.2.R, man/heatmap.2.Rd: - Integrated my
	  extensions into the R 1.8.0 version of heatmap.
	  - Add Rd documentation.

2003-11-19  warnes

	* [r228] man/bandplot.Rd: Remove extranious NULL that confused R
	  CMD check.

2003-11-18  warnes

	* [r226] man/barplot2.Rd: - Tiny fix to remove R CMD check error.
	* [r225] man/smartlegend.Rd: - Added missing closing brace.
	* [r224] R/overplot.R: - Convert from MS-Dos to Unix line endings.
	  - Reformat to 80 columns.

2003-11-10  warnes

	* [r220] R/heatmap.2.R, R/overplot.R, R/plotmeans.R, R/space.R,
	  R/wapply.R: - Add files contributed by Arni Magnusson
	  <arnima@u.washington.edu>. As well as some of my own.

2003-08-19  warnes

	* [r219] R/heatmap.2.R: - Copy of local changes.
	* [r218] R/heatmap.2.R: - Checkin before re-integrating local
	  changes.

2003-06-19  warnes

	* [r201] R/heatmap.2.R: - Added enhanced heatmap function.

2003-06-09  warnes

	* [r200] man/smartlegend.Rd: - Add help text for smartlegend.
	* [r199] R/smartlegend.R: - New function smartlegend().

2003-04-22  warnes

	* [r191] R/plotmeans.R: - Fixeed warning messing caused when
	  'connect' is a vector.
	* [r187] 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.

2003-04-04  warnes

	* [r182] R/balloonplot.R, man/qqnorm.aov.Rd: - Change occurences of
	  'T' to 'TRUE'
	* [r179] 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
	* [r178] 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.

2003-04-02  warnes

	* [r175] R/textplot.R, man/textplot.Rd: - Added textplot function
	  and friends, as well as documentation.

2003-03-08  warnes

	* [r171] man/balloonplot.Rd: - Forgot to update arglist in \usage
	  section.
	* [r169] 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  warnes

	* [r168] R/hist2d.R, R/qqnorm.aov.R: - Minor changes to code to
	  allow the package to be provided as an
	  S-Plus chapter.
	* [r167] 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.
	* [r166] R/lowess.R: - Specify where the defualt lowess function
	  should be found.
	  - Use getFunction in S-Plus instead of 'get'

2003-01-30  warnes

	* [r159] R/barplot2.R, man/barplot2.Rd: - Added argument 'add' to
	  allow for the addition of a barplot to an
	  existing graphic. Default is FALSE

2003-01-20  warnes

	* [r156] R/balloonplot.R, man/balloonplot.Rd: - Updated balloonplot
	  help page.
	* [r155] 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  warnes

	* [r154] R/balloonplot.R, man/balloonplot.Rd: - Initial checkin of
	  balloonplot functions and documentation.
	* [r153] man/space.Rd: - Added reference to and comparison example
	  of sunflowerplot.
	  - Added code to put example plots on same plot window using
	  par(mfrow=...).

2003-01-02  warnes

	* [r150] R/barplot2.R: - Changed assignment statements that used
	  "=" to "<-" to avoid syntax
	  errors in older versions of the S language.
	* [r149] R/lowess.R: - Added wrapper code so that R-specific
	  fiddling won't be executed
	  under S-Plus.
	* [r147] R/qqnorm.aov.R, man/qqnorm.aov.Rd: - Renamed first
	  parameter to match qqnorm generic.
	* [r146] man/qqnorm.aov.Rd: Added additional help text from Kjeitl.

2002-12-31  warnes

	* [r145] 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  warnes

	* [r143] 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.

2002-10-30  warnes

	* [r139] R/plot.lm.R: - Commented out plot.lm() code since recent
	  changes in R have broken it.

2002-10-11  warnes

	* [r131] R/barplot2.R: - Fixed log scale errors in legend() call

2002-10-01  warnes

	* [r130] man/hist2d.Rd: - Added examples of using 'contour' and
	  'filled.contour' for display.

2002-09-24  warnes

	* [r121] 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  warnes

	* [r119] man/barplot2.Rd: - Fixed syntax errors in barplot2.Rd and
	  CrossTable.Rd
	  - Fixed incorrect translation of 'F' (distribution) to 'FALSE' in
	  glh.test.Rd
	* [r117] R/boxplot.n.R, R/hist2d.R, R/lowess.R, R/residplot.R,
	  man/bandplot.Rd, man/hist2d.Rd, man/lowess.Rd, man/plotCI.Rd,
	  man/space.Rd: - Modified all files to include CVS Id and Log
	  tags.
	* [r116] R/barplot2.R, 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  warnes

	* [r114] R/hist2d.R, R/wapply.R: - 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.

2002-04-09  warneg

	* [r109] R/bandplot.R, R/boxplot.n.R, R/hist2d.R, R/plot.lm.R,
	  R/plotCI.R, R/plotmeans.R, R/residplot.R, R/space.R, R/wapply.R,
	  man/bandplot.Rd, man/boxplot.n.Rd, man/hist2d.Rd,
	  man/plotmeans.Rd, man/space.Rd, man/wapply.Rd: Checkin for
	  version 0.5.3

2002-03-27  warneg

	* [r107] man/lowess.Rd: Added "..." argument to lowess.default.
	* [r106] 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  warneg

	* [r104] R/lowess.R, man/lowess.Rd: - Changed methods to include
	  '...' to match the generic.
	  - Updated for version 0.5.1
	* [r100] man/hist2d.Rd: Initial checkin.

2002-03-20  warneg

	* [r94] R/plotmeans.R: - Changes to add compatibility with S-Plus
	  2000
	* [r93] R/plotCI.R: - Changes to add compatibility with S-Plus
	  2000.
	* [r92] R/boxplot.n.R: - Updated to work in S-Plus 2000 as well as
	  R.

2002-03-05  warneg

	* [r88] R/plotmeans.R: - Replace "T" with "TRUE". Problems arrive
	  when there is a variable named "T".

2002-02-20  warneg

	* [r81] man/lowess.Rd, man/plotCI.Rd, man/space.Rd: Minor changes,
	  typo and formatting fixes.
	* [r80] 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.

2002-02-16  warneg

	* [r78] man/bandplot.Rd: Added bandplot documentation.
	* [r77] 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.
	* [r76] 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  warneg

	* [r74] R/space.R: - Add na.rm parameter and make the default TRUE.
	* [r73] R/hist2d.R: Initial checkin.
	* [r72] R/plotCI.R: - When err="x", 'col' was being used to plot
	  bars, rather than 'barcol'.
	* [r71] R/plotCI.R: - fixed typo, when err="x", lty was 'slty'
	  causing an error.

2001-12-12  warneg

	* [r54] man/space.Rd: - Quoted underscore character in my email
	  address.
	  - Added correct keyword.
	* [r52] man/plotmeans.Rd: Added documentation for xaxt parameter.
	* [r51] R/lowess.R: Updated to explicitly list control arguments to
	  lowess.formula.
	* [r50] man/lowess.Rd: Initial checkin. Code copied from R source
	  package and extended.

2001-12-07  warneg

	* [r46] man/wapply.Rd: Fixed an problem where \code was incorrectly
	  delimited by parens
	  rather than curly brackets.
	* [r42] R/lowess.R, R/plot.lm.R, R/residplot.R, man/space.Rd:
	  Initial checkin.
	* [r41] R/space.R: - Added cvs tags.
	* [r40] 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.

2001-12-05  warneg

	* [r33] R/plotmeans.R: - Added ability to use the t-distribution to
	  compute confidence
	  intervals. This is controlled using the 'use.t' parameter.
	* [r31] man/plotmeans.Rd: - Added documentation of use.t parameter.
	* [r30] man/wapply.Rd: - Clarified how the width of the window is
	  computed when method="nobs".
	* [r29] 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.

2001-10-26  warneg

	* [r28] R/plotmeans.R: Added correct handling of 'xaxt="n"'.

2001-10-16  warneg

	* [r27] man/wapply.Rd: Fixed unbalanced brace.
	* [r26] man/plotCI.Rd: Added minbar and maxbar parameters.
	* [r25] man/plotmeans.Rd: Forgot to add minbar and maxbar to usage
	  section.
	* [r24] man/plotmeans.Rd: Added description of minbar and maxbar.
	* [r23] R/plotCI.R: - Added minbar and maxbar parameters
	  - Added cvs id and log tags to header
	* [r22] R/plotmeans.R: Added cvs id and log tag to file header
	* [r21] R/plotmeans.R: Added minbar and maxbar parameters.
	* [r20] man/plotmeans.Rd: Added description of minsd parameter.
	* [r19] R/plotmeans.R: Added minsd parameter.

2001-09-18  warneg

	* [r18] R/plotCI.R, R/plotmeans.R: Release 0.3.2

2001-09-01  warneg

	* [r16] man/wapply.Rd: Release 0.3.0

2001-08-31  warneg

	* [r15] R/wapply.R: Used wrong character in header (% instead of
	  #). Fixed.
	* [r14] R/bandplot.R: Used wrong comment character (% instead of #)
	  in header. Fixed.

2001-08-25  warneg

	* [r10] R/wapply.R: Initial checkin.
	* [r9] man/boxplot.n.Rd, man/plotmeans.Rd: Added CVS header.
	* [r8] man/wapply.Rd: Initial Checkin

2001-05-30  warneg

	* [r2] ., R, R/boxplot.n.R, R/plotCI.R, R/plotmeans.R, man,
	  man/boxplot.n.Rd, man/plotCI.Rd, man/plotmeans.Rd: Initial
	  revision