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From: <wa...@us...> - 2006-11-14 18:29:54
|
Revision: 1011
http://svn.sourceforge.net/r-gregmisc/?rev=1011&view=rev
Author: warnes
Date: 2006-11-14 10:29:49 -0800 (Tue, 14 Nov 2006)
Log Message:
-----------
Create 2.3.2 tag
Added Paths:
-----------
tags/gdata-2.3.2/gdata/
Copied: tags/gdata-2.3.2/gdata (from rev 1010, trunk/gdata)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2006-11-14 18:29:38
|
Revision: 1010
http://svn.sourceforge.net/r-gregmisc/?rev=1010&view=rev
Author: warnes
Date: 2006-11-14 10:29:35 -0800 (Tue, 14 Nov 2006)
Log Message:
-----------
Update output file to match (trivial) changes in the test code.
Modified Paths:
--------------
trunk/gplots/tests/heatmap2Test.Rout.save
Modified: trunk/gplots/tests/heatmap2Test.Rout.save
===================================================================
--- trunk/gplots/tests/heatmap2Test.Rout.save 2006-11-14 18:13:02 UTC (rev 1009)
+++ trunk/gplots/tests/heatmap2Test.Rout.save 2006-11-14 18:29:35 UTC (rev 1010)
@@ -1,6 +1,7 @@
-R : Copyright 2005, The R Foundation for Statistical Computing
-Version 2.1.1 (2005-06-20), ISBN 3-900051-07-0
+R version 2.4.0 (2006-10-03)
+Copyright (C) 2006 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -11,12 +12,9 @@
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for a HTML browser interface to help.
+'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
-[1] "Repostitories set to: CRAN, CRANextra, BioC, Omegahat -> ~/.Rprofile"
-> invisible(options(echo = TRUE))
-> .libPaths("~/Rlib")
> library(gplots)
Loading required package: gtools
Loading required package: gdata
@@ -29,13 +27,11 @@
lowess
>
-> #source("/home/jainn02/projects/gregmisc/gplots/R/heatmap.2.R")
+> data(mtcars)
+> x <- as.matrix(mtcars)
+> rc <- rainbow(nrow(x), start=0, end=.3)
+> cc <- rainbow(ncol(x), start=0, end=.3)
>
-> data(mtcars)
-> x <- as.matrix(mtcars)
-> rc <- rainbow(nrow(x), start=0, end=.3)
-> cc <- rainbow(ncol(x), start=0, end=.3)
->
> heatmap.2(x) ## default - dendrogram plotted and reordering done.
> heatmap.2(x, dendrogram="none") ## no dendrogram plotted, but reordering done.
> heatmap.2(x, dendrogram="row") ## row dendrogram plotted and row reordering done.
@@ -108,6 +104,4 @@
$ rowInd: int [1:32] 31 17 16 15 5 25 29 24 7 6 ...
$ colInd: int [1:11] 2 9 8 11 6 5 10 7 1 4 ...
>
-> proc.time()
-[1] 3.65 0.47 6.82 0.01 0.00
>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2006-11-14 18:13:04
|
Revision: 1009
http://svn.sourceforge.net/r-gregmisc/?rev=1009&view=rev
Author: warnes
Date: 2006-11-14 10:13:02 -0800 (Tue, 14 Nov 2006)
Log Message:
-----------
Create 2.3.2 tag
Added Paths:
-----------
tags/gdata-2.3.2/
Copied: tags/gdata-2.3.2 (from rev 1008, trunk/gdata)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2006-11-14 18:09:04
|
Revision: 1008
http://svn.sourceforge.net/r-gregmisc/?rev=1008&view=rev
Author: warnes
Date: 2006-11-14 10:07:31 -0800 (Tue, 14 Nov 2006)
Log Message:
-----------
Update ChangeLog and NEWS files for release 2.3.2.
Modified Paths:
--------------
trunk/gplots/ChangeLog
trunk/gplots/NEWS
Modified: trunk/gplots/ChangeLog
===================================================================
--- trunk/gplots/ChangeLog 2006-11-14 17:59:51 UTC (rev 1007)
+++ trunk/gplots/ChangeLog 2006-11-14 18:07:31 UTC (rev 1008)
@@ -1,200 +1,262 @@
+2006-11-14 17:56 warnes
+
+ * man/heatmap.2.Rd: Correct problem with labeled correlation matrix
+ example. Thanks to Jean Vidal for reporting the error..
+
+2006-08-02 22:21 warnes
+
+ * trunk/BalloonPlotPaper/BalloonPlot.pdf,
+ trunk/BalloonPlotPaper/BalloonPlot.tex,
+ trunk/MSOfficeUtil/DESCRIPTION,
+ trunk/PathwayModeling/thesispaper/slides.tex,
+ trunk/RMCMC/DESCRIPTION, trunk/RMCMC/man/make.density.Rd,
+ trunk/Rlsf/DESCRIPTION, trunk/Rlsf/man/lsf.numcpu.Rd,
+ trunk/Rlsf/man/lsf.parRapply.Rd, trunk/Rlsf/man/scat.Rd,
+ trunk/bwRF/DESCRIPTION, trunk/bwRF/man/RF.Rd,
+ trunk/exp.ssize/inst/doc/ssize.pdf,
+ trunk/exp.ssize/inst/doc/ssize.tex, trunk/fork/DESCRIPTION,
+ trunk/fork/man/exit.Rd, trunk/fork/man/fork.Rd,
+ trunk/fork/man/getpid.Rd, trunk/fork/man/kill.Rd,
+ trunk/fork/man/signame.Rd, trunk/fork/man/wait.Rd,
+ trunk/gdata/inst/doc/gregmisc.tex,
+ trunk/gdata/man/ConvertMedUnits.Rd,
+ trunk/gdata/man/aggregate.table.Rd, trunk/gdata/man/combine.Rd,
+ trunk/gdata/man/interleave.Rd, trunk/gdata/man/matchcols.Rd,
+ trunk/gdata/man/nobs.Rd, trunk/gdata/man/read.xls.Rd,
+ trunk/gdata/man/rename.vars.Rd, trunk/gdata/man/reorder.Rd,
+ trunk/gdata/man/trim.Rd, trunk/gdata/man/unmatrix.Rd,
+ trunk/gdata/man/upperTriangle.Rd,
+ trunk/gmodels/man/fast.prcomp.Rd,
+ trunk/gmodels/man/fit.contrast.Rd, trunk/gmodels/man/glh.test.Rd,
+ trunk/gmodels/man/make.contrasts.Rd, 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,
+ trunk/gregmisc/DESCRIPTION,
+ trunk/gregmisc/gregmisc/DESCRIPTION.standalone,
+ trunk/gregmisc/inst/doc/gregmisc.tex,
+ trunk/gtools/man/addLast.Rd, trunk/gtools/man/assert.Rd,
+ trunk/gtools/man/capture.Rd, trunk/gtools/man/combinations.Rd,
+ trunk/gtools/man/defmacro.Rd, trunk/gtools/man/dirichlet.Rd,
+ trunk/gtools/man/foldchange.Rd, trunk/gtools/man/invalid.Rd,
+ trunk/gtools/man/logit.Rd, trunk/gtools/man/mixedsort.Rd,
+ trunk/gtools/man/oddeven.Rd, trunk/gtools/man/permute.Rd,
+ trunk/gtools/man/quantcut.Rd, trunk/gtools/man/running.Rd,
+ trunk/gtools/man/scat.Rd, trunk/gtools/man/setTCPNoDelay.Rd,
+ trunk/nws/DESCRIPTION, trunk/qvalue/DESCRIPTION,
+ trunk/qvalue/man/print.qvalue.Rd, trunk/ssize/DESCRIPTION,
+ trunk/ssize/man/pow.Rd: Update my email address
+
+2006-06-26 21:08 nj7w
+
+ * R/heatmap.2.R: Fixed a bug which displayed warnings when Rowv and
+ Colv were specified as dendrograms
+
+2006-03-10 17:24 warnes
+
+ * tests/heatmap2Test.R: Remove code that added a local path
+
+2006-03-09 22:53 nj7w
+
+ * tests/heatmap2Test.R, tests/heatmap2Test.Rout.save: Added the
+ correct library path where gplots is installed locally and
+ corresponding .save file
+
+2006-03-09 22:40 nj7w
+
+ * tests/heatmap2Test.R: Updated the tests file
+
+2006-03-09 22:39 nj7w
+
+ * R/heatmap.2.R: Removed the condition Colv != Rowv as it has
+ already been taken care of
+
+2006-03-09 22:17 nj7w
+
+ * rtPCR.rda: Deleted rtPCR.rda from the main directory
+
+2006-03-09 22:09 nj7w
+
+ * ChangeLog: Added ChangeLog
+
+2006-03-07 18:18 nj7w
+
+ * DESCRIPTION, NEWS: Updated ChangeLog and NEWS
+
+2006-03-07 18:10 nj7w
+
+ * tests, tests/heatmap2Test.R, tests/heatmap2Test.Rout.save: Added
+ the tests and fixed corrupted files
+
2006-03-07 16:22 nj7w
- * trunk/gplots/data/rtPCR.rda: Replaced the corrupted rtPCR.rda
- file in data directory
+ * data/rtPCR.rda: Replaced the corrupted rtPCR.rda file in data
+ directory
2006-03-07 16:14 nj7w
- * trunk/gplots/tests: Removed the corrputed tests directory
+ * tests: Removed the corrputed tests directory
2006-03-07 16:12 nj7w
- * trunk/gplots/data/rtPCR.rda, trunk/gplots/rtPCR.rda: Replaced
- the corrupted rtPCR.rda file in data directory
+ * data/rtPCR.rda, rtPCR.rda: Replaced the corrupted rtPCR.rda file
+ in data directory
2006-03-03 21:03 nj7w
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd:
- Updated the code and man page to make sure the Rowv and Colv
- values are properly handled
+ * 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 21:43 warnes
- * trunk/gplots/R/balloonplot.R: Adjust row total placement to
- adjust for width of the totals
+ * R/balloonplot.R: Adjust row total placement to adjust for width
+ of the totals
2006-03-02 21:26 warnes
- * trunk/gplots/DESCRIPTION, trunk/gplots/R/balloonplot.R,
- trunk/gplots/man/1: Row totals in ballonplot were in reverse
- order. Fixed.
+ * DESCRIPTION, R/balloonplot.R, man/1: Row totals in ballonplot
+ were in reverse order. Fixed.
2006-02-23 22:00 nj7w
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/tests/heatmap2Test.R:
- Add ability to scale the color key using the new 'keysize'
- argument.
+ * R/heatmap.2.R, tests/heatmap2Test.R: Add ability to scale the
+ color key using the new 'keysize' argument.
2006-02-23 21:34 nj7w
- * trunk/gplots/tests, trunk/gplots/tests/heatmap2Test.R,
- trunk/gplots/tests/heatmap2Test.Rout.save: Add tests for
- heatmap.2
+ * tests, tests/heatmap2Test.R, tests/heatmap2Test.Rout.save: Add
+ tests for heatmap.2
2006-02-23 21:25 nj7w
- * trunk/gplots/inst/doc/Figure1.eps,
- trunk/gplots/inst/doc/Table.eps, trunk/gplots/inst/doc/bka.bst,
- trunk/gplots/inst/doc/heatmap2.R,
- trunk/gplots/inst/doc/heatmap2.tex,
- trunk/gplots/inst/doc/regression_rank_image.Rda,
- trunk/gplots/inst/doc/regression_rank_image_II.Rda: Move heatmap
- and ballonplot paper source materials to their respective cvs
- modules
+ * 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
2006-02-23 21:20 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.R,
- trunk/gplots/inst/doc/BalloonPlot.tex,
- trunk/gplots/inst/doc/Figure1.pdf,
- trunk/gplots/inst/doc/Figure2.pdf,
- trunk/gplots/inst/doc/Figure3.pdf,
- trunk/gplots/inst/doc/Figure4.pdf,
- trunk/gplots/inst/doc/Rnews.sty,
- trunk/gplots/inst/doc/SurvivedPop.pdf,
- trunk/gplots/inst/doc/SurvivedPopWhite.pdf,
- trunk/gplots/inst/doc/SurvivedProp.pdf,
- trunk/gplots/inst/doc/TotalPop.pdf: Moved balloonplot paper
- materials to BallonPlotPaper cvs module
+ * 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
2006-02-23 21:18 nj7w
- * trunk/gplots/inst/doc/colSeparator.pdf,
- trunk/gplots/inst/doc/logData.pdf,
- trunk/gplots/inst/doc/logDataColDendrogram.pdf,
- trunk/gplots/inst/doc/logDataColOrd.pdf,
- trunk/gplots/inst/doc/logDataColOrdNo.pdf,
- trunk/gplots/inst/doc/logDataRowDendrogram.pdf,
- trunk/gplots/inst/doc/origScale.pdf,
- trunk/gplots/inst/doc/rowSeparator.pdf,
- trunk/gplots/inst/doc/scaled.pdf: Remove heatmap paper files and
- move them to the HeatmapPaper cvs module.
+ * 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.
2006-02-23 19:57 nj7w
- * trunk/gplots/inst/doc/colSeparator.pdf,
- trunk/gplots/inst/doc/logData.pdf,
- trunk/gplots/inst/doc/logDataColDendrogram.pdf,
- trunk/gplots/inst/doc/logDataColOrd.pdf,
- trunk/gplots/inst/doc/logDataColOrdNo.pdf,
- trunk/gplots/inst/doc/logDataRowDendrogram.pdf,
- trunk/gplots/inst/doc/origScale.pdf,
- trunk/gplots/inst/doc/rowSeparator.pdf,
- trunk/gplots/inst/doc/scaled.pdf: Added figures for heatmap2
- paper
+ * 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
2006-02-23 19:54 nj7w
- * trunk/gplots/inst/doc/regression_rank_image.Rda,
- trunk/gplots/inst/doc/regression_rank_image_II.Rda: Added the
- .Rda files for the heatmap2 paper
+ * inst/doc/regression_rank_image.Rda,
+ inst/doc/regression_rank_image_II.Rda: Added the .Rda files for
+ the heatmap2 paper
2006-02-23 19:52 nj7w
- * trunk/gplots/inst/doc/heatmap2.tex: Added the source - (tex
- file) of the heatmap paper
+ * inst/doc/heatmap2.tex: Added the source - (tex file) of the
+ heatmap paper
2006-02-23 19:51 nj7w
- * trunk/gplots/inst/doc/heatmap2.R: Added the code for the figures
- of heatmap paper
+ * inst/doc/heatmap2.R: Added the code for the figures of heatmap
+ paper
2006-02-21 22:19 nj7w
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/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.
+ * 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 23:10 warnes
- * trunk/gplots/inst/doc/BalloonPlot.R,
- trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex,
- trunk/gplots/inst/doc/Figure1.pdf,
- trunk/gplots/inst/doc/Figure2.pdf,
- trunk/gplots/inst/doc/Figure3.pdf,
- trunk/gplots/inst/doc/Figure4.pdf: more updates
+ * 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
2006-01-12 23:01 warnes
- * trunk/gplots/inst/doc/bka.bst: Add Biometrica bibliography style
- file
+ * inst/doc/bka.bst: Add Biometrica bibliography style file
2006-01-12 22:34 warnes
- * trunk/gplots/inst/doc/BalloonPlot.tex: A little more.
+ * inst/doc/BalloonPlot.tex: A little more.
2006-01-12 22:32 warnes
- * trunk/gplots/inst/doc/BalloonPlot.tex: Updates to respond to
- referee.
+ * inst/doc/BalloonPlot.tex: Updates to respond to referee.
2006-01-12 19:59 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.tex: Added references
+ * inst/doc/BalloonPlot.tex: Added references
2005-12-13 17:01 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.tex: Fixed Nitin's company name
+ * inst/doc/BalloonPlot.tex: Fixed Nitin's company name
2005-12-13 16:18 nj7w
- * trunk/gplots/ChangeLog, trunk/gplots/NEWS, trunk/gtools/NEWS:
- Updated NEWS and removed ChangeLog
+ * ChangeLog, NEWS, trunk/gtools/NEWS: Updated NEWS and removed
+ ChangeLog
2005-12-12 22:20 nj7w
- * trunk/gplots/R/plotmeans.R: Fixed bug in plotmeans - based on
- Stefano Calza's suggestion
+ * R/plotmeans.R: Fixed bug in plotmeans - based on Stefano Calza's
+ suggestion
2005-12-07 18:52 nj7w
- * trunk/gplots/DESCRIPTION: Updated version number
+ * DESCRIPTION: Updated version number
2005-12-07 18:50 nj7w
- * trunk/gplots/NAMESPACE, trunk/gplots/R/plot.lm.R,
- trunk/gplots/man/plot.lm2.Rd: Added plot.lm
+ * NAMESPACE, R/plot.lm.R, man/plot.lm2.Rd: Added plot.lm
2005-12-07 18:48 nj7w
- * trunk/gplots/man/barplot2.Rd: Changed the default grey colors to
- heat colors, if height is matrix
- * trunk/gplots/R/barplot2.R: Changed the default greay colors to
- heat colors, if height is matrix
+ * man/barplot2.Rd: Changed the default grey colors to heat colors,
+ if height is matrix
+2005-12-07 18:48 nj7w
+
+ * R/barplot2.R: Changed the default greay colors to heat colors, if
+ height is matrix
+
2005-12-06 22:41 nj7w
- * trunk/gplots/man/barplot2.Rd: Fixed minor error in documentation
- of barplot2
+ * man/barplot2.Rd: Fixed minor error in documentation of barplot2
2005-12-02 21:11 warnes
- * trunk/gplots/R/plot.lm.R: Remove .Alias calls, since .Alias is
- defunct.
+ * R/plot.lm.R: Remove .Alias calls, since .Alias is defunct.
2005-12-01 16:54 nj7w
* trunk/gmodels/man/ci.Rd, trunk/gmodels/man/coefFrame.Rd,
trunk/gmodels/man/estimable.Rd,
trunk/gmodels/man/fit.contrast.Rd,
- trunk/gmodels/man/make.contrasts.Rd,
- trunk/gplots/man/balloonplot.Rd, trunk/gplots/man/bandplot.Rd,
- trunk/gplots/man/boxplot.n.Rd, trunk/gplots/man/colorpanel.Rd,
- trunk/gplots/man/overplot.Rd, trunk/gplots/man/plotmeans.Rd,
- trunk/gplots/man/textplot.Rd, trunk/gplots/man/wapply.Rd,
- trunk/gtools/man/combinations.Rd,
+ trunk/gmodels/man/make.contrasts.Rd, 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, trunk/gtools/man/combinations.Rd,
trunk/gtools/man/foldchange.Rd, trunk/gtools/man/invalid.Rd,
trunk/gtools/man/logit.Rd, trunk/gtools/man/mixedsort.Rd,
trunk/gtools/man/oddeven.Rd, trunk/gtools/man/quantcut.Rd,
@@ -202,187 +264,179 @@
2005-11-23 22:05 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.R,
- trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex,
- trunk/gplots/inst/doc/Figure2.pdf: Updated Figure 2 colors
+ * inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.pdf,
+ inst/doc/BalloonPlot.tex, inst/doc/Figure2.pdf: Updated Figure 2
+ colors
2005-11-18 20:40 warnes
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/Figure1.pdf,
- trunk/gplots/inst/doc/Figure2.pdf,
- trunk/gplots/inst/doc/Figure3.pdf,
- trunk/gplots/inst/doc/Figure4.pdf: Latest version of the pdf
- files
+ * 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
2005-11-18 20:37 warnes
- * trunk/gplots/inst/doc/BalloonPlot.tex: Nitin works for the
- Cambrige Group, not Pfizer.
+ * inst/doc/BalloonPlot.tex: Nitin works for the Cambrige Group, not
+ Pfizer.
2005-11-18 20:34 warnes
- * trunk/gplots/inst/doc/BalloonPlot.tex: Minor text rewording.
+ * inst/doc/BalloonPlot.tex: Minor text rewording.
2005-11-18 20:31 warnes
- * trunk/gplots/inst/doc/BalloonPlot.R,
- trunk/gplots/inst/doc/BalloonPlot.tex: More edits.
+ * inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex: More edits.
2005-11-18 19:50 warnes
- * trunk/gplots/R/balloonplot.R: Recent changes to align row totals
- with the overall total broke how
+ * 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.
2005-11-18 01:17 warnes
- * trunk/gplots/DESCRIPTION, trunk/gplots/R/balloonplot.R,
- trunk/gplots/R/plot.lm.R, trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/man/balloonplot.Rd: - Update documentation for
- balloonplot to match the latest code.
+ * 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'
2005-11-18 00:16 warnes
- * trunk/gplots/R/colorpanel.R: More changes: colorpanel now allows
- only 2 colors to be specified if
+ * R/colorpanel.R: More changes: colorpanel now allows only 2 colors
+ to be specified if
no 'middle' color is desired.
2005-11-17 22:08 warnes
- * trunk/gplots/R/balloonplot.R: Allow user to control removal of
- duplicate entries in balloonplot.
+ * R/balloonplot.R: Allow user to control removal of duplicate
+ entries in balloonplot.
2005-11-17 22:06 warnes
- * trunk/gplots/R/colorpanel.R, trunk/gplots/man/colorpanel.Rd:
- Extend colorpanel to handle just two-colors in addition to three.
+ * R/colorpanel.R, man/colorpanel.Rd: Extend colorpanel to handle
+ just two-colors in addition to three.
2005-11-09 22:39 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.pdf: Updated the pdf file
+ * inst/doc/BalloonPlot.pdf: Updated the pdf file
2005-11-09 22:38 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.R,
- trunk/gplots/inst/doc/BalloonPlot.tex: Updated the changes
+ * inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex: Updated the
+ changes
2005-11-09 22:29 nj7w
- * trunk/gplots/inst/doc/Figure4.pdf: Modified figure 4
- * trunk/gplots/inst/doc/BalloonPlot.R: Updated code
+ * inst/doc/Figure4.pdf: Modified figure 4
+2005-11-09 22:29 nj7w
+
+ * inst/doc/BalloonPlot.R: Updated code
+
2005-11-09 22:20 nj7w
- * trunk/gplots/inst/doc/Figure3.pdf: Modified figure 3
- * trunk/gplots/inst/doc/Figure2.pdf: Modified figure 2
+ * inst/doc/Figure3.pdf: Modified figure 3
+2005-11-09 22:20 nj7w
+
+ * inst/doc/Figure2.pdf: Modified figure 2
+
2005-11-09 22:19 nj7w
- * trunk/gplots/inst/doc/Figure1.pdf: Modified figure 1
+ * inst/doc/Figure1.pdf: Modified figure 1
2005-11-08 16:19 nj7w
- * trunk/gplots/man/plotCI.Rd: Updated Greg's email
+ * man/plotCI.Rd: Updated Greg's email
2005-11-07 16:58 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex: Minor modifications to
- fit the code properly on pdf
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Minor
+ modifications to fit the code properly on pdf
2005-11-07 14:22 warnes
- * trunk/gplots/inst/doc/BalloonPlot.R: Add R code that generates
- plots
+ * inst/doc/BalloonPlot.R: Add R code that generates plots
2005-11-07 14:18 warnes
- * trunk/gplots/inst/doc/Figure2.pdf,
- trunk/gplots/inst/doc/Figure3.pdf,
- trunk/gplots/inst/doc/Figure4.pdf: Add figures to CVS
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex,
- trunk/gplots/inst/doc/Figure1.pdf: Text changes
+ * inst/doc/Figure2.pdf, inst/doc/Figure3.pdf, inst/doc/Figure4.pdf:
+ Add figures to CVS
+2005-11-07 14:18 warnes
+
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex,
+ inst/doc/Figure1.pdf: Text changes
+
2005-11-04 21:48 warnes
- * trunk/gplots/R/balloonplot.R: Fix some alignment issues.
+ * R/balloonplot.R: Fix some alignment issues.
2005-11-04 19:05 warnes
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/Table.pdf: Remove Table.pdf since it is no
- longer needed
+ * inst/doc/BalloonPlot.pdf, inst/doc/Table.pdf: Remove Table.pdf
+ since it is no longer needed
2005-11-04 19:04 warnes
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex,
- trunk/gplots/inst/doc/Figure1.pdf: Nitin's Changes
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex,
+ inst/doc/Figure1.pdf: Nitin's Changes
2005-11-04 19:00 warnes
- * trunk/gplots/inst/doc/SurvivedPop.pdf,
- trunk/gplots/inst/doc/SurvivedPopWhite.pdf,
- trunk/gplots/inst/doc/SurvivedProp.pdf,
- trunk/gplots/inst/doc/TotalPop.pdf: Add figure plots
+ * inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
+ inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Add figure
+ plots
2005-11-04 18:59 warnes
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex: Fix paths
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Fix paths
2005-10-20 18:36 nj7w
- * trunk/gplots/inst/doc/Figure1.eps,
- trunk/gplots/inst/doc/Table.eps: added the eps version of figures
+ * inst/doc/Figure1.eps, inst/doc/Table.eps: added the eps version
+ of figures
2005-10-20 18:35 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.pdf: Updated BallonPlot.pdf
+ * inst/doc/BalloonPlot.pdf: Updated BallonPlot.pdf
2005-10-20 18:34 nj7w
- * trunk/gplots/inst/doc/SurvivedPop.pdf,
- trunk/gplots/inst/doc/SurvivedPopWhite.pdf,
- trunk/gplots/inst/doc/SurvivedProp.pdf,
- trunk/gplots/inst/doc/TotalPop.pdf: Removed Old Figure
+ * inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
+ inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Removed Old
+ Figure
2005-10-20 18:31 nj7w
- * trunk/gplots/inst/doc/Figure1.pdf,
- trunk/gplots/inst/doc/Table.pdf: Added the new figure - for
- total popluation - Balloonplot
+ * inst/doc/Figure1.pdf, inst/doc/Table.pdf: Added the new figure -
+ for total popluation - Balloonplot
2005-10-20 18:29 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.tex: Modified the BallonPlot
- article
+ * inst/doc/BalloonPlot.tex: Modified the BallonPlot article
2005-10-20 14:12 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.tex: Added references
+ * inst/doc/BalloonPlot.tex: Added references
2005-10-19 16:57 arnima
- * trunk/gplots/man/rich.color.Rd: The last example now displays
- the correct heat.colors.
+ * man/rich.color.Rd: The last example now displays the correct
+ heat.colors.
Default 'palette' argument is now a single string, not a vector.
2005-10-19 16:56 arnima
- * trunk/gplots/R/rich.color.R: Default 'palette' argument is now a
- single string, not a vector.
+ * R/rich.color.R: Default 'palette' argument is now a single
+ string, not a vector.
2005-10-14 19:13 warnes
- * trunk/gplots/DESCRIPTION, trunk/gplots/R/balloonplot.R,
- trunk/gplots/man/balloonplot.Rd: Formatting fixes:
+ * 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
@@ -390,54 +444,50 @@
2005-10-13 20:00 warnes
- * trunk/gplots/man/balloonplot.Rd: Add example using Titanic data
- that exercises the multi-factor
+ * man/balloonplot.Rd: Add example using Titanic data that exercises
+ the multi-factor
display.
2005-10-11 21:20 warnes
- * trunk/gplots/R/balloonplot.R: Initial changes to allow multiple
- x and y factor variables. Yet to
+ * 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 19:39 warnes
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex: more minor fixes
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: more minor
+ fixes
2005-10-04 19:29 warnes
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex: fix spacing
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: fix spacing
2005-10-04 19:08 warnes
- * trunk/gplots/inst/doc/Rnews.sty: Inlcude Rnews.sty
+ * inst/doc/Rnews.sty: Inlcude Rnews.sty
2005-10-04 19:07 warnes
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex: Some textual edits.
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Some textual
+ edits.
2005-10-03 16:23 nj7w
- * trunk/gplots/inst/doc/SurvivedPop.pdf,
- trunk/gplots/inst/doc/SurvivedPopWhite.pdf,
- trunk/gplots/inst/doc/SurvivedProp.pdf,
- trunk/gplots/inst/doc/TotalPop.pdf: Added figures for the R-News
- Article
+ * 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 21:02 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex: Updated the documentation
- - added the name of the person who asked the question
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Updated the
+ documentation - added the name of the person who asked the
+ question
2005-09-29 20:29 nj7w
- * trunk/gplots/inst, trunk/gplots/inst/doc,
- trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex: Added R-news article
+ * inst, inst/doc, inst/doc/BalloonPlot.pdf,
+ inst/doc/BalloonPlot.tex: Added R-news article
2005-09-12 15:44 nj7w
@@ -446,47 +496,47 @@
trunk/gdata/man/nobs.Rd, trunk/gdata/man/read.xls.Rd,
trunk/gdata/man/rename.vars.Rd, trunk/gdata/man/trim.Rd,
trunk/gdata/man/unmatrix.Rd, trunk/gmodels/man/fast.prcomp.Rd,
- trunk/gmodels/man/glh.test.Rd, trunk/gplots/man/hist2d.Rd,
- trunk/gplots/man/ooplot.Rd, trunk/gplots/man/residplot.Rd,
- trunk/gplots/man/sinkplot.Rd, trunk/gplots/man/smartlegend.Rd,
- trunk/gplots/man/space.Rd, trunk/gtools/man/assert.Rd,
+ trunk/gmodels/man/glh.test.Rd, man/hist2d.Rd, man/ooplot.Rd,
+ man/residplot.Rd, man/sinkplot.Rd, man/smartlegend.Rd,
+ man/space.Rd, trunk/gtools/man/assert.Rd,
trunk/gtools/man/dirichlet.Rd, trunk/gtools/man/permute.Rd,
trunk/gtools/man/scat.Rd: Updated Greg's email
2005-09-12 14:45 nj7w
- * trunk/gplots/R/balloonplot.R: Updated version of balloonplot -
- by Romain Francois <fra...@fr...>
+ * R/balloonplot.R: Updated version of balloonplot - by Romain
+ Francois <fra...@fr...>
2005-09-09 20:34 nj7w
- * trunk/gplots/ChangeLog, trunk/gplots/DESCRIPTION: Updated the
- version and ChangeLog
+ * ChangeLog, DESCRIPTION: Updated the version and ChangeLog
2005-09-09 20:32 nj7w
- * trunk/gplots/R/balloonplot.R, trunk/gplots/man/balloonplot.Rd:
- Changes in ballon plot based on Romain Francois
- (fra...@fr...) suggestions
+ * R/balloonplot.R, man/balloonplot.Rd: Changes in ballon plot based
+ on Romain Francois (fra...@fr...) suggestions
2005-09-06 21:41 nj7w
- * trunk/gplots/DESCRIPTION: Updated package dependencies
- * trunk/gplots/NEWS: Added NEWS
+ * DESCRIPTION: Updated package dependencies
+2005-09-06 21:41 nj7w
+
+ * NEWS: Added NEWS
+
2005-09-02 23:10 nj7w
- * trunk/gmodels/ChangeLog, trunk/gplots/ChangeLog: Added ChangeLog
+ * trunk/gmodels/ChangeLog, ChangeLog: Added ChangeLog
2005-08-31 16:28 nj7w
- * trunk/gdata/DESCRIPTION, trunk/gmodels/DESCRIPTION,
- trunk/gplots/DESCRIPTION: Added DESCRIPTION file
+ * trunk/gdata/DESCRIPTION, trunk/gmodels/DESCRIPTION, DESCRIPTION:
+ Added DESCRIPTION file
2005-08-31 16:27 nj7w
* trunk/gdata/DESCRIPTION.in, trunk/gmodels/DESCRIPTION.in,
- trunk/gplots/DESCRIPTION.in: removed DESCRIPTION.in
+ DESCRIPTION.in: removed DESCRIPTION.in
2005-06-09 14:20 nj7w
@@ -498,8 +548,7 @@
trunk/gdata/R/matchcols.R, trunk/gdata/R/nobs.R,
trunk/gdata/R/read.xls.R, trunk/gdata/R/rename.vars.R,
trunk/gdata/R/reorder.R, trunk/gdata/R/trim.R,
- trunk/gdata/R/unmatrix.R,
- trunk/gdata/inst/perl/IO/AtomicFile.pm,
+ trunk/gdata/R/unmatrix.R, trunk/gdata/inst/perl/IO/AtomicFile.pm,
trunk/gdata/inst/perl/IO/InnerFile.pm,
trunk/gdata/inst/perl/IO/Lines.pm,
trunk/gdata/inst/perl/IO/Scalar.pm,
@@ -518,24 +567,15 @@
trunk/gmodels/man/CrossTable.Rd, trunk/gmodels/man/ci.Rd,
trunk/gmodels/man/coefFrame.Rd, trunk/gmodels/man/estimable.Rd,
trunk/gmodels/man/fast.prcomp.Rd,
- trunk/gmodels/man/fit.contrast.Rd,
- trunk/gmodels/man/glh.test.Rd,
- trunk/gmodels/man/make.contrasts.Rd,
- trunk/gplots/R/balloonplot.R, trunk/gplots/R/bandplot.R,
- trunk/gplots/R/boxplot.n.R, trunk/gplots/R/colorpanel.R,
- trunk/gplots/R/heatmap.2.R, trunk/gplots/R/hist2d.R,
- trunk/gplots/R/lowess.R, trunk/gplots/R/ooplot.R,
- trunk/gplots/R/overplot.R, trunk/gplots/R/plotCI.R,
- trunk/gplots/R/plotmeans.R, trunk/gplots/R/qqnorm.aov.R,
- trunk/gplots/R/residplot.R, trunk/gplots/R/rich.color.R,
- trunk/gplots/R/sinkplot.R, trunk/gplots/R/smartlegend.R,
- trunk/gplots/R/space.R, trunk/gplots/R/textplot.R,
- trunk/gplots/R/wapply.R, trunk/gplots/man/1,
- trunk/gplots/man/bandplot.Rd, trunk/gplots/man/barplot2.Rd,
- trunk/gplots/man/boxplot.n.Rd, trunk/gplots/man/hist2d.Rd,
- trunk/gplots/man/lowess.Rd, trunk/gplots/man/plotCI.Rd,
- trunk/gplots/man/plotmeans.Rd, trunk/gplots/man/residplot.Rd,
- trunk/gplots/man/space.Rd, trunk/gplots/man/wapply.Rd,
+ trunk/gmodels/man/fit.contrast.Rd, trunk/gmodels/man/glh.test.Rd,
+ trunk/gmodels/man/make.contrasts.Rd, 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,
trunk/gtools/R/RSCompat.S, trunk/gtools/R/combinations.R,
trunk/gtools/R/dirichlet.R, trunk/gtools/R/foldchange.R,
trunk/gtools/R/invalid.R, trunk/gtools/R/logit.R,
@@ -553,22 +593,21 @@
2005-06-09 14:15 nj7w
- * trunk/gplots/R/barplot2.R: Changes based on Marc Schwartz's
- suggestions to handel 0's and NA's appropriately.
+ * R/barplot2.R: Changes based on Marc Schwartz's suggestions to
+ handel 0's and NA's appropriately.
2005-05-13 18:59 nj7w
* trunk/gdata/R/read.xls.R, trunk/gmodels/man/CrossTable.Rd,
- trunk/gplots/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.
+ 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 14:23 warnes
- * trunk/gplots/R/overplot.R: Explicitly reference package
- containing lowess.formula in
+ * R/overplot.R: Explicitly reference package containing
+ lowess.formula in
panel.overplot(). This should fix the error reported by Troels
Ring
<tr...@gv...>.
@@ -577,57 +616,55 @@
* trunk/gdata/NAMESPACE, trunk/gdata/man/elem.Rd,
trunk/gdata/man/env.Rd, trunk/gdata/man/ll.Rd,
- trunk/gdata/man/read.xls.Rd, trunk/gplots/R/heatmap.2.R,
- trunk/gplots/man/heatmap.2.Rd, trunk/gplots/man/rich.color.Rd,
- trunk/gplots/man/sinkplot.Rd, trunk/gplots/man/textplot.Rd: ***
- empty log message ***
+ trunk/gdata/man/read.xls.Rd, R/heatmap.2.R, man/heatmap.2.Rd,
+ man/rich.color.Rd, man/sinkplot.Rd, man/textplot.Rd: *** empty
+ log message ***
2005-02-25 23:22 warnes
* trunk/gdata/R/elem.R, trunk/gdata/R/env.R, trunk/gdata/R/ll.R,
trunk/gdata/man/Args.Rd, trunk/gdata/man/env.Rd,
- trunk/gdata/man/ll.Rd, trunk/gplots/man/rich.color.Rd: Integrate
- changes submitted by Arni Magnusson
+ trunk/gdata/man/ll.Rd, man/rich.color.Rd: Integrate changes
+ submitted by Arni Magnusson
2005-02-25 22:31 warnes
- * trunk/gplots/NAMESPACE: Add dependency imports from 'stats'
- package.
+ * NAMESPACE: Add dependency imports from 'stats' package.
2005-02-22 21:01 warnes
- * trunk/gplots/R/bandplot.R: Fix problem in passing graphical
- parameters (xlim,etc).@
+ * R/bandplot.R: Fix problem in passing graphical parameters
+ (xlim,etc).@
2005-02-08 16:41 warnes
- * trunk/gplots/DESCRIPTION.in: Improve package title.
+ * DESCRIPTION.in: Improve package title.
2005-02-08 16:40 warnes
- * trunk/gplots/R/heatmap.2.R: Ignore missing values when computing
- symmetric range.
+ * R/heatmap.2.R: Ignore missing values when computing symmetric
+ range.
2005-02-02 19:25 warnes
- * trunk/gplots/man/plotmeans.Rd: Add more extensive example.
+ * man/plotmeans.Rd: Add more extensive example.
2005-01-14 19:05 warnes
- * trunk/gplots/R/textplot.R: Code can be simplified because R now
- supports selecting a fixed width font.
+ * R/textplot.R: Code can be simplified because R now supports
+ selecting a fixed width font.
2005-01-12 20:50 warnes
* trunk/gdata/DESCRIPTION.in, trunk/gmodels/DESCRIPTION.in,
- trunk/gplots/DESCRIPTION.in, trunk/gtools/DESCRIPTION.in: Add
- dependency on R 1.9.0+ to prevent poeple from installing on old
+ DESCRIPTION.in, trunk/gtools/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 01:06 warnes
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd: 1.
- Add new parameters for controlling color key:
+ * 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
@@ -640,8 +677,7 @@
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
+ 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
@@ -649,8 +685,8 @@
2004-11-03 19:43 warnes
- * trunk/gplots/R/heatmap.2.R: Fix bugs in layout of cell notes.
- They were being plotted top down
+ * 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.
@@ -659,18 +695,19 @@
* trunk/gdata/DESCRIPTION, trunk/gdata/DESCRIPTION.in,
trunk/gdata/NAMESPACE, trunk/gdata/man/.Rhistory,
trunk/gmodels/DESCRIPTION, trunk/gmodels/DESCRIPTION.in,
- trunk/gplots/DESCRIPTION, trunk/gplots/DESCRIPTION.in,
- trunk/gplots/man/sinkplot.Rd, trunk/gplots/man/textplot.Rd,
+ DESCRIPTION, DESCRIPTION.in, man/sinkplot.Rd, man/textplot.Rd,
trunk/gregmisc/.Rhistory, trunk/gregmisc/DESCRIPTION,
trunk/gtools/DESCRIPTION, trunk/gtools/DESCRIPTION.in,
trunk/gtools/man/running.Rd: Updated to pass R CMD check.
2004-09-03 22:50 warneg
- * trunk/gplots/man/textplot.Rd: Provide explicit package for call
- to nobs.
- * trunk/gplots/man/heatmap.2.Rd: Fix typos.
+ * man/textplot.Rd: Provide explicit package for call to nobs.
+2004-09-03 22:50 warneg
+
+ * man/heatmap.2.Rd: Fix typos.
+
2004-09-03 17:27 warneg
* trunk/gdata/DESCRIPTION, trunk/gdata/DESCRIPTION.in,
@@ -688,58 +725,49 @@
trunk/gmodels/R/fast.prcomp.R, trunk/gmodels/R/fit.contrast.R,
trunk/gmodels/R/glh.test.R, trunk/gmodels/R/make.contrasts.R,
trunk/gmodels/man/estimable.Rd,
- trunk/gmodels/man/fit.contrast.Rd,
- trunk/gmodels/man/glh.test.Rd,
- trunk/gmodels/man/make.contrasts.Rd, trunk/gplots/DESCRIPTION,
- trunk/gplots/NAMESPACE, trunk/gplots/R/balloonplot.R,
- trunk/gplots/R/bandplot.R, trunk/gplots/R/barplot2.R,
- trunk/gplots/R/boxplot.n.R, trunk/gplots/R/colorpanel.R,
- trunk/gplots/R/heatmap.2.R, trunk/gplots/R/hist2d.R,
- trunk/gplots/R/lowess.R, trunk/gplots/R/ooplot.R,
- trunk/gplots/R/overplot.R, trunk/gplots/R/plotCI.R,
- trunk/gplots/R/plotmeans.R, trunk/gplots/R/qqnorm.aov.R,
- trunk/gplots/R/residplot.R, trunk/gplots/R/rich.color.R,
- trunk/gplots/R/sinkplot.R, trunk/gplots/R/smartlegend.R,
- trunk/gplots/R/space.R, trunk/gplots/R/textplot.R,
- trunk/gplots/R/wapply.R, trunk/gtools/DESCRIPTION,
- trunk/gtools/NAMESPACE, trunk/gtools/R/dirichlet.R,
- trunk/gtools/R/foldchange.R, trunk/gtools/R/invalid.R,
- trunk/gtools/R/mixedsort.R, trunk/gtools/R/oddeven.R,
- trunk/gtools/R/permute.R, trunk/gtools/R/quantcut.R,
- trunk/gtools/R/running.R, trunk/gtools/man/running.Rd: initial
- bundle checkin
+ trunk/gmodels/man/fit.contrast.Rd, trunk/gmodels/man/glh.test.Rd,
+ trunk/gmodels/man/make.contrasts.Rd, 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,
+ trunk/gtools/DESCRIPTION, trunk/gtools/NAMESPACE,
+ trunk/gtools/R/dirichlet.R, trunk/gtools/R/foldchange.R,
+ trunk/gtools/R/invalid.R, trunk/gtools/R/mixedsort.R,
+ trunk/gtools/R/oddeven.R, trunk/gtools/R/permute.R,
+ trunk/gtools/R/quantcut.R, trunk/gtools/R/running.R,
+ trunk/gtools/man/running.Rd: initial bundle checkin
2004-09-02 17:14 warneg
* trunk/gdata/DESCRIPTION, trunk/gdata/DESCRIPTION.in,
trunk/gdata/NAMESPACE, trunk/gdata/man/.Rhistory,
trunk/gmodels/DESCRIPTION, trunk/gmodels/DESCRIPTION.in,
- trunk/gmodels/NAMESPACE, trunk/gplots/DESCRIPTION,
- trunk/gplots/DESCRIPTION.in, trunk/gplots/NAMESPACE,
- trunk/gplots/man/1, trunk/gplots/man/residplot.Rd,
- trunk/gregmisc/.Rhistory, trunk/gtools/DESCRIPTION,
- trunk/gtools/DESCRIPTION.in, trunk/gtools/NAMESPACE: Initial
- revision
+ trunk/gmodels/NAMESPACE, DESCRIPTION, DESCRIPTION.in, NAMESPACE,
+ man/1, man/residplot.Rd, trunk/gregmisc/.Rhistory,
+ trunk/gtools/DESCRIPTION, trunk/gtools/DESCRIPTION.in,
+ trunk/gtools/NAMESPACE: Initial revision
2004-07-29 14:49 warnes
- * trunk/gplots/R/plotCI.R, trunk/gplots/man/plotCI.Rd: Integrate
- changes from the version of plotCI maintained by Martin Maechler.
+ * R/plotCI.R, man/plotCI.Rd: Integrate changes from the version of
+ plotCI maintained by Martin Maechler.
2004-06-30 19:32 warnes
- * trunk/gplots/R/textplot.R: Remove commented-out code.
+ * R/textplot.R: Remove commented-out code.
2004-06-30 19:26 warnes
- * trunk/gplots/R/textplot.R: Fixed text size calculations
+ * R/textplot.R: Fixed text size calculations
2004-06-28 20:16 warnes
- * trunk/gplots/R/barplot2.R, trunk/gplots/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
+ * 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
@@ -748,234 +776,223 @@
2004-06-24 16:57 warnes
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd: Add
- ability to specify color of NA cells.
+ * R/heatmap.2.R, man/heatmap.2.Rd: Add ability to specify color of
+ NA cells.
2004-05-27 15:11 warnes
- * trunk/gplots/man/plotCI.Rd: Fix spelling error.
+ * man/plotCI.Rd: Fix spelling error.
2004-05-26 14:56 warnes
- * trunk/gplots/R/overplot.R: One more fix to get it right.
+ * R/overplot.R: One more fix to get it right.
2004-05-26 13:50 warnes
- * trunk/gplots/R/overplot.R: Use triple-colon operator ':::' to
- access plot.formula from the graphics package.
+ * R/overplot.R: Use triple-colon operator ':::' to access
+ plot.formula from the graphics package.
2004-05-26 13:19 warnes
- * trunk/gplots/man/rich.color.Rd: Replace 'F' by 'FALSE' to pass R
- CMD check.
+ * man/rich.color.Rd: Replace 'F' by 'FALSE' to pass R CMD check.
2004-05-25 18:32 warnes
- * trunk/gplots/R/overplot.R: Work around bug in R 1.9.X due to
- plot.formula() not having the same
+ * 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 17:33 warnes
- * trunk/gplots/R/rich.color.R, trunk/gplots/man/rich.color.Rd: Add
- rich.colors() submitted by Arni Magnusson
- <arnima@u.washington.edu>.
+ * R/rich.color.R, man/rich.color.Rd: Add rich.colors() submitted by
+ Arni Magnusson <arnima@u.washington.edu>.
2004-05-25 02:58 warnes
- * trunk/gplots/R/ooplot.R, trunk/gplots/man/ooplot.Rd: ??
+ * R/ooplot.R, man/ooplot.Rd: ??
2004-05-24 23:43 warnes
- * trunk/gplots/R/plotCI.R, trunk/gplots/R/plotmeans.R: Modified to
- use invalid() to check arguments instead of missing().
+ * 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 15:44 warnes
- * trunk/gplots/R/ooplot.R, trunk/gplots/man/ooplot.Rd: Integrate
- changes from Lodewijk Bonebakker <bon...@co...>
+ * R/ooplot.R, man/ooplot.Rd: Integrate changes from Lodewijk
+ Bonebakker <bon...@co...>
2004-04-13 13:42 warnes
- * trunk/gplots/R/space.R, trunk/gplots/man/space.Rd: Add ability
- to space points along 'y' direction.
+ * R/space.R, man/space.Rd: Add ability to space points along 'y'
+ direction.
2004-04-02 19:06 warnes
- * trunk/gplots/R/smartlegend.R: Fixed smartlegend() positioning
- when x and/or y axis are log-scale.
+ * R/smartlegend.R: Fixed smartlegend() positioning when x and/or y
+ axis are log-scale.
2004-03-30 19:04 warnes
- * trunk/gplots/R/textplot.R, trunk/gregmisc/DESCRIPTION: - Fix bug
- in textplot() reported by Wright, Kevin
- <kev...@pi...>.
+ * R/textplot.R, trunk/gregmisc/DESCRIPTION: - Fix bug in textplot()
+ reported by Wright, Kevin <kev...@pi...>.
2004-03-26 22:27 warnes
- * trunk/gplots/man/textplot.Rd: Update to match changes in
- textplot() code.
+ * man/textplot.Rd: Update to match changes in textplot() code.
2004-03-26 22:25 warnes
- * trunk/gplots/man/ooplot.Rd: Remove Windows EOL characters.
+ * man/ooplot.Rd: Remove Windows EOL characters.
2004-03-26 22:20 warnes
- * trunk/gplots/man/barplot2.Rd: - Remove some commented-out code.
+ * man/barplot2.Rd: - Remove some commented-out code.
- Remove cvs log tag.
2004-03-26 22:16 warnes
- * trunk/gplots/R/textplot.R: Misc changes.
+ * R/textplot.R: Misc changes.
2004-02-17 22:22 warnes
- * trunk/gplots/man/ooplot.Rd: Minor fix to ooplot documentation.
+ * man/ooplot.Rd: Minor fix to ooplot documentation.
2004-02-17 22:21 warnes
- * trunk/gplots/R/ooplot.R, trunk/gplots/man/ooplot.Rd: Integrate
- ooplot updates provided by Lodewijk Bonebakker
+ * R/ooplot.R, man/ooplot.Rd: Integrate ooplot updates provided by
+ Lodewijk Bonebakker
<bon...@co...>
2004-02-02 16:26 warnes
- * trunk/gplots/R/colorpanel.R, trunk/gplots/man/colorpanel.Rd: -
- Add colorpanel function, which generates a smoothly varying band
- of
+ * 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 12:07 warnes
- * trunk/gplots/man/textplot.Rd: - Correct arguments to halign to
- match code.
+ * man/textplot.Rd: - Correct arguments to halign to match code.
2004-01-21 05:17 warnes
- * trunk/gplots/R/lowess.R: Track R 1.9.0's move of 'lowess' from
- the base package to the (new)
+ * R/lowess.R: Track R 1.9.0's move of 'lowess' from the base
+ package to the (new)
stats package.
2004-01-21 04:44 warnes
- * trunk/gplots/man/sinkplot.Rd: - Fix sinkplot() example by
- replacing 'T' with 'TRUE'.
+ * man/sinkplot.Rd: - Fix sinkplot() example by replacing 'T' with
+ 'TRUE'.
2004-01-21 04:42 warnes
- * trunk/gplots/man/ooplot.Rd: - Add some more details to the
- ooplot() documentation. The
+ * man/ooplot.Rd: - Add some more details to the ooplot()
+ documentation. The
documentation is *not* complete.
2004-01-21 04:31 warnes
- * trunk/gplots/R/textplot.R, trunk/gtools/R/capture.R: - Mark
- sprint() as depreciated.
+ * R/textplot.R, trunk/gtools/R/capture.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
+ displayed. Previouslt, character vectors were plotted on top of
+ each
other.
2004-01-19 23:43 warnes
- * trunk/gplots/R/sinkplot.R, trunk/gplots/man/sinkplot.Rd: New
- function sinkplot(), as requested on R-devel by Kevin Wright
+ * R/sinkplot.R, man/sinkplot.Rd: New function sinkplot(), as
+ requested on R-devel by Kevin Wright
<kw...@es...> in
https://www.stat.math.ethz.ch/pipermail/r-devel/2004-January/028483.html.
2004-01-15 05:14 warnes
- * trunk/gplots/R/ooplot.R, trunk/gplots/man/ooplot.Rd: Add initial
- code and docs for ooplot() function submitted by Lodewijk
+ * R/ooplot.R, man/ooplot.Rd: Add initial code and docs for ooplot()
+ function submitted by Lodewijk
Bonebakker <bon...@co...>.
2003-12-03 02:46 warnes
- * trunk/gdata/man/elem.Rd, trunk/gdata/man/ll.Rd,
- trunk/gplots/man/lowess.Rd, trunk/gplots/man/textplot.Rd,
- trunk/gplots/man/wapply.Rd, trunk/gtools/man/foldchange.Rd: -
+ * trunk/gdata/man/elem.Rd, trunk/gdata/man/ll.Rd, man/lowess.Rd,
+ man/textplot.Rd, man/wapply.Rd, trunk/gtools/man/foldchange.Rd: -
match function argument defaults with 'usage'
2003-12-03 02:42 warnes
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd: - Fix
- buglets in heatmap function
+ * R/heatmap.2.R, man/heatmap.2.Rd: - Fix buglets in heatmap
+ function
- Make a slight enhancement to the example code.
2003-12-02 22:49 warnes
- * trunk/gplots/R/heatmap.2.R: Integrated some suggestions from
- Sean Davis <sd...@ma...>.
+ * R/heatmap.2.R: Integrated some suggestions from Sean Davis
+ <sd...@ma...>.
2003-12-02 18:22 warnes
- * trunk/gplots/man/heatmap.2.Rd: - Make final example use 16
- colors instead of 8. This looks nicer.
+ * man/heatmap.2.Rd: - Make final example use 16 colors instead of
+ 8. This looks nicer.
2003-12-02 16:58 warnes
- * trunk/gplots/man/barplot2.Rd: - Remove '%' character from
- example code to avoid errors.
+ * man/barplot2.Rd: - Remove '%' character from example code to
+ avoid errors.
2003-12-02 16:54 warnes
- * trunk/gplots/R/plotCI.R: - Add '...' parameter to call to text
- to allow user to control size/color/etc.
+ * R/plotCI.R: - Add '...' parameter to call to text to allow user
+ to control size/color/etc.
2003-12-01 16:00 warnes
- * trunk/gplots/man/barplot2.Rd: - updated to match changes to
- barplot() in base.
+ * man/barplot2.Rd: - updated to match changes to barplot() in base.
2003-12-01 15:59 warnes
- * trunk/gplots/data, trunk/gplots/data/rtPCR.rda: - Renamed
- rtPCR.Rda to rtPCR.rda so that R will properly load the file
+ * data, data/rtPCR.rda: - Renamed rtPCR.Rda to rtPCR.rda so that R
+ will properly load the file
when data(rtPCR) is executed.
2003-12-01 15:55 warnes
- * trunk/gplots/R/barplot2.R: - Follow patches applied to barplot()
- in base.
+ * R/barplot2.R: - Follow patches applied to barplot() in base.
2003-11-24 21:32 warnes
- * trunk/gplots/man/heatmap.2.Rd: Fix unbalanced braces.
+ * man/heatmap.2.Rd: Fix unbalanced braces.
2003-11-24 15:09 warnes
- * trunk/gplots/R/overplot.R, trunk/gplots/man/overplot.Rd: Fix
- errors reported by R CMD check.
+ * R/overplot.R, man/overplot.Rd: Fix errors reported by R CMD
+ check.
2003-11-21 23:13 warnes
- * trunk/gplots/man/overplot.Rd: Added missing closing brace.
+ * man/overplot.Rd: Added missing closing brace.
2003-11-21 23:08 warnes
- * trunk/gplots/man/rtPCR.Rd: Initial addition of these files.
- Used in examples of overplot().
+ * man/rtPCR.Rd: Initial addition of these files. Used in examples
+ of overplot().
2003-11-21 22:59 warnes
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd:
- Applied my enhancements to the heatmap() code from R 1.8.0, and
- added
+ * 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 22:58 warnes
- * trunk/gplots/R/overplot.R, trunk/gplots/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.
+ * 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
@@ -983,30 +1000,29 @@
2003-11-21 19:50 warnes
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd: -
- Integrated my extensions into the R 1.8.0 version of heatmap.
+ * 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 14:52 warnes
- * trunk/gplots/man/bandplot.Rd: Remove extranious NULL that
- confused R CMD check.
+ * man/bandplot.Rd: Remove extranious NULL that confused R CMD
+ check.
2003-11-18 18:59 warnes
- * trunk/gplots/man/barplot2.Rd: - Tiny fix to remove R CMD check
- error.
+ * man/barplot2.Rd: - Tiny fix to remove R CMD check error.
2003-11-18 18:58 warnes
- * trunk/gplots/man/smartlegend.Rd: - Added missing closing brace.
+ * man/smartlegend.Rd: - Added missing closing brace.
2003-11-18 18:45 warnes
* trunk/gdata/R/elem.R, trunk/gdata/R/env.R,
trunk/gdata/R/is.what.R, trunk/gdata/R/keep.R,
- trunk/gdata/R/ll.R, trunk/gplots/R/overplot.R: - Convert from
- MS-Dos to Unix line endings.
+ trunk/gdata/R/ll.R, R/overplot.R: - Convert from MS-Dos to Unix
+ line endings.
- Reformat to 80 columns.
2003-11-10 22:11 warnes
@@ -1015,61 +1031,56 @@
trunk/gdata/R/is.what.R, trunk/gdata/R/keep.R,
trunk/gdata/R/ll.R, trunk/gdata/man/elem.Rd,
trunk/gdata/man/env.Rd, trunk/gdata/man/is.what.Rd,
- trunk/gdata/man/keep.Rd, trunk/gdata/man/ll.Rd,
- trunk/gplots/R/heatmap.2.R, trunk/gplots/R/overplot.R,
- trunk/gplots/R/plotmeans.R, trunk/gplots/R/space.R,
- trunk/gplots/R/wapply.R, trunk/gregmisc/DESCRIPTION,
- trunk/gtools/R/capture.R, trunk/gtools/man/capture.Rd: - Add
- files contributed by Arni Magnusson
+ trunk/gdata/man/keep.Rd, trunk/gdata/man/ll.Rd, R/heatmap.2.R,
+ R/overplot.R, R/plotmeans.R, R/space.R, R/wapply.R,
+ trunk/gregmisc/DESCRIPTION, trunk/gtools/R/capture.R,
+ trunk/gtools/man/capture.Rd: - Add files contributed by Arni
+ Magnusson
<arnima@u.washington.edu>. As well as some of my own.
2003-08-19 14:58 warnes
- * trunk/gplots/R/heatmap.2.R: - Copy of local changes.
+ * R/heatmap.2.R: - Copy of local changes.
2003-08-19 14:57 warnes
- * trunk/gplots/R/heatmap.2.R: - Checkin before re-integrating
- local changes.
+ * R/heatmap.2.R: - Checkin before re-integrating local changes.
2003-06-19 21:23 warnes
- * trunk/gplots/R/heatmap.2.R: - Added enhanced heatmap function.
+ * R/heatmap.2.R: - Added enhanced heatmap function.
2003-06-09 15:10 warnes
- * trunk/gplots/man/smartlegend.Rd: - Add help text for smartlegend.
+ * man/smartlegend.Rd: - Add help text for smartlegend.
2003-06-09 14:57 warnes
- * trunk/gplots/R/smartlegend.R: - New function smartlegend().
+ * R/smartlegend.R: - New function smartlegend().
2003-04-22 17:28 warnes
- * trunk/gplots/R/plotmeans.R: - Fixeed warning messing caused when
- 'connect' is a vector.
+ * R/plotmeans.R: - Fixeed warning messing caused when 'connect' is
+ a vector.
2003-04-22 15:34 warnes
- * trunk/gplots/R/barplot2.R: Update from Marc Schwartz, modified
- by Gregory 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.
+ to remove R v1.7.0 if() based error msgs for vector conditions.
2003-04-04 13:49 warnes
- * trunk/gplots/R/balloonplot.R, trunk/gplots/man/qqnorm.aov.Rd,
- trunk/gtools/R/dirichlet.R: - Change occurences of 'T' to 'TRUE'
+ * R/balloonplot.R, man/qqnorm.aov.Rd, trunk/gtools/R/dirichlet.R: -
+ Change occurences of 'T' to 'TRUE'
2003-04-04 13:44 warnes
- * trunk/gplots/man/textplot.Rd: - Updated to match changes in
- textplot function:
+ * man/textplot.Rd: - Updated to match changes in textplot function:
- Added textplot.character
- - Renamed arguments "col.margin" and "row.margin" to "cmar",
- and
+ - 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
@@ -1077,65 +1088,62 @@
2003-04-04 13:41 warnes
- * trunk/gplots/R/textplot.R: - Added textplot.character to handle
- character strings.
+ * 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 22:29 warnes
- * trunk/gplots/R/textplot.R, trunk/gplots/man/textplot.Rd: - Added
- textplot function and friends, as well as documentation.
+ * R/textplot.R, man/textplot.Rd: - Added textplot function and
+ friends, as well as documentation.
2003-03-08 16:30 warnes
- * trunk/gplots/man/balloonplot.Rd: - Forgot to update arglist in
- \usage section.
+ * man/balloonplot.Rd: - Forgot to update arglist in \usage section.
2003-03-08 16:22 warnes
- * trunk/gplots/R/balloonplot.R, trunk/gplots/man/balloonplot.Rd: -
- Added parameters for rotation of and amount of space allocated
- for
+ * 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 15:48 warnes
- * trunk/gmodels/R/fast.prcomp.R, trunk/gplots/R/hist2d.R,
- trunk/gplots/R/qqnorm.aov.R, trunk/gregmisc/DESCRIPTION,
- trunk/gtools/R/RSCompat.S: - Minor changes to code to allow the
- package to be provided as an
+ * trunk/gmodels/R/fast.prcomp.R, R/hist2d.R, R/qqnorm.aov.R,
+ trunk/gregmisc/DESCRIPTION, trunk/gtools/R/RSCompat.S: - Minor
+ changes to code to allow the package to be provided as an
S-Plus chapter.
2003-03-07 15:43 warnes
- * trunk/gplots/R/lowess.R: - Add 'NULL' as the last element of if
- statement that defines
+ * 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 15:41 warnes
- * trunk/gplots/R/lowess.R: - Specify where the defualt lowess
- function should be found.
+ * R/lowess.R: - Specify where the defualt lowess function should be
+ found.
- Use getFunction in S-Plus instead of 'get'
2003-01-30 21:43 warnes
- * trunk/gplots/R/barplot2.R, trunk/gplots/man/barplot2.Rd: - Added
- argument 'add' to allow for the addition of a barplot to an
+ * 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 18:35 warnes
- * trunk/gplots/R/balloonplot.R, trunk/gplots/man/balloonplot.Rd: -
- Updated balloonplot help page.
+ * R/balloonplot.R, man/balloonplot.Rd: - Updated balloonplot help
+ page.
2003-01-20 17:13 warnes
- * trunk/gplots/R/wapply.R, trunk/gplots/man/wapply.Rd: - Updated
- wapply.R to allow specification of evaluation points when
+ * 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
@@ -1144,62 +1152,58 @@
2003-01-03 21:34 warnes
- * trunk/gplots/R/balloonplot.R, trunk/gplots/man/balloonplot.Rd: -
- Initial checkin of balloonplot functions and documentation.
+ * R/balloonplot.R, man/balloonplot.Rd: - Initial checkin of
+ balloonplot functions and documentation.
2003-01-03 19:23 warnes
- * trunk/gplots/man/space.Rd: - Added reference to and comparison
- example of sunflowerplot.
+ * 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 16:09 warnes
- * trunk/gplots/R/barplot2.R: - Changed assignment statements that
- used "=" to "<-" to avoid syntax
+ * R/barplot2.R: - Changed assignment statements that used "=" to
+ "<-" to avoid syntax
errors in older versions of the S language.
2003-01-02 16:07 warnes
- * trunk/gplots/R/lowess.R: - Added wrapper code so that R-specific
- fiddling won't be executed
+ * R/lowess.R: - Added wrapper code so that R-specific fiddling
+ won't be executed
under S-Plus.
2003-01-02 15:40 warnes
- * trunk/gplots/R/qqnorm.aov.R, trunk/gplots/man/qqnorm.aov.Rd: -
- Renamed first parameter to match qqnorm generic.
+ * R/qqnorm.aov.R, man/qqnorm.aov.Rd: - Renamed first parameter to
+ match qqnorm generic.
2003-01-02 15:14 warnes
- * trunk/gplots/man/qqnorm.aov.Rd: Added additional help text from
- Kjeitl.
+ * man/qqnorm.aov.Rd: Added additional help text from Kjeitl.
2002-12-31 19:50 warnes
- * trunk/gplots/R/qqnorm.aov.R, trunk/gplots/man/qqnorm.aov.Rd:
- Initial checkin of qqnorm.aov function and documentation
- submitted by
+ * R/qqnorm.aov.R, man/qqnorm.aov.Rd: Initial checkin of qqnorm.aov
+ function and documentation submitted by
Kjetil Halvorsen <kj...@ju...>.
2002-11-04 14:21 warnes
- * trunk/gplots/R/barplot2.R, trunk/gplots/man/barplot2.Rd: Updates
- from Marc Schwartz:
+ * 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
+ - 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
+ 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.
@@ -1207,23 +1211,22 @@
2002-10-30 02:21 warnes
- * trunk/gplots/R/plot.lm.R: - Commented out plot.lm() code since
- recent changes in R have broken it.
+ * R/plot.lm.R: - Commented out plot.lm() code since recent changes
+ in R have broken it.
2002-10-11 18:02 warnes
- * trunk/gplots/R/barplot2.R: - Fixed log scale errors in legend()
- call
+ * R/barplot2.R: - Fixed log scale errors in legend() call
2002-10-01 18:16 warnes
- * trunk/gplots/man/hist2d.Rd: - Added examples of using 'contour'
- and 'filled.contour' for display.
+ * man/hist2d.Rd: - Added examples of using 'contour' and
+ 'filled.contour' for display.
2002-09-24 14:53 warnes
- * trunk/gplots/R/plotmeans.R: - Changed digits=options("digits")
- which produces a list of length 1
+ * 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().
@@ -1231,10 +1234,10 @@
2002-09-23 14:27 warnes
* trunk/gmodels/man/CrossTable.Rd, trunk/gmodels/man/glh.test.Rd,
- trunk/gplots/man/barplot2.Rd: - Fixed syntax errors in
- barplot2.Rd and CrossTable.Rd
- - Fixed incorrect translation of 'F' (distribution) to 'FALSE'
- in glh.test.Rd
+ man/barplot2.Rd: - Fixed syntax errors in barplot2.Rd and
...
[truncated message content] |
|
From: <wa...@us...> - 2006-11-14 18:00:14
|
Revision: 1007
http://svn.sourceforge.net/r-gregmisc/?rev=1007&view=rev
Author: warnes
Date: 2006-11-14 09:59:51 -0800 (Tue, 14 Nov 2006)
Log Message:
-----------
Update version number
Modified Paths:
--------------
trunk/gplots/DESCRIPTION
Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION 2006-11-14 17:57:22 UTC (rev 1006)
+++ trunk/gplots/DESCRIPTION 2006-11-14 17:59:51 UTC (rev 1007)
@@ -4,7 +4,7 @@
Depends: R (>= 1.9.0), gtools, gdata, stats
Recommends: datasets
Suggests: gtools, gdata
-Version: 2.3.1
+Version: 2.3.2
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker and Thomas Lumley
Maintainer: Gregory R. Warnes <wa...@bs...>
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|
|
From: <gg...@us...> - 2006-11-10 23:52:04
|
Revision: 1004
http://svn.sourceforge.net/r-gregmisc/?rev=1004&view=rev
Author: ggorjan
Date: 2006-11-10 15:51:57 -0800 (Fri, 10 Nov 2006)
Log Message:
-----------
just formatting
Modified Paths:
--------------
trunk/gdata/NAMESPACE
trunk/gdata/NEWS
Modified: trunk/gdata/NAMESPACE
===================================================================
--- trunk/gdata/NAMESPACE 2006-11-03 01:49:02 UTC (rev 1003)
+++ trunk/gdata/NAMESPACE 2006-11-10 23:51:57 UTC (rev 1004)
@@ -44,27 +44,25 @@
importFrom(stats, reorder)
importFrom(gtools, mixedsort)
-S3method(nobs, data.frame)
-S3method(nobs, default)
-S3method(nobs, lm)
-S3method(trim, character)
-S3method(trim, default)
-S3method(trim, factor)
-S3method(trim, list)
-S3method(trim, data.frame)
S3method(reorder, factor)
+## drop.levels stuff
S3method(drop.levels, default)
S3method(drop.levels, factor)
S3method(drop.levels, list)
S3method(drop.levels, data.frame)
+## mapLevels stuff
S3method(mapLevels, default)
S3method(mapLevels, character)
S3method(mapLevels, factor)
S3method(mapLevels, list)
S3method(mapLevels, data.frame)
+S3method("mapLevels<-", default)
+S3method("mapLevels<-", list)
+S3method("mapLevels<-", data.frame)
+
S3method(print, levelsMap)
S3method(print, listLevelsMap)
@@ -77,10 +75,12 @@
S3method(unique, levelsMap)
S3method(sort, levelsMap)
-S3method("mapLevels<-", default)
-S3method("mapLevels<-", list)
-S3method("mapLevels<-", data.frame)
+## nobs stuff
+S3method(nobs, data.frame)
+S3method(nobs, default)
+S3method(nobs, lm)
+## unknown stuff
S3method(isUnknown, default)
S3method(isUnknown, POSIXlt)
S3method(isUnknown, list)
@@ -96,3 +96,10 @@
S3method(NAToUnknown, factor)
S3method(NAToUnknown, list)
S3method(NAToUnknown, data.frame)
+
+## trim stuff
+S3method(trim, character)
+S3method(trim, default)
+S3method(trim, factor)
+S3method(trim, list)
+S3method(trim, data.frame)
Modified: trunk/gdata/NEWS
===================================================================
--- trunk/gdata/NEWS 2006-11-03 01:49:02 UTC (rev 1003)
+++ trunk/gdata/NEWS 2006-11-10 23:51:57 UTC (rev 1004)
@@ -14,7 +14,7 @@
- Added c() method for factors based on mapLevels() functions.
-- Added write.fwf, which writes file in *F*ixed *W*idth *f*ormat.
+- Added write.fwf, which writes file in *F*ixed *W*idth *F*ormat.
CHANGES FROM 2.1.X to 2.3.0 (2006-09-19)
---------------------------------------
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|
|
From: <gg...@us...> - 2006-11-03 01:49:09
|
Revision: 1003
http://svn.sourceforge.net/r-gregmisc/?rev=1003&view=rev
Author: ggorjan
Date: 2006-11-02 17:49:02 -0800 (Thu, 02 Nov 2006)
Log Message:
-----------
ignores
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Name: svn:ignore
+ *.Rcheck
*.tar.gz
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|
|
From: <gg...@us...> - 2006-11-02 15:08:48
|
Revision: 1002
http://svn.sourceforge.net/r-gregmisc/?rev=1002&view=rev
Author: ggorjan
Date: 2006-11-02 07:08:32 -0800 (Thu, 02 Nov 2006)
Log Message:
-----------
typos
Modified Paths:
--------------
trunk/gdata/man/mapLevels.Rd
trunk/gdata/man/unknown.Rd
Modified: trunk/gdata/man/mapLevels.Rd
===================================================================
--- trunk/gdata/man/mapLevels.Rd 2006-10-30 22:54:51 UTC (rev 1001)
+++ trunk/gdata/man/mapLevels.Rd 2006-11-02 15:08:32 UTC (rev 1002)
@@ -2,7 +2,7 @@
%--------------------------------------------------------------------------
% What: Mapping levels
% $Id: mapLevels.Rd,v 1.1 2006/03/29 13:47:10 ggorjan Exp ggorjan $
-% Time-stamp: <2006-10-15 18:36:28 ggorjan>
+% Time-stamp: <2006-11-01 00:15:57 ggorjan>
%--------------------------------------------------------------------------
\name{mapLevels}
@@ -144,7 +144,7 @@
applied to \dQuote{character} or \dQuote{factor}. Methods for
\dQuote{list} and \dQuote{data.frame} can work only on mentioned atomic
components/columns and can accept either \dQuote{levelsMap} or
-\dQuote{listLevelsMap}. Recycling occours, if length of \code{value} is not
+\dQuote{listLevelsMap}. Recycling occurs, if length of \code{value} is not
the same as number of components/columns of a \dQuote{list/data.frame}.
}
Modified: trunk/gdata/man/unknown.Rd
===================================================================
--- trunk/gdata/man/unknown.Rd 2006-10-30 22:54:51 UTC (rev 1001)
+++ trunk/gdata/man/unknown.Rd 2006-11-02 15:08:32 UTC (rev 1002)
@@ -2,7 +2,7 @@
%--------------------------------------------------------------------------
% What: Change given unknown value to NA and vice versa man page
% $Id$
-% Time-stamp: <2006-10-15 03:52:48 ggorjan>
+% Time-stamp: <2006-11-01 00:15:08 ggorjan>
%--------------------------------------------------------------------------
\name{unknownToNA}
@@ -60,9 +60,10 @@
This functions were written to handle different variants of
\dQuote{other \code{NA}} like representations that are usually used in
various external data sources. \code{unknownToNA} can help to change
-unknown values to NA for work in \R, while \code{NAToUnknown} is meant
-for the opposite and would usually be used prior to export of data from
-\R. \code{isUnknown} is utility function for testing for unknown values.
+unknown values to \code{NA} for work in \R, while \code{NAToUnknown} is
+meant for the opposite and would usually be used prior to export of data
+from \R. \code{isUnknown} is utility function for testing for unknown
+values.
All functions are generic and the following classes were tested to work
with latest version: \dQuote{integer}, \dQuote{numeric},
@@ -75,10 +76,10 @@
coercing to vector is applied. Argument \code{unknown} can be feed also
with \dQuote{list} in \dQuote{list} and \dQuote{data.frame} methods.
-If names \dQuote{list} or \dQuote{vector} is passed to argument
+If named \dQuote{list} or \dQuote{vector} is passed to argument
\code{unknown} and \code{x} is also named, matching of names will occur.
-Recycling occours in all \dQuote{list} and \dQuote{data.frame} methods,
+Recycling occurs in all \dQuote{list} and \dQuote{data.frame} methods,
when \code{unknown} argument is not of the same length as \code{x} and
\code{unknown} is not named.
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|
|
From: <gg...@us...> - 2006-10-30 22:54:56
|
Revision: 1001
http://svn.sourceforge.net/r-gregmisc/?rev=1001&view=rev
Author: ggorjan
Date: 2006-10-30 14:54:51 -0800 (Mon, 30 Oct 2006)
Log Message:
-----------
some more examples for use of read.fwf after write.fwf
Modified Paths:
--------------
trunk/gdata/man/write.fwf.Rd
Modified: trunk/gdata/man/write.fwf.Rd
===================================================================
--- trunk/gdata/man/write.fwf.Rd 2006-10-30 22:34:19 UTC (rev 1000)
+++ trunk/gdata/man/write.fwf.Rd 2006-10-30 22:54:51 UTC (rev 1001)
@@ -2,7 +2,7 @@
%--------------------------------------------------------------------------
% What: Write fixed width format man page
% $Id$
-% Time-stamp: <2006-10-30 20:01:16 ggorjan>
+% Time-stamp: <2006-10-30 23:52:00 ggorjan>
%--------------------------------------------------------------------------
\name{write.fwf}
@@ -179,21 +179,22 @@
formatInfo <- write.fwf(x=testData, file=file, formatInfo=TRUE)
## Read exported data back to R (note +1 due to separator)
+ ## ... without header
+ read.fwf(file=file, widths=formatInfo$width + 1, header=FALSE, skip=1,
+ strip.white=TRUE)
+
+ ## ... with header - via postimport modfication
tmp <- read.fwf(file=file, widths=formatInfo$width + 1, skip=1,
strip.white=TRUE)
- colnames(tmp) <- unlist(strsplit(readLines(con=file, n=1), split=" "))
+ colnames(tmp) <- read.table(file=file, nrow=1, as.is=TRUE)
tmp
- \dontrun{
- ## How to persuade read.fwf to accept header properly?
- read.fwf(file=file, widths=formatInfo$width + 1, header=TRUE)
+ ## ... with header - persuading read.fwf to accept header properly
+ ## (thanks to Marc Schwartz)
+ read.fwf(file=file, widths=formatInfo$width + 1, strip.white=TRUE,
+ skip=1, col.names=read.table(file=file, nrow=1, as.is=TRUE))
- }
-
- ## This works, but without header
- read.fwf(file=file, widths=formatInfo$width + 1, header=FALSE, skip=1)
-
- ## This works, but we have to use quotes
+ ## ... with header - with the use of quotes
write.fwf(x=testData, file=file, quote=TRUE)
read.table(file=file, header=TRUE, strip.white=TRUE)
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|
|
From: <gg...@us...> - 2006-10-30 22:34:27
|
Revision: 1000
http://svn.sourceforge.net/r-gregmisc/?rev=1000&view=rev
Author: ggorjan
Date: 2006-10-30 14:34:19 -0800 (Mon, 30 Oct 2006)
Log Message:
-----------
ignore for report files
Property Changed:
----------------
trunk/gdata/inst/unitTests/
Property changes on: trunk/gdata/inst/unitTests
___________________________________________________________________
Name: svn:ignore
+ report.txt
report.html
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|
|
From: <gg...@us...> - 2006-10-30 19:19:05
|
Revision: 999
http://svn.sourceforge.net/r-gregmisc/?rev=999&view=rev
Author: ggorjan
Date: 2006-10-30 11:18:52 -0800 (Mon, 30 Oct 2006)
Log Message:
-----------
Id tag from source
Modified Paths:
--------------
trunk/gdata/tests/tests.write.fwf.Rout.save
Modified: trunk/gdata/tests/tests.write.fwf.Rout.save
===================================================================
--- trunk/gdata/tests/tests.write.fwf.Rout.save 2006-10-30 19:07:20 UTC (rev 998)
+++ trunk/gdata/tests/tests.write.fwf.Rout.save 2006-10-30 19:18:52 UTC (rev 999)
@@ -21,7 +21,7 @@
> ### tests.write.fwf.R
> ###------------------------------------------------------------------------
> ### What: Tests for write.fwf
-> ### $Id$
+> ### $Id: tests.write.fwf.R 997 2006-10-30 19:04:53Z ggorjan $
> ### Time-stamp: <2006-10-30 19:54:59 ggorjan>
> ###------------------------------------------------------------------------
>
@@ -187,5 +187,5 @@
> ### tests.write.fwf.R ends
>
> proc.time()
-[1] 1.283 0.028 1.311 0.000 0.000
+[1] 1.279 0.038 1.306 0.000 0.000
>
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|
|
From: <gg...@us...> - 2006-10-30 19:07:30
|
Revision: 998
http://svn.sourceforge.net/r-gregmisc/?rev=998&view=rev
Author: ggorjan
Date: 2006-10-30 11:07:20 -0800 (Mon, 30 Oct 2006)
Log Message:
-----------
removing unused import
Modified Paths:
--------------
trunk/gdata/NAMESPACE
Modified: trunk/gdata/NAMESPACE
===================================================================
--- trunk/gdata/NAMESPACE 2006-10-30 19:04:53 UTC (rev 997)
+++ trunk/gdata/NAMESPACE 2006-10-30 19:07:20 UTC (rev 998)
@@ -41,7 +41,7 @@
NAToUnknown
)
-importFrom(stats, reorder, na.omit)
+importFrom(stats, reorder)
importFrom(gtools, mixedsort)
S3method(nobs, data.frame)
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|
|
From: <gg...@us...> - 2006-10-30 19:05:08
|
Revision: 997
http://svn.sourceforge.net/r-gregmisc/?rev=997&view=rev
Author: ggorjan
Date: 2006-10-30 11:04:53 -0800 (Mon, 30 Oct 2006)
Log Message:
-----------
Id tag
Property Changed:
----------------
trunk/gdata/R/write.fwf.R
trunk/gdata/inst/unitTests/runit.write.fwf.R
trunk/gdata/man/write.fwf.Rd
trunk/gdata/tests/tests.write.fwf.R
Property changes on: trunk/gdata/R/write.fwf.R
___________________________________________________________________
Name: svn:keywords
+ Id
Property changes on: trunk/gdata/inst/unitTests/runit.write.fwf.R
___________________________________________________________________
Name: svn:keywords
+ Id
Property changes on: trunk/gdata/man/write.fwf.Rd
___________________________________________________________________
Name: svn:keywords
+ Id
Property changes on: trunk/gdata/tests/tests.write.fwf.R
___________________________________________________________________
Name: svn:keywords
+ Id
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|
|
From: <gg...@us...> - 2006-10-30 19:02:47
|
Revision: 996
http://svn.sourceforge.net/r-gregmisc/?rev=996&view=rev
Author: ggorjan
Date: 2006-10-30 11:02:13 -0800 (Mon, 30 Oct 2006)
Log Message:
-----------
write.fwf
Modified Paths:
--------------
trunk/gdata/NAMESPACE
trunk/gdata/NEWS
Added Paths:
-----------
trunk/gdata/R/write.fwf.R
trunk/gdata/inst/unitTests/runit.write.fwf.R
trunk/gdata/man/write.fwf.Rd
trunk/gdata/tests/tests.write.fwf.R
trunk/gdata/tests/tests.write.fwf.Rout.save
Modified: trunk/gdata/NAMESPACE
===================================================================
--- trunk/gdata/NAMESPACE 2006-10-30 17:27:38 UTC (rev 995)
+++ trunk/gdata/NAMESPACE 2006-10-30 19:02:13 UTC (rev 996)
@@ -25,7 +25,7 @@
unmatrix,
upperTriangle,
"upperTriangle<-",
-## write.fwf,
+ write.fwf,
## mapLevels stuff
mapLevels,
@@ -85,7 +85,7 @@
S3method(isUnknown, POSIXlt)
S3method(isUnknown, list)
S3method(isUnknown, data.frame)
-## S3method(isUnknown, matrix)
+S3method(isUnknown, matrix)
S3method(unknownToNA, default)
S3method(unknownToNA, factor)
Modified: trunk/gdata/NEWS
===================================================================
--- trunk/gdata/NEWS 2006-10-30 17:27:38 UTC (rev 995)
+++ trunk/gdata/NEWS 2006-10-30 19:02:13 UTC (rev 996)
@@ -12,6 +12,10 @@
- Added "unknown" methods for matrices.
+- Added c() method for factors based on mapLevels() functions.
+
+- Added write.fwf, which writes file in *F*ixed *W*idth *f*ormat.
+
CHANGES FROM 2.1.X to 2.3.0 (2006-09-19)
---------------------------------------
Added: trunk/gdata/R/write.fwf.R
===================================================================
--- trunk/gdata/R/write.fwf.R (rev 0)
+++ trunk/gdata/R/write.fwf.R 2006-10-30 19:02:13 UTC (rev 996)
@@ -0,0 +1,104 @@
+### write.fwf.R
+###------------------------------------------------------------------------
+### What: Write fixed width format
+### $Id$
+### Time-stamp: <2006-10-30 18:58:40 ggorjan>
+###------------------------------------------------------------------------
+
+write.fwf <- function(x, file="", append=FALSE, quote=FALSE, sep=" ",
+ na="", rownames=FALSE, colnames=TRUE, rowCol=NULL,
+ justify="right", formatInfo=FALSE, quoteInfo=TRUE, ...)
+{
+ if(!(is.data.frame(x) || is.matrix(x)))
+ stop("'x' must be a data.frame or matrix")
+ if(rownames) {
+ x <- cbind(rownames(x), x)
+ rowColVal <- ifelse(!is.null(rowCol), rowCol, "row")
+ colnames(x)[1] <- rowColVal
+ }
+ colnamesMy <- colnames(x)
+
+ ## --- Format info ---
+
+ if(formatInfo) {
+ retFormat <- data.frame(colname=colnamesMy,
+ nlevels=0,
+ position=0,
+ width=0,
+ digits=0,
+ exp=0)
+ retFormat$colname <- as.character(retFormat$colname)
+
+ isNum <- sapply(x, is.numeric)
+ ## is.numeric picks also Date and POSIXt
+ isNum <- isNum & !(sapply(x, inherits, what="Date") |
+ sapply(x, inherits, what="POSIXt"))
+
+ ## Numeric is a bit special and we need to get info before format turns
+ ## all to character
+ if(any(isNum)) {
+ tmp <- lapply(x[, isNum, drop=FALSE], format.info, ...)
+ tmp1 <- sapply(tmp, length)
+ tmp <- t(as.data.frame(tmp))
+ j <- 1
+ for(i in which(isNum)) {
+ retFormat[i, 4:(3+tmp1[j])] <- tmp[j, 1:tmp1[j]]
+ ## length 1 for exp should mean 1 and not 1+1
+ if(tmp1[j] > 2 && tmp[j, 3] > 1)
+ retFormat[i, "exp"] <- retFormat[i, "exp"] + 1
+ j <- j + 1
+ }
+ }
+ }
+
+ ## --- Format ---
+
+ x <- apply(X=x, MARGIN=2,
+ FUN=function(z) {
+ ## NAToUnknown is used since format corces NA to "NA" and
+ ## then argument na in write.table does not do its job
+ format(gdata:::NAToUnknown.default(as.character(z),
+ unknown=as.character(na)),
+ justify=justify, ...) })
+ if(formatInfo) {
+ if(any(!isNum)) { # need apply as x is now a matrix
+ retFormat[!isNum, "width"] <- apply(X=x[, !isNum, drop=FALSE], MARGIN=2,
+ FUN=function(z) format.info(z)[1])
+ retFormat[!isNum, "nlevels"] <- apply(X=x[, !isNum, drop=FALSE], MARGIN=2,
+ FUN=function(z) length(unique(z)))
+ }
+ }
+
+ ## --- Write ---
+
+ if(colnames) {
+ if(rownames && is.null(rowCol)) colnamesMy <- colnamesMy[-1]
+ write.table(t(as.matrix(colnamesMy)), file=file, append=append,
+ quote=quote, sep=sep, row.names=FALSE, col.names=FALSE, ...)
+ }
+
+ write.table(x=x, file=file, append=(colnames || append), quote=quote,
+ sep=sep, row.names=FALSE, col.names=FALSE, ...)
+
+ ## --- Return format and fixed width information ---
+
+ if(formatInfo) {
+ ## be carefull with these ifelse constructs
+ retFormat$position[1] <- ifelse(quote, ifelse(quoteInfo, 1, 2), 1)
+ if(ifelse(quote, quoteInfo, FALSE)) retFormat$width <- retFormat$width + 2
+ N <- nrow(retFormat)
+ for(i in 2:N) {
+ retFormat$position[i] <- retFormat$position[i - 1] +
+ retFormat$width[i - 1] + nchar(x=sep, type="chars") +
+ ifelse(quote, ifelse(quoteInfo, 0, 1), 0)
+ }
+ if(rownames && is.null(rowCol)) {
+ retFormat <- retFormat[-1,]
+ rownames(retFormat) <- 1:(N-1)
+ }
+ return(retFormat)
+ }
+}
+
+###------------------------------------------------------------------------
+### write.fwf.R ends here
Added: trunk/gdata/inst/unitTests/runit.write.fwf.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.write.fwf.R (rev 0)
+++ trunk/gdata/inst/unitTests/runit.write.fwf.R 2006-10-30 19:02:13 UTC (rev 996)
@@ -0,0 +1,97 @@
+### runit.write.fwf.R
+###------------------------------------------------------------------------
+### What: Unit tests for write.fwf
+### $Id$
+### Time-stamp: <2006-10-30 18:49:04 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+ library("RUnit")
+ library("gdata")
+}
+
+### }}}
+### {{{ --- write.fwf ---
+
+test.write.fwf <- function()
+{
+
+ ## 'x' must be a data.frame or matrix
+ checkException(write.fwf(1:10))
+ checkException(write.fwf(list(1:10)))
+
+ testData <- data.frame(num1=c(1:10, NA),
+ num2=c(NA, seq(from=1, to=5.5, by=0.5)),
+ num3=c(NA, rnorm(n=10, mean=1e6, sd=3e5)),
+ int1=c(as.integer(1:4), NA, as.integer(5:10)),
+ fac1=factor(c(NA, letters[1:10])),
+ fac2=factor(c(letters[6:15], NA)),
+ cha1=c(letters[17:26], NA),
+ cha2=c(NA, letters[26:17]),
+ stringsAsFactors=FALSE)
+ levels(testData$fac1) <- c(levels(testData$fac1), "unusedLevel")
+ testData$Date <- as.Date("1900-1-1")
+ testData$Date[2] <- NA
+ testData$POSIXt <- as.POSIXct(strptime("1900-1-1 01:01:01", format="%Y-%m-%d %H:%M:%S"))
+ testData$POSIXt[5] <- NA
+
+ ## --- output ---
+ ## in regular tests
+
+ ## --- formatInfo ---
+
+ ## default output
+ formatInfoT <- data.frame(colname=c("num1", "num2"),
+ nlevels=c(0, 0),
+ position=c(1, 4),
+ width=c(2, 3),
+ digits=c(0, 1),
+ exp=c(0, 0),
+ stringsAsFactors=FALSE)
+ formatInfo <- write.fwf(testData[, c("num1", "num2")], formatInfo=TRUE)
+ checkEquals(formatInfo, formatInfoT)
+
+ ## rowCol
+ formatInfoTR <- data.frame(colname=c("row", "num1", "num2"),
+ nlevels=c(11, 0, 0),
+ position=c(1, 4, 7),
+ width=c(2, 2, 3),
+ digits=c(0, 0, 1),
+ exp=c(0, 0, 0),
+ stringsAsFactors=FALSE)
+ formatInfoR <- write.fwf(testData[, c("num1", "num2")], formatInfo=TRUE,
+ rownames=TRUE, rowCol="row")
+ checkEquals(formatInfoR, formatInfoTR)
+
+ ## quoteInfo alone does not have any effect
+ formatInfoI <- write.fwf(testData[, c("num1", "num2")], formatInfo=TRUE,
+ quoteInfo=TRUE)
+ checkEquals(formatInfoI, formatInfoT)
+
+ ## quote
+ formatInfoQ <- write.fwf(testData[, c("num1", "num2")], formatInfo=TRUE,
+ quote=TRUE)
+ formatInfoTQ <- formatInfoT
+ formatInfoTQ$position <- c(1, 6)
+ formatInfoTQ$width <- c(4, 5)
+ checkEquals(formatInfoQ, formatInfoTQ)
+
+ ## quote without quoteInfo
+ formatInfoQI <- write.fwf(testData[, c("num1", "num2")], formatInfo=TRUE,
+ quote=TRUE, quoteInfo=FALSE)
+ formatInfoTQI <- formatInfoT
+ formatInfoTQI$position <- c(2, 6)
+ checkEquals(formatInfoQI, formatInfoTQI)
+}
+
+### }}}
+### {{{ Dear Emacs
+## Local variables:
+## folded-file: t
+## End:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.write.fwf.R ends here
Added: trunk/gdata/man/write.fwf.Rd
===================================================================
--- trunk/gdata/man/write.fwf.Rd (rev 0)
+++ trunk/gdata/man/write.fwf.Rd 2006-10-30 19:02:13 UTC (rev 996)
@@ -0,0 +1,208 @@
+% write.fwf.Rd
+%--------------------------------------------------------------------------
+% What: Write fixed width format man page
+% $Id$
+% Time-stamp: <2006-10-30 20:01:16 ggorjan>
+%--------------------------------------------------------------------------
+
+\name{write.fwf}
+
+\alias{write.fwf}
+
+\concept{data output}
+\concept{data export}
+
+\title{Write object in fixed width format}
+
+\description{
+\code{write.fwf} writes object in *f*ixed *w*idth *f*ormat.
+}
+
+\usage{
+
+write.fwf(x, file="", append=FALSE, quote=FALSE, sep=" ", na="",
+ rownames=FALSE, colnames=TRUE, rowCol=NULL, justify="right",
+ formatInfo=FALSE, quoteInfo=TRUE, \ldots)
+
+}
+
+\arguments{
+ \item{x}{data.frame or matrix, the object to be written}
+ \item{file}{character, name of file or connection, look in
+ \code{\link{write.table}} for more}
+ \item{append}{logical, append to existing data in \code{file}}
+ \item{quote}{logical, quote data in output}
+ \item{na}{character, the string to use for missing values
+ i.e. \code{NA} in the output}
+ \item{sep}{character, separator between columns in output}
+ \item{rownames}{logical, print row names}
+ \item{colnames}{logical, print column names}
+ \item{rowCol}{character, rownames column name}
+ \item{justify}{character, allignment of character columns}
+ \item{formatInfo}{logical, return information on number of levels,
+ widths and format}
+ \item{quoteInfo}{logical, should \code{formatInfo} account for quotes}
+ \item{\ldots}{further arguments to \code{\link{format.info}},
+ \code{\link{format}} and \code{\link{write.table}}}
+}
+
+\details{
+
+Output is similar to \code{print(x)} or \code{format(x)}. Formating is
+done completely by \code{\link{format}} on a column basis. Columns in
+the output are by default separated with a space i.e. empty column with
+a width of one character, but that can be changed with \code{sep}
+argument as passed to \code{\link{write.table}} via \ldots.
+
+\code{quote} can be used to quote fields in the output. Since all
+columns of \code{x} are converted to character during the output, all
+columns will be quoted! The following is needed for \code{read.fwf} or
+any other tools outside \R. If quotes are used, \code{\link{read.table}}
+can be easily used to read the data back into \R. Check examples. Do read
+details on \code{quoteInfo}.
+
+Use only *true* character i.e. not "\t" or similar for \code{sep} as
+number of characters in \code{sep} is needed internally.
+
+Use \code{na} to convert missing/unknown values. Only single value can
+be specified. Take a look at \code{\link{NAToUnknown}} if you need
+greater flexibility.
+
+If \code{rowCol} is not \code{NULL} and \code{rownames=TRUE} rownames
+will also have column name with \code{rowCol} value. This is mainly for
+flexibility with tools outside \R. Note that (at least in \R 2.4.0) it
+is not "easy" to import data back to \R with \code{\link{read.fwf}} if
+you also export rownames. That is the reason, that default is
+\code{rownames=FALSE}.
+
+Information about format of output can be returned if
+\code{formatInfo=TRUE}. Returned value is described in value
+section. Result is provided by \code{\link{format.info}} and care was
+taken to handle numeric properly. If output contains rownames, returned
+value accounts for this. Additionally, if \code{rowCol} is not
+\code{NULL} then returned value contains also information about format
+of rownames.
+
+If \code{quote=TRUE} output is wider due to quotes. Return value (with
+\code{formatInfo=TRUE}) can account for this in two ways; controlled
+with argument \code{quoteInfo}. However, note that there is no way to
+properly read data back to \R if \code{quote=TRUE & quoteInfo=FALSE} was
+specifed for export. \code{quoteInfo} applies only when
+\code{quote=TRUE}. Assume there is a file with quoted data as shown
+bellow (column numbers in first three line are only for demonstration of
+the values in the output).
+
+\preformatted{
+123456789 12345678 # for position
+123 1234567 123456 # for width with quoteInfo=TRUE
+ 1 12345 1234 # for width with quoteInfo=FALSE
+"a" "hsgdh" " 9"
+" " " bb" " 123"
+}
+
+With \code{quoteInfo=TRUE} \code{write.fwf} will return (symbolically)
+
+\preformatted{
+colname position width
+V1 1 3
+V2 5 7
+V3 13 6
+}
+
+or (with \code{quoteInfo=FALSE})
+
+\preformatted{
+colname position width
+V1 2 1
+V2 6 5
+V3 14 4
+}
+
+}
+
+\value{
+
+Besides its effect to write/export data \code{write.fwf} can provide
+information on format and width. A data.frame is returned with the
+following columns:
+ \item{colname}{name of the column}
+ \item{nlevels}{number of unique values (unused levels of factors are
+ dropped), 0 for numeric column}
+ \item{position}{starting column number in the output}
+ \item{width}{width of the column}
+ \item{digits}{number of digits after the decimal point}
+ \item{exp}{width of exponent in exponential representation; 0 means
+ there is no exponential representation, while 1 represents exponent
+ of length one i.e. \code{1e+6} and 2 \code{1e+06} or \code{1e+16}}
+}
+
+\author{Gregor Gorjanc}
+
+\seealso{
+ \code{\link{format.info}}, \code{\link{format}},
+ \code{\link{NAToUnknown}}, \code{\link{write.table}},
+ \code{\link{read.fwf}}, \code{\link{read.table}} and
+ \code{\link{trim}}
+}
+
+\examples{
+
+ ## Some data
+ testData <- data.frame(num1=c(1:10, NA),
+ num2=c(NA, seq(from=1, to=5.5, by=0.5)),
+ num3=c(NA, rnorm(n=10, mean=1e6, sd=3e5)),
+ int1=c(as.integer(1:4), NA, as.integer(5:10)),
+ fac1=factor(c(NA, letters[1:10])),
+ fac2=factor(c(letters[6:15], NA)),
+ cha1=c(letters[17:26], NA),
+ cha2=c(NA, letters[26:17]),
+ stringsAsFactors=FALSE)
+ levels(testData$fac1) <- c(levels(testData$fac1), "unusedLevel")
+ testData$Date <- as.Date("1900-1-1")
+ testData$Date[2] <- NA
+ testData$POSIXt <- as.POSIXct(strptime("1900-1-1 01:01:01",
+ format="\%Y-\%m-\%d \%H:\%M:\%S"))
+ testData$POSIXt[5] <- NA
+
+ ## Default
+ write.fwf(x=testData)
+
+ ## NA should be - or ------------
+ write.fwf(x=testData, na="-")
+ write.fwf(x=testData, na="------------")
+
+ ## Some other separator than space
+ write.fwf(x=testData[, 1:4], sep="-mySep-")
+
+ ## Write to file and report format and fixed width information
+ file <- tempfile("test.txt")
+ formatInfo <- write.fwf(x=testData, file=file, formatInfo=TRUE)
+
+ ## Read exported data back to R (note +1 due to separator)
+ tmp <- read.fwf(file=file, widths=formatInfo$width + 1, skip=1,
+ strip.white=TRUE)
+ colnames(tmp) <- unlist(strsplit(readLines(con=file, n=1), split=" "))
+ tmp
+
+ \dontrun{
+ ## How to persuade read.fwf to accept header properly?
+ read.fwf(file=file, widths=formatInfo$width + 1, header=TRUE)
+
+ }
+
+ ## This works, but without header
+ read.fwf(file=file, widths=formatInfo$width + 1, header=FALSE, skip=1)
+
+ ## This works, but we have to use quotes
+ write.fwf(x=testData, file=file, quote=TRUE)
+ read.table(file=file, header=TRUE, strip.white=TRUE)
+
+ ## Tidy up
+ unlink(file)
+}
+
+\keyword{print}
+\keyword{file}
+
+%--------------------------------------------------------------------------
+% write.fwf.Rd ends here
Added: trunk/gdata/tests/tests.write.fwf.R
===================================================================
--- trunk/gdata/tests/tests.write.fwf.R (rev 0)
+++ trunk/gdata/tests/tests.write.fwf.R 2006-10-30 19:02:13 UTC (rev 996)
@@ -0,0 +1,61 @@
+### tests.write.fwf.R
+###------------------------------------------------------------------------
+### What: Tests for write.fwf
+### $Id$
+### Time-stamp: <2006-10-30 19:54:59 ggorjan>
+###------------------------------------------------------------------------
+
+library(gdata)
+
+## --- Test data ---
+
+num <- c(733070.345678, 1214213.78765456, 553823.798765678,
+ 1085022.8876545678, 571063.88765456, 606718.3876545678,
+ 1053686.6, 971024.187656, 631193.398765456, 879431.1)
+
+testData <- data.frame(num1=c(1:10, NA),
+ num2=c(NA, seq(from=1, to=5.5, by=0.5)),
+ num3=c(NA, num),
+ int1=c(as.integer(1:4), NA, as.integer(5:10)),
+ fac1=factor(c(NA, letters[1:10])),
+ fac2=factor(c(letters[6:15], NA)),
+ cha1=c(letters[17:26], NA),
+ cha2=c(NA, letters[26:17]),
+ stringsAsFactors=FALSE)
+levels(testData$fac1) <- c(levels(testData$fac1), "unusedLevel")
+testData$Date <- as.Date("1900-1-1")
+testData$Date[2] <- NA
+testData$POSIXt <- as.POSIXct(strptime("1900-1-1 01:01:01", format="%Y-%m-%d %H:%M:%S"))
+testData$POSIXt[5] <- NA
+
+## --- Tests ---
+
+## Default
+write.fwf(testData)
+
+## NA should be - or ------------
+write.fwf(x=testData, na="-")
+write.fwf(x=testData, na="------------")
+
+## Some other separator than space
+write.fwf(testData[, 1:4], sep="-mySep-")
+
+## With quotes
+write.fwf(testData, quote=TRUE)
+
+## Without rownames
+write.fwf(testData, rownames=FALSE)
+
+## Without colnames
+write.fwf(testData, colnames=FALSE)
+
+## Without rownames and colnames
+write.fwf(testData, rownames=FALSE, colnames=FALSE)
+
+## With rownames and colnames and rowCol
+write.fwf(testData, rowCol="HI!")
+
+## formatInfo in unit tests
+
+###------------------------------------------------------------------------
+### tests.write.fwf.R ends
Added: trunk/gdata/tests/tests.write.fwf.Rout.save
===================================================================
--- trunk/gdata/tests/tests.write.fwf.Rout.save (rev 0)
+++ trunk/gdata/tests/tests.write.fwf.Rout.save 2006-10-30 19:02:13 UTC (rev 996)
@@ -0,0 +1,191 @@
+
+R version 2.4.0 (2006-10-03)
+Copyright (C) 2006 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+ Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> invisible(options(echo = TRUE))
+> ### tests.write.fwf.R
+> ###------------------------------------------------------------------------
+> ### What: Tests for write.fwf
+> ### $Id$
+> ### Time-stamp: <2006-10-30 19:54:59 ggorjan>
+> ###------------------------------------------------------------------------
+>
+> library(gdata)
+>
+> ## --- Test data ---
+>
+> num <- c(733070.345678, 1214213.78765456, 553823.798765678,
++ 1085022.8876545678, 571063.88765456, 606718.3876545678,
++ 1053686.6, 971024.187656, 631193.398765456, 879431.1)
+>
+> testData <- data.frame(num1=c(1:10, NA),
++ num2=c(NA, seq(from=1, to=5.5, by=0.5)),
++ num3=c(NA, num),
++ int1=c(as.integer(1:4), NA, as.integer(5:10)),
++ fac1=factor(c(NA, letters[1:10])),
++ fac2=factor(c(letters[6:15], NA)),
++ cha1=c(letters[17:26], NA),
++ cha2=c(NA, letters[26:17]),
++ stringsAsFactors=FALSE)
+> levels(testData$fac1) <- c(levels(testData$fac1), "unusedLevel")
+> testData$Date <- as.Date("1900-1-1")
+> testData$Date[2] <- NA
+> testData$POSIXt <- as.POSIXct(strptime("1900-1-1 01:01:01", format="%Y-%m-%d %H:%M:%S"))
+> testData$POSIXt[5] <- NA
+>
+> ## --- Tests ---
+>
+> ## Default
+> write.fwf(testData)
+num1 num2 num3 int1 fac1 fac2 cha1 cha2 Date POSIXt
+ 1 1 f q 1900-01-01 1900-01-01 01:01:01
+ 2 1.0 733070.3 2 a g r z 1900-01-01 01:01:01
+ 3 1.5 1214213.8 3 b h s y 1900-01-01 1900-01-01 01:01:01
+ 4 2.0 553823.8 4 c i t x 1900-01-01 1900-01-01 01:01:01
+ 5 2.5 1085022.9 d j u w 1900-01-01
+ 6 3.0 571063.9 5 e k v v 1900-01-01 1900-01-01 01:01:01
+ 7 3.5 606718.4 6 f l w u 1900-01-01 1900-01-01 01:01:01
+ 8 4.0 1053686.6 7 g m x t 1900-01-01 1900-01-01 01:01:01
+ 9 4.5 971024.2 8 h n y s 1900-01-01 1900-01-01 01:01:01
+10 5.0 631193.4 9 i o z r 1900-01-01 1900-01-01 01:01:01
+ 5.5 879431.1 10 j q 1900-01-01 1900-01-01 01:01:01
+>
+> ## NA should be - or ------------
+> write.fwf(x=testData, na="-")
+num1 num2 num3 int1 fac1 fac2 cha1 cha2 Date POSIXt
+ 1 - - 1 - f q - 1900-01-01 1900-01-01 01:01:01
+ 2 1.0 733070.3 2 a g r z - 1900-01-01 01:01:01
+ 3 1.5 1214213.8 3 b h s y 1900-01-01 1900-01-01 01:01:01
+ 4 2.0 553823.8 4 c i t x 1900-01-01 1900-01-01 01:01:01
+ 5 2.5 1085022.9 - d j u w 1900-01-01 -
+ 6 3.0 571063.9 5 e k v v 1900-01-01 1900-01-01 01:01:01
+ 7 3.5 606718.4 6 f l w u 1900-01-01 1900-01-01 01:01:01
+ 8 4.0 1053686.6 7 g m x t 1900-01-01 1900-01-01 01:01:01
+ 9 4.5 971024.2 8 h n y s 1900-01-01 1900-01-01 01:01:01
+10 5.0 631193.4 9 i o z r 1900-01-01 1900-01-01 01:01:01
+ - 5.5 879431.1 10 j - - q 1900-01-01 1900-01-01 01:01:01
+> write.fwf(x=testData, na="------------")
+num1 num2 num3 int1 fac1 fac2 cha1 cha2 Date POSIXt
+ 1 ------------ ------------ 1 ------------ f q ------------ 1900-01-01 1900-01-01 01:01:01
+ 2 1.0 733070.3 2 a g r z ------------ 1900-01-01 01:01:01
+ 3 1.5 1214213.8 3 b h s y 1900-01-01 1900-01-01 01:01:01
+ 4 2.0 553823.8 4 c i t x 1900-01-01 1900-01-01 01:01:01
+ 5 2.5 1085022.9 ------------ d j u w 1900-01-01 ------------
+ 6 3.0 571063.9 5 e k v v 1900-01-01 1900-01-01 01:01:01
+ 7 3.5 606718.4 6 f l w u 1900-01-01 1900-01-01 01:01:01
+ 8 4.0 1053686.6 7 g m x t 1900-01-01 1900-01-01 01:01:01
+ 9 4.5 971024.2 8 h n y s 1900-01-01 1900-01-01 01:01:01
+ 10 5.0 631193.4 9 i o z r 1900-01-01 1900-01-01 01:01:01
+------------ 5.5 879431.1 10 j ------------ ------------ q 1900-01-01 1900-01-01 01:01:01
+>
+> ## Some other separator than space
+> write.fwf(testData[, 1:4], sep="-mySep-")
+num1-mySep-num2-mySep-num3-mySep-int1
+ 1-mySep- -mySep- -mySep- 1
+ 2-mySep- 1-mySep- 733070.345678-mySep- 2
+ 3-mySep-1.5-mySep-1214213.78765456-mySep- 3
+ 4-mySep- 2-mySep-553823.798765678-mySep- 4
+ 5-mySep-2.5-mySep-1085022.88765457-mySep-
+ 6-mySep- 3-mySep- 571063.88765456-mySep- 5
+ 7-mySep-3.5-mySep-606718.387654568-mySep- 6
+ 8-mySep- 4-mySep- 1053686.6-mySep- 7
+ 9-mySep-4.5-mySep- 971024.187656-mySep- 8
+10-mySep- 5-mySep-631193.398765456-mySep- 9
+ -mySep-5.5-mySep- 879431.1-mySep-10
+>
+> ## With quotes
+> write.fwf(testData, quote=TRUE)
+"num1" "num2" "num3" "int1" "fac1" "fac2" "cha1" "cha2" "Date" "POSIXt"
+" 1" " " " " " 1" " " "f" "q" " " "1900-01-01" "1900-01-01 01:01:01"
+" 2" "1.0" " 733070.3" " 2" "a" "g" "r" "z" " " "1900-01-01 01:01:01"
+" 3" "1.5" "1214213.8" " 3" "b" "h" "s" "y" "1900-01-01" "1900-01-01 01:01:01"
+" 4" "2.0" " 553823.8" " 4" "c" "i" "t" "x" "1900-01-01" "1900-01-01 01:01:01"
+" 5" "2.5" "1085022.9" " " "d" "j" "u" "w" "1900-01-01" " "
+" 6" "3.0" " 571063.9" " 5" "e" "k" "v" "v" "1900-01-01" "1900-01-01 01:01:01"
+" 7" "3.5" " 606718.4" " 6" "f" "l" "w" "u" "1900-01-01" "1900-01-01 01:01:01"
+" 8" "4.0" "1053686.6" " 7" "g" "m" "x" "t" "1900-01-01" "1900-01-01 01:01:01"
+" 9" "4.5" " 971024.2" " 8" "h" "n" "y" "s" "1900-01-01" "1900-01-01 01:01:01"
+"10" "5.0" " 631193.4" " 9" "i" "o" "z" "r" "1900-01-01" "1900-01-01 01:01:01"
+" " "5.5" " 879431.1" "10" "j" " " " " "q" "1900-01-01" "1900-01-01 01:01:01"
+>
+> ## Without rownames
+> write.fwf(testData, rownames=FALSE)
+num1 num2 num3 int1 fac1 fac2 cha1 cha2 Date POSIXt
+ 1 1 f q 1900-01-01 1900-01-01 01:01:01
+ 2 1.0 733070.3 2 a g r z 1900-01-01 01:01:01
+ 3 1.5 1214213.8 3 b h s y 1900-01-01 1900-01-01 01:01:01
+ 4 2.0 553823.8 4 c i t x 1900-01-01 1900-01-01 01:01:01
+ 5 2.5 1085022.9 d j u w 1900-01-01
+ 6 3.0 571063.9 5 e k v v 1900-01-01 1900-01-01 01:01:01
+ 7 3.5 606718.4 6 f l w u 1900-01-01 1900-01-01 01:01:01
+ 8 4.0 1053686.6 7 g m x t 1900-01-01 1900-01-01 01:01:01
+ 9 4.5 971024.2 8 h n y s 1900-01-01 1900-01-01 01:01:01
+10 5.0 631193.4 9 i o z r 1900-01-01 1900-01-01 01:01:01
+ 5.5 879431.1 10 j q 1900-01-01 1900-01-01 01:01:01
+>
+> ## Without colnames
+> write.fwf(testData, colnames=FALSE)
+ 1 1 f q 1900-01-01 1900-01-01 01:01:01
+ 2 1.0 733070.3 2 a g r z 1900-01-01 01:01:01
+ 3 1.5 1214213.8 3 b h s y 1900-01-01 1900-01-01 01:01:01
+ 4 2.0 553823.8 4 c i t x 1900-01-01 1900-01-01 01:01:01
+ 5 2.5 1085022.9 d j u w 1900-01-01
+ 6 3.0 571063.9 5 e k v v 1900-01-01 1900-01-01 01:01:01
+ 7 3.5 606718.4 6 f l w u 1900-01-01 1900-01-01 01:01:01
+ 8 4.0 1053686.6 7 g m x t 1900-01-01 1900-01-01 01:01:01
+ 9 4.5 971024.2 8 h n y s 1900-01-01 1900-01-01 01:01:01
+10 5.0 631193.4 9 i o z r 1900-01-01 1900-01-01 01:01:01
+ 5.5 879431.1 10 j q 1900-01-01 1900-01-01 01:01:01
+>
+> ## Without rownames and colnames
+> write.fwf(testData, rownames=FALSE, colnames=FALSE)
+ 1 1 f q 1900-01-01 1900-01-01 01:01:01
+ 2 1.0 733070.3 2 a g r z 1900-01-01 01:01:01
+ 3 1.5 1214213.8 3 b h s y 1900-01-01 1900-01-01 01:01:01
+ 4 2.0 553823.8 4 c i t x 1900-01-01 1900-01-01 01:01:01
+ 5 2.5 1085022.9 d j u w 1900-01-01
+ 6 3.0 571063.9 5 e k v v 1900-01-01 1900-01-01 01:01:01
+ 7 3.5 606718.4 6 f l w u 1900-01-01 1900-01-01 01:01:01
+ 8 4.0 1053686.6 7 g m x t 1900-01-01 1900-01-01 01:01:01
+ 9 4.5 971024.2 8 h n y s 1900-01-01 1900-01-01 01:01:01
+10 5.0 631193.4 9 i o z r 1900-01-01 1900-01-01 01:01:01
+ 5.5 879431.1 10 j q 1900-01-01 1900-01-01 01:01:01
+>
+> ## With rownames and colnames and rowCol
+> write.fwf(testData, rowCol="HI!")
+num1 num2 num3 int1 fac1 fac2 cha1 cha2 Date POSIXt
+ 1 1 f q 1900-01-01 1900-01-01 01:01:01
+ 2 1.0 733070.3 2 a g r z 1900-01-01 01:01:01
+ 3 1.5 1214213.8 3 b h s y 1900-01-01 1900-01-01 01:01:01
+ 4 2.0 553823.8 4 c i t x 1900-01-01 1900-01-01 01:01:01
+ 5 2.5 1085022.9 d j u w 1900-01-01
+ 6 3.0 571063.9 5 e k v v 1900-01-01 1900-01-01 01:01:01
+ 7 3.5 606718.4 6 f l w u 1900-01-01 1900-01-01 01:01:01
+ 8 4.0 1053686.6 7 g m x t 1900-01-01 1900-01-01 01:01:01
+ 9 4.5 971024.2 8 h n y s 1900-01-01 1900-01-01 01:01:01
+10 5.0 631193.4 9 i o z r 1900-01-01 1900-01-01 01:01:01
+ 5.5 879431.1 10 j q 1900-01-01 1900-01-01 01:01:01
+>
+> ## formatInfo in unit tests
+>
+> ###------------------------------------------------------------------------
+> ### tests.write.fwf.R ends
+>
+> proc.time()
+[1] 1.283 0.028 1.311 0.000 0.000
+>
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|
|
From: <gg...@us...> - 2006-10-30 17:27:49
|
Revision: 995
http://svn.sourceforge.net/r-gregmisc/?rev=995&view=rev
Author: ggorjan
Date: 2006-10-30 09:27:38 -0800 (Mon, 30 Oct 2006)
Log Message:
-----------
Id tag
Property Changed:
----------------
trunk/gdata/inst/unitTests/runit.reorder.factor.R
Property changes on: trunk/gdata/inst/unitTests/runit.reorder.factor.R
___________________________________________________________________
Name: svn:keywords
+ Id
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2006-10-30 17:26:47
|
Revision: 994
http://svn.sourceforge.net/r-gregmisc/?rev=994&view=rev
Author: ggorjan
Date: 2006-10-30 09:26:32 -0800 (Mon, 30 Oct 2006)
Log Message:
-----------
added unit tests for reorder.factor
Added Paths:
-----------
trunk/gdata/inst/unitTests/runit.reorder.factor.R
Added: trunk/gdata/inst/unitTests/runit.reorder.factor.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.reorder.factor.R (rev 0)
+++ trunk/gdata/inst/unitTests/runit.reorder.factor.R 2006-10-30 17:26:32 UTC (rev 994)
@@ -0,0 +1,64 @@
+### runit.reorder.factor.R
+###------------------------------------------------------------------------
+### What: Tests for reorder.factor
+### $Id$
+### Time-stamp: <2006-10-30 18:25:05 ggorjan>
+###------------------------------------------------------------------------
+
+### {{{ --- Test setup ---
+
+if(FALSE) {
+ library("RUnit")
+ library("gdata")
+}
+
+### }}}
+### {{{ --- reorder.factor ---
+
+test.reorder.factor <- function()
+{
+ tmp <- Sys.getlocale(category="LC_COLLATE")
+ Sys.setlocale(category="LC_COLLATE", locale="C")
+
+ ## Create a 4 level example factor
+ levs <- c("PLACEBO", "300 MG", "600 MG", "1200 MG")
+ trt <- factor(rep(x=levs, times=c(22, 24, 28, 26)))
+
+ ## Change the order to something useful
+ ## default "mixedsort" ordering
+ trt2 <- reorder(trt)
+ levsTest <- c("300 MG", "600 MG", "1200 MG", "PLACEBO")
+ checkIdentical(levels(trt2), levsTest)
+
+ ## using indexes:
+ trt3 <- reorder(trt, new.order=c(4, 2, 3, 1))
+ levsTest <- c("PLACEBO", "300 MG", "600 MG", "1200 MG")
+ checkIdentical(levels(trt3), levsTest)
+
+ ## using label names:
+ trt4 <- reorder(trt, new.order=c("PLACEBO", "300 MG", "600 MG", "1200 MG"))
+ levsTest <- c("PLACEBO", "300 MG", "600 MG", "1200 MG")
+ checkIdentical(levels(trt4), levsTest)
+
+ ## using frequency
+ trt5 <- reorder(trt, X=as.numeric(trt), FUN=length)
+ levsTest <- c("PLACEBO", "300 MG", "1200 MG", "600 MG")
+ checkIdentical(levels(trt5), levsTest)
+
+ ## drop out the '300 MG' level
+ trt6 <- reorder(trt, new.order=c("PLACEBO", "600 MG", "1200 MG"))
+ levsTest <- c("PLACEBO", "600 MG", "1200 MG")
+ checkIdentical(levels(trt6), levsTest)
+
+ Sys.setlocale(category="LC_COLLATE", locale=tmp)
+}
+
+### }}}
+### {{{ Dear Emacs
+## Local variables:
+## folded-file: t
+## End:
+### }}}
+
+###------------------------------------------------------------------------
+### runit.reorder.factor.R ends here
Property changes on: trunk/gdata/inst/unitTests/runit.reorder.factor.R
___________________________________________________________________
Name: svn:keyword
+ Id
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|
|
From: <gg...@us...> - 2006-10-30 17:10:39
|
Revision: 993
http://svn.sourceforge.net/r-gregmisc/?rev=993&view=rev
Author: ggorjan
Date: 2006-10-30 09:10:08 -0800 (Mon, 30 Oct 2006)
Log Message:
-----------
mapply keeps names in R 2.4; POSIX unit tests solved; $ should work now
Modified Paths:
--------------
trunk/gdata/R/mapLevels.R
trunk/gdata/R/unknown.R
trunk/gdata/inst/unitTests/runit.unknown.R
Property Changed:
----------------
trunk/gdata/R/c.factor.R
trunk/gdata/R/mapLevels.R
trunk/gdata/R/unknown.R
trunk/gdata/inst/unitTests/runit.drop.levels.R
trunk/gdata/inst/unitTests/runit.mapLevels.R
trunk/gdata/inst/unitTests/runit.trim.R
trunk/gdata/inst/unitTests/runit.unknown.R
trunk/gdata/man/c.factor.Rd
trunk/gdata/man/unknown.Rd
trunk/gdata/tests/doRUnit.R
Property changes on: trunk/gdata/R/c.factor.R
___________________________________________________________________
Name: svn:keywords
+ Id
Modified: trunk/gdata/R/mapLevels.R
===================================================================
--- trunk/gdata/R/mapLevels.R 2006-10-29 16:08:40 UTC (rev 992)
+++ trunk/gdata/R/mapLevels.R 2006-10-30 17:10:08 UTC (rev 993)
@@ -1,7 +1,7 @@
### mapLevels.R
###------------------------------------------------------------------------
### What: Mapping levels
-### $Id: mapLevels.R,v 1.1 2006/03/29 13:47:15 ggorjan Exp ggorjan $
+### $Id$
### Time-stamp: <2006-10-29 16:45:20 ggorjan>
###------------------------------------------------------------------------
Property changes on: trunk/gdata/R/mapLevels.R
___________________________________________________________________
Name: svn:keywords
+ Id
Modified: trunk/gdata/R/unknown.R
===================================================================
--- trunk/gdata/R/unknown.R 2006-10-29 16:08:40 UTC (rev 992)
+++ trunk/gdata/R/unknown.R 2006-10-30 17:10:08 UTC (rev 993)
@@ -1,12 +1,11 @@
### unknown.R
###------------------------------------------------------------------------
### What: Change given unknown value to NA and vice versa
-### $Id$
-### Time-stamp: <2006-10-29 17:08:21 ggorjan>
+### $Id:$
+### Time-stamp: <2006-10-30 18:06:17 ggorjan>
###------------------------------------------------------------------------
### {{{ isUnknown
-
###------------------------------------------------------------------------
isUnknown <- function(x, unknown=NA, ...)
@@ -34,10 +33,7 @@
isUnknown.list <- function(x, unknown=NA, ...) {
unknown <- gdata:::.unknownList(x=x, unknown=unknown)
- ## FIXME - do I still need attributes here; R 2.4
- ## attrX <- attributes(x)
x <- mapply(FUN="isUnknown", x=x, unknown=unknown, ..., SIMPLIFY=FALSE)
- ## attributes(x) <- attrX
x
}
@@ -53,7 +49,6 @@
### }}}
### {{{ unknownToNA
-
###------------------------------------------------------------------------
unknownToNA <- function(x, unknown, warning=FALSE, ...)
@@ -87,11 +82,8 @@
unknownToNA.list <- function(x, unknown, warning=FALSE, ...)
{
unknown <- gdata:::.unknownList(x=x, unknown=unknown)
- ## FIXME - do I still need attributes here; R 2.4
- ## attrX <- attributes(x)
x <- mapply(FUN="unknownToNA", x=x, unknown=unknown, warning=warning,
SIMPLIFY=FALSE)
- ## attributes(x) <- attrX
return(x)
}
@@ -103,7 +95,6 @@
### }}}
### {{{ NAToUnknown
-
###------------------------------------------------------------------------
NAToUnknown <- function(x, unknown, force=FALSE, call.=FALSE, ...)
@@ -148,11 +139,8 @@
NAToUnknown.list <- function(x, unknown, force=FALSE, call.=FALSE, ...)
{
unknown <- gdata:::.unknownList(x=x, unknown=unknown)
- ## FIXME - do I still need attributes here; R 2.4
- ## attrX <- attributes(x)
x <- mapply(FUN="NAToUnknown", x=x, unknown=unknown, force=force,
call.=call., SIMPLIFY=FALSE)
- ## attributes(x) <- attrX
x
}
Property changes on: trunk/gdata/R/unknown.R
___________________________________________________________________
Name: svn:keywords
+ Id
Property changes on: trunk/gdata/inst/unitTests/runit.drop.levels.R
___________________________________________________________________
Name: svn:keywords
+ Id
Property changes on: trunk/gdata/inst/unitTests/runit.mapLevels.R
___________________________________________________________________
Name: svn:keywords
+ Id
Property changes on: trunk/gdata/inst/unitTests/runit.trim.R
___________________________________________________________________
Name: svn:keywords
+ Id
Modified: trunk/gdata/inst/unitTests/runit.unknown.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.unknown.R 2006-10-29 16:08:40 UTC (rev 992)
+++ trunk/gdata/inst/unitTests/runit.unknown.R 2006-10-30 17:10:08 UTC (rev 993)
@@ -2,7 +2,7 @@
###------------------------------------------------------------------------
### What: Tests for Change given unknown value to NA and vice versa methods
### $Id$
-### Time-stamp: <2006-10-29 17:06:04 ggorjan>
+### Time-stamp: <2006-10-30 17:46:21 ggorjan>
###------------------------------------------------------------------------
### {{{ --- Test setup ---
@@ -48,28 +48,31 @@
xFacUnkLevTest <- c(1, 0, 0, 0, 0, 0, 0, 0, 1)
xFacUnkLevTest <- as.logical(xFacUnkLevTest)
-dateUnk <- as.Date("1900-1-1")
-xDate <- c(as.Date("2006-08-31"), NA)
-xDateUnk <- c(as.Date("2006-08-31"), dateUnk)
-xDateTest <- c(FALSE, TRUE)
+dateUnk <- as.Date("2006-08-14")
+tmp <- as.Date("2006-08-15")
+xDate <- c(tmp, NA)
+xDateUnk <- c(tmp, dateUnk)
+xDateTest <- c(FALSE, TRUE)
-xDate1Unk <- c(as.Date("2006-08-31"), dateUnk, NA)
-xDate1Test <- c(FALSE, TRUE, FALSE)
+xDate1Unk <- c(tmp, dateUnk, NA)
+xDate1Test <- c(FALSE, TRUE, FALSE)
-POSIXltUnk <- strptime("1900-1-1", format="%Y-%m-%d")
-xPOSIXlt <- c(strptime("2006-08-31", format="%Y-%m-%d"), NA)
-xPOSIXltUnk <- c(strptime("2006-08-31", format="%Y-%m-%d"), POSIXltUnk)
-xPOSIXltTest <- c(FALSE, TRUE)
+POSIXltUnk <- strptime("2006-08-14", format="%Y-%m-%d")
+tmp <- strptime("2006-08-15", format="%Y-%m-%d")
+xPOSIXlt <- c(tmp, NA)
+xPOSIXltUnk <- c(tmp, POSIXltUnk)
+xPOSIXltTest <- c(FALSE, TRUE)
-xPOSIXlt1Unk <- c(strptime("2006-08-31", format="%Y-%m-%d"), POSIXltUnk, NA)
-xPOSIXlt1Test <- c(FALSE, TRUE, FALSE)
+xPOSIXlt1Unk <- c(tmp, POSIXltUnk, NA)
+xPOSIXlt1Test <- c(FALSE, TRUE, FALSE)
-POSIXctUnk <- as.POSIXct(strptime("1900-1-1 01:01:01", format="%Y-%m-%d %H:%M:%S"))
-xPOSIXct <- c(as.POSIXct(strptime("2006-08-31 01:01:01", format="%Y-%m-%d %H:%M:%S")), NA)
-xPOSIXctUnk <- c(as.POSIXct(strptime("2006-08-31 01:01:01", format="%Y-%m-%d %H:%M:%S")), POSIXctUnk)
+POSIXctUnk <- as.POSIXct(strptime("2006-08-14 01:01:01", format="%Y-%m-%d %H:%M:%S"))
+tmp <- as.POSIXct(strptime("2006-08-15 01:01:01", format="%Y-%m-%d %H:%M:%S"))
+xPOSIXct <- c(tmp, NA)
+xPOSIXctUnk <- c(tmp, POSIXctUnk)
xPOSIXctTest <- xPOSIXltTest
-xPOSIXct1Unk <- c(as.POSIXct(strptime("2006-08-31 01:01:01", format="%Y-%m-%d %H:%M:%S")), POSIXctUnk, NA)
+xPOSIXct1Unk <- c(tmp, POSIXctUnk, NA)
xPOSIXct1Test <- xPOSIXlt1Test
### }}}
@@ -427,8 +430,7 @@
## Date-time classes
checkIdentical(NAToUnknown(xDate, unknown=dateUnk), xDateUnk)
- ## FIXME
- ## checkIdentical(NAToUnknown(xPOSIXlt, unknown=POSIXltUnk), xPOSIXltUnk)
+ checkIdentical(NAToUnknown(xPOSIXlt, unknown=POSIXltUnk), xPOSIXltUnk)
checkIdentical(NAToUnknown(xPOSIXct, unknown=POSIXctUnk), xPOSIXctUnk)
## --- lists and data.frames ---
Property changes on: trunk/gdata/inst/unitTests/runit.unknown.R
___________________________________________________________________
Name: svn:keywords
+ Id
Property changes on: trunk/gdata/man/c.factor.Rd
___________________________________________________________________
Name: svn:keywords
+ Id
Property changes on: trunk/gdata/man/unknown.Rd
___________________________________________________________________
Name: svn:keywords
+ Id
Property changes on: trunk/gdata/tests/doRUnit.R
___________________________________________________________________
Name: svn:keywords
+ Id
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2006-10-29 16:08:52
|
Revision: 992
http://svn.sourceforge.net/r-gregmisc/?rev=992&view=rev
Author: ggorjan
Date: 2006-10-29 08:08:40 -0800 (Sun, 29 Oct 2006)
Log Message:
-----------
fixed problem in tests; added unknown methods and tests for matrices
Modified Paths:
--------------
trunk/gdata/NEWS
trunk/gdata/R/unknown.R
trunk/gdata/inst/unitTests/runit.unknown.R
trunk/gdata/man/unknown.Rd
Modified: trunk/gdata/NEWS
===================================================================
--- trunk/gdata/NEWS 2006-10-29 15:47:33 UTC (rev 991)
+++ trunk/gdata/NEWS 2006-10-29 16:08:40 UTC (rev 992)
@@ -10,6 +10,8 @@
- trim() gains ... argument.
+- Added "unknown" methods for matrices.
+
CHANGES FROM 2.1.X to 2.3.0 (2006-09-19)
---------------------------------------
Modified: trunk/gdata/R/unknown.R
===================================================================
--- trunk/gdata/R/unknown.R 2006-10-29 15:47:33 UTC (rev 991)
+++ trunk/gdata/R/unknown.R 2006-10-29 16:08:40 UTC (rev 992)
@@ -2,14 +2,15 @@
###------------------------------------------------------------------------
### What: Change given unknown value to NA and vice versa
### $Id$
-### Time-stamp: <2006-09-10 03:52:39 ggorjan>
+### Time-stamp: <2006-10-29 17:08:21 ggorjan>
###------------------------------------------------------------------------
### {{{ isUnknown
+
###------------------------------------------------------------------------
isUnknown <- function(x, unknown=NA, ...)
- UseMethod("isUnknown")
+ UseMethod("isUnknown", x=x)
isUnknown.default <- function(x, unknown=NA, ...)
{
@@ -21,10 +22,12 @@
isUnknown.POSIXlt <- function(x, unknown=NA, ...)
{
+ ## FIXME: codetools say
+ ## isUnknown.POSIXlt: wrong number of arguments to as.character
if(is.list(unknown) && !inherits(x=unknown, what="POSIXlt")) {
unknown <- lapply(unknown, FUN=as.character, ...)
} else {
- unknown <- as.character(unknown, ...)
+ unknown <- as.character(x=unknown, ...)
}
isUnknown.default(x=as.character(x), unknown=unknown)
}
@@ -32,9 +35,9 @@
isUnknown.list <- function(x, unknown=NA, ...) {
unknown <- gdata:::.unknownList(x=x, unknown=unknown)
## FIXME - do I still need attributes here; R 2.4
- attrX <- attributes(x)
+ ## attrX <- attributes(x)
x <- mapply(FUN="isUnknown", x=x, unknown=unknown, ..., SIMPLIFY=FALSE)
- attributes(x) <- attrX
+ ## attributes(x) <- attrX
x
}
@@ -44,14 +47,19 @@
x
}
+isUnknown.matrix <- function(x, unknown=NA, ...)
+ apply(X=x, MARGIN=ifelse(ncol(x) > nrow(x), 1, 2), FUN=isUnknown,
+ unknown=unknown)
+
### }}}
### {{{ unknownToNA
+
###------------------------------------------------------------------------
-unknownToNA <- function(x, unknown, warning=FALSE)
+unknownToNA <- function(x, unknown, warning=FALSE, ...)
UseMethod("unknownToNA")
-unknownToNA.default <- function(x, unknown, warning=FALSE)
+unknownToNA.default <- function(x, unknown, warning=FALSE, ...)
{
if(warning) {
if(any(is.na(x)))
@@ -61,7 +69,7 @@
x
}
-unknownToNA.factor <- function(x, unknown, warning=FALSE)
+unknownToNA.factor <- function(x, unknown, warning=FALSE, ...)
{
## could put this func into default method, but I need unlisted unknown
## for levels handling
@@ -76,18 +84,18 @@
factor(x, levels=levs)
}
-unknownToNA.list <- function(x, unknown, warning=FALSE)
+unknownToNA.list <- function(x, unknown, warning=FALSE, ...)
{
unknown <- gdata:::.unknownList(x=x, unknown=unknown)
## FIXME - do I still need attributes here; R 2.4
- attrX <- attributes(x)
+ ## attrX <- attributes(x)
x <- mapply(FUN="unknownToNA", x=x, unknown=unknown, warning=warning,
SIMPLIFY=FALSE)
- attributes(x) <- attrX
+ ## attributes(x) <- attrX
return(x)
}
-unknownToNA.data.frame <- function(x, unknown, warning=FALSE)
+unknownToNA.data.frame <- function(x, unknown, warning=FALSE, ...)
{
x[] <- unknownToNA.list(x=x, unknown=unknown, warning=warning)
x
@@ -95,12 +103,13 @@
### }}}
### {{{ NAToUnknown
+
###------------------------------------------------------------------------
-NAToUnknown <- function(x, unknown, force=FALSE, call.=FALSE)
+NAToUnknown <- function(x, unknown, force=FALSE, call.=FALSE, ...)
UseMethod("NAToUnknown")
-NAToUnknown.default <- function(x, unknown, force=FALSE, call.=FALSE)
+NAToUnknown.default <- function(x, unknown, force=FALSE, call.=FALSE, ...)
{
if(length(as.character(unknown)) != 1) # as.character allows also POSIXlt
stop("'unknown' must be a single value")
@@ -120,7 +129,7 @@
x
}
-NAToUnknown.factor <- function(x, unknown, force=FALSE, call.=FALSE)
+NAToUnknown.factor <- function(x, unknown, force=FALSE, call.=FALSE, ...)
{
if(length(unknown) != 1)
stop("'unknown' must be a single value")
@@ -136,18 +145,18 @@
x
}
-NAToUnknown.list <- function(x, unknown, force=FALSE, call.=FALSE)
+NAToUnknown.list <- function(x, unknown, force=FALSE, call.=FALSE, ...)
{
unknown <- gdata:::.unknownList(x=x, unknown=unknown)
## FIXME - do I still need attributes here; R 2.4
- attrX <- attributes(x)
+ ## attrX <- attributes(x)
x <- mapply(FUN="NAToUnknown", x=x, unknown=unknown, force=force,
call.=call., SIMPLIFY=FALSE)
- attributes(x) <- attrX
+ ## attributes(x) <- attrX
x
}
-NAToUnknown.data.frame <- function(x, unknown, force=FALSE, call.=FALSE)
+NAToUnknown.data.frame <- function(x, unknown, force=FALSE, call.=FALSE, ...)
{
x[] <- NAToUnknown.list(x=x, unknown=unknown, force=force, call.=call.)
x
Modified: trunk/gdata/inst/unitTests/runit.unknown.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.unknown.R 2006-10-29 15:47:33 UTC (rev 991)
+++ trunk/gdata/inst/unitTests/runit.unknown.R 2006-10-29 16:08:40 UTC (rev 992)
@@ -2,7 +2,7 @@
###------------------------------------------------------------------------
### What: Tests for Change given unknown value to NA and vice versa methods
### $Id$
-### Time-stamp: <2006-09-07 15:33:50 ggorjan>
+### Time-stamp: <2006-10-29 17:06:04 ggorjan>
###------------------------------------------------------------------------
### {{{ --- Test setup ---
@@ -125,7 +125,7 @@
xDFUnk1 <- as.data.frame(xListNUnk1)
xDFUnk1$cha <- as.character(xDFUnk1$cha)
xDFUnk1Test <- as.data.frame(xListUnk1Test)
-colnames(xDFUnk1Test) <- names(xListNUnk1)
+names(xDFUnk1Test) <- names(xListNUnk1)
unkC2 <- c(0, "notAvail")
xListUnk2 <- list(as.integer(c(unkC2[1], 1, 2, unkC2[1], 5, 6, 7, 8, 9)),
@@ -165,6 +165,20 @@
factor(c("A", NA, NA, "NA", "NA", 9999, NA, "-", NA)))
### }}}
+### {{{ --- Matrix ---
+
+matUnk <- 9999
+mat <- matrix(1:25, nrow=5, ncol=5)
+mat[1, 2] <- NA; mat[1, 4] <- NA; mat[2, 2] <- NA;
+mat[3, 2] <- NA; mat[3, 5] <- NA; mat[5, 4] <- NA;
+matUnk1 <- mat
+matUnk1[1, 2] <- matUnk; matUnk1[1, 4] <- matUnk; matUnk1[2, 2] <- matUnk;
+matUnk1[3, 2] <- matUnk; matUnk1[3, 5] <- matUnk; matUnk1[5, 4] <- matUnk;
+matUnkTest <- matUnk1Test <- is.na(mat)
+
+matUnk2Test <- matUnkTest | mat == 1
+
+### }}}
### {{{ --- Use of unknown=list(.default=, ...) or similarly named vector ---
D1 <- "notAvail"
@@ -280,6 +294,11 @@
## list(.default=, 99) ERROR as we do not know where to apply 99
checkException(isUnknown(x=xListNUnk, unknown=unkLND2E))
+ ## --- matrix ---
+
+ checkIdentical(isUnknown(x=mat, unknown=NA), matUnkTest)
+ checkIdentical(isUnknown(x=matUnk1, unknown=matUnk), matUnkTest)
+ checkIdentical(isUnknown(x=matUnk1, unknown=c(1, matUnk)), matUnk2Test)
}
### }}}
@@ -310,8 +329,7 @@
## Date-time classes
checkIdentical(unknownToNA(xDateUnk, unknown=dateUnk), xDate)
- ## FIXME uncomment in R 2.4
- ## checkIdentical(unknownToNA(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXlt)
+ checkIdentical(unknownToNA(xPOSIXltUnk, unknown=POSIXltUnk), xPOSIXlt)
checkIdentical(unknownToNA(xPOSIXctUnk, unknown=POSIXctUnk), xPOSIXct)
## --- lists and data.frames ---
@@ -368,6 +386,10 @@
checkIdentical(unknownToNA(x=xListNUnkD3, unknown=unkLND3), xListN)
## list(.default=, 99) ERROR as we do not know where to apply 99
checkException(unknownToNA(x=xListNUnk, unknown=unkLND2E))
+
+ ## --- matrix ---
+
+ checkEquals(unknownToNA(x=matUnk1, unknown=matUnk), mat)
}
### }}}
@@ -405,7 +427,7 @@
## Date-time classes
checkIdentical(NAToUnknown(xDate, unknown=dateUnk), xDateUnk)
- ## FIXME uncomment in R 2.4
+ ## FIXME
## checkIdentical(NAToUnknown(xPOSIXlt, unknown=POSIXltUnk), xPOSIXltUnk)
checkIdentical(NAToUnknown(xPOSIXct, unknown=POSIXctUnk), xPOSIXctUnk)
@@ -464,6 +486,9 @@
## list(.default=, 99) ERROR as we do not know where to apply 99
checkException(NAToUnknown(x=xListN, unknown=unkLND2E))
+ ## --- matrix ---
+
+ checkEquals(NAToUnknown(x=mat, unknown=matUnk), matUnk1)
}
### }}}
Modified: trunk/gdata/man/unknown.Rd
===================================================================
--- trunk/gdata/man/unknown.Rd 2006-10-29 15:47:33 UTC (rev 991)
+++ trunk/gdata/man/unknown.Rd 2006-10-29 16:08:40 UTC (rev 992)
@@ -2,7 +2,7 @@
%--------------------------------------------------------------------------
% What: Change given unknown value to NA and vice versa man page
% $Id$
-% Time-stamp: <2006-09-07 15:38:12 ggorjan>
+% Time-stamp: <2006-10-15 03:52:48 ggorjan>
%--------------------------------------------------------------------------
\name{unknownToNA}
@@ -12,6 +12,7 @@
\alias{isUnknown.POSIXlt}
\alias{isUnknown.list}
\alias{isUnknown.data.frame}
+\alias{isUnknown.matrix}
\alias{unknownToNA}
\alias{unknownToNA.default}
@@ -39,8 +40,8 @@
\usage{
isUnknown(x, unknown=NA, \ldots)
-unknownToNA(x, unknown, warning=FALSE)
-NAToUnknown(x, unknown, force=FALSE, call.=FALSE)
+unknownToNA(x, unknown, warning=FALSE, \ldots)
+NAToUnknown(x, unknown, force=FALSE, call.=FALSE, \ldots)
}
@@ -49,7 +50,8 @@
\item{unknown}{generic, value used instead of \code{NA}}
\item{warning}{logical, issue warning if \code{x} already has \code{NA}}
\item{force}{logical, force to apply already existing value in \code{x}}
- \item{\ldots}{arguments pased to as.character POSIXlt method}
+ \item{\ldots}{arguments pased to other methods (as.character for POSIXlt
+ in case of isUnknown)}
\item{call.}{logical, look in \code{\link{warning}}}
}
@@ -65,8 +67,8 @@
All functions are generic and the following classes were tested to work
with latest version: \dQuote{integer}, \dQuote{numeric},
\dQuote{character}, \dQuote{factor}, \dQuote{Date}, \dQuote{POSIXct},
-\dQuote{POSIXlt}, \dQuote{list}, \dQuote{data.frame}. For others default
-method might work just fine.
+\dQuote{POSIXlt}, \dQuote{list}, \dQuote{data.frame} and
+\dQuote{matrix}. For others default method might work just fine.
\code{unknownToNA} and \code{isUnknown} can cope with multiple values in
\code{unknown}, but those should be given as a \dQuote{vector}. If not,
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2006-10-29 15:47:44
|
Revision: 991
http://svn.sourceforge.net/r-gregmisc/?rev=991&view=rev
Author: ggorjan
Date: 2006-10-29 07:47:33 -0800 (Sun, 29 Oct 2006)
Log Message:
-----------
sort is generic now; mapply keeps names in R 2.4.0; some codetools suggestions fixed
Modified Paths:
--------------
trunk/gdata/R/drop.levels.R
trunk/gdata/R/mapLevels.R
trunk/gdata/inst/unitTests/runit.mapLevels.R
trunk/gdata/man/mapLevels.Rd
trunk/gdata/tests/doRUnit.R
Modified: trunk/gdata/R/drop.levels.R
===================================================================
--- trunk/gdata/R/drop.levels.R 2006-10-29 15:34:19 UTC (rev 990)
+++ trunk/gdata/R/drop.levels.R 2006-10-29 15:47:33 UTC (rev 991)
@@ -1,6 +1,6 @@
drop.levels <- function(x, reorder=TRUE, ...)
- UseMethod("drop.levels")
+ UseMethod("drop.levels", x=x)
drop.levels.default <- function(x, reorder=TRUE, ...)
x
Modified: trunk/gdata/R/mapLevels.R
===================================================================
--- trunk/gdata/R/mapLevels.R 2006-10-29 15:34:19 UTC (rev 990)
+++ trunk/gdata/R/mapLevels.R 2006-10-29 15:47:33 UTC (rev 991)
@@ -2,7 +2,7 @@
###------------------------------------------------------------------------
### What: Mapping levels
### $Id: mapLevels.R,v 1.1 2006/03/29 13:47:15 ggorjan Exp ggorjan $
-### Time-stamp: <2006-09-10 03:54:56 ggorjan>
+### Time-stamp: <2006-10-29 16:45:20 ggorjan>
###------------------------------------------------------------------------
### {{{ mapLevels
@@ -12,7 +12,7 @@
mapLevels <- function(x, codes=TRUE, sort=TRUE, drop=FALSE,
combine=FALSE, ...)
{
- UseMethod("mapLevels")
+ UseMethod("mapLevels", x=x)
}
mapLevels.default <- function(x, codes=TRUE, sort=TRUE, drop=FALSE,
@@ -88,10 +88,10 @@
.unlistLevelsMap <- function(x, ind=FALSE)
{
y <- unlist(x, use.names=FALSE)
- length <- sapply(x, FUN=length)
- names(y) <- rep(names(x), times=length)
+ len <- sapply(x, FUN=length)
+ names(y) <- rep(names(x), times=len)
if(ind) {
- return(list(y, rep(1:length(x), times=length), length))
+ return(list(y, rep(1:length(x), times=len), len))
} else {
return(y)
}
@@ -214,6 +214,7 @@
{
x <- list(...)
class(x) <- "listLevelsMap"
+ ## we use recursive=TRUE here because ... is a lists of lists
c(x, sort=sort, recursive=TRUE)
}
@@ -231,7 +232,7 @@
x <- unlist(x, recursive=FALSE)
## how to merge components with the same name?
class(x) <- "levelsMap"
- if(sort) x <- sort.levelsMap(x)
+ if(sort) x <- sort(x)
x <- unique(x)
}
x
@@ -330,13 +331,7 @@
dQuote("listLevelsMap"), dQuote("levelsMap")))
}
}
- ## FIXME: mapply drops names
- if(!is.null(names(x))) {
- isNamed <- TRUE
- namesX <- names(x)
- }
x <- mapply(FUN="mapLevels<-", x=x, value=value, SIMPLIFY=FALSE)
- if(isNamed) names(x) <- namesX
x
}
Modified: trunk/gdata/inst/unitTests/runit.mapLevels.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.mapLevels.R 2006-10-29 15:34:19 UTC (rev 990)
+++ trunk/gdata/inst/unitTests/runit.mapLevels.R 2006-10-29 15:47:33 UTC (rev 991)
@@ -2,16 +2,280 @@
###------------------------------------------------------------------------
### What: Unit tests for mapLevels et al.
### $Id$
-### Time-stamp: <2006-08-31 02:24:20 ggorjan>
+### Time-stamp: <2006-10-29 16:41:41 ggorjan>
###------------------------------------------------------------------------
-### {{{ --- Test setup ---
if(FALSE) {
library("RUnit")
library("gdata")
}
### }}}
-### {{{ mapLevels, is.*, as.*, [.*
test.mapLevels <- function()
{
## Integer and numeric
checkException(mapLevels(1:3)) # wrong class(x)
checkException(mapLevels(1.5)) # wrong class(x)
## Factor
f <- factor(c("B", "C", "A"))
fMapInt <- list(A=as.integer(1), B=as.integer(2), C=as.integer(3))
fMapInt1 <- list(B=as.integer(1), C=as.integer(2))
fMapCha <- list(A="A", B="B", C="C")
fMapInt <- as.levelsMap(fMapInt)
fMapInt1 <- as.levelsMap(fMapInt1)
fMapCha <- as.levelsMap(fMapCha)
fMapCha1 <- fMapCha[c(1, 3)] # this will test also [.levelsMap
checkIdentical(mapLevels(f), fMapInt)
checkTrue(is.levelsMap(mapLevels(f))) # test for is.levelsMap
checkTrue(is.levelsMap(fMapInt)) # test for as.levelsMap
checkTrue(!gdata:::.isCharacterMap(fMapInt))
checkIdentical(mapLevels(f, sort=FALSE), fMapInt) # sort is not used for factors
checkIdentical(mapLevels(f[1:2], drop=TRUE), fMapInt1)
checkIdentical(mapLevels(f, codes=FALSE), fMapCha)
checkIdentical(mapLevels(f[c(2, 3)], drop=TRUE, codes=FALSE), fMapCha1)
## Character
cha <- c("Z", "M", "A")
chaMapInt <- list(A=as.integer(1), M=as.integer(2), Z=as.integer(3))
chaMapIntO <- list(Z=as.integer(1), M=as.integer(2), A=as.integer(3))
chaMapInt1 <- list(M=as.integer(1), Z=as.integer(2))
chaMapCha <- list(A="A", M="M", Z="Z")
chaMapInt <- as.levelsMap(chaMapInt)
chaMapIntO <- as.levelsMap(chaMapIntO)
chaMapInt1 <- as.levelsMap(chaMapInt1)
chaMapCha <- as.levelsMap(chaMapCha)
checkIdentical(mapLevels(cha), chaMapInt)
checkIdentical(mapLevels(cha, sort=FALSE), chaMapIntO) # sort works for characters
checkIdentical(mapLevels(cha[1:2], drop=TRUE), chaMapInt1)
checkIdentical(mapLevels(cha, codes=FALSE), chaMapCha)
## List
l <- list(f=f, cha=cha)
l1 <- list(cha=cha, f=f)
l2 <- list(cha=cha, f=f, i=1:10)
lMapInt <- list(f=fMapInt, cha=chaMapInt)
lMapCha <- list(f=fMapCha, cha=chaMapCha)
lMapInt <- as.listLevelsMap(lMapInt)
lMapCha <- as.listLevelsMap(lMapCha)
lMapChaC <- as.list(sort(unique(c(cha, as.character(f)))))
lMapChaCO <- as.list(unique(c(cha, as.character(f))))
names(lMapChaC) <- unlist(lMapChaC)
names(lMapChaCO) <- unlist(lMapChaCO)
lMapChaC <- as.levelsMap(lMapChaC)
lMapChaCO <- as.levelsMap(lMapChaCO)
checkIdentical(mapLevels(l), lMapInt)
checkTrue(is.listLevelsMap(mapLevels(l))) # test for is.listLevelsMap
checkTrue(is.listLevelsMap(lMapInt)) # test for as.listLevelsMap
checkIdentical(mapLevels(l, codes=FALSE), lMapCha)
checkException(mapLevels(l, combine=TRUE)) # can not combine integer maps
checkIdentical(mapLevels(l, codes=FALSE, combine=TRUE), lMapChaC)
checkIdentical(mapLevels(l1, codes=FALSE, combine=TRUE), lMapChaC)
checkIdentical(mapLevels(l1, codes=FALSE, combine=TRUE, sort=FALSE), lMapChaCO)
checkException(mapLevels(l2)) # only char and factor
## Data.frame
df <- data.frame(f1=factor(c("G", "Abc", "Abc", "D", "F")),
f2=factor(c("Abc", "Abc", "B", "D", "K")),
cha=c("jkl", "A", "D", "K", "L"),
int=1:5)
dfMapInt <- list(f1=mapLevels(df$f1), f2=mapLevels(df$f2), cha=mapLevels(df$cha))
dfMapInt <- as.listLevelsMap(dfMapInt)
dfMapInt1 <- dfMapInt[c(1, 3)] # this will test also [.listLevelsMap
checkException(mapLevels(df)) # wrong class of int
checkIdentical(mapLevels(df[, 1:3]), dfMapInt)
checkIdentical(mapLevels(df[, c(1, 3)]), dfMapInt1)
}
### }}}
-### {{{ .check*
test.checkLevelsMap <- function(x)
{
## --- levelsMap ---
## not a list
checkException(gdata:::.checkLevelsMap(x="A", method="raw"))
## list without names
checkException(gdata:::.checkLevelsMap(x=list("A"), method="raw"))
fMapInt <- list(A=as.integer(1), B=as.integer(2), C=as.integer(3))
## x should be levelsMap
checkException(gdata:::.checkLevelsMap(x=fMapInt, method="class"))
## --- listLevelsMap ---
map <- list(as.levelsMap(fMapInt), as.levelsMap(fMapInt))
map1 <- list(fMapInt, fMapInt)
class(map1) <- "listLevelsMap"
## x should be a listLevelsMap
checkException(gdata:::.checkListLevelsMap(x=map, method="class"))
## x should be also a list of levelsMaps
checkException(gdata:::.checkListLevelsMap(x=map1, method="class"))
## the rest is done with levelsMap tests
}
### }}}
-### {{{ c.*
test.cLevelsMap <- function()
{
f1 <- factor(letters[c(2, 1)])
f2 <- factor(letters[c(3, 1, 2)])
mapCha1 <- mapLevels(f1, codes=FALSE) # get maps
mapCha2 <- mapLevels(f2, codes=FALSE)
mapCha1S <- mapLevels(as.character(f1), codes=FALSE, sort=FALSE)
mapCha2S <- mapLevels(as.character(f2), codes=FALSE, sort=FALSE)
mapChaTest <- list(a="a", b="b")
mapChaTest1 <- list(a="a", b="b", c="c")
mapChaTest2 <- list(c="c", a="a", b="b")
class(mapChaTest) <- class(mapChaTest1) <- class(mapChaTest2) <- "levelsMap"
mapChaTest3 <- list(mapChaTest, mapChaTest1, mapChaTest, mapChaTest1)
class(mapChaTest3) <- "listLevelsMap"
checkIdentical(c(mapCha1), mapChaTest)
checkIdentical(c(mapCha2, mapCha1), mapChaTest1)
checkIdentical(c(mapCha2S, mapCha1S, sort=FALSE), mapChaTest2)
l <- list(f1, f2)
mapCha <- mapLevels(l, codes=FALSE)
checkIdentical(c(mapCha, mapCha), mapChaTest3)
checkIdentical(c(mapCha, recursive=TRUE), mapChaTest1)
checkException(c(mapLevels(f1))) # can not combine integer “levelsMaps”
## Example with maps of different length of components
map1 <- list(A=c("a", "e", "i", "o", "u"), B="b", C="c", C="m",
D=c("d", "e"), F="f")
map2 <- list(A=c("a", "z", "w", "y", "x"), F="f", G=c("g", "h", "j"),
i="i", k=c("k", "l"), B="B")
map0Test <- list(A=c("a", "e", "i", "o", "u"), B="b", C="c", C="m",
D=c("d", "e"), F="f",
A=c("z", "w", "y", "x"), G=c("g", "h", "j"),
i="i", k=c("k", "l"), B="B")
map0Test <- as.levelsMap(map0Test)
mapTest <- sort.levelsMap(map0Test)
map1 <- as.levelsMap(map1)
map2 <- as.levelsMap(map2)
map <- c(map1, map2)
map0 <- c(map1, map2, sort=FALSE)
checkIdentical(map, mapTest)
checkIdentical(map0, map0Test)
}
### }}}
-### {{{ unique
test.uniqueLevelsMap <- function()
{
map <- list(A=c(1, 2, 1, 3), B=4, C=1, C=5, D=c(6, 8), E=7, B=4,
D=c(6, 8))
map1 <- map
map1[[1]] <- map[[1]][c(1, 2, 4)]
map1[[7]] <- NULL # remove B=4
map1[[7]] <- NULL # remove D=c(6, 8)
## unique (used in as.levelsMap), will remove duplicates (A=1)
checkIdentical(as.levelsMap(map1), as.levelsMap(map))
}
### }}}
-### {{{ mapLevels<-
"test.mapLevels<-" <- function()
{
## Some errors
checkException("mapLevels<-"(1.1, value=2)) # wrong class(x)
checkException("mapLevels<-"(complex(1.1), value=2)) # wrong class(x)
f <- factor(c("A", "B", "C"))
fMapInt <- mapLevels(f)
## can not apply integer "levelsMap" to "character"
checkException("mapLevels<-"(as.character(f), value=fMapInt))
fMapCha <- mapLevels(f, codes=FALSE)
## can not apply character levelsMap to "integer"
checkException("mapLevels<-"(as.integer(f), value=chaMapCha))
fMapFuzz <- fMapInt
fMapFuzz[[1]] <- "A"
## all components of 'value' must be of the same class
checkException("mapLevels<-"(as.character(f), value=fMapFuzz))
checkException("mapLevels<-"(as.integer(f), value=fMapFuzz))
## x integer, value integer levelsMap
f <- factor(letters[c(10, 15, 1, 2)])
fMapInt <- mapLevels(f)
fInt <- as.integer(f)
mapLevels(fInt) <- fMapInt
checkIdentical(fInt, f)
## x factor, value integer levelsMap
fInt <- factor(as.integer(f))
mapLevels(fInt) <- fMapInt
checkIdentical(fInt, f)
## above is essentially the same as levels<-.factor
fInt1 <- factor(as.integer(f))
levels(fInt1) <- fMapInt
checkIdentical(fInt1, f)
## x character, value character levelsMap
cha <- c("B", "A", "C")
chaMapCha <- as.levelsMap(list(A1="A", B2="B", C3="C"))
mapLevels(cha) <- chaMapCha
chaTest <- factor(c("B2", "A1", "C3"))
checkIdentical(cha, chaTest)
## and a bit more for components of length > 1
cha <- c("G", "I", "B", "A", "C", "D", "Z")
chaMapCha <- as.levelsMap(list(A1=c("A", "G", "I"), B2="B", C3=c("C", "D")))
mapLevels(cha) <- chaMapCha
chaTest <- factor(c("A1", "A1", "B2", "A1", "C3", "C3", NA))
checkIdentical(cha, chaTest)
## x factor, value character levelsMap
f <- factor(c("G", "I", "B", "A", "C", "D", "Z"))
fMapCha <- as.levelsMap(list(A1=c("A", "G", "I"), B2="B", C3=c("C", "D")))
mapLevels(f) <- fMapCha
fTest <- factor(c("A1", "A1", "B2", "A1", "C3", "C3", NA))
checkIdentical(f, fTest)
## Two factors and character map
f1 <- factor(letters[1:10])
f2 <- factor(letters[5:14])
checkIdentical(as.integer(f1), as.integer(f2)) # the same integer codes
mapCha1 <- mapLevels(f1, codes=FALSE) # get maps
mapCha2 <- mapLevels(f2, codes=FALSE)
mapCha <- c(mapCha1, mapCha2) # combine maps
## apply map
mapLevels(f1) <- mapCha # the same as levels(f1) <- mapCha
mapLevels(f2) <- mapCha # the same as levels(f2) <- mapCha
checkIdentical(as.integer(f1), 1:10) # \ internal codes are now
checkIdentical(as.integer(f2), 5:14) # / "consistent" among factors
## The same with list
l <- list(f1=f1, f2=f2)
mapCha <- mapLevels(l, codes=FALSE, combine=TRUE)
mapLevels(l) <- mapCha
checkIdentical(as.integer(l$f1), 1:10) # \ internal codes are now
checkIdentical(as.integer(l$f2), 5:14) # / "consistent" among factors
## and data.frame
df <- data.frame(f1=f1, f2=f2)
mapCha <- mapLevels(df, codes=FALSE, combine=TRUE)
mapLevels(df) <- mapCha
checkIdentical(as.integer(df$f1), 1:10) # \ internal codes are now
checkIdentical(as.integer(df$f2), 5:14) # / "consistent" among factors
}
### }}}
-### {{{ Dear Emacs
## Local variables:
## folded-file: t
## End:
### }}}
+### {{{ --- Test setup ---
+if(FALSE) {
+ library("RUnit")
+ library("gdata")
+}
+
+### }}}
+### {{{ mapLevels, is.*, as.*, [.*
+
+test.mapLevels <- function()
+{
+ ## Integer and numeric
+ checkException(mapLevels(1:3)) # wrong class(x)
+ checkException(mapLevels(1.5)) # wrong class(x)
+
+ ## Factor
+ f <- factor(c("B", "C", "A"))
+ fMapInt <- list(A=as.integer(1), B=as.integer(2), C=as.integer(3))
+ fMapInt1 <- list(B=as.integer(1), C=as.integer(2))
+ fMapCha <- list(A="A", B="B", C="C")
+ fMapInt <- as.levelsMap(fMapInt)
+ fMapInt1 <- as.levelsMap(fMapInt1)
+ fMapCha <- as.levelsMap(fMapCha)
+ fMapCha1 <- fMapCha[c(1, 3)] # this will test also [.levelsMap
+ checkIdentical(mapLevels(f), fMapInt)
+ checkTrue(is.levelsMap(mapLevels(f))) # test for is.levelsMap
+ checkTrue(is.levelsMap(fMapInt)) # test for as.levelsMap
+ checkTrue(!gdata:::.isCharacterMap(fMapInt))
+ checkIdentical(mapLevels(f, sort=FALSE), fMapInt) # sort is not used for factors
+ checkIdentical(mapLevels(f[1:2], drop=TRUE), fMapInt1)
+ checkIdentical(mapLevels(f, codes=FALSE), fMapCha)
+ checkIdentical(mapLevels(f[c(2, 3)], drop=TRUE, codes=FALSE), fMapCha1)
+
+ ## Character
+ cha <- c("Z", "M", "A")
+ chaMapInt <- list(A=as.integer(1), M=as.integer(2), Z=as.integer(3))
+ chaMapIntO <- list(Z=as.integer(1), M=as.integer(2), A=as.integer(3))
+ chaMapInt1 <- list(M=as.integer(1), Z=as.integer(2))
+ chaMapCha <- list(A="A", M="M", Z="Z")
+ chaMapInt <- as.levelsMap(chaMapInt)
+ chaMapIntO <- as.levelsMap(chaMapIntO)
+ chaMapInt1 <- as.levelsMap(chaMapInt1)
+ chaMapCha <- as.levelsMap(chaMapCha)
+ checkIdentical(mapLevels(cha), chaMapInt)
+ checkIdentical(mapLevels(cha, sort=FALSE), chaMapIntO) # sort works for characters
+ checkIdentical(mapLevels(cha[1:2], drop=TRUE), chaMapInt1)
+ checkIdentical(mapLevels(cha, codes=FALSE), chaMapCha)
+
+ ## List
+ l <- list(f=f, cha=cha)
+ l1 <- list(cha=cha, f=f)
+ l2 <- list(cha=cha, f=f, i=1:10)
+ lMapInt <- list(f=fMapInt, cha=chaMapInt)
+ lMapCha <- list(f=fMapCha, cha=chaMapCha)
+ lMapInt <- as.listLevelsMap(lMapInt)
+ lMapCha <- as.listLevelsMap(lMapCha)
+ lMapChaC <- as.list(sort(unique(c(cha, as.character(f)))))
+ lMapChaCO <- as.list(unique(c(cha, as.character(f))))
+ names(lMapChaC) <- unlist(lMapChaC)
+ names(lMapChaCO) <- unlist(lMapChaCO)
+ lMapChaC <- as.levelsMap(lMapChaC)
+ lMapChaCO <- as.levelsMap(lMapChaCO)
+ checkIdentical(mapLevels(l), lMapInt)
+ checkTrue(is.listLevelsMap(mapLevels(l))) # test for is.listLevelsMap
+ checkTrue(is.listLevelsMap(lMapInt)) # test for as.listLevelsMap
+ checkIdentical(mapLevels(l, codes=FALSE), lMapCha)
+ checkException(mapLevels(l, combine=TRUE)) # can not combine integer maps
+ checkIdentical(mapLevels(l, codes=FALSE, combine=TRUE), lMapChaC)
+ checkIdentical(mapLevels(l1, codes=FALSE, combine=TRUE), lMapChaC)
+ checkIdentical(mapLevels(l1, codes=FALSE, combine=TRUE, sort=FALSE), lMapChaCO)
+ checkException(mapLevels(l2)) # only char and factor
+
+ ## Data.frame
+ df <- data.frame(f1=factor(c("G", "Abc", "Abc", "D", "F")),
+ f2=factor(c("Abc", "Abc", "B", "D", "K")),
+ cha=c("jkl", "A", "D", "K", "L"),
+ int=1:5)
+ dfMapInt <- list(f1=mapLevels(df$f1), f2=mapLevels(df$f2), cha=mapLevels(df$cha))
+ dfMapInt <- as.listLevelsMap(dfMapInt)
+ dfMapInt1 <- dfMapInt[c(1, 3)] # this will test also [.listLevelsMap
+ checkException(mapLevels(df)) # wrong class of int
+ checkIdentical(mapLevels(df[, 1:3]), dfMapInt)
+ checkIdentical(mapLevels(df[, c(1, 3)]), dfMapInt1)
+}
+
+### }}}
+### {{{ .check*
+
+test.checkLevelsMap <- function(x)
+{
+ ## --- levelsMap ---
+
+ ## not a list
+ checkException(gdata:::.checkLevelsMap(x="A", method="raw"))
+ ## list without names
+ checkException(gdata:::.checkLevelsMap(x=list("A"), method="raw"))
+ fMapInt <- list(A=as.integer(1), B=as.integer(2), C=as.integer(3))
+ ## x should be levelsMap
+ checkException(gdata:::.checkLevelsMap(x=fMapInt, method="class"))
+
+ ## --- listLevelsMap ---
+
+ map <- list(as.levelsMap(fMapInt), as.levelsMap(fMapInt))
+ map1 <- list(fMapInt, fMapInt)
+ class(map1) <- "listLevelsMap"
+ ## x should be a listLevelsMap
+ checkException(gdata:::.checkListLevelsMap(x=map, method="class"))
+ ## x should be also a list of levelsMaps
+ checkException(gdata:::.checkListLevelsMap(x=map1, method="class"))
+ ## the rest is done with levelsMap tests
+}
+
+### }}}
+### {{{ c.*
+
+test.cLevelsMap <- function()
+{
+ f1 <- factor(letters[c(2, 1)])
+ f2 <- factor(letters[c(3, 1, 2)])
+ mapCha1 <- mapLevels(f1, codes=FALSE) # get maps
+ mapCha2 <- mapLevels(f2, codes=FALSE)
+ mapCha1S <- mapLevels(as.character(f1), codes=FALSE, sort=FALSE)
+ mapCha2S <- mapLevels(as.character(f2), codes=FALSE, sort=FALSE)
+ mapChaTest <- list(a="a", b="b")
+ mapChaTest1 <- list(a="a", b="b", c="c")
+ mapChaTest2 <- list(c="c", a="a", b="b")
+ class(mapChaTest) <- class(mapChaTest1) <- class(mapChaTest2) <- "levelsMap"
+ mapChaTest3 <- list(mapChaTest, mapChaTest1, mapChaTest, mapChaTest1)
+ class(mapChaTest3) <- "listLevelsMap"
+ checkIdentical(c(mapCha1), mapChaTest)
+ checkIdentical(c(mapCha2, mapCha1), mapChaTest1)
+ checkIdentical(c(mapCha2S, mapCha1S, sort=FALSE), mapChaTest2)
+
+ l <- list(f1, f2)
+ mapCha <- mapLevels(l, codes=FALSE)
+ checkIdentical(c(mapCha, mapCha), mapChaTest3)
+ checkIdentical(c(mapCha, recursive=TRUE), mapChaTest1)
+
+ checkException(c(mapLevels(f1))) # can not combine integer “levelsMaps”
+
+ ## Example with maps of different length of components
+ map1 <- list(A=c("a", "e", "i", "o", "u"), B="b", C="c", C="m",
+ D=c("d", "e"), F="f")
+ map2 <- list(A=c("a", "z", "w", "y", "x"), F="f", G=c("g", "h", "j"),
+ i="i", k=c("k", "l"), B="B")
+ map0Test <- list(A=c("a", "e", "i", "o", "u"), B="b", C="c", C="m",
+ D=c("d", "e"), F="f",
+ A=c("z", "w", "y", "x"), G=c("g", "h", "j"),
+ i="i", k=c("k", "l"), B="B")
+ map0Test <- as.levelsMap(map0Test)
+ mapTest <- sort(map0Test)
+ map1 <- as.levelsMap(map1)
+ map2 <- as.levelsMap(map2)
+ map <- c(map1, map2)
+ map0 <- c(map1, map2, sort=FALSE)
+ checkIdentical(map, mapTest)
+ checkIdentical(map0, map0Test)
+}
+
+### }}}
+### {{{ unique
+
+test.uniqueLevelsMap <- function()
+{
+ map <- list(A=c(1, 2, 1, 3), B=4, C=1, C=5, D=c(6, 8), E=7, B=4,
+ D=c(6, 8))
+ map1 <- map
+ map1[[1]] <- map[[1]][c(1, 2, 4)]
+ map1[[7]] <- NULL # remove B=4
+ map1[[7]] <- NULL # remove D=c(6, 8)
+ ## unique (used in as.levelsMap), will remove duplicates (A=1)
+ checkIdentical(as.levelsMap(map1), as.levelsMap(map))
+}
+
+### }}}
+### {{{ mapLevels<-
+
+"test.mapLevels<-" <- function()
+{
+ ## Some errors
+ checkException("mapLevels<-"(1.1, value=2)) # wrong class(x)
+ checkException("mapLevels<-"(complex(1.1), value=2)) # wrong class(x)
+
+ f <- factor(c("A", "B", "C"))
+ fMapInt <- mapLevels(f)
+ ## can not apply integer "levelsMap" to "character"
+ checkException("mapLevels<-"(as.character(f), value=fMapInt))
+
+ fMapCha <- mapLevels(f, codes=FALSE)
+ ## can not apply character levelsMap to "integer"
+ checkException("mapLevels<-"(as.integer(f), value=chaMapCha))
+
+ fMapFuzz <- fMapInt
+ fMapFuzz[[1]] <- "A"
+ ## all components of 'value' must be of the same class
+ checkException("mapLevels<-"(as.character(f), value=fMapFuzz))
+ checkException("mapLevels<-"(as.integer(f), value=fMapFuzz))
+
+ ## x integer, value integer levelsMap
+ f <- factor(letters[c(10, 15, 1, 2)])
+ fMapInt <- mapLevels(f)
+ fInt <- as.integer(f)
+ mapLevels(fInt) <- fMapInt
+ checkIdentical(fInt, f)
+
+ ## x factor, value integer levelsMap
+ fInt <- factor(as.integer(f))
+ mapLevels(fInt) <- fMapInt
+ checkIdentical(fInt, f)
+
+ ## above is essentially the same as levels<-.factor
+ fInt1 <- factor(as.integer(f))
+ levels(fInt1) <- fMapInt
+ checkIdentical(fInt1, f)
+
+ ## x character, value character levelsMap
+ cha <- c("B", "A", "C")
+ chaMapCha <- as.levelsMap(list(A1="A", B2="B", C3="C"))
+ mapLevels(cha) <- chaMapCha
+ chaTest <- factor(c("B2", "A1", "C3"))
+ checkIdentical(cha, chaTest)
+ ## and a bit more for components of length > 1
+ cha <- c("G", "I", "B", "A", "C", "D", "Z")
+ chaMapCha <- as.levelsMap(list(A1=c("A", "G", "I"), B2="B", C3=c("C", "D")))
+ mapLevels(cha) <- chaMapCha
+ chaTest <- factor(c("A1", "A1", "B2", "A1", "C3", "C3", NA))
+ checkIdentical(cha, chaTest)
+
+ ## x factor, value character levelsMap
+ f <- factor(c("G", "I", "B", "A", "C", "D", "Z"))
+ fMapCha <- as.levelsMap(list(A1=c("A", "G", "I"), B2="B", C3=c("C", "D")))
+ mapLevels(f) <- fMapCha
+ fTest <- factor(c("A1", "A1", "B2", "A1", "C3", "C3", NA))
+ checkIdentical(f, fTest)
+
+ ## Two factors and character map
+ f1 <- factor(letters[1:10])
+ f2 <- factor(letters[5:14])
+ checkIdentical(as.integer(f1), as.integer(f2)) # the same integer codes
+ mapCha1 <- mapLevels(f1, codes=FALSE) # get maps
+ mapCha2 <- mapLevels(f2, codes=FALSE)
+ mapCha <- c(mapCha1, mapCha2) # combine maps
+ ## apply map
+ mapLevels(f1) <- mapCha # the same as levels(f1) <- mapCha
+ mapLevels(f2) <- mapCha # the same as levels(f2) <- mapCha
+ checkIdentical(as.integer(f1), 1:10) # \ internal codes are now
+ checkIdentical(as.integer(f2), 5:14) # / "consistent" among factors
+
+ ## The same with list
+ l <- list(f1=f1, f2=f2)
+ mapCha <- mapLevels(l, codes=FALSE, combine=TRUE)
+ mapLevels(l) <- mapCha
+ checkIdentical(as.integer(l$f1), 1:10) # \ internal codes are now
+ checkIdentical(as.integer(l$f2), 5:14) # / "consistent" among factors
+
+ ## and data.frame
+ df <- data.frame(f1=f1, f2=f2)
+ mapCha <- mapLevels(df, codes=FALSE, combine=TRUE)
+ mapLevels(df) <- mapCha
+ checkIdentical(as.integer(df$f1), 1:10) # \ internal codes are now
+ checkIdentical(as.integer(df$f2), 5:14) # / "consistent" among factors
+
+}
+
+### }}}
+### {{{ Dear Emacs
+## Local variables:
+## folded-file: t
+## End:
+### }}}
+
###------------------------------------------------------------------------
### runit.mapLevels.R ends here
Modified: trunk/gdata/man/mapLevels.Rd
===================================================================
--- trunk/gdata/man/mapLevels.Rd 2006-10-29 15:34:19 UTC (rev 990)
+++ trunk/gdata/man/mapLevels.Rd 2006-10-29 15:47:33 UTC (rev 991)
@@ -2,7 +2,7 @@
%--------------------------------------------------------------------------
% What: Mapping levels
% $Id: mapLevels.Rd,v 1.1 2006/03/29 13:47:10 ggorjan Exp ggorjan $
-% Time-stamp: <2006-08-31 02:43:29 ggorjan>
+% Time-stamp: <2006-10-15 18:36:28 ggorjan>
%--------------------------------------------------------------------------
\name{mapLevels}
@@ -144,7 +144,7 @@
applied to \dQuote{character} or \dQuote{factor}. Methods for
\dQuote{list} and \dQuote{data.frame} can work only on mentioned atomic
components/columns and can accept either \dQuote{levelsMap} or
-\dQuote{levelsMap}. Recycling occours, if length of \code{value} is not
+\dQuote{listLevelsMap}. Recycling occours, if length of \code{value} is not
the same as number of components/columns of a \dQuote{list/data.frame}.
}
Modified: trunk/gdata/tests/doRUnit.R
===================================================================
--- trunk/gdata/tests/doRUnit.R 2006-10-29 15:34:19 UTC (rev 990)
+++ trunk/gdata/tests/doRUnit.R 2006-10-29 15:47:33 UTC (rev 991)
@@ -2,7 +2,7 @@
###------------------------------------------------------------------------
### What: Run RUnit tests
### $Id$
-### Time-stamp: <2006-09-18 13:14:34 ggorjan>
+### Time-stamp: <2006-10-29 16:37:40 ggorjan>
###------------------------------------------------------------------------
if(require("RUnit", quietly=TRUE)) {
@@ -26,8 +26,7 @@
## --- Testing ---
## Define tests
- testSuite <- defineTestSuite(name=paste(pkg, "unit testing"),
- dirs=path)
+ testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), dirs=path)
## Run
tests <- runTestSuite(testSuite)
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|
|
From: <gg...@us...> - 2006-10-29 15:34:33
|
Revision: 990
http://svn.sourceforge.net/r-gregmisc/?rev=990&view=rev
Author: ggorjan
Date: 2006-10-29 07:34:19 -0800 (Sun, 29 Oct 2006)
Log Message:
-----------
sort is generic from R 2.4.0
Modified Paths:
--------------
trunk/gdata/DESCRIPTION
trunk/gdata/NAMESPACE
Modified: trunk/gdata/DESCRIPTION
===================================================================
--- trunk/gdata/DESCRIPTION 2006-10-29 15:28:26 UTC (rev 989)
+++ trunk/gdata/DESCRIPTION 2006-10-29 15:34:19 UTC (rev 990)
@@ -1,7 +1,7 @@
Package: gdata
Title: Various R programming tools for data manipulation
Description: Various R programming tools for data manipulation
-Depends: R (>= 1.9.0)
+Depends: R (>= 2.4.0)
Imports: gtools
Version: 2.3.1
Author: Gregory R. Warnes. Includes R source code and/or documentation
Modified: trunk/gdata/NAMESPACE
===================================================================
--- trunk/gdata/NAMESPACE 2006-10-29 15:28:26 UTC (rev 989)
+++ trunk/gdata/NAMESPACE 2006-10-29 15:34:19 UTC (rev 990)
@@ -25,6 +25,7 @@
unmatrix,
upperTriangle,
"upperTriangle<-",
+## write.fwf,
## mapLevels stuff
mapLevels,
@@ -32,7 +33,6 @@
as.listLevelsMap,
is.levelsMap,
is.listLevelsMap,
- sort.levelsMap, ## FIXME remove in R 2.4
"mapLevels<-",
## unknown stuff
@@ -44,15 +44,15 @@
importFrom(stats, reorder, na.omit)
importFrom(gtools, mixedsort)
-S3method(nobs,data.frame)
-S3method(nobs,default)
-S3method(nobs,lm)
+S3method(nobs, data.frame)
+S3method(nobs, default)
+S3method(nobs, lm)
S3method(trim, character)
S3method(trim, default)
S3method(trim, factor)
S3method(trim, list)
S3method(trim, data.frame)
-S3method(reorder,factor)
+S3method(reorder, factor)
S3method(drop.levels, default)
S3method(drop.levels, factor)
@@ -75,7 +75,7 @@
S3method(c, listLevelsMap)
S3method(unique, levelsMap)
-## S3method(sort, levelsMap) ## FIXME uncomment in R 2.4
+S3method(sort, levelsMap)
S3method("mapLevels<-", default)
S3method("mapLevels<-", list)
@@ -85,6 +85,7 @@
S3method(isUnknown, POSIXlt)
S3method(isUnknown, list)
S3method(isUnknown, data.frame)
+## S3method(isUnknown, matrix)
S3method(unknownToNA, default)
S3method(unknownToNA, factor)
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|
|
From: <gg...@us...> - 2006-10-29 15:28:35
|
Revision: 989
http://svn.sourceforge.net/r-gregmisc/?rev=989&view=rev
Author: ggorjan
Date: 2006-10-29 07:28:26 -0800 (Sun, 29 Oct 2006)
Log Message:
-----------
trim() gains ... argument; version bump
Modified Paths:
--------------
trunk/gdata/DESCRIPTION
trunk/gdata/NEWS
trunk/gdata/R/trim.R
trunk/gdata/man/trim.Rd
Modified: trunk/gdata/DESCRIPTION
===================================================================
--- trunk/gdata/DESCRIPTION 2006-10-29 12:55:08 UTC (rev 988)
+++ trunk/gdata/DESCRIPTION 2006-10-29 15:28:26 UTC (rev 989)
@@ -3,7 +3,7 @@
Description: Various R programming tools for data manipulation
Depends: R (>= 1.9.0)
Imports: gtools
-Version: 2.3.0
+Version: 2.3.1
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker, Gregor Gorjanc, and Thomas Lumley
Maintainer: Gregory Warnes <gre...@ur...>
Modified: trunk/gdata/NEWS
===================================================================
--- trunk/gdata/NEWS 2006-10-29 12:55:08 UTC (rev 988)
+++ trunk/gdata/NEWS 2006-10-29 15:28:26 UTC (rev 989)
@@ -8,6 +8,8 @@
reorder(trt, new.order=c("PLACEBO", "300 MG", "600 MG", "1200 MG"))
+- trim() gains ... argument.
+
CHANGES FROM 2.1.X to 2.3.0 (2006-09-19)
---------------------------------------
Modified: trunk/gdata/R/trim.R
===================================================================
--- trunk/gdata/R/trim.R 2006-10-29 12:55:08 UTC (rev 988)
+++ trunk/gdata/R/trim.R 2006-10-29 15:28:26 UTC (rev 989)
@@ -1,30 +1,34 @@
# $Id$
-trim <- function(s, recode.factor=TRUE)
+trim <- function(s, recode.factor=TRUE, ...)
UseMethod("trim", s)
-trim.default <- function(s, recode.factor=TRUE)
+trim.default <- function(s, recode.factor=TRUE, ...)
s
-trim.character <- function(s, recode.factor=TRUE)
+trim.character <- function(s, recode.factor=TRUE, ...)
{
s <- sub(pattern="^ +", replacement="", x=s)
s <- sub(pattern=" +$", replacement="", x=s)
s
}
-trim.factor <- function(s, recode.factor=TRUE)
+trim.factor <- function(s, recode.factor=TRUE, ...)
{
levels(s) <- trim(levels(s))
- if(recode.factor) s <- reorder.factor(s, sort=sort)
+ if(recode.factor) {
+ dots <- list(x=s, ...)
+ if(is.null(dots$sort)) dots$sort <- sort
+ s <- do.call(what=reorder.factor, args=dots)
+ }
s
}
-trim.list <- function(s, recode.factor=TRUE)
- lapply(s, trim, recode.factor=recode.factor)
+trim.list <- function(s, recode.factor=TRUE, ...)
+ lapply(s, trim, recode.factor=recode.factor, ...)
-trim.data.frame <- function(s, recode.factor=TRUE)
+trim.data.frame <- function(s, recode.factor=TRUE, ...)
{
- s[] <- trim.list(s, recode.factor=recode.factor)
+ s[] <- trim.list(s, recode.factor=recode.factor, ...)
s
}
Modified: trunk/gdata/man/trim.Rd
===================================================================
--- trunk/gdata/man/trim.Rd 2006-10-29 12:55:08 UTC (rev 988)
+++ trunk/gdata/man/trim.Rd 2006-10-29 15:28:26 UTC (rev 989)
@@ -6,11 +6,13 @@
related objects.
}
\usage{
-trim(s, recode.factor=TRUE)
+trim(s, recode.factor=TRUE, \ldots)
}
\arguments{
\item{s}{object to be processed}
- \item{recode.factor}{Should levels of a factor be recoded, see below}
+ \item{recode.factor}{should levels of a factor be recoded, see below}
+ \item{\ldots}{arguments passed to other methods, currently only to
+ \code{\link{reorder.factor}} for factors}
}
\details{
@@ -20,19 +22,22 @@
factor \code{s} trims \code{\link{levels}}. There are also methods for
\code{list} and \code{data.frame}.
-Trimming character strings can change the sort order in some
-locales. For factors, this can affect the coding of levels. By
-default, factor levels are recoded to match the trimmed sort order, but
-this can be disabled by setting \code{recode.factor=FALSE}.
+Trimming character strings can change the sort order in some locales.
+For factors, this can affect the coding of levels. By default, factor
+levels are recoded to match the trimmed sort order, but this can be
+disabled by setting \code{recode.factor=FALSE}. Recoding is done with
+\code{\link{reorder.factor}}.
}
\value{
\code{s} with all leading and trailing spaces removed in its elements.
}
-\author{ Gregory R. Warnes \email{wa...@bs...} with
+\author{Gregory R. Warnes \email{wa...@bs...} with
contributions by Gregor Gorjanc}
\seealso{ \code{\link[base]{sub}}, \code{\link[base]{gsub}} as well as
- argument \code{strip.white} in \code{\link{read.table}}}
+ argument \code{strip.white} in \code{\link{read.table}} and
+ \code{\link{reorder.factor}}
+}
\examples{
s <- " this is an example string "
trim(s)
@@ -43,17 +48,14 @@
trim(f)
levels(trim(f))
-trim(f,recode.factor=FALSE)
-levels(trim(f,recode.factor=FALSE))
+trim(f, recode.factor=FALSE)
+levels(trim(f, recode.factor=FALSE))
-
l <- list(s=rep(s, times=6), f=f, i=1:6)
trim(l)
df <- as.data.frame(l)
trim(df)
-
-
}
\keyword{manip}
\keyword{character}
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|
|
From: <gg...@us...> - 2006-10-29 12:55:20
|
Revision: 988
http://svn.sourceforge.net/r-gregmisc/?rev=988&view=rev
Author: ggorjan
Date: 2006-10-29 04:55:08 -0800 (Sun, 29 Oct 2006)
Log Message:
-----------
Fixed collision bug with stats version of reorder.factor
Modified Paths:
--------------
trunk/gdata/NEWS
trunk/gdata/R/reorder.R
trunk/gdata/man/reorder.Rd
Modified: trunk/gdata/NEWS
===================================================================
--- trunk/gdata/NEWS 2006-10-27 21:15:22 UTC (rev 987)
+++ trunk/gdata/NEWS 2006-10-29 12:55:08 UTC (rev 988)
@@ -1,3 +1,13 @@
+CHANGES IN 2.3.1 (2006-10-29)
+---------------------------------------
+
+- Arguments as well as their position of reorder.factor have been changed
+ to conform with reorder.factor method in stats package, due to collision
+ bug. Argument 'make.ordered' is now 'order' and old argument 'order' is
+ now 'new.order'! Therefore, you have to implicitly specify new.order i.e.
+
+ reorder(trt, new.order=c("PLACEBO", "300 MG", "600 MG", "1200 MG"))
+
CHANGES FROM 2.1.X to 2.3.0 (2006-09-19)
---------------------------------------
@@ -12,7 +22,7 @@
- Extended trim() to handle a variety of data types data.frames,
lists, factors, etc. Code changes contributed by Gregor Gorjanc.
-
+
- Added resample() command that acts like sample() except that it
_always_ samples from the arguments provided, even if only a single
argument is present. This differs from sample() which behaves
@@ -54,6 +64,4 @@
- Updated ll.Rd documentation
- - Fixed bug in Args.R, is.what.R, ll.R
-
-
+ - Fixed bug in Args.R, is.what.R, ll.R
Modified: trunk/gdata/R/reorder.R
===================================================================
--- trunk/gdata/R/reorder.R 2006-10-27 21:15:22 UTC (rev 987)
+++ trunk/gdata/R/reorder.R 2006-10-29 12:55:08 UTC (rev 988)
@@ -3,31 +3,26 @@
# Reorder the levels of a factor.
reorder.factor <- function(x,
- order,
X,
FUN,
- sort=mixedsort,
- make.ordered = is.ordered(x),
- ... )
- {
- constructor <- if (make.ordered) ordered else factor
+ ...,
+ order=is.ordered(x),
+ new.order,
+ sort=mixedsort)
+{
+ constructor <- if (order) ordered else factor
- if (!missing(order))
+ if (!missing(new.order))
{
- if (is.numeric(order))
- order = levels(x)[order]
+ if (is.numeric(new.order))
+ new.order <- levels(x)[new.order]
else
- order = order
+ new.order <- new.order
}
else if (!missing(FUN))
- order = names(sort(tapply(X, x, FUN, ...)))
+ new.order <- names(sort(tapply(X, x, FUN, ...)))
else
- order = sort(levels(x))
+ new.order <- sort(levels(x))
- constructor( x, levels=order)
-
- }
-
-
-
-
+ constructor(x, levels=new.order)
+}
Modified: trunk/gdata/man/reorder.Rd
===================================================================
--- trunk/gdata/man/reorder.Rd 2006-10-27 21:15:22 UTC (rev 987)
+++ trunk/gdata/man/reorder.Rd 2006-10-29 12:55:08 UTC (rev 988)
@@ -1,6 +1,5 @@
% $Id$
-
\name{reorder.factor}
\alias{reorder.factor}
\title{Reorder the Levels of a Factor}
@@ -9,61 +8,61 @@
}
\usage{
\method{reorder}{factor}(x,
- order,
X,
FUN,
- sort=mixedsort,
- make.ordered = is.ordered(x),
- ... )
+ ...,
+ order=is.ordered(x),
+ new.order,
+ sort=mixedsort)
}
\arguments{
- \item{x}{factor.}
- \item{order}{A vector of indexes or a vector of label names giving the
- order of the new factor levels.}
+ \item{x}{factor}
\item{X}{auxillary data vector}
\item{FUN}{function to be applied to subsets of \code{X} determined by
- \code{x}, to determine factor order.}
- \item{sort}{function to use to sort the factor level names}
- \item{make.ordered}{logical value indicating whether the returned
- object should be an \code{'ordered'} factor.}
- \item{...}{Optional parameters to FUN.}
+ \code{x}, to determine factor order}
+ \item{...}{optional parameters to \code{FUN}}
+ \item{order}{logical value indicating whether the returned
+ object should be an \code{\link{ordered}} factor}
+ \item{new.order}{a vector of indexes or a vector of label names giving
+ the order of the new factor levels}
+ \item{sort}{function to use to sort the factor level names, used only
+ when \code{new.order} is missing}
}
\details{
- This function changes the order of the levels of a factor. It can do
- so via three different mechanisms, depending on whether \code{order},
- \code{X} \emph{and} \code{FUN}, or \code{sort} are provided.
+ This function changes the order of the levels of a factor. It can do
+ so via three different mechanisms, depending on whether, \code{X}
+ \emph{and} \code{FUN}, \code{new.order} or \code{sort} are provided.
- If \code{order} is provided: For a numeric vector, the new factor level names
- are constructed by reordering the factor levels according to the
- numeric values. For vectors, \code{order} gives the list of new factor
- level names. In either case levels omitted from \code{order} will
- become missing values.
-
If \code{X} \emph{and} \code{Fun} are provided: The data in \code{X}
- is grouped by the levels of \code{data} and \code{FUN} is applied.
+ is grouped by the levels of \code{x} and \code{FUN} is applied.
The groups are then sorted by this value, and the resulting order is
used for the new factor level names.
+ If \code{new.order} is provided: For a numeric vector, the new factor
+ level names are constructed by reordering the factor levels according
+ to the numeric values. For vectors, \code{new.order} gives the list of
+ new factor level names. In either case levels omitted from
+ \code{new.order} will become missing (\code{NA}) values.
+
If \code{sort} is provided (as it is by default): The new
factor level names are generated by applying the supplied function
- to the existing factor level names. With \code{order="mixedsort"} the
+ to the existing factor level names. With \code{sort=mixedsort} the
factor levels are sorted so that combined numeric and character
strings are sorted in according to character rules on the character
- sections (including ignoring case), and be numeric rules for the
- numeric sections. See \code{mixedsort} for details.
-
+ sections (including ignoring case), and the numeric rules for the
+ numeric sections. See \code{\link[gtools]{mixedsort}} for details.
}
\value{
- A new factor with the levels ordered as specified.
+ A new factor with reordered levels
}
-\author{ Gregory R. Warnes \email{wa...@bs...}}
+\author{Gregory R. Warnes \email{wa...@bs...}}
-\seealso{ \code{\link{factor}}, \code{\link[stats]{reorder}} }
+\seealso{\code{\link{factor}} and \code{\link[stats]{reorder}}}
\examples{
# Create a 4 level example factor
- trt <- factor( sample( c("PLACEBO","300 MG", "600 MG", "1200 MG"),
+ trt <- factor( sample( c("PLACEBO", "300 MG", "600 MG", "1200 MG"),
100, replace=TRUE ) )
summary(trt)
# Note that the levels are not in a meaningful order.
@@ -73,18 +72,17 @@
trt2 <- reorder(trt)
summary(trt2)
# using indexes:
- trt3 <- reorder(trt, c(4,2,3,1))
+ trt3 <- reorder(trt, new.order=c(4, 2, 3, 1))
summary(trt3)
# using label names:
- trt4 <- reorder(trt, c("PLACEBO","300 MG", "600 MG", "1200 MG") )
+ trt4 <- reorder(trt, new.order=c("PLACEBO", "300 MG", "600 MG", "1200 MG"))
summary(trt4)
# using frequency
trt5 <- reorder(trt, X=as.numeric(trt), FUN=length)
summary(trt5)
-
# drop out the '300 MG' level
- trt6 <- reorder(trt, c("PLACEBO", "600 MG", "1200 MG") )
+ trt6 <- reorder(trt, new.order=c("PLACEBO", "600 MG", "1200 MG"))
summary(trt6)
}
\keyword{ manip }
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From: <wa...@us...> - 2006-10-27 21:15:40
|
Revision: 987
http://svn.sourceforge.net/r-gregmisc/?rev=987&view=rev
Author: warnes
Date: 2006-10-27 14:15:22 -0700 (Fri, 27 Oct 2006)
Log Message:
-----------
Add c() method for factor objects, submitted by Gregor Gorjanc
Added Paths:
-----------
trunk/gdata/R/c.factor.R
trunk/gdata/man/c.factor.Rd
Added: trunk/gdata/R/c.factor.R
===================================================================
--- trunk/gdata/R/c.factor.R (rev 0)
+++ trunk/gdata/R/c.factor.R 2006-10-27 21:15:22 UTC (rev 987)
@@ -0,0 +1,18 @@
+# $Id$
+
+c.factor <- function(...,
+ recursive=FALSE # ignored
+ )
+{
+ dots <- list(...) # recursive below is not related to one above!
+ mapCha <- c(mapLevels(dots, codes=FALSE), recursive=TRUE)
+ class(mapCha) <- "levelsMap"
+ dots <- unlist(lapply(dots, "mapLevels<-", mapCha))
+ mapLevels(dots) <- mapLevels(as.character(mapCha))
+ dots
+}
+
+
+
+
+
Added: trunk/gdata/man/c.factor.Rd
===================================================================
--- trunk/gdata/man/c.factor.Rd (rev 0)
+++ trunk/gdata/man/c.factor.Rd 2006-10-27 21:15:22 UTC (rev 987)
@@ -0,0 +1,35 @@
+%% $Id$
+
+\name{c.factor}
+\alias{c.factor}
+\title{Combine factors, properly handling levels}
+\description{
+ This method for \code{c} combines factors while properly preserves level
+ information.
+}
+\usage{
+c.factor(..., recursive = FALSE)
+}
+\arguments{
+ \item{\dots}{ factors to be combined }
+ \item{recursive}{ ignored }
+}
+\details{
+
+}
+\value{
+ A single factor object. The levels on the new object are created by
+ concatinating the levels of the provided factors, with any duplicate
+ level names merged, and with the factor coding modified appropriately.
+}
+\author{Gregor Gorjan}
+\seealso{ \code{\link[base]{c}} }
+\examples{
+f1 <- factor(letters[1:10])
+f2 <- factor(letters[5:14])
+
+c(f1,f2)
+
+}
+\keyword{manip}
+
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From: <wa...@us...> - 2006-09-19 21:09:44
|
Revision: 986
http://svn.sourceforge.net/r-gregmisc/?rev=986&view=rev
Author: warnes
Date: 2006-09-19 14:08:40 -0700 (Tue, 19 Sep 2006)
Log Message:
-----------
Update NEWS file for 2.3.0 release
Modified Paths:
--------------
trunk/gdata/NEWS
Modified: trunk/gdata/NEWS
===================================================================
--- trunk/gdata/NEWS 2006-09-19 20:52:46 UTC (rev 985)
+++ trunk/gdata/NEWS 2006-09-19 21:08:40 UTC (rev 986)
@@ -1,3 +1,25 @@
+CHANGES FROM 2.1.X to 2.3.0 (2006-09-19)
+---------------------------------------
+
+- Added mapLevels(), which produces a map with information on levels and/or
+ internal integer codes. Contributed by Gregor Gorjanc.
+
+- Extended dropLevels() to work on the factors contained in a data
+ frame, as well as individual factors.
+
+- Add unknown(), which changes given unknown value to NA and vice
+ versa. Contributed by Gregor Gorjanc.
+
+- Extended trim() to handle a variety of data types data.frames,
+ lists, factors, etc. Code changes contributed by Gregor Gorjanc.
+
+- Added resample() command that acts like sample() except that it
+ _always_ samples from the arguments provided, even if only a single
+ argument is present. This differs from sample() which behaves
+ differently in this case.
+
+- Updated my email address.
+
CHANGES IN GDATA 2.1.2
-----------------------
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From: <wa...@us...> - 2006-09-19 20:54:50
|
Revision: 985
http://svn.sourceforge.net/r-gregmisc/?rev=985&view=rev
Author: warnes
Date: 2006-09-19 13:52:46 -0700 (Tue, 19 Sep 2006)
Log Message:
-----------
Explicitly set the local in runit.trim.R to one where leading spaces affect sort order so that the unit test works properly.
Modified Paths:
--------------
trunk/gdata/inst/unitTests/runit.trim.R
Modified: trunk/gdata/inst/unitTests/runit.trim.R
===================================================================
--- trunk/gdata/inst/unitTests/runit.trim.R 2006-09-18 20:33:30 UTC (rev 984)
+++ trunk/gdata/inst/unitTests/runit.trim.R 2006-09-19 20:52:46 UTC (rev 985)
@@ -17,6 +17,9 @@
test.trim <- function()
{
+ tmp <- Sys.getlocale(category="LC_COLLATE")
+ Sys.setlocale(category="LC_COLLATE", locale="C")
+
sTrim <- " this is an example string "
sTrimR <- "this is an example string"
@@ -37,6 +40,8 @@
)
checkIdentical(trim(lTrim), lTrimR)
checkIdentical(trim(dfTrim), dfTrimR)
+
+ Sys.setlocale(category="LC_COLLATE", locale=tmp)
}
### }}}
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