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From: <wa...@us...> - 2015-04-14 22:02:44
|
Revision: 1929
http://sourceforge.net/p/r-gregmisc/code/1929
Author: warnes
Date: 2015-04-14 22:02:42 +0000 (Tue, 14 Apr 2015)
Log Message:
-----------
Update ChangeLog
Modified Paths:
--------------
trunk/gdata/inst/ChangeLog
Modified: trunk/gdata/inst/ChangeLog
===================================================================
--- trunk/gdata/inst/ChangeLog 2015-04-14 22:02:01 UTC (rev 1928)
+++ trunk/gdata/inst/ChangeLog 2015-04-14 22:02:42 UTC (rev 1929)
@@ -1,5 +1,8 @@
2015-04-14 warnes
+ * [r1928] man/write.fwf.Rd: Remove editorializing
+ * [r1927] inst/ChangeLog, inst/NEWS: Update NEWS and ChangeLog for
+ gdata 2.15.0
* [r1926] R/write.fwf.R, man/write.fwf.Rd: Add 'scientific'
argument to write.fwf to allow control of whether numeric values
can be displated using scientific notation.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2015-04-14 22:02:04
|
Revision: 1928
http://sourceforge.net/p/r-gregmisc/code/1928
Author: warnes
Date: 2015-04-14 22:02:01 +0000 (Tue, 14 Apr 2015)
Log Message:
-----------
Remove editorializing
Modified Paths:
--------------
trunk/gdata/man/write.fwf.Rd
Modified: trunk/gdata/man/write.fwf.Rd
===================================================================
--- trunk/gdata/man/write.fwf.Rd 2015-04-14 21:55:54 UTC (rev 1927)
+++ trunk/gdata/man/write.fwf.Rd 2015-04-14 22:02:01 UTC (rev 1928)
@@ -64,9 +64,7 @@
\details{
While *F*ixed *w*idth *f*ormat is no longer widely used, it remains
-common in some disciplines. When possible, we recommend using
-standardized format (e.g. *c*omma *s*eparated *v*alues; see
-\code{\link{read.csv}}) when possible.
+common in some disciplines.
Output is similar to \code{print(x)} or \code{format(x)}. Formatting is
done completely by \code{\link{format}} on a column basis. Columns in
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2015-04-14 21:56:01
|
Revision: 1927
http://sourceforge.net/p/r-gregmisc/code/1927
Author: warnes
Date: 2015-04-14 21:55:54 +0000 (Tue, 14 Apr 2015)
Log Message:
-----------
Update NEWS and ChangeLog for gdata 2.15.0
Modified Paths:
--------------
trunk/gdata/inst/ChangeLog
trunk/gdata/inst/NEWS
Modified: trunk/gdata/inst/ChangeLog
===================================================================
--- trunk/gdata/inst/ChangeLog 2015-04-14 21:52:53 UTC (rev 1926)
+++ trunk/gdata/inst/ChangeLog 2015-04-14 21:55:54 UTC (rev 1927)
@@ -1,3 +1,12 @@
+2015-04-14 warnes
+
+ * [r1926] R/write.fwf.R, man/write.fwf.Rd: Add 'scientific'
+ argument to write.fwf to allow control of whether numeric values
+ can be displated using scientific notation.
+ * [r1925] inst/perl/xls2csv.pl: Replace depricated PERL function
+ POSIX::isnumeric with equivalent regexp
+ * [r1924] inst/ChangeLog: Add gdata ChangeLog to SVN
+
2015-04-10 warnes
* [r1922] DESCRIPTION, NAMESPACE, inst/NEWS: Update files for gdata
Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS 2015-04-14 21:52:53 UTC (rev 1926)
+++ trunk/gdata/inst/NEWS 2015-04-14 21:55:54 UTC (rev 1927)
@@ -9,7 +9,16 @@
- New functions left() and right() to return the leftmost or
rightmost n (default to 6) columns of a matrix or dataframe.
+- New 'scienfic' argument to write.fwf(). Set 'scientific=FALSE' to
+ prevent numeric columns from being displayed using scientific
+ notification.
+Other changes:
+
+- Replaced depricated PERL function POSIX::isdigit with equivalent
+ regular expression.
+
+
Changes in 2.14.0 (2014-08-27)
------------------------------
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2015-04-14 21:53:00
|
Revision: 1926
http://sourceforge.net/p/r-gregmisc/code/1926
Author: warnes
Date: 2015-04-14 21:52:53 +0000 (Tue, 14 Apr 2015)
Log Message:
-----------
Add 'scientific' argument to write.fwf to allow control of whether numeric values can be displated using scientific notation.
Modified Paths:
--------------
trunk/gdata/R/write.fwf.R
trunk/gdata/man/write.fwf.Rd
Modified: trunk/gdata/R/write.fwf.R
===================================================================
--- trunk/gdata/R/write.fwf.R 2015-04-14 20:52:26 UTC (rev 1925)
+++ trunk/gdata/R/write.fwf.R 2015-04-14 21:52:53 UTC (rev 1926)
@@ -20,6 +20,7 @@
width=NULL,
eol="\n",
qmethod=c("escape", "double"),
+ scientific=TRUE,
...)
{
## --- Setup ---
@@ -29,6 +30,14 @@
if(length(na) > 1)
stop("only single value can be defined for 'na'")
+ if(!scientific)
+ {
+ option.scipen <- getOption("scipen")
+ on.exit( function() options("scipen"=option.scipen) )
+ options("scipen"=100)
+ }
+
+
if(rownames) {
x <- cbind(rownames(x), x)
rowColVal <- ifelse(!is.null(rowCol), rowCol, "row")
Modified: trunk/gdata/man/write.fwf.Rd
===================================================================
--- trunk/gdata/man/write.fwf.Rd 2015-04-14 20:52:26 UTC (rev 1925)
+++ trunk/gdata/man/write.fwf.Rd 2015-04-14 21:52:53 UTC (rev 1926)
@@ -23,7 +23,7 @@
write.fwf(x, file="", append=FALSE, quote=FALSE, sep=" ", na="",
rownames=FALSE, colnames=TRUE, rowCol=NULL, justify="left",
formatInfo=FALSE, quoteInfo=TRUE, width=NULL, eol="\n",
- qmethod=c("escape", "double"), \dots)
+ qmethod=c("escape", "double"), scientific=TRUE, \dots)
}
@@ -54,6 +54,8 @@
'"escape"' (default), in which case the quote character is
escaped in C style by a backslash, or '"double"', in which
case it is doubled. You can specify just the initial letter.}
+ \item{scientific}{logical, if TRUE, allow numeric values to be
+ formatted using scientific notation.}
\item{\dots}{further arguments to
\code{\link{format.info}} and \code{\link{format}}
}
@@ -61,10 +63,10 @@
\details{
-*F*ixed *w*idth *f*ormat is not used widely anymore. Use some other
-format (say *c*omma *s*eparated *v*alues; see \code{\link{read.csv}}) if
-you can. However, if you need fixed width format then \code{write.fwf}
-can help you.
+While *F*ixed *w*idth *f*ormat is no longer widely used, it remains
+common in some disciplines. When possible, we recommend using
+standardized format (e.g. *c*omma *s*eparated *v*alues; see
+\code{\link{read.csv}}) when possible.
Output is similar to \code{print(x)} or \code{format(x)}. Formatting is
done completely by \code{\link{format}} on a column basis. Columns in
@@ -217,15 +219,22 @@
## Force wider columns
write.fwf(x=testData[, 1:5], width=20)
+ ## Show effect of 'scienfic' option
+ testData$num3 <- testData$num3 * 1e8
+ write.fwf(testData, scientific=TRUE)
+ write.fwf(testData, scientific=FALSE)
+ testData$num3 <- testData$num3 / 1e8
+
## Write to file and report format and fixed width information
file <- tempfile()
formatInfo <- write.fwf(x=testData, file=file, formatInfo=TRUE)
+ formatInfo
## 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)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2015-04-14 20:52:29
|
Revision: 1925
http://sourceforge.net/p/r-gregmisc/code/1925
Author: warnes
Date: 2015-04-14 20:52:26 +0000 (Tue, 14 Apr 2015)
Log Message:
-----------
Replace depricated PERL function POSIX::isnumeric with equivalent regexp
Modified Paths:
--------------
trunk/gdata/inst/perl/xls2csv.pl
Modified: trunk/gdata/inst/perl/xls2csv.pl
===================================================================
--- trunk/gdata/inst/perl/xls2csv.pl 2015-04-14 19:43:15 UTC (rev 1924)
+++ trunk/gdata/inst/perl/xls2csv.pl 2015-04-14 20:52:26 UTC (rev 1925)
@@ -118,7 +118,7 @@
if(defined($ARGV[2]) )
{
- if ( isdigit($ARGV[2]) )
+ if ( $ARGV[2] =~ m|^\d+$| )
{
$sheetnumber = $ARGV[2];
die "Sheetnumber must be an integer larger than 0.\n" if $sheetnumber < 1;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2015-04-14 19:43:26
|
Revision: 1924
http://sourceforge.net/p/r-gregmisc/code/1924
Author: warnes
Date: 2015-04-14 19:43:15 +0000 (Tue, 14 Apr 2015)
Log Message:
-----------
Add gdata ChangeLog to SVN
Added Paths:
-----------
trunk/gdata/inst/ChangeLog
Added: trunk/gdata/inst/ChangeLog
===================================================================
--- trunk/gdata/inst/ChangeLog (rev 0)
+++ trunk/gdata/inst/ChangeLog 2015-04-14 19:43:15 UTC (rev 1924)
@@ -0,0 +1,1695 @@
+2015-04-10 warnes
+
+ * [r1922] DESCRIPTION, NAMESPACE, inst/NEWS: Update files for gdata
+ 2.15.0
+
+2015-04-08 warnes
+
+ * [r1919] R/first.R, man/first.Rd, man/left.Rd: Move
+ first/last/left/right to from gtools to gdata
+
+2014-08-28 warnes
+
+ * [r1883] R/trim.R, inst/NEWS, inst/perl/xls2csv.pl,
+ inst/xls/ExampleExcelFile.xls, inst/xls/ExampleExcelFile.xlsx,
+ inst/xls/ExampleExcelFile_1900.xls,
+ inst/xls/ExampleExcelFile_1900.xlsx,
+ inst/xls/ExampleExcelFile_1904.xls,
+ inst/xls/ExampleExcelFile_1904.xlsx, tests/test.read.xls.R,
+ tests/test.read.xls.Rout.save, tests/tests.write.fwf.Rout.save:
+ Everything works now!
+ * [r1882] inst/perl/Spreadsheet/ParseExcel/FmtDefault.pm: Suppress
+ annoying warnings in Spreadsheet::ParseXLS::FmtDefalt.
+ * [r1881] inst/xls/ExampleExcelFile_1900.xls,
+ inst/xls/ExampleExcelFile_1900.xlsx,
+ inst/xls/ExampleExcelFile_1904.xls,
+ inst/xls/ExampleExcelFile_1904.xlsx, tests/test.read.xls.R: Add
+ tests and corresponding test files for 1900 and 1904 based
+ XLX/XLSX files
+ * [r1880] inst/perl/Spreadsheet/XLSX,
+ inst/perl/Spreadsheet/XLSX.pm, inst/perl/install_modules.pl,
+ inst/perl/module_tools.pl, inst/perl/sheetCount.pl,
+ inst/perl/supportedFormats.pl: Complete transition from
+ Spreadsheet::XLSX to Spreadsheet::ParseXLSX
+ * [r1879] inst/perl/xls2csv.pl: Handle Excel files created on the
+ Mac, where by default Excel uses
+ 1904-01-01 as the baseline for dates, rather than the usual
+ 1900-01-01.
+ * [r1878] inst/perl/Crypt/.exists, inst/perl/XML/.exists: Remove
+ dotfiles
+ * [r1877] DESCRIPTION, inst/NEWS: Update for release
+ * [r1876] inst/xls/wide.xls, inst/xls/wide.xlsx: Add test for
+ handling fo very wide xls and xlsx files.
+ * [r1875] tests/test.read.xls.R: Add test for handling fo very wide
+ xls and xlsx files.
+ * [r1874] inst/perl/module_tools.pl, inst/perl/sheetCount.pl,
+ inst/perl/xls2csv.pl: Modify code to use latest version of
+ Spreadsheet::ParseExcel and to replace Spreadsheet::XLSX woth
+ Spreadsheet::ParseXLSX
+ * [r1873] inst/perl/Crypt, inst/perl/Crypt/.exists,
+ inst/perl/Crypt/RC4.pm, inst/perl/Digest, inst/perl/Digest/Perl,
+ inst/perl/Digest/Perl/MD5.pm, inst/perl/Graphics,
+ inst/perl/Graphics/ColorUtils.pm,
+ inst/perl/Spreadsheet/ParseExcel.pm,
+ inst/perl/Spreadsheet/ParseExcel/Cell.pm,
+ inst/perl/Spreadsheet/ParseExcel/Dump.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtDefault.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtJapan.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtJapan2.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtUnicode.pm,
+ inst/perl/Spreadsheet/ParseExcel/Font.pm,
+ inst/perl/Spreadsheet/ParseExcel/Format.pm,
+ inst/perl/Spreadsheet/ParseExcel/SaveParser.pm,
+ inst/perl/Spreadsheet/ParseExcel/SaveParser/Workbook.pm,
+ inst/perl/Spreadsheet/ParseExcel/SaveParser/Worksheet.pm,
+ inst/perl/Spreadsheet/ParseExcel/Utility.pm,
+ inst/perl/Spreadsheet/ParseExcel/Workbook.pm,
+ inst/perl/Spreadsheet/ParseExcel/Worksheet.pm,
+ inst/perl/Spreadsheet/ParseXLSX.pm,
+ inst/perl/Spreadsheet/XLSX.pm, inst/perl/XML,
+ inst/perl/XML/.exists, inst/perl/XML/Twig, inst/perl/XML/Twig.pm,
+ inst/perl/XML/Twig/XPath.pm: Update Spreadsheet::ParseExcel, add
+ Spreadsheet:ParseXLSX, add dependencies
+
+2014-04-05 warnes
+
+ * [r1801] tests/unitTests/runit.unknown.R: Apply same changes to
+ NAToUnknown that were previously applied to
+ unknownToNA for POSIXlt.
+ * [r1800] inst/NEWS: Update NEWS with latest changes
+ * [r1799] R/nobs.R: Call stats::nobs instead of
+ stats:::nobs.default within
+ gdata::nobs.default. This avoids R CMD check warning.
+ * [r1798] tests/unitTests/runit.unknown.R: Don't compare optional
+ POSIXlt field. Explicitly compare POSIXlt, with special handling
+ of '-1' unknown value.
+ * [r1797] R/mapLevels.R, R/unknown.R: Don't use gdata:::<foo>
+ prefix to access gdata function <foo>
+ * [r1796] DESCRIPTION: Fix syntax error in DESCRIPTION file.
+ * [r1795] tests/runRUnitTests.R: Package name needs to be defined
+ outside of if test.
+ * [r1794] vignettes/Rnews.sty: Style file needed
+ * [r1793] R/unknown.R, tests/unitTests/runit.unknown.R: The issue
+ Brian pointed out was an error in the isUnknown() code, not an
+ error in the unit tests!
+ * [r1792] tests/unitTests/runit.unknown.R: Apply changes Brian
+ recommned to NAtoUnknown as well as unknownToNA.
+ * [r1791] inst/NEWS: Update NEWS file
+ * [r1790] inst/doc/Rnews.dtx: Don't need latex .dtx source file
+ * [r1789] inst/doc/mapLevels.Rnw, inst/doc/unknown.Rnw, vignettes,
+ vignettes/mapLevels.Rnw, vignettes/unknown.Rnw: Move vignettes
+ from inst/doc/ to vignettes/
+ * [r1788] R/aggregate.table.R, man/aggregate.table.Rd,
+ man/gdata-defunct.Rd: Change 'aggregate.table' from deprecated to
+ defunct.
+ * [r1787] DESCRIPTION, inst/unitTests, man/gdata-package.Rd,
+ tests/runRUnitTests.R, tests/unitTests: Complete changes so that
+ the unit tests are run as part of R CMD check
+ * [r1786] DESCRIPTION, inst/NEWS: Update NEWS for gdata 2.13.4
+ * [r1785] NAMESPACE: Update NAMESPACE file to remove deleted
+ function
+ * [r1784] inst/unitTests/Makefile, inst/unitTests/runit.bindData.R,
+ inst/unitTests/runit.cbindX.R,
+ inst/unitTests/runit.drop.levels.R,
+ inst/unitTests/runit.getDateTimeParts.R,
+ inst/unitTests/runit.mapLevels.R, inst/unitTests/runit.nPairs.R,
+ inst/unitTests/runit.reorder.factor.R,
+ inst/unitTests/runit.trim.R, inst/unitTests/runit.trimSum.R,
+ inst/unitTests/runit.unknown.R,
+ inst/unitTests/runit.wideByFactor.R,
+ inst/unitTests/runit.write.fwf.R, tests/Makefile,
+ tests/runRUnitTests.R, tests/runit.bindData.R,
+ tests/runit.cbindX.R, tests/runit.drop.levels.R,
+ tests/runit.getDateTimeParts.R, tests/runit.mapLevels.R,
+ tests/runit.nPairs.R, tests/runit.reorder.factor.R,
+ tests/runit.trim.R, tests/runit.trimSum.R, tests/runit.unknown.R,
+ tests/runit.wideByFactor.R, tests/runit.write.fwf.R: Move unit
+ test files back to inst/unitTests. Fix up runRUnitTests.R to work
+ properly in the new location
+ * [r1783] tests/runit.unknown.R: - For unit tests, don't check for
+ equality of optional POSIXlt
+ components. (Bug reported by Brian Ripley).
+ * [r1782] R/runRUnitTests.R, inst/unitTests/Makefile,
+ inst/unitTests/runRUnitTests.R, inst/unitTests/runit.bindData.R,
+ inst/unitTests/runit.cbindX.R,
+ inst/unitTests/runit.drop.levels.R,
+ inst/unitTests/runit.getDateTimeParts.R,
+ inst/unitTests/runit.mapLevels.R, inst/unitTests/runit.nPairs.R,
+ inst/unitTests/runit.reorder.factor.R,
+ inst/unitTests/runit.trim.R, inst/unitTests/runit.trimSum.R,
+ inst/unitTests/runit.unknown.R,
+ inst/unitTests/runit.wideByFactor.R,
+ inst/unitTests/runit.write.fwf.R, man/runRUnitTests.Rd,
+ tests/Makefile, tests/runRUnitTests.R, tests/runit.bindData.R,
+ tests/runit.cbindX.R, tests/runit.drop.levels.R,
+ tests/runit.getDateTimeParts.R, tests/runit.mapLevels.R,
+ tests/runit.nPairs.R, tests/runit.reorder.factor.R,
+ tests/runit.trim.R, tests/runit.trimSum.R, tests/runit.unknown.R,
+ tests/runit.wideByFactor.R, tests/runit.write.fwf.R: Move unit
+ test code into the (now) standard location
+
+2014-03-19 arnima
+
+ * [r1777] R/keep.R: change warning message to R standards
+
+2013-12-18 arnima
+
+ * [r1758] R/ll.R: Retain original list order unless sort=FALSE;
+ also stop if unnamed list
+
+2013-12-16 warnes
+
+ * [r1757] R/trim.R: Trim will now remove all types of
+ leading/trailing whitespace by using
+ the [:blank:] character class.
+
+2013-06-29 warnes
+
+ * [r1692] inst/NEWS: Update NEWS for second try for gdata 2.13.2
+ * [r1691] R/ll.R: Simplify ll() by stuffing list arguments into an
+ environment, avoiding the need to use attach/detach.
+
+2013-06-28 warnes
+
+ * [r1685] inst/NEWS: Update NEWS for gdata 2.13.2
+ * [r1684] tests/test.read.xls.Rout.save,
+ tests/tests.write.fwf.Rout.save: Minor update to
+ tests/*.Rout.save
+ * [r1683] R/ll.R: Add on.exit() handler to ensure a matching detach
+ occurs when attach is used in ll()
+ * [r1682] DESCRIPTION: Update for gdata 2.13.2
+ * [r1681] R/aggregate.table.R: Improve deprecated message
+
+2013-03-24 warnes
+
+ * [r1645] tests/test.read.xls.Rout.save,
+ tests/tests.write.fwf.Rout.save: Update test files for code
+ changes
+ * [r1644] inst/NEWS: Fix formatting in NEWS
+ * [r1643] DESCRIPTION, inst/NEWS, man/read.xls.Rd,
+ man/sheetCount.Rd, tests/test.read.xls.R: Replaced calls to
+ depreciated function ".path.package" with the new public function
+ "path.package".
+
+2013-01-14 warnes
+
+ * [r1639] R/installXLSXsupport.R, R/sheetCount.R, R/xls2sep.R,
+ R/xlsFormats.R: Replace (obsolete) '.path.package' with
+ 'find.package' function.
+
+2012-09-20 warnes
+
+ * [r1622] man/MedUnits.Rd, man/ans.Rd, man/duplicated2.Rd: Correct
+ .Rd file errors detected by 'R CMD check'.
+ * [r1621] NAMESPACE: Add duplicated() and ans() to the NAMESPACE.
+ * [r1620] DESCRIPTION, inst/NEWS: Update for gdata 2.13.0.
+ * [r1619] man/ConvertMedUnits.Rd: Fix typographic error.
+ * [r1618] R/ans.R, R/duplicated2.R, man/ans.Rd, man/duplicated2.Rd:
+ Add 'ans()' and 'duplicated()' contributed by Liviu Andronic.
+
+2012-09-19 warnes
+
+ * [r1617] data/MedUnits.rda: Correct column names. Unit columns
+ were reversed and misspelled.
+ * [r1616] R/sheetCount.R: Add ignore.stderr to system command in
+ sheetCmd() to prevent stderr
+ messages from being included in the captured output from the perl
+ script.
+
+2012-09-12 warnes
+
+ * [r1606] DESCRIPTION, inst/NEWS: Update for gdata 2.12.0
+ * [r1605] R/aggregate.table.R, man/aggregate.table.Rd:
+ 'stats::aggregate' was made into a generic on 27-Jan-2010, so
+ that
+ attempting to call 'aggregate' on a 'table' object will now
+ incorrectly call 'aggregate.table'. Since 'aggregate.table' can
+ be
+ replaced by a call to tapply using two index vectors, e.g.
+ aggregate.table(x, by1=a, by2=b, mean)
+ can be replaced by
+ tapply(x, INDEX=list(a, b), FUN=mean),
+ the 'aggregate.table' function will now display a warning that it
+ is depreciated and recommending the equivalent call to tapply. It
+ will be removed entirely in a future version of gdata.
+ * [r1604] .Rinstignore: Don't ignore .Rnw files, but do ignore .svn
+ files.
+
+2012-09-11 warnes
+
+ * [r1603] man/interleave.Rd: Clarify workding of DROP argument to
+ interleave().
+ * [r1602] man/interleave.Rd: Replace call to aggregate.table() with
+ equivalent tapply() call since aggregate.table() is being
+ depreciated.
+
+2012-08-22 warnes
+
+ * [r1601] DESCRIPTION, inst/NEWS: Update DESCRIPTION and NEWS for
+ gdate 2.11.1.
+ * [r1600] man/read.xls.Rd: Add example for read.xls() that shows
+ how to use the fileEncoding
+ argument to read in latin-1 encoded data.
+ * [r1599] tests/latin-1.xls, tests/test.read.xls.R,
+ tests/test.read.xls.Rout.save: Add XLSX test for latin-1
+ characters, and look for them in their new
+ location in inst/xls/.
+ * [r1598] inst/xls/latin-1.xls, inst/xls/latin-1.xlsx: add XLSX
+ version of latin-1.xls
+ * [r1597] tests/latin-1.xls, tests/test.read.xls.R,
+ tests/test.read.xls.Rout.save: Add test file and code to ensure
+ that read.xls() can properly handle
+ files with alternative encodings. latin-1.xls contains each of
+ the
+ non-ascii latin-1 special characters in both the column headings
+ and
+ the body of the file.
+ * [r1596] R/read.xls.R: Change code to have R read the csv/tab data
+ from the file rather than
+ from the connetion we made, so that file encodings can be
+ properly handled.
+ * [r1595] R/read.xls.R: Always close the connection.
+
+2012-08-13 warnes
+
+ * [r1594] inst/perl/xls2csv.pl: Remove trailing space from output
+ line.
+
+2012-06-18 warnes
+
+ * [r1567] inst/NEWS: Update NEWS for 2.11.0 release.
+ * [r1566] DESCRIPTION: Bump version number and add
+ SystemRequirements for perl.
+ * [r1565] R/xls2sep.R, inst/perl/xls2csv.pl, man/read.xls.Rd,
+ tests/test.read.xls.R, tests/test.read.xls.Rout.save: read.xls()
+ and supporting functions now allow blank lines to be
+ preserved, rather than skipped, by supplying the argument
+ "blank.lines.skip=FALSE". The underlying perl function has been
+ extended to suppor this via an optional "-s" argument which, when
+ present, *preserves* blank lines during the conversion.
+
+2012-06-13 warnes
+
+ * [r1564] DESCRIPTION, R/nobs.R, inst/NEWS: - nobs.default needs to
+ handle logical vectors in addition to numeric
+ vectors.
+ - update DESCRIPTION and NEWS for 2.10.6.
+ * [r1563] R/nobs.R: nobs.default needs to handle logical as well as
+ numeric vectors.
+
+2012-06-08 warnes
+
+ * [r1562] DESCRIPTION, tests/test.read.xls.Rout.save: Update
+ DESCRIPTION and tests
+ * [r1561] tests/test.read.xls.R: fix incorrect function name
+ * [r1560] DESCRIPTION, man/installXLSXsupport.Rd: Mark example for
+ installXLSXsupport() to not be executed durin R CMD check.
+ * [r1559] DESCRIPTION: stats:::nobs.default and stats::nobs.lm
+ require R > 2.13.0, so add this as a dependency.
+
+2012-06-06 warnes
+
+ * [r1552] DESCRIPTION, inst/NEWS: Update for release 2.10.2
+ * [r1551] R/nobs.R: Fix bugs in nobs.default.
+ * [r1550] tests/test.read.xls.Rout.save,
+ tests/tests.write.fwf.Rout.save: Update to reflect warning on
+ startup that 'nobs' hides 'stats::nobs'.
+ * [r1549] man/nobs.Rd: Remove stray non-ASCII characters.
+ * [r1548] R/nobs.R: The nobs() dispatch method must be defined in
+ the gdata namespace to
+ pick up the definition of gdata::nobs.default.
+ * [r1547] DESCRIPTION, inst/NEWS: Update DESCRIPTION and NEWS for
+ 2.10.1 release.
+ * [r1546] NAMESPACE, R/nobs.R, man/nobs.Rd: Define aliases for
+ 'nobs' and 'nobs.lm' to support backward
+ compatibility for packages depending on gdata.
+ * [r1545] DESCRIPTION, inst/NEWS: Update DESCRIPTION and NEWS for
+ 2.10.0 release
+ * [r1544] NAMESPACE, R/startsWith.R, man/startsWith.Rd: - Add
+ manual page and NAMESPACE entry for startsWith().
+ - Add 'ignore.case' argument to startsWith().
+ * [r1543] tests/test.read.xls.Rout.save: Update to match new code.
+ * [r1542] man/read.xls.Rd: Replace non-ASCII characters.
+ * [r1541] R/read.xls.R, man/read.xls.Rd, tests/test.read.xls.R: Add
+ na.strings to read.xls call to convert "#DIV/0!" to NA.
+
+2012-06-05 warnes
+
+ * [r1540] NAMESPACE: Remove nobs method dispatch and lm methods
+ since these are now provided by the stats package.
+ * [r1539] R/env.R: Spell out arguments to ls() to avoid R CMD check
+ warnings.
+ * [r1538] .Rinstignore: Add .Rinstignore file to omit latex style
+ and source files from distributed inst/doc directory.
+ * [r1537] R/ConvertMedUnits.R: - Add NULL definition of MedUnits to
+ avoid R CMD check warning.
+ - Specify local environment when calling data() so that MedUnits
+ gets
+ defined in the function's environment rather than the global
+ environment.
+ * [r1536] R/ls.funs.R: Fix error in ls.funs() that occurs when
+ there are no objects in the environment.
+ * [r1535] R/object.size.R: Avoid warning by calling
+ utils::object.size rather than Internal(object.size(x))
+
+2012-05-31 warnes
+
+ * [r1534] R/nobs.R, man/nobs.Rd: - Remove dispatch function 'nobs'
+ and method 'nobs.lm' since these are
+ now provided by the R 'stats' package.
+
+2012-05-04 warnes
+
+ * [r1532] DESCRIPTION: Update for next release
+ * [r1531] NAMESPACE, R/ls.funs.R, man/ls.funs.Rd: Add ls.funs() to
+ show functions defined in the specified environment.
+ * [r1530] man/is.what.Rd: Fix enumerate syntax.
+
+2012-04-03 warnes
+
+ * [r1522] R/startsWith.R: Add startsWith() function.
+
+2011-10-05 warnes
+
+ * [r1516] man/read.xls.Rd: Fix typo
+
+2011-09-30 warnes
+
+ * [r1515] inst/NEWS: Update DESCRIPTION and README for 2.9.0
+ release.
+ * [r1514] DESCRIPTION: Update DESCRIPTION and README for 2.9.0
+ release.
+
+2011-09-20 warnes
+
+ * [r1508] man/read.xls.Rd: Improve xls2csv() man page
+ * [r1507] NAMESPACE: Add case() function, a vector equivalent of
+ the switch() function
+ * [r1506] R/case.R, man/case.Rd: Add case() function, a vector
+ equivalent of the switch() function
+
+2011-09-02 warnes
+
+ * [r1500] NAMESPACE: Add 'centerText' function to center text
+ strings for a specified width.
+ * [r1499] R/centerText.R, man/centerText.Rd: Add 'centerText'
+ function to center text strings for a specified width.
+
+2011-04-16 warnes
+
+ * [r1469] DESCRIPTION, inst/NEWS: Update for release 2.8.2
+
+2011-04-15 warnes
+
+ * [r1468] R/dQuote.ascii.R, R/installXLSXsupport.R, R/read.xls.R,
+ R/sheetCount.R, R/xls2sep.R: Fix errors on windows when R or Perl
+ install path includes spaces by properly quoting the path.
+ * [r1467] R/xlsFormats.R: Fix error in xlsFormat() on windows when
+ R or Perl install path includes spaces by quoting the path.
+
+2011-01-15 ggorjan
+
+ * [r1465] NAMESPACE, R/nPairs.R, inst/NEWS,
+ inst/unitTests/runit.nPairs.R, man/nPairs.Rd: Adding summary
+ method for nPairs
+
+2010-11-12 warnes
+
+ * [r1462] inst/NEWS: Update NEWS for gdata 2.8.1
+ * [r1461] DESCRIPTION: Update DEScription file for 2.8.1 release
+ * [r1460] tests/test.read.xls.Rout.save,
+ tests/tests.write.fwf.Rout.save: Update test output to match
+ latest code
+ * [r1459] R/write.fwf.R, man/write.fwf.Rd,
+ tests/test.write.fwf.eol.R: Modify write.fwf() to capture and
+ pass on additional arguments for
+ write.table(). This resolves a bug reported by Jan Wijffels.
+
+2010-11-01 arnima
+
+ * [r1453] man/Args.Rd: Minor improvement in Args.Rd help page
+
+2010-10-19 warnes
+
+ * [r1452] R/onAttach.R, R/xls2sep.R: Avoid use of file.access()
+ which is unreliable on Windows network shares.
+
+2010-07-08 ggrothendieck2
+
+ * [r1448] R/xls2sep.R: findPerl call added to xls2sep
+
+2010-07-07 ggrothendieck2
+
+ * [r1447] man/read.xls.Rd: small improvements to read.xls.Rd
+
+2010-05-03 warnes
+
+ * [r1439] NAMESPACE, R/installXLSXModules.R,
+ R/installXLSXsupport.R, R/onAttach.R, inst/NEWS,
+ man/installXLSXsupport.Rd, man/xlsFormats.Rd: Rename
+ installXLSXModules() to installXLSXsupport() and provide
+ documentation for it.
+ * [r1438] inst/NEWS: Update news for gdata 2.8.0
+ * [r1437] DESCRIPTION, NAMESPACE, R/installXLSXModules.R,
+ R/onAttach.R, inst/perl/install_modules.pl,
+ inst/perl/module_tools.pl, tests/test.read.xls.R: Add .onAttach
+ function to check & inform user if perl is available, to check
+ whether XLS and XLSX formats are avaiable, and to run the (new)
+ installXLSXModules() functon to attempt to install the necessar
+ libraries if not. Added installXLSXModules() function.
+
+2010-05-02 warnes
+
+ * [r1436] man/xlsFormats.Rd: Correct error in xlsFormat example
+ * [r1435] DESCRIPTION, NAMESPACE, R/dQuote.ascii.R, R/findPerl.R,
+ R/read.xls.R, R/xlsFormats.R, inst/doc/gregmisc.tex,
+ inst/perl/install_modules.pl, inst/perl/module_tools.pl,
+ inst/perl/sheetCount.pl, inst/perl/supportedFormats.pl,
+ inst/perl/xls2csv.pl, man/ConvertMedUnits.Rd,
+ man/aggregate.table.Rd, man/combine.Rd, man/interleave.Rd,
+ man/matchcols.Rd, man/nobs.Rd, man/read.xls.Rd,
+ man/rename.vars.Rd, man/reorder.Rd, man/resample.Rd,
+ man/sheetCount.Rd, man/trim.Rd, man/unmatrix.Rd,
+ man/upperTriangle.Rd, man/xlsFormats.Rd, src,
+ tests/test.read.xls.R, tests/test.read.xls.Rout.save,
+ tests/tests.write.fwf.Rout.save: Update perl code to work (but
+ generate warnings) when Zlib or SpreadSheet::XLXS is not
+ instaled. Also update Greg's email address
+
+2010-02-21 ggrothendieck2
+
+ * [r1423] R/read.xls.R, man/read.xls.Rd: isOpen problems fixed
+ (isOpen must have changed in R since this worked in earlier
+ versions). Also nba.xls link in read.xls.Rd disappeared. Replaced
+ with similar link.
+
+2010-02-20 ggrothendieck2
+
+ * [r1422] INSTALL: improved INSTALL file
+
+2010-02-19 ggrothendieck2
+
+ * [r1421] INSTALL, R/dQuote.ascii.R, R/read.xls.R, R/sheetCount.R,
+ inst/NEWS: added findPerl to locate ActiveState Perl on Windows
+ if perl= not specified and Rtools perl would have otherwise been
+ used. Also added INSTALL file.
+
+2010-01-28 warnes
+
+ * [r1419] DESCRIPTION, inst/NEWS: Update for release 2.7.1
+ * [r1418] R/xls2sep.R: xls2sep(): Show output of perl call when
+ verbose=T
+ * [r1417] src/build.bat: More Win32 fixes
+ * [r1416] src/Makefile, src/Makefile.win, src/build.bat: More work
+ on Win32 building
+ * [r1415] src/Makefile, src/Makefile.win, src/build.bat: Support
+ building Compress::Raw::Zlib perl package under windows.
+
+2010-01-26 warnes
+
+ * [r1413] inst/NEWS: Fix typos
+ * [r1412] R/sheetCount.R: Show more details in sheetCount() when
+ verbose=TRUE
+
+2010-01-24 warnes
+
+ * [r1411] R/xls2sep.R: Replace two calls to 'dQuote', to
+ 'dQuote.ascii'
+ * [r1408] inst/doc/mapLevels.pdf, inst/doc/unknown.pdf: Remove
+ auto-generated pdf files from svn
+ * [r1407] src/Makefile: create 'distclean' to remove perl binary
+ dir, currently mac-only
+ * [r1406] R/read.xls.R, R/xls2sep.R: Make read.xls() and xls2sep()
+ quieter when verbose=FALSE
+ * [r1405] tests/test.read.xls.R, tests/test.read.xls.Rout.save: Add
+ tests for read.xls, sheetCount, and sheetNames
+ * [r1404] src/Makefile: Modify makefile to 1) clean up after build,
+ 2) make tar non-verbose
+ * [r1403] R/read.xls.R, R/sheetCount.R: Close connections when
+ done.
+ * [r1402] man/read.xls.Rd: Fix typo
+ * [r1401] man/read.xls.Rd, man/sheetNames.Rd: Fix R CMD CHECK
+ errors
+ * [r1400] src/Compress-Raw-Zlib-2.024,
+ src/Compress-Raw-Zlib-2.024.tar.gz, src/Makefile: Use the
+ original gz file for Compress::Raw::Zlib to avoid issues with
+ 'non-platform-independent' filename error in R CMD CHECK
+ * [r1399] inst/perl/Archive/README-Archive-Zip,
+ inst/perl/Archive/README-Archive::Zip: Rename files to remove R
+ CMD check error
+ * [r1398] DESCRIPTION, inst/NEWS, inst/doc/mapLevels.pdf,
+ inst/doc/unknown.pdf: Update for 2.7.0 release
+ * [r1397] NAMESPACE: Add new functions to NAMESPACE
+ * [r1396] src, src/Compress-Raw-Zlib-2.024,
+ src/Compress-Raw-Zlib-2.024/Changes,
+ src/Compress-Raw-Zlib-2.024/MANIFEST,
+ src/Compress-Raw-Zlib-2.024/META.yml,
+ src/Compress-Raw-Zlib-2.024/Makefile.PL,
+ src/Compress-Raw-Zlib-2.024/README,
+ src/Compress-Raw-Zlib-2.024/Zlib.xs,
+ src/Compress-Raw-Zlib-2.024/config.in,
+ src/Compress-Raw-Zlib-2.024/examples,
+ src/Compress-Raw-Zlib-2.024/examples/filtdef,
+ src/Compress-Raw-Zlib-2.024/examples/filtinf,
+ src/Compress-Raw-Zlib-2.024/fallback,
+ src/Compress-Raw-Zlib-2.024/fallback/constants.h,
+ src/Compress-Raw-Zlib-2.024/fallback/constants.xs,
+ src/Compress-Raw-Zlib-2.024/lib,
+ src/Compress-Raw-Zlib-2.024/lib/Compress,
+ src/Compress-Raw-Zlib-2.024/lib/Compress/Raw,
+ src/Compress-Raw-Zlib-2.024/lib/Compress/Raw/Zlib.pm,
+ src/Compress-Raw-Zlib-2.024/pod,
+ src/Compress-Raw-Zlib-2.024/pod/FAQ.pod,
+ src/Compress-Raw-Zlib-2.024/ppport.h,
+ src/Compress-Raw-Zlib-2.024/private,
+ src/Compress-Raw-Zlib-2.024/private/MakeUtil.pm,
+ src/Compress-Raw-Zlib-2.024/t,
+ src/Compress-Raw-Zlib-2.024/t/000prereq.t,
+ src/Compress-Raw-Zlib-2.024/t/01version.t,
+ src/Compress-Raw-Zlib-2.024/t/02zlib.t,
+ src/Compress-Raw-Zlib-2.024/t/07bufsize.t,
+ src/Compress-Raw-Zlib-2.024/t/09limitoutput.t,
+ src/Compress-Raw-Zlib-2.024/t/18lvalue.t,
+ src/Compress-Raw-Zlib-2.024/t/99pod.t,
+ src/Compress-Raw-Zlib-2.024/t/Test,
+ src/Compress-Raw-Zlib-2.024/t/Test/Builder.pm,
+ src/Compress-Raw-Zlib-2.024/t/Test/More.pm,
+ src/Compress-Raw-Zlib-2.024/t/Test/Simple.pm,
+ src/Compress-Raw-Zlib-2.024/t/compress,
+ src/Compress-Raw-Zlib-2.024/t/compress/CompTestUtils.pm,
+ src/Compress-Raw-Zlib-2.024/typemap,
+ src/Compress-Raw-Zlib-2.024/zlib-src,
+ src/Compress-Raw-Zlib-2.024/zlib-src/adler32.c,
+ src/Compress-Raw-Zlib-2.024/zlib-src/compress.c,
+ src/Compress-Raw-Zlib-2.024/zlib-src/crc32.c,
+ src/Compress-Raw-Zlib-2.024/zlib-src/crc32.h,
+ src/Compress-Raw-Zlib-2.024/zlib-src/deflate.c,
+ src/Compress-Raw-Zlib-2.024/zlib-src/deflate.h,
+ src/Compress-Raw-Zlib-2.024/zlib-src/infback.c,
+ src/Compress-Raw-Zlib-2.024/zlib-src/inffast.c,
+ src/Compress-Raw-Zlib-2.024/zlib-src/inffast.h,
+ src/Compress-Raw-Zlib-2.024/zlib-src/inffixed.h,
+ src/Compress-Raw-Zlib-2.024/zlib-src/inflate.c,
+ src/Compress-Raw-Zlib-2.024/zlib-src/inflate.h,
+ src/Compress-Raw-Zlib-2.024/zlib-src/inftrees.c,
+ src/Compress-Raw-Zlib-2.024/zlib-src/inftrees.h,
+ src/Compress-Raw-Zlib-2.024/zlib-src/trees.c,
+ src/Compress-Raw-Zlib-2.024/zlib-src/trees.h,
+ src/Compress-Raw-Zlib-2.024/zlib-src/uncompr.c,
+ src/Compress-Raw-Zlib-2.024/zlib-src/zconf.h,
+ src/Compress-Raw-Zlib-2.024/zlib-src/zlib.h,
+ src/Compress-Raw-Zlib-2.024/zlib-src/zutil.c,
+ src/Compress-Raw-Zlib-2.024/zlib-src/zutil.h, src/Makefile: Add
+ Compress::Raw::Zlib code
+ * [r1395] man/read.xls.Rd, man/sheetCount.Rd: Add/Update
+ documentation
+ * [r1394] R/xls2sep.R: Minor formatting change
+ * [r1393] inst/xls/ExampleExcelFile.xls,
+ inst/xls/ExampleExcelFile.xlsx: Add additional example files
+ * [r1392] inst/perl/sheetCount.pl, inst/perl/sheetNames.pl,
+ inst/perl/xls2csv.pl: Combine sheetCount.pl and sheetNames.pl and
+ modify to support Excel 2007 'xlsx' format
+ * [r1391] inst/perl/Spreadsheet/XLSX.pm,
+ inst/perl/Spreadsheet/XLSX/Fmt2007.pm, inst/perl/xls2csv.pl:
+ Complete changes to handle Excel 2007 'xlsx' files
+ * [r1390] inst/perl/Archive, inst/perl/Archive/README-Archive::Zip,
+ inst/perl/Archive/Zip, inst/perl/Archive/Zip.pm,
+ inst/perl/Archive/Zip/Archive.pm,
+ inst/perl/Archive/Zip/BufferedFileHandle.pm,
+ inst/perl/Archive/Zip/DirectoryMember.pm,
+ inst/perl/Archive/Zip/FAQ.pod,
+ inst/perl/Archive/Zip/FileMember.pm,
+ inst/perl/Archive/Zip/Member.pm,
+ inst/perl/Archive/Zip/MemberRead.pm,
+ inst/perl/Archive/Zip/MockFileHandle.pm,
+ inst/perl/Archive/Zip/NewFileMember.pm,
+ inst/perl/Archive/Zip/StringMember.pm,
+ inst/perl/Archive/Zip/Tree.pm,
+ inst/perl/Archive/Zip/ZipFileMember.pm,
+ inst/perl/OLE/README-OLE-Storage_Lite,
+ inst/perl/Spreadsheet/README-ParseExcel,
+ inst/perl/Spreadsheet/README-XLS, inst/perl/Spreadsheet/XLSX,
+ inst/perl/Spreadsheet/XLSX.pm,
+ inst/perl/Spreadsheet/XLSX/Fmt2007.pm,
+ inst/perl/Spreadsheet/XLSX/Utility2007.pm, inst/perl/VERSIONS:
+ Add additional Perl modules to support Excel 2007 'xlsx' files
+
+2010-01-24 ggrothendieck2
+
+ * [r1389] NAMESPACE, man/sheetNames.Rd: added sheetNames.Rd
+ (documenting sheetNames/sheetCount) and updated NAMESPACE file.
+ * [r1388] inst/NEWS: fixed spacing problem in NEWS
+
+2010-01-23 warnes
+
+ * [r1387] inst/perl/xls2csv.pl: Check if parsing the xls file
+ succeeds... Current code doesn't handle new XML-based format
+ * [r1386] inst/perl/Spreadsheet/XLSX: Remove perl
+ 'Spreadsheet:XLSX' module since it depends on Compress-Raw-Zlib,
+ which probably won't be available on most machines, and I don't
+ have time to figure out how to get R to build it properly when
+ gdata is installed.
+ * [r1385] inst/perl/Spreadsheet/XLSX,
+ inst/perl/Spreadsheet/XLSX/Fmt2007.pm,
+ inst/perl/Spreadsheet/XLSX/Utility2007.pm: Add perl
+ 'Spreadsheet:XLSX' module to support new Excel XML format files
+ * [r1384] R/xls2sep.R: Add xls2tsv() convenience wrapper to
+ xls2sep()
+ * [r1383] R/read.xls.R, R/xls2sep.R: Update to match new xls2csv.pl
+ code, allow specification of sheets by name, support CSV and TAB
+ delimited files using the same code, other minor changes.
+ * [r1382] R/sheetCount.R: Add sheetNames() function to extract the
+ names from XLS files
+ * [r1381] inst/bin/xls2csv.bat: Fix xls2csv.bat
+ * [r1380] inst/perl/xls2csv.pl: If only one sheet is present in the
+ file, don't insert the sheet name into the filename
+ * [r1379] inst/xls/ExampleExcelFile.xls,
+ inst/xls/ExampleExcelFile.xlsx: Add additional test/example Excel
+ files
+ * [r1378] inst/perl/xls2csv.pl, inst/perl/xls2tab.pl,
+ inst/perl/xls2tsv.pl: Modify xls2csv.pl script to:
+ - Use tab-delimiter and .tsv or .tab extension if called with the
+ name
+ xls2tsv.pl or xls2tab.pl, respectively. This allows a single
+ source
+ file and two symlinks to be used intstead of maintaining several
+ almost-identical files.
+ - Allow selection of sheets by name
+ - Provide better error checking
+ - Other code improvements
+ * [r1377] inst/perl/sheetCount.pl, inst/perl/sheetNames.pl: Add
+ perl scripts to extract worksheet names and sheet count from
+ Excel files
+
+2010-01-22 warnes
+
+ * [r1376] inst/perl/OLE/Storage_Lite.pm: Upgrade Perl
+ OLE::StorageLight module to version 0.19
+ * [r1375] inst/perl/Spreadsheet/ParseExcel.pm,
+ inst/perl/Spreadsheet/ParseExcel/Cell.pm,
+ inst/perl/Spreadsheet/ParseExcel/Dump.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtDefault.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtJapan.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtJapan2.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtUnicode.pm,
+ inst/perl/Spreadsheet/ParseExcel/Font.pm,
+ inst/perl/Spreadsheet/ParseExcel/Format.pm,
+ inst/perl/Spreadsheet/ParseExcel/SaveParser,
+ inst/perl/Spreadsheet/ParseExcel/SaveParser.pm,
+ inst/perl/Spreadsheet/ParseExcel/SaveParser/Workbook.pm,
+ inst/perl/Spreadsheet/ParseExcel/SaveParser/Worksheet.pm,
+ inst/perl/Spreadsheet/ParseExcel/Utility.pm,
+ inst/perl/Spreadsheet/ParseExcel/Workbook.pm,
+ inst/perl/Spreadsheet/ParseExcel/Worksheet.pm: Upgrade perl
+ Spreadsheet::ParseExcel to version 0.56
+ * [r1374] DESCRIPTION: Add complete list of contributors
+
+2010-01-22 arnima
+
+ * [r1373] man/keep.Rd: Minor improvement in help page
+ * [r1371] R/Args.R, R/env.R, R/is.what.R, R/keep.R, R/ll.R,
+ man/Args.Rd, man/env.Rd, man/is.what.Rd, man/keep.Rd, man/ll.Rd:
+ Many small improvements to documentation of Arni's five functions
+
+2010-01-22 warnes
+
+ * [r1370] R/dQuote.ascii.R, R/read.xls.R, R/sheetCount.R,
+ R/xls2sep.R: - Move xls2csv(), xls2tab(), xls2sep() to a separate
+ file
+ - Move qQuote.ascii to a separate file
+
+ - Bug Fix: xls2csv(), xls2tab() failed to pass the provided
+ 'perl'
+ parameter to xls2sep()
+
+ - New Feature: xls2sep() (and hence xls2csv, xls2tab, and
+ read.xls)
+ now supports ftp URLs.
+
+2009-12-06 arnima
+
+ * [r1369] R/Args.R, man/Args.Rd: Minor improvements of Args().
+ * [r1368] R/ll.R, man/ll.Rd: Improved ll() so user can limit output
+ to specified classes
+
+2009-11-16 arnima
+
+ * [r1366] R/ll.R: ll(.GlobalEnv) does not crash anymore
+
+2009-08-20 warnes
+
+ * [r1357] man/cbindX.Rd, man/getDateTimePart.Rd, man/mapLevels.Rd,
+ man/nPairs.Rd, man/trim.Rd, man/trimSum.Rd, man/unknown.Rd,
+ man/write.fwf.Rd: Replace \ldots with \dots to make the new R CMD
+ CHECK happy.
+
+2009-08-19 warnes
+
+ * [r1355] DESCRIPTION: Update for 2.6.1 release
+ * [r1354] inst/unitTests/runit.getDateTimeParts.R: Modify unit
+ tests to avoid issues related to zime zones.
+
+2009-08-05 warnes
+
+ * [r1353] inst/doc/mapLevels.pdf, inst/doc/unknown.pdf: Update
+ vignettes for 2.6.0 release
+ * [r1352] man/frameApply.Rd: Fix formatting warning in frameApply
+ man page
+
+2009-07-16 ggorjan
+
+ * [r1350] man/write.fwf.Rd: Reverting recent change and clarifying
+ the meaning.
+
+2009-07-16 warnes
+
+ * [r1349] inst/doc/mapLevels.pdf, inst/doc/unknown.pdf,
+ man/resample.Rd: Add contents of \value section for resample()
+ man page
+ * [r1348] tests/tests.write.fwf.Rout.save: Update test output to
+ remove R CMD check warning
+ * [r1347] inst/NEWS: Update ChangeLog and NEWS for gdata 2.6.0
+ release
+ * [r1346] DESCRIPTION: Update DESCRIPTION file for gdata 2.6.0
+ * [r1345] inst/doc/gregmisc.tex, inst/doc/mapLevels.pdf,
+ inst/doc/unknown.pdf, man/ConvertMedUnits.Rd,
+ man/aggregate.table.Rd, man/combine.Rd, man/interleave.Rd,
+ man/matchcols.Rd, man/nobs.Rd, man/rename.vars.Rd,
+ man/reorder.Rd, man/trim.Rd, man/unmatrix.Rd,
+ man/upperTriangle.Rd: Correct Greg's email address
+ * [r1344] man/write.fwf.Rd: Correct minor typos in write.fwf() man
+ page
+ * [r1343] man/resample.Rd: Correct page for resample()
+ * [r1342] NAMESPACE, R/read.xls.R, inst/perl/xls2tab.pl,
+ man/read.xls.Rd: Add support for using tab for field separator
+ during translation from xls format in read.xls
+
+2009-04-19 arnima
+
+ * [r1314] R/env.R, R/ll.R: Changed object.size(object) to
+ unclass(object.size(object)).
+
+2008-12-31 ggorjan
+
+ * [r1312] NAMESPACE, inst/NEWS: Documenting changes and exporting
+ the functions.
+ * [r1311] R/object.size.R, man/humanReadable.Rd,
+ man/object.size.Rd: Enhanced function object.size that returns
+ the size of multiple objects. There is also a handy print method
+ that can print size of an object in "human readable" format when
+ options(humanReadable=TRUE) or print(object.size(x),
+ humanReadable=TRUE).
+ * [r1310] R/wideByFactor.R, inst/unitTests/runit.wideByFactor.R,
+ man/wideByFactor.Rd: New function wideByFactor that reshapes
+ given dataset by a given factor - it creates a "multivariate"
+ data.frame.
+ * [r1309] R/nPairs.R, inst/unitTests/runit.nPairs.R, man/nPairs.Rd:
+ New function nPairs that gives the number of variable pairs in a
+ data.frame or a matrix.
+ * [r1308] R/getDateTimeParts.R,
+ inst/unitTests/runit.getDateTimeParts.R, man/getDateTimePart.Rd:
+ New functions getYear, getMonth, getDay, getHour, getMin, and
+ getSec for extracting the date/time parts from objects of a
+ date/time class.
+ * [r1307] R/bindData.R, inst/unitTests/runit.bindData.R,
+ man/bindData.Rd: New function bindData that binds two data frames
+ into a multivariate data frame in a different way than merge.
+ * [r1306] R/runRUnitTests.R, inst/unitTests/Makefile,
+ inst/unitTests/runRUnitTests.R, man/gdata-package.Rd,
+ man/runRUnitTests.Rd, tests/doRUnit.R: New function
+ .runRUnitTestsGdata that enables run of all RUnit tests during
+ the R CMD check as well as directly from within R.
+
+2008-12-20 ggorjan
+
+ * [r1305] NAMESPACE, R/trimSum.R, inst/NEWS,
+ inst/unitTests/runit.trimSum.R, man/trimSum.Rd:
+ * [r1304] tests/tests.write.fwf.Rout.save: To remove some output in
+ the R CMD check
+
+2008-08-05 ggorjan
+
+ * [r1300] DESCRIPTION, NAMESPACE, R/cbindX.R, R/write.fwf.R,
+ inst/NEWS, inst/doc/mapLevels.pdf, inst/doc/unknown.pdf,
+ inst/unitTests/runit.cbindX.R, inst/unitTests/runit.write.fwf.R,
+ man/cbindX.Rd, man/write.fwf.Rd, tests/tests.write.fwf.R,
+ tests/tests.write.fwf.Rout.save: - Increased version to 2.5.0
+
+ - New function cbindX that can bind objects with different number
+ of rows.
+
+ - write.fwf gains width argument. Unknown values can increase or
+ decrease
+ the width of the columns. Additional tests and documentation
+ fixes.
+
+2008-06-30 arnima
+
+ * [r1299] R/env.R, R/ll.R, man/env.Rd, man/ll.Rd: Simplified
+ default 'unit' argument from c("KB","MB","bytes") to "KB".
+
+2008-05-13 warnes
+
+ * [r1270] inst/NEWS, inst/doc/mapLevels.pdf, inst/doc/unknown.pdf:
+ Update NEWS file for 2.4.2
+ * [r1269] R/read.xls.R: Use path.expand() to give proper full path
+ to xls file to be translated by read.xls()
+ * [r1268] R/read.xls.R: Modifed read.xls() failed to return the
+ converted data... fixed.
+ * [r1267] inst/perl/Spreadsheet/ParseExcel/Utility.pm: Correct
+ broken patch for open-office support
+ * [r1266] DESCRIPTION, R/read.xls.R: For read.xls() and xls2csv():
+ - Implement more informative log messages when verbose=TRUE
+ - Quote temporary file name to avoid errors when calling perl to
+ do the work.
+ - Add better error messages, particularly when perl fails to
+ generate an
+ output .csv file.
+
+ Update version number in DESCRIPTION.
+
+2008-05-12 warnes
+
+ * [r1265] inst/perl/Spreadsheet/ParseExcel/Utility.pm: Patch to
+ correct issue with OpenOffice-created XLS files. Thanks to
+ Robert Burns for pointing out the patch at
+ http://rt.cpan.org/Public/Bug/Display.html?id=7206
+
+2008-03-25 warnes
+
+ * [r1250] DESCRIPTION, inst/NEWS, inst/doc/mapLevels.pdf,
+ inst/doc/unknown.pdf: Update for version 2.4.1
+ * [r1249] inst/xls/iris.xls: Example iris.xls file didn't complete
+ & properly formatted iris data set. Fixed.
+ * [r1248] inst/perl/IO/AtomicFile.pm, inst/perl/IO/InnerFile.pm,
+ inst/perl/IO/Lines.pm, inst/perl/IO/Scalar.pm,
+ inst/perl/IO/ScalarArray.pm, inst/perl/IO/Stringy.pm,
+ inst/perl/IO/Wrap.pm, inst/perl/IO/WrapTie.pm,
+ inst/perl/OLE/Storage_Lite.pm,
+ inst/perl/Spreadsheet/ParseExcel.pm,
+ inst/perl/Spreadsheet/ParseExcel/Dump.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtDefault.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtJapan.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtJapan2.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtUnicode.pm,
+ inst/perl/Spreadsheet/ParseExcel/SaveParser.pm,
+ inst/perl/Spreadsheet/ParseExcel/Utility.pm: Update perl modules
+ to latest versions
+
+2008-03-24 warnes
+
+ * [r1247] man/read.xls.Rd: Fix typo in win32 example for read.xls()
+
+2008-03-11 warnes
+
+ * [r1246] NAMESPACE: Add xls2csv to exported function list
+
+2008-01-30 warnes
+
+ * [r1241] ChangeLog, DESCRIPTION, inst/NEWS: Update DESCRIPTION and
+ NEWS for release 2.4.0
+
+2008-01-29 arnima
+
+ * [r1240] man/keep.Rd: Added argument 'all'.
+ * [r1239] R/keep.R: Added argument 'all'.
+
+2007-10-22 warnes
+
+ * [r1196] DESCRIPTION: Clarify GPL version
+
+2007-09-10 ggorjan
+
+ * [r1169] man/upperTriangle.Rd: removed unmatched brace
+ * [r1168] man/gdata-package.Rd: adding alias
+
+2007-09-06 ggorjan
+
+ * [r1162] man/gdata-package.Rd: keyword
+
+2007-08-21 ggorjan
+
+ * [r1154] man/gdata-package.Rd: package help page
+ * [r1153] NEWS, inst/NEWS: move
+ * [r1152] NEWS: move
+
+2007-08-20 ggorjan
+
+ * [r1151] inst/doc/mapLevels.tex: clean
+ * [r1150] inst/doc/mapLevels.Rnw, inst/doc/mapLevels.pdf,
+ inst/doc/mapLevels.tex: a real vignette
+ * [r1149] inst/doc/unknown.Rnw, inst/doc/unknown.pdf,
+ inst/doc/unknown.tex: a real vignette
+ * [r1148] man/unknown.Rd: additional keyword for searchig
+
+2007-08-17 ggorjan
+
+ * [r1147] man/unknown.Rd: keyword
+
+2007-07-22 arnima
+
+ * [r1103] R/Args.R, R/keep.R: Reverted back to
+ as.character(substitute(x)), so user can run keep(x),
+ keep("x"), Args(x), and Args("x").
+
+2007-07-21 arnima
+
+ * [r1102] R/keep.R: Changed as.character(substitute()) to
+ deparse(substitute()), following
+ help(substitute) recommendation.
+ * [r1101] R/Args.R: Changed as.character(substitute()) to
+ deparse(substitute()), following
+ help(substitute) recommendation.
+
+2007-07-10 warnes
+
+ * [r1099] R/read.xls.R, man/read.xls.Rd: Update read.xls() code and
+ docs with enhacements by Gabor Grothendieck
+
+2007-06-06 ggorjan
+
+ * [r1097] inst/doc/unknown.pdf, inst/doc/unknown.tex: last edits
+ from newsletter
+ * [r1096] R/drop.levels.R, man/drop.levels.Rd: drop levels as
+ suggested by Brian Ripley
+ * [r1095] inst/unitTests/Makefile, tests/doRUnit.R: better
+ integration of unit tests
+ * [r1094] R/mapLevels.R, R/unknown.R: making codetools happy
+
+2007-01-28 arnima
+
+ * [r1042] R/keep.R: Throw warnings rather than errors
+
+2007-01-27 arnima
+
+ * [r1041] R/keep.R: Meaningful error message is given when
+ requested object does not exist
+ * [r1040] R/is.what.R: is.* tests that return NA are not reported
+ is.what recursion is avoided
+
+2006-11-30 ggorjan
+
+ * [r1035] R/unknown.R: minor commet to the code
+ * [r1034] inst/doc/mapLevels.pdf, inst/doc/mapLevels.tex:
+ description of mapLevels methods
+ * [r1033] inst/doc/unknown.pdf, inst/doc/unknown.tex: description
+ of unknown methods
+
+2006-11-16 ggorjan
+
+ * [r1013] R/c.factor.R, man/c.factor.Rd: seems that c.factor was
+ not a good idea and there were better examples posted on r-devel
+ list
+
+2006-11-14 ggorjan
+
+ * [r1012] man/combine.Rd, man/frameApply.Rd: Removed executable
+ property
+
+2006-11-10 ggorjan
+
+ * [r1004] NAMESPACE, NEWS: just formatting
+
+2006-11-02 ggorjan
+
+ * [r1002] man/mapLevels.Rd, man/unknown.Rd: typos
+
+2006-10-30 ggorjan
+
+ * [r1001] man/write.fwf.Rd: some more examples for use of read.fwf
+ after write.fwf
+ * [r1000] inst/unitTests: ignore for report files
+ * [r999] tests/tests.write.fwf.Rout.save: Id tag from source
+ * [r998] NAMESPACE: removing unused import
+ * [r997] R/write.fwf.R, inst/unitTests/runit.write.fwf.R,
+ man/write.fwf.Rd, tests/tests.write.fwf.R: Id tag
+ * [r996] NAMESPACE, NEWS, R/write.fwf.R,
+ inst/unitTests/runit.write.fwf.R, man/write.fwf.Rd,
+ tests/tests.write.fwf.R, tests/tests.write.fwf.Rout.save:
+ write.fwf
+ * [r995] inst/unitTests/runit.reorder.factor.R: Id tag
+ * [r994] inst/unitTests/runit.reorder.factor.R: added unit tests
+ for reorder.factor
+ * [r993] R/c.factor.R, R/mapLevels.R, R/unknown.R,
+ inst/unitTests/runit.drop.levels.R,
+ inst/unitTests/runit.mapLevels.R, inst/unitTests/runit.trim.R,
+ inst/unitTests/runit.unknown.R, man/c.factor.Rd, man/unknown.Rd,
+ tests/doRUnit.R: mapply keeps names in R 2.4; POSIX unit tests
+ solved; $ should work now
+
+2006-10-29 ggorjan
+
+ * [r992] NEWS, R/unknown.R, inst/unitTests/runit.unknown.R,
+ man/unknown.Rd: fixed problem in tests; added unknown methods and
+ tests for matrices
+ * [r991] R/drop.levels.R, R/mapLevels.R,
+ inst/unitTests/runit.mapLevels.R, man/mapLevels.Rd,
+ tests/doRUnit.R: sort is generic now; mapply keeps names in R
+ 2.4.0; some codetools suggestions fixed
+ * [r990] DESCRIPTION, NAMESPACE: sort is generic from R 2.4.0
+ * [r989] DESCRIPTION, NEWS, R/trim.R, man/trim.Rd: trim() gains ...
+ argument; version bump
+ * [r988] NEWS, R/reorder.R, man/reorder.Rd: Fixed collision bug
+ with stats version of reorder.factor
+
+2006-10-27 warnes
+
+ * [r987] R/c.factor.R, man/c.factor.Rd: Add c() method for factor
+ objects, submitted by Gregor Gorjanc
+
+2006-09-19 warnes
+
+ * [r986] NEWS: Update NEWS file for 2.3.0 release
+ * [r985] inst/unitTests/runit.trim.R: Explicitly set the local in
+ runit.trim.R to one where leading spaces affect sort order so
+ that the unit test works properly.
+
+2006-09-18 warnes
+
+ * [r984] inst/doc/Rnews.sty: Update Rnews.sty to the latest version
+ * [r983] R/trim.R, inst/unitTests/Makefile,
+ inst/unitTests/runit.trim.R, man/trim.Rd, tests/doRUnit.R:
+ Integrate fixes for trim() from Gregor and myself.
+ * [r982] inst/unitTests/report.html, inst/unitTests/report.txt:
+ Remove unneeded files.
+
+2006-09-13 warnes
+
+ * [r981] R/unknown.R, inst/unitTests, inst/unitTests/Makefile,
+ inst/unitTests/report.html, inst/unitTests/report.txt,
+ inst/unitTests/runit.drop.levels.R,
+ inst/unitTests/runit.mapLevels.R, inst/unitTests/runit.trim.R,
+ inst/unitTests/runit.unknown.R, man/unknown.Rd, tests,
+ tests/doRUnit.R: Add unknown() and unit test files
+ * [r980] NAMESPACE, R/drop.levels.R, R/mapLevels.R, R/trim.R: More
+ fixes from Gregor Gorjanc
+ * [r979] DESCRIPTION, NAMESPACE, R/combineLevels.R, R/mapFactor.R,
+ R/mapLevels.R, man/combineLevels.Rd, man/mapFactor.Rd,
+ man/mapLevels.Rd: Add mapLevels functions from Gregor Gorjanc,
+ along with associated unit tests.
+
+2006-08-03 warnes
+
+ * [r978] DESCRIPTION, NAMESPACE, R/combineLevels.R, R/mapFactor.R,
+ man/combineLevels.Rd, man/mapFactor.Rd: Add Gregor Gorjanc's
+ mapFactor() and combineLevels() functions.
+
+2006-08-02 warnes
+
+ * [r977] inst/doc/gregmisc.tex, man/ConvertMedUnits.Rd,
+ man/aggregate.table.Rd, man/combine.Rd, man/interleave.Rd,
+ man/matchcols.Rd, man/nobs.Rd, man/read.xls.Rd,
+ man/rename.vars.Rd, man/reorder.Rd, man/trim.Rd, man/unmatrix.Rd,
+ man/upperTriangle.Rd: Update my email address
+ * [r976] data/MedUnits.rda: Remove MedUnits.rda to convert to
+ binary format
+ * [r975] data/MedUnits.rda: Remove MedUnits.rda to convert to
+ binary format
+ * [r974] DESCRIPTION: Update version number
+ * [r973] NAMESPACE, R/drop.levels.R, R/trim.R, man/drop.levels.Rd,
+ man/trim.Rd: Integrate changes suggested by Gregor Gorjanc
+
+2006-03-14 nj7w
+
+ * [r940] NAMESPACE, R/trim.R, man/resample.Rd: Fixed R CMD check
+ errors and added trim.default to NAMESPACE
+
+2006-03-13 nj7w
+
+ * [r939] R/trim.R: Added trim.character and trim.factor as per
+ Gregor's suggestions
+
+2006-01-03 warnes
+
+ * [r839] NAMESPACE, R/resample.R, man/resample.Rd: Add resample()
+ function, which generates a random sample or
+ permutation from the elements of the supplied vector, even if the
+ vector has length 1. This avoide the problems caused by
+ base::sample()'s special case for vectors of length 1, where it
+ attempts to sample from 1:x.
+
+2005-12-13 nj7w
+
+ * [r806] ChangeLog, NEWS: Updated news and removed changelog
+
+2005-12-12 nj7w
+
+ * [r798] DESCRIPTION, man/interleave.Rd: Updated version number for
+ CRAN release
+
+2005-12-08 warnes
+
+ * [r789] R/interleave.R: Andrew Burgess reported that interleave()
+ converts 1-column matrixes
+ to vectors and provided a patch. A slight modification of his
+ patch
+ has been applied. There is now a 'drop' argument, which controls
+ whether 'unnecessary' dimensions are dropped. The default is
+ FALSE.
+
+2005-12-04 warnes
+
+ * [r779] man/interleave.Rd: Andrew Burgess reported that
+ interleave() converts 1-column matrixes
+ to vectors and provided a patch. A slight modification of his
+ patch
+ has been applied. There is now a 'drop' argument, which controls
+ whether 'unnecessary' dimensions are dropped. The default is
+ FALSE.
+
+2005-12-01 nj7w
+
+ * [r775] man/combine.Rd, man/reorder.Rd: Updated Greg's email
+ address
+ * [r774] man/drop.levels.Rd, man/frameApply.Rd, man/ll.Rd,
+ man/read.xls.Rd: Updated Jim's email address
+
+2005-11-21 arnima
+
+ * [r744] R/ll.R: Suppressed warning message in attach() call.
+
+2005-10-27 warnes
+
+ * [r716] DESCRIPTION: Bump version number again to show that I
+ fixed a bug.
+ * [r715] DESCRIPTION, R/upperTriangle.R: Update version number
+ * [r714] man/frameApply.Rd, man/reorder.Rd: Remove explicit loading
+ of gtools in examples, so that failure to
+ import functions from gtools gets properly caught by running the
+ examples.
+ * [r713] man/upperTriangle.Rd: Add missing close-bracket
+ * [r712] NAMESPACE: Add upperTriangle and friends
+ * [r711] R/upperTriangle.R, man/upperTriangle.Rd: Add functions for
+ extracting, modifying upper and lower trianglular
+ components of matrices.
+
+2005-10-19 arnima
+
+ * [r695] R/is.what.R: Replaced the "not.using" vector with a more
+ robust try(get(test)) to find out whether a particular is.*
+ function returns a logical of length one.
+
+2005-09-12 nj7w
+
+ * [r671] man/aggregate.table.Rd, man/interleave.Rd,
+ man/matchcols.Rd, man/nobs.Rd, man/read.xls.Rd,
+ man/rename.vars.Rd, man/trim.Rd, man/unmatrix.Rd: Updated Greg's
+ email
+
+2005-09-06 nj7w
+
+ * [r661] man/reorder.Rd: Added library(gtools) in the example
+ * [r660] NAMESPACE: Removed gtools dependency from NAMESPACE, as it
+ was being used only in an example, and was giving warning
+ * [r659] DESCRIPTION: Added Suggests field
+
+2005-09-02 nj7w
+
+ * [r658] man/frameApply.Rd: Updated the example in frameApply
+ * [r656] NEWS: Added NEWS
+ * [r654] ChangeLog: ChangeLog
+
+2005-08-31 nj7w
+
+ * [r644] DESCRIPTION: Added DESCRIPTION file
+ * [r643] DESCRIPTION.in: removed DESCRIPTION.in
+
+2005-07-20 nj7w
+
+ * [r631] man/ll.Rd: updated documentation
+ * [r630] R/Args.R: ## Args() was using a different search path from
+ args(), e.g.
+ rep <- function(local) return(NULL)
+ args()
+ Args()
+ ## Fixed
+ * [r629] R/is.what.R: ## is.what() was giving needless warnings for
+ functions, e.g.
+ is.what(plot)
+ ## Fixed
+ * [r628] R/ll.R: ## ll() was crashing if argument was a list of
+ length zero, e.g.
+ x <- list()
+ ll(x)
+ ## Fixed, and added sort.elements (see new help page)
+
+2005-06-09 nj7w
+
+ * [r625] R/Args.R, R/aggregate.table.R, R/combine.R, R/elem.R,
+ R/env.R, R/frameApply.R, R/interleave.R, R/is.what.R, R/keep.R,
+ R/ll.R, R/matchcols.R, R/nobs.R, R/read.xls.R, R/rename.vars.R,
+ R/reorder.R, R/trim.R, R/unmatrix.R, inst/perl/IO/AtomicFile.pm,
+ inst/perl/IO/InnerFile.pm, inst/perl/IO/Lines.pm,
+ inst/perl/IO/Scalar.pm, inst/perl/IO/Scalar.pm.html,
+ inst/perl/IO/ScalarArray.pm, inst/perl/IO/Stringy.pm,
+ inst/perl/IO/Wrap.pm, inst/perl/IO/WrapTie.pm,
+ man/aggregate.table.Rd, man/combine.Rd, man/drop.levels.Rd,
+ man/interleave.Rd, man/nobs.Rd, man/rename.vars.Rd,
+ man/reorder.Rd: Updating the version number, and various help
+ files to synchronize splitting of gregmisc bundle in 4 individual
+ components.
+
+2005-06-07 nj7w
+
+ * [r622] R/drop.levels.R: Reverting to the previous version of
+ drop.levels.R by replacing
+ sapply(...) with as.data.frame(lapply(...)) because sapply has
+ the undesirable effect of converting the object to a matrix,
+ which in turn coerces the factors to numeric.
+
+2005-05-13 nj7w
+
+ * [r621] R/read.xls.R: 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.
+
+2005-04-02 warnes
+
+ * [r600] NAMESPACE, R/drop.levels.R, man/drop.levels.Rd: Move
+ drop.levels() from gtools to gdata.
+ * [r598] NAMESPACE, R/frameApply.R, man/frameApply.Rd: Move
+ frameApply() to gdata package.
+
+2005-03-31 warnes
+
+ * [r586] man/elem.Rd: Comment out example to avoid R CMD check
+ warnings
+
+2005-03-22 warnes
+
+ * [r578] NAMESPACE, R/ConvertMedUnits.R, data/MedUnits.Rda,
+ data/MedUnits.rda, man/ConvertMedUnits.Rd, man/MedUnits.Rd: Fixes
+ to pass `R CMD check'.
+ * [r577] R/Args.R, R/env.R, R/ll.R, man/Args.Rd: Integrated fixes
+ from Arni.
+ * [r576] man/read.xls.Rd: Improve documentation of 'perl' argument
+ and give examples.
+
+2005-03-09 warnes
+
+ * [r573] R/ConvertMedUnits.R, man/ConvertMedUnits.Rd,
+ man/MedUnits.Rd: - Add ConvertMedUnits() plus documentation
+ - Add documentation for MedUnits data set.
+ * [r572] data/MedUnits.Rda: Update MedUnits data file.
+ * [r571] data/MedUnits.tab: Don't need both .Rda and .tab forms of
+ the data.
+ * [r570] data, data/MedUnits.Rda, data/MedUnits.tab: Add MedUnits
+ data set, which provides conversions between American
+ 'Conventional' and Standard Intertional (SI) medical units.
+
+2005-03-01 warnes
+
+ * [r566] man/elem.Rd, man/ll.Rd: - Remove 'elem' call from ll
+ example.
+ - Add note to 'elem' man page that it is depreciated and 'll'
+ should
+ be used instead.
+
+2005-02-26 nj7w
+
+ * [r565] NAMESPACE, man/elem.Rd, man/env.Rd, man/ll.Rd,
+ man/read.xls.Rd: *** empty log message ***
+
+2005-02-25 warnes
+
+ * [r564] NAMESPACE: Remove ll methods since the base function now
+ handles lists and data frames.
+ * [r563] R/elem.R, R/env.R, R/ll.R, man/Args.Rd, man/env.Rd,
+ man/ll.Rd: Integrate changes submitted by Arni Magnusson
+
+2005-01-31 warnes
+
+ * [r529] R/read.xls.R, man/read.xls.Rd: Add ability to specify the
+ perl executable and path.
+
+2005-01-28 warnes
+
+ * [r526] DESCRIPTION.in, NAMESPACE: Add dependency on stats.
+
+2005-01-12 warnes
+
+ * [r515] DESCRIPTION.in: Add dependency on R 1.9.0+ to prevent
+ poeple from installing on old
+ versions of R which don't support namespaces.
+
+2004-12-27 warnes
+
+ * [r509] man/unmatrix.Rd: Update usage to match code.
+ * [r508] R/unmatrix.R: Replace 'F' with 'FALSE'.
+
+2004-10-12 warneg
+
+ * [r465] R/unmatrix.R, man/unmatrix.Rd: Add unmatrix() function
+
+2004-09-27 warneg
+
+ * [r461] DESCRIPTION, DESCRIPTION.in, NAMESPACE, man/.Rhistory:
+ Updated to pass R CMD check.
+
+2004-09-03 warneg
+
+ * [r455] inst/xls, inst/xls/iris.xls: added to cvs.
+ * [r454] inst/perl/xls2csv.pl: Checkin xls2csv.pl. Should have been
+ in long ago, must have been an oversight
+ * [r451] R/read.xls.R: Need to look for files using the new package
+ name.
+ * [r449] man/read.xls.Rd: Need to use the new package name when
+ looking for iris.xls.
+ * [r448] man/ll.Rd: Add ll.list to the to the list of functions
+ described
+ * [r447] NAMESPACE: Add ll and friends to the namespace
+ * [r446] DESCRIPTION, DESCRIPTION.in, NAMESPACE, R/Args.R,
+ R/aggregate.table.R, R/combine.R, R/elem.R, R/env.R,
+ R/interleave.R, R/is.what.R, R/keep.R, R/ll.R, R/matchcols.R,
+ R/nobs.R, R/read.xls.R, R/rename.vars.R, R/reorder.R, R/trim.R,
+ man/reorder.Rd: initial bundle checkin
+
+2004-09-02 warneg
+
+ * [r442] DESCRIPTION, DESCRIPTION.in, NAMESPACE, man/.Rhistory:
+ Initial revision
+
+2004-08-27 warnes
+
+ * [r441] R/reorder.R, man/reorder.Rd: Fixed bug in mixedsort, and
+ modified reorder.factor to use mixedsort.
+
+2004-07-29 warnes
+
+ * [r427] inst/perl, inst/perl/IO, inst/perl/IO/AtomicFile.pm,
+ inst/perl/IO/InnerFile.pm, inst/perl/IO/Lines.pm,
+ inst/perl/IO/Scalar.pm, inst/perl/IO/Scalar.pm.html,
+ inst/perl/IO/ScalarArray.pm, inst/perl/IO/Stringy.pm,
+ inst/perl/IO/Wrap.pm, inst/perl/IO/WrapTie.pm, inst/perl/OLE,
+ inst/perl/OLE/Storage_Lite.pm, inst/perl/Spreadsheet,
+ inst/perl/Spreadsheet/ParseExcel,
+ inst/perl/Spreadsheet/ParseExcel.pm,
+ inst/perl/Spreadsheet/ParseExcel/Dump.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtDefault.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtJapan.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtJapan2.pm,
+ inst/perl/Spreadsheet/ParseExcel/FmtUnicode.pm,
+ inst/perl/Spreadsheet/ParseExcel/SaveParser.pm,
+ inst/perl/Spreadsheet/ParseExcel/Utility.pm: Add perl modules to
+ CVS.
+
+2004-07-27 warnes
+
+ * [r425] man/read.xls.Rd: Fix typos/spelling.
+ * [r424] man/read.xls.Rd: Add note that Perl is required for
+ read.xls to work properly.
+
+2004-07-16 warnes
+
+ * [r420] R/read.xls.R: Remove the temporary csv file if reading it
+ in fails.
+
+2004-06-22 warnes
+
+ * [r377] R/ll.R, man/ll.Rd: Add S3 methods for data frames and
+ lists.
+
+2004-06-08 warnes
+
+ * [r371] inst/bin, inst/bin/xls2csv, inst/bin/xls2csv.bat: Moved
+ from gregmisc/src/.
+ * [r370] inst/tools: Remove the files in src, instead provide
+ "pre-installed" perl packages
+ in inst/perl.
+
+2004-06-05 warnes
+
+ * [r365] inst/tools/Makefile: Fix typo.
+ * [r364] inst/tools/Makefile: Fix Unix makefile so that it works
+ when invoked directly.
+ * [r363] inst/tools/Makefile: Fixes for Windows
+ * [r362] man/read.xls.Rd: Minor enhancment to read.xls example.
+ * [r361] inst/tools/Makefile, inst/xls: - Merge Makefile.win into
+ Makefile. Makefile.win now just redirects
+ to Makefile.
+ - Update xls2csv.bat and xls2csv shell script to correctly obtain
+ thier installion path and infer the location of the perl code and
+ libraries.
+ - The xls2csv.pl script now assumes that the libraries it needs
+ are
+ installed into the same directory where it is.
+
+2004-06-04 warnes
+
+ * [r360] inst/tools/Makefile: More changes, indended to improve
+ installation reliabilty and to make
+ Makefile and Makefile.win as similar as possible.
+
+2004-05-27 warnes
+
+ * [r358] inst/tools/Makefile: Clean should remove scripts from
+ source directory.
+ * [r357] inst/perl: Moved to xls2csv.pl.in.
+ * [r354] inst/perl/xls2csv.pl, inst/tools/Makefile: More fixes.
+ * [r353] man/elem.Rd: Fix missing brace.
+ * [r352] man/elem.Rd: Add explicit package name to see also links.
+ * [r351] inst/perl/xls2csv.pl, inst/tools/Makefile: More xls2csv
+ perl module support changes.
+ * [r350] inst/tools/Makefile: More changes to fix local
+ installation of perl modules.
+
+2004-05-26 warnes
+
+ * [r345] man/read.xls.Rd: Escape underscores in email addresses so
+ Latex is happy.
+
+2004-05-25 warnes
+
+ * [r339] inst/perl/xls2csv.pl, inst/tools/Makefile: More changes to
+ xls2csv code.
+ * [r337] R/Args.R, man/Args.Rd: Add Args() function contributed by
+ Arni Magnusson <arnima@u.washington.edu>.
+ * [r335] R/read.xls.R: - Change to call perl directly rather than
+ depending on the installed
+ shell script. This should make the code more portable to
+ MS-Windows
+ systes.
+
+ - Add additional commants..
+ * [r332] inst/tools/Makefile: Makefile now modifies xls2csv.bat
+ xls2csv.pl and xls2csv to contain an
+ explicit path to the perl script/libraries.
+ * [r330] inst/tools/Makefile: R CMD build calls the clean target to
+ purge build files from the
+ source tree when packaging. To get use this behavior correctly,
+ I've
+ renamed the clean target to cleanup and distclean target to
+ clean.
+ * [r329] R/read.xls.R, man/read.xls.Rd: Add read.xls(), a function
+ to read Microsoft Excel files by
+ translating them to csv files via the xls2csv.pl script.
+ * [r326] inst/tools/Makefile: More fixes. Seems to work now.
+
+2004-05-24 warnes
+
+ * [r325] inst/perl, inst/perl/xls2csv.pl, inst/tools,
+ inst/tools/Makefile, inst/xls, inst/xls/iris.xls: Add files to
+ enable inclusion and installation of xls2csv.pl as part
+ of the package.
+
+2004-04-01 warnes
+
+ * [r312] R/rename.vars.R, man/rename.vars.Rd: Add function
+ remove.vars().
+
+2004-03-26 warnes
+
+ * [r307] man/reorder.Rd: Contents of package 'mva' moveed to
+ 'stats'.
+ * [r298] R/is.what.R: - Fix is.what() for use under R 1.9.0
+ - is.what() now uses is.* functions found in any attached frame
+
+2004-01-21 warnes
+
+ * [r282] R/reorder.R, man/reorder.Rd: - Add ... argument to match
+ generic provided in mva.
+
+2004-01-19 warnes
+
+ * [r275] R/elem.R, R/env.R, R/ll.R, man/keep.Rd, man/ll.Rd: -
+ Integrated (partial) patch submitted by Arni Magnusson to clarify
+ help text.
+ - Modifed code to use match.arg().
+
+2003-12-15 warnes
+
+ * [r271] R/env.R: - Applied patch from Arni that fixed a bug that
+ caused env() to crash
+ if any environment was completely empty
+
+2003-12-03 warnes
+
+ * [r253] man/elem.Rd, man/ll.Rd: - match function argument defaults
+ with 'usage'
+
+2003-12-02 warnes
+
+ * [r249] man/ll.Rd: Add one argument, to match code.
+
+2003-12-01 warnes
+
+ * [r244] R/elem.R, R/env.R, R/is.what.R, R/keep.R, R/ll.R: - Apply
+ changes submitted by Arni Magnusson
+
+2003-11-19 warnes
+
+ * [r229] man/env.Rd, man/is.what.Rd, man/keep.Rd, man/ll.Rd:
+ Changes to pass R CMD check.
+
+2003-11-18 warnes
+
+ * [r224] R/elem.R, R/env.R, R/is.what.R, R/keep.R, R/ll.R: -
+ Convert from MS-Dos to Unix line endings.
+ - Reformat to 80 columns.
+
+2003-11-17 warnes
+
+ * [r223] man/elem.Rd: Replace 'T' with 'TRUE' to remove R CMD check
+ error.
+ * [r222] man/aggregate.table.Rd: Fix syntax error.
+
+2003-11-10 warnes
+
+ * [r220] R/elem.R, R/env.R, R/is.what.R, R/keep.R, R/ll.R,
+ man/elem.Rd, man/env.Rd, man/is.what.Rd, man/keep.Rd, man/ll.Rd:
+ - Add files contributed by Arni Magnusson
+ <arnima@u.washington.edu>. As well as some of my own.
+
+2003-06-07 warnes
+
+ * [r198] man/aggregate.table.Rd, man/interleave.Rd: - Fixed error
+ in examples. Had sqrt(var(x)/(n-1)) for the standard
+ error of the mean instead of sqrt(var(x)/n).
+
+2003-05-23 warnes
+
+ * [r197] R/matchcols.R, man/matchcols.Rd: - Fixed typos
+ * [r196] R/matchcols.R, man/matchcols.Rd: - library() backported
+ from 1.7-devel. This version of the function
+ adds the "pos=" argument to specify where in the search path the
+ library should be placed.
+
+ - updated .First.lib to use library(...pos=3) for MASS to avoid
+ the
+ 'genotype' data set in MASS from masking the genotype funciton in
+ genetics when it loads gregmisc
+
+ - Added logit() inv.logit() matchcols() function and
+ corresponding docs
+
+2003-05-20 warnes
+
+ * [r195] R/interleave.R: - Omit ...
[truncated message content] |
|
From: <wa...@us...> - 2015-04-14 19:39:24
|
Revision: 1923
http://sourceforge.net/p/r-gregmisc/code/1923
Author: warnes
Date: 2015-04-14 19:39:22 +0000 (Tue, 14 Apr 2015)
Log Message:
-----------
Fix typo
Modified Paths:
--------------
trunk/gtools/DESCRIPTION
Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION 2015-04-10 03:15:42 UTC (rev 1922)
+++ trunk/gtools/DESCRIPTION 2015-04-14 19:39:22 UTC (rev 1923)
@@ -1,23 +1,26 @@
Package: gtools
Title: Various R Programming Tools
Description: Functions to assist in R programming, including:
- - assist in developing, updating, and maintaning R and R packages ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat'),
- - calculate the logit and inverse logit transformations ('logit', 'inv.logit')
- - test if a value is missing, empty or contains only NA and NULL values ('invalid')
- - manipulate R's .Last function ('addLast')
- - define macros ('defmacro'),
- - detect odd and even integers ('odd', 'even')
- - convert strings containig non-ascii characters (like single quotes) to plain ASCII ('ASCIIfy'),
- - perform a binary search ('binseach')
- - sort strings containing both numeric and character components ('mixedsort')
- - create a factor variable from the quantiles of a continuous variable ('quantcut')
- - enumerate permutations and combinations ('combinations', 'permutation'),
- - calculate and convert betwen fold-change and log-ratio ('foldchange', 'logratio2foldchange', 'foldchange2logratio'),
- - calculate probablities and generate random numbers from dirichlet distributions ('rdirichlet', 'ddirichlet')
- - apply a function over adjacent subsets of a vector ('running')
- - Modify the TCP\_NODELAY ('de-Nagle') flag for socket objects
- - Efficient rbind of data frames, even if the column names don't match ('smartbind')
- - Generate significance stars from p-values ('stars.pval')
+ - assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion',
+ 'getDependencies', 'keywords', 'scat'),
+ - calculate the logit and inverse logit transformations ('logit', 'inv.logit'),
+ - test if a value is missing, empty or contains only NA and NULL values ('invalid'),
+ - manipulate R's .Last function ('addLast'),
+ - define macros ('defmacro'),
+ - detect odd and even integers ('odd', 'even'),
+ - convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'),
+ - perform a binary search ('binsearch'),
+ - sort strings containing both numeric and character components ('mixedsort'),
+ - create a factor variable from the quantiles of a continuous variable ('quantcut'),
+ - enumerate permutations and combinations ('combinations', 'permutation'),
+ - calculate and convert between fold-change and log-ratio ('foldchange',
+ 'logratio2foldchange', 'foldchange2logratio'),
+ - calculate probabilities and generate random numbers from Dirichlet distributions
+ ('rdirichlet', 'ddirichlet'),
+ - apply a function over adjacent subsets of a vector ('running'),
+ - Modify the TCP\_NODELAY ('de-Nagle') flag for socket objects,
+ - Efficient 'rbind' of data frames, even if the column names don't match ('smartbind'),
+ - Generate significance stars from p-values ('stars.pval').
Version: 3.4.2
Date: 2015-04-06
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2015-04-10 03:15:49
|
Revision: 1922
http://sourceforge.net/p/r-gregmisc/code/1922
Author: warnes
Date: 2015-04-10 03:15:42 +0000 (Fri, 10 Apr 2015)
Log Message:
-----------
Update files for gdata 2.15.0
Modified Paths:
--------------
trunk/gdata/DESCRIPTION
trunk/gdata/NAMESPACE
trunk/gdata/inst/NEWS
Modified: trunk/gdata/DESCRIPTION
===================================================================
--- trunk/gdata/DESCRIPTION 2015-04-09 19:46:55 UTC (rev 1921)
+++ trunk/gdata/DESCRIPTION 2015-04-10 03:15:42 UTC (rev 1922)
@@ -1,11 +1,11 @@
Package: gdata
-Title: Various R programming tools for data manipulation
+Title: Various R Programming Tools for Data Manipulation
Description: Various R programming tools for data manipulation
Depends: R (>= 2.13.0)
SystemRequirements: perl
Imports: gtools
-Version: 2.14.0
-Date: 2014-08-27
+Version: 2.15.0
+Date: 2015-04-06
Author: Gregory R. Warnes, Ben Bolker, Gregor Gorjanc, Gabor
Grothendieck, Ales Korosec, Thomas Lumley, Don MacQueen, Arni
Magnusson, Jim Rogers, and others
Modified: trunk/gdata/NAMESPACE
===================================================================
--- trunk/gdata/NAMESPACE 2015-04-09 19:46:55 UTC (rev 1921)
+++ trunk/gdata/NAMESPACE 2015-04-10 03:15:42 UTC (rev 1922)
@@ -14,11 +14,14 @@
duplicated2,
elem,
env,
+ first,
frameApply,
installXLSXsupport,
interleave,
is.what,
keep,
+ last,
+ left,
ll,
ls.funs,
lowerTriangle,
@@ -31,6 +34,7 @@
remove.vars,
reorder.factor,
resample,
+ right,
sheetCount,
sheetNames,
startsWith,
@@ -151,3 +155,13 @@
S3method(trim, factor)
S3method(trim, list)
S3method(trim, data.frame)
+
+## first, last, left, right
+S3method(first, default)
+S3method(first, list )
+S3method(last, default)
+S3method(last, list )
+S3method(left, data.frame)
+S3method(left, matrix)
+S3method(right, data.frame)
+S3method(right, matrix)
Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS 2015-04-09 19:46:55 UTC (rev 1921)
+++ trunk/gdata/inst/NEWS 2015-04-10 03:15:42 UTC (rev 1922)
@@ -1,3 +1,15 @@
+Changes in 2.15.0 (2015-04-06)
+------------------------------
+
+New features:
+
+- New functions first() and last() to retrun the first or last
+ element of a vector or list.
+
+- New functions left() and right() to return the leftmost or
+ rightmost n (default to 6) columns of a matrix or dataframe.
+
+
Changes in 2.14.0 (2014-08-27)
------------------------------
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2015-04-09 19:46:58
|
Revision: 1921
http://sourceforge.net/p/r-gregmisc/code/1921
Author: warnes
Date: 2015-04-09 19:46:55 +0000 (Thu, 09 Apr 2015)
Log Message:
-----------
Update gtools ChangeLog
Modified Paths:
--------------
trunk/gtools/inst/ChangeLog
Modified: trunk/gtools/inst/ChangeLog
===================================================================
--- trunk/gtools/inst/ChangeLog 2015-04-09 19:45:21 UTC (rev 1920)
+++ trunk/gtools/inst/ChangeLog 2015-04-09 19:46:55 UTC (rev 1921)
@@ -1,3 +1,16 @@
+2015-04-09 warnes
+
+ * [r1920] DESCRIPTION, NAMESPACE, R/loadedPackages.R,
+ R/na.replace.R, inst/ChangeLog, inst/NEWS, man/loadedPackages.Rd,
+ man/na.replace.Rd: Move first()/last()/left()/right() to gdata.
+ Add new functions na.replace() and loadedPackages().
+ Add more text to package description.
+
+2015-04-08 warnes
+
+ * [r1919] NAMESPACE, R/first.R, man/first.Rd, man/left.Rd: Move
+ first/last/left/right to from gtools to gdata
+
2015-04-06 warnes
* [r1918] man/dirichlet.Rd: Correct URL
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2015-04-09 19:45:29
|
Revision: 1920
http://sourceforge.net/p/r-gregmisc/code/1920
Author: warnes
Date: 2015-04-09 19:45:21 +0000 (Thu, 09 Apr 2015)
Log Message:
-----------
Move first()/last()/left()/right() to gdata.
Add new functions na.replace() and loadedPackages().
Add more text to package description.
Modified Paths:
--------------
trunk/gtools/DESCRIPTION
trunk/gtools/NAMESPACE
trunk/gtools/inst/ChangeLog
trunk/gtools/inst/NEWS
Added Paths:
-----------
trunk/gtools/R/loadedPackages.R
trunk/gtools/R/na.replace.R
trunk/gtools/man/loadedPackages.Rd
trunk/gtools/man/na.replace.Rd
Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION 2015-04-08 19:55:41 UTC (rev 1919)
+++ trunk/gtools/DESCRIPTION 2015-04-09 19:45:21 UTC (rev 1920)
@@ -1,8 +1,25 @@
Package: gtools
-Title: Various R programming tools
-Description: Various R programming tools
-Version: 3.5.0
-Date: 2014-10-09
+Title: Various R Programming Tools
+Description: Functions to assist in R programming, including:
+ - assist in developing, updating, and maintaning R and R packages ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat'),
+ - calculate the logit and inverse logit transformations ('logit', 'inv.logit')
+ - test if a value is missing, empty or contains only NA and NULL values ('invalid')
+ - manipulate R's .Last function ('addLast')
+ - define macros ('defmacro'),
+ - detect odd and even integers ('odd', 'even')
+ - convert strings containig non-ascii characters (like single quotes) to plain ASCII ('ASCIIfy'),
+ - perform a binary search ('binseach')
+ - sort strings containing both numeric and character components ('mixedsort')
+ - create a factor variable from the quantiles of a continuous variable ('quantcut')
+ - enumerate permutations and combinations ('combinations', 'permutation'),
+ - calculate and convert betwen fold-change and log-ratio ('foldchange', 'logratio2foldchange', 'foldchange2logratio'),
+ - calculate probablities and generate random numbers from dirichlet distributions ('rdirichlet', 'ddirichlet')
+ - apply a function over adjacent subsets of a vector ('running')
+ - Modify the TCP\_NODELAY ('de-Nagle') flag for socket objects
+ - Efficient rbind of data frames, even if the column names don't match ('smartbind')
+ - Generate significance stars from p-values ('stars.pval')
+Version: 3.4.2
+Date: 2015-04-06
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes <gr...@wa...>
License: LGPL-2.1
Modified: trunk/gtools/NAMESPACE
===================================================================
--- trunk/gtools/NAMESPACE 2015-04-08 19:55:41 UTC (rev 1919)
+++ trunk/gtools/NAMESPACE 2015-04-09 19:45:21 UTC (rev 1920)
@@ -19,10 +19,12 @@
invalid,
keywords,
lastAdd,
+ loadedPackages,
logit,
logratio2foldchange,
mixedorder,
mixedsort,
+ na.replace,
odd,
permutations,
permute,
Added: trunk/gtools/R/loadedPackages.R
===================================================================
--- trunk/gtools/R/loadedPackages.R (rev 0)
+++ trunk/gtools/R/loadedPackages.R 2015-04-09 19:45:21 UTC (rev 1920)
@@ -0,0 +1,12 @@
+loadedPackages <- function(silent=FALSE)
+{
+ packageNames <- loadedNamespaces()
+ packageVersions <- sapply(packageNames, function(package) paste(packageVersion(package), sep=".") )
+ packagePaths <- find.package(packageNames)
+ inSearchPath <- match(packageNames, gsub('^package:', '', grep('^package:', search(), value=TRUE)))
+ retval <- data.frame(Name=packageNames, Version=packageVersions, Path=packagePaths, SearchPath=inSearchPath)
+ retval$SearchPath <- na.replace(retval$SearchPath, '-')
+ retval <- retval[order(inSearchPath),]
+ if(!silent) print(retval)
+ retval
+}
Added: trunk/gtools/R/na.replace.R
===================================================================
--- trunk/gtools/R/na.replace.R (rev 0)
+++ trunk/gtools/R/na.replace.R 2015-04-09 19:45:21 UTC (rev 1920)
@@ -0,0 +1,5 @@
+na.replace <- function(x, replace)
+{
+ x[is.na(x)] <- replace
+ x
+}
Modified: trunk/gtools/inst/ChangeLog
===================================================================
--- trunk/gtools/inst/ChangeLog 2015-04-08 19:55:41 UTC (rev 1919)
+++ trunk/gtools/inst/ChangeLog 2015-04-09 19:45:21 UTC (rev 1920)
@@ -1,5 +1,8 @@
2015-04-06 warnes
+ * [r1918] man/dirichlet.Rd: Correct URL
+ * [r1917] inst/ChangeLog, inst/NEWS: Update NEWS and ChangeLog for
+ gtools 3.5.0
* [r1916] inst/ChangeLog: Add ChangeLog files to repository
* [r1915] R/keywords.R: Implement fix to keywords() needed for
R-3.4.1, as suggested by Kurt
Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS 2015-04-08 19:55:41 UTC (rev 1919)
+++ trunk/gtools/inst/NEWS 2015-04-09 19:45:21 UTC (rev 1920)
@@ -1,13 +1,13 @@
-gtools 3.5.0 - 2015-04-06
+gtools 3.4.2 - 2015-04-06
-------------------------
New features:
-- New functions first() and last() to retrun the first or last
- element of a vector or list.
+- New function loadedPackages() to display name, version, and path of
+ loaded packages (package namespaces).
-- New functions left() and right() to return the leftmost or
- rightmost n (default to 6) columns of a matrix or dataframe.
+- New function: na.replace() to replace missing values within a
+ vector with a specified value.`
Bug fixes:
Added: trunk/gtools/man/loadedPackages.Rd
===================================================================
--- trunk/gtools/man/loadedPackages.Rd (rev 0)
+++ trunk/gtools/man/loadedPackages.Rd 2015-04-09 19:45:21 UTC (rev 1920)
@@ -0,0 +1,37 @@
+\name{loadedPackages}
+\alias{loadedPackages}
+\title{
+ Provide Name, Version, and Path of Loaded Package Namespaces
+}
+\description{
+ Provide name, version, and path of loaded package namespaces
+}
+\usage{
+loadedPackages(silent = FALSE)
+}
+\arguments{
+ \item{silent}{Logical indicating whether the results should be printed}
+}
+\value{
+ Data frame containing one row per loaded package namespace, with columns:
+ \item{Package}{Package name}
+ \item{Version}{Version string}
+ \item{Path}{Path to package files}
+ \item{SearchPath}{Either the index of the package namespace in the current
+ search path, or '-' if the package namespace is not in the search
+ path. '1' corresponds to the top of the search path (the first namespace
+ searched for values). }
+}
+\author{
+ Gregory R. Warnes \email{gr...@wa...}
+}
+\seealso{
+ \code{\link[base]{loadedNamespaces}},
+ \code{\link[utils]{packageVersion}},
+ \code{\link[base]{search}},
+ \code{\link[base]{find.package}}
+}
+\examples{
+ loadedPackages()
+}
+\keyword{package}
Added: trunk/gtools/man/na.replace.Rd
===================================================================
--- trunk/gtools/man/na.replace.Rd (rev 0)
+++ trunk/gtools/man/na.replace.Rd 2015-04-09 19:45:21 UTC (rev 1920)
@@ -0,0 +1,34 @@
+\name{na.replace}
+\alias{na.replace}
+\title{
+ Replace Missing Values
+}
+\description{
+ Replace missing values
+}
+\usage{
+na.replace(x, replace)
+}
+\arguments{
+ \item{x}{vector possibly contining missing (\code{NA}) values.}
+ \item{replace}{scalar replacement value}
+}
+\details{
+ This is a convenience function that is the same as
+ x[is.na(x)] <- replace
+}
+\value{
+ Vector with missing values (\code{NA}) replaced by the
+ value of \code{replace}.
+}
+\author{
+ Gregory R. Warnes \email{gr...@wa...}
+}
+\seealso{
+ \code{\link[base]{is.na}}, \code{\link[stats]{na.omit}}
+}
+\examples{
+ x <- c(1,2,3,NA,6,7,8,NA,NA)
+ na.replace(x, '999')
+}
+\keyword{ manip }
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|
|
From: <wa...@us...> - 2015-04-08 19:55:43
|
Revision: 1919
http://sourceforge.net/p/r-gregmisc/code/1919
Author: warnes
Date: 2015-04-08 19:55:41 +0000 (Wed, 08 Apr 2015)
Log Message:
-----------
Move first/last/left/right to from gtools to gdata
Modified Paths:
--------------
trunk/gtools/NAMESPACE
Added Paths:
-----------
trunk/gdata/R/first.R
trunk/gdata/man/first.Rd
trunk/gdata/man/left.Rd
Removed Paths:
-------------
trunk/gtools/R/first.R
trunk/gtools/man/first.Rd
trunk/gtools/man/left.Rd
Copied: trunk/gdata/R/first.R (from rev 1914, trunk/gtools/R/first.R)
===================================================================
--- trunk/gdata/R/first.R (rev 0)
+++ trunk/gdata/R/first.R 2015-04-08 19:55:41 UTC (rev 1919)
@@ -0,0 +1,30 @@
+first <- function(x) UseMethod("first")
+last <- function(x) UseMethod("last")
+
+left <- function(x, n=6) UseMethod("left")
+right <- function(x, n=6) UseMethod("left")
+
+
+first.default <- function(x) x[1]
+last.default <- function(x) x[length(x)]
+
+
+first.list <- function(x) x[[1]]
+last.list <- function(x) x[[length(x)]]
+
+
+left.data.frame <- function(x, n=6)
+{
+ n <- min(n, ncol(x))
+ x[, 1:n]
+}
+left.matrix <- left.data.frame
+
+
+right.data.frame <- function(x, n=6)
+{
+ n <- min(n, ncol(x))
+ x[, (ncol(x)-n+1):ncol(x)]
+}
+right.matrix <- right.data.frame
+
Copied: trunk/gdata/man/first.Rd (from rev 1913, trunk/gtools/man/first.Rd)
===================================================================
--- trunk/gdata/man/first.Rd (rev 0)
+++ trunk/gdata/man/first.Rd 2015-04-08 19:55:41 UTC (rev 1919)
@@ -0,0 +1,47 @@
+\name{first}
+\alias{first}
+\alias{first.default}
+\alias{first.list}
+\alias{last}
+\alias{last.default}
+\alias{last.list}
+\title{Return first or last element of a vector or list}
+\description{
+ Return first or last element of a vector or list
+}
+\usage{
+first(x)
+last(x)
+\method{first}{default}(x)
+\method{last}{default}(x)
+\method{first}{list}(x)
+\method{last}{list}(x)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+ \item{x}{vector or list}
+}
+\value{
+ The first or last element of \code{x}.
+}
+\author{
+ Gregory R. Warnes \email{gr...@wa...}
+}
+\seealso{
+ \code{\link[utils]{head}},
+ \code{\link[utils]{tail}},
+ \code{\link{left}},
+ \code{\link{right}}
+}
+\examples{
+## works for vectors..
+v <- 1:10
+first(v)
+last(v)
+
+## and for lists
+l <- list(a=1, b=2, c=3)
+first(l)
+last(l)
+}
+\keyword{ manip }
Copied: trunk/gdata/man/left.Rd (from rev 1913, trunk/gtools/man/left.Rd)
===================================================================
--- trunk/gdata/man/left.Rd (rev 0)
+++ trunk/gdata/man/left.Rd 2015-04-08 19:55:41 UTC (rev 1919)
@@ -0,0 +1,39 @@
+\name{left}
+\alias{right}
+\alias{left}
+\title{Return the leftmost or rightmost columns of a matrix or dataframe}
+\description{
+ Return the leftmost or rightmost or columns of a matrix or dataframe
+}
+\usage{
+right(x, n = 6)
+left(x, n=6)
+}
+\arguments{
+ \item{x}{Matrix or dataframe}
+ \item{n}{Number of columns to return}
+}
+\value{
+ An object consisting of the leftmost or rightmost \code{n} columns
+ of \code{x}.
+}
+\author{
+ Gregory R. Warnes \email{gr...@wa...}
+}
+\seealso{
+ \code{\link{first}},
+ \code{\link{last}},
+ \code{\link[utils]{head}},
+ \code{\link[utils]{tail}}
+}
+\examples{
+ m <- matrix( 1:100, ncol=10 )
+ colnames(m) <- paste("Col",1:10, sep="_")
+ left(m)
+ right(m)
+
+ d <- as.data.frame(m)
+ left(d)
+ right(d)
+}
+\keyword{ manip }
Modified: trunk/gtools/NAMESPACE
===================================================================
--- trunk/gtools/NAMESPACE 2015-04-06 22:09:54 UTC (rev 1918)
+++ trunk/gtools/NAMESPACE 2015-04-08 19:55:41 UTC (rev 1919)
@@ -12,15 +12,12 @@
ddirichlet,
defmacro,
even,
- first,
foldchange,
foldchange2logratio,
getDependencies,
inv.logit,
invalid,
keywords,
- last,
- left,
lastAdd,
logit,
logratio2foldchange,
@@ -30,7 +27,6 @@
permutations,
permute,
quantcut,
- right,
rdirichlet,
running,
scat,
@@ -40,16 +36,3 @@
stars.pval,
strmacro
)
-
-S3method(first, default)
-S3method(first, list )
-
-S3method(last, default)
-S3method(last, list )
-
-S3method(left, data.frame)
-S3method(left, matrix)
-
-S3method(right, data.frame)
-S3method(right, matrix)
-
Deleted: trunk/gtools/R/first.R
===================================================================
--- trunk/gtools/R/first.R 2015-04-06 22:09:54 UTC (rev 1918)
+++ trunk/gtools/R/first.R 2015-04-08 19:55:41 UTC (rev 1919)
@@ -1,30 +0,0 @@
-first <- function(x) UseMethod("first")
-last <- function(x) UseMethod("last")
-
-left <- function(x, n=6) UseMethod("left")
-right <- function(x, n=6) UseMethod("left")
-
-
-first.default <- function(x) x[1]
-last.default <- function(x) x[length(x)]
-
-
-first.list <- function(x) x[[1]]
-last.list <- function(x) x[[length(x)]]
-
-
-left.data.frame <- function(x, n=6)
-{
- n <- min(n, ncol(x))
- x[, 1:n]
-}
-left.matrix <- left.data.frame
-
-
-right.data.frame <- function(x, n=6)
-{
- n <- min(n, ncol(x))
- x[, (ncol(x)-n+1):ncol(x)]
-}
-right.matrix <- right.data.frame
-
Deleted: trunk/gtools/man/first.Rd
===================================================================
--- trunk/gtools/man/first.Rd 2015-04-06 22:09:54 UTC (rev 1918)
+++ trunk/gtools/man/first.Rd 2015-04-08 19:55:41 UTC (rev 1919)
@@ -1,47 +0,0 @@
-\name{first}
-\alias{first}
-\alias{first.default}
-\alias{first.list}
-\alias{last}
-\alias{last.default}
-\alias{last.list}
-\title{Return first or last element of a vector or list}
-\description{
- Return first or last element of a vector or list
-}
-\usage{
-first(x)
-last(x)
-\method{first}{default}(x)
-\method{last}{default}(x)
-\method{first}{list}(x)
-\method{last}{list}(x)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
- \item{x}{vector or list}
-}
-\value{
- The first or last element of \code{x}.
-}
-\author{
- Gregory R. Warnes \email{gr...@wa...}
-}
-\seealso{
- \code{\link[utils]{head}},
- \code{\link[utils]{tail}},
- \code{\link{left}},
- \code{\link{right}}
-}
-\examples{
-## works for vectors..
-v <- 1:10
-first(v)
-last(v)
-
-## and for lists
-l <- list(a=1, b=2, c=3)
-first(l)
-last(l)
-}
-\keyword{ manip }
Deleted: trunk/gtools/man/left.Rd
===================================================================
--- trunk/gtools/man/left.Rd 2015-04-06 22:09:54 UTC (rev 1918)
+++ trunk/gtools/man/left.Rd 2015-04-08 19:55:41 UTC (rev 1919)
@@ -1,39 +0,0 @@
-\name{left}
-\alias{right}
-\alias{left}
-\title{Return the leftmost or rightmost columns of a matrix or dataframe}
-\description{
- Return the leftmost or rightmost or columns of a matrix or dataframe
-}
-\usage{
-right(x, n = 6)
-left(x, n=6)
-}
-\arguments{
- \item{x}{Matrix or dataframe}
- \item{n}{Number of columns to return}
-}
-\value{
- An object consisting of the leftmost or rightmost \code{n} columns
- of \code{x}.
-}
-\author{
- Gregory R. Warnes \email{gr...@wa...}
-}
-\seealso{
- \code{\link{first}},
- \code{\link{last}},
- \code{\link[utils]{head}},
- \code{\link[utils]{tail}}
-}
-\examples{
- m <- matrix( 1:100, ncol=10 )
- colnames(m) <- paste("Col",1:10, sep="_")
- left(m)
- right(m)
-
- d <- as.data.frame(m)
- left(d)
- right(d)
-}
-\keyword{ manip }
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|
|
From: <wa...@us...> - 2015-04-06 22:09:57
|
Revision: 1918
http://sourceforge.net/p/r-gregmisc/code/1918
Author: warnes
Date: 2015-04-06 22:09:54 +0000 (Mon, 06 Apr 2015)
Log Message:
-----------
Correct URL
Modified Paths:
--------------
trunk/gtools/man/dirichlet.Rd
Modified: trunk/gtools/man/dirichlet.Rd
===================================================================
--- trunk/gtools/man/dirichlet.Rd 2015-04-06 22:04:28 UTC (rev 1917)
+++ trunk/gtools/man/dirichlet.Rd 2015-04-06 22:09:54 UTC (rev 1918)
@@ -33,8 +33,8 @@
}
\author{
Code original posted by Ben Bolker to R-News on Fri Dec 15 2000. See
- \url{http://www.r-project.org/nocvs/mail/r-help/2000/3865.html}. Ben
- attributed the code to Ian Wilson \email{i.w...@ma...}.
+ \url{https://stat.ethz.ch/pipermail/r-help/2000-December/009561.html}.
+ Ben attributed the code to Ian Wilson \email{i.w...@ma...}.
Subsequent modifications by Gregory R. Warnes
\email{gr...@wa...}.
}
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|
|
From: <wa...@us...> - 2015-04-06 22:04:30
|
Revision: 1917
http://sourceforge.net/p/r-gregmisc/code/1917
Author: warnes
Date: 2015-04-06 22:04:28 +0000 (Mon, 06 Apr 2015)
Log Message:
-----------
Update NEWS and ChangeLog for gtools 3.5.0
Modified Paths:
--------------
trunk/gtools/inst/ChangeLog
trunk/gtools/inst/NEWS
Modified: trunk/gtools/inst/ChangeLog
===================================================================
--- trunk/gtools/inst/ChangeLog 2015-04-06 21:52:12 UTC (rev 1916)
+++ trunk/gtools/inst/ChangeLog 2015-04-06 22:04:28 UTC (rev 1917)
@@ -1,5 +1,18 @@
+2015-04-06 warnes
+
+ * [r1916] inst/ChangeLog: Add ChangeLog files to repository
+ * [r1915] R/keywords.R: Implement fix to keywords() needed for
+ R-3.4.1, as suggested by Kurt
+ Hornik.
+ * [r1914] NAMESPACE, R/first.R: - Export S3 methods for first(),
+ last(), left() and right().
+ - Ensure code matches man page for first(), last(), left(), and
+ right().
+
2014-10-09 warnes
+ * [r1897] DESCRIPTION, inst/NEWS: Update for 3.5.0 release of
+ gtools
* [r1896] R/first.R: Make right() and left() S3 methods for classes
data.frame and matrix
Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS 2015-04-06 21:52:12 UTC (rev 1916)
+++ trunk/gtools/inst/NEWS 2015-04-06 22:04:28 UTC (rev 1917)
@@ -1,4 +1,4 @@
-gtools 3.5.0 - 2014-10-08
+gtools 3.5.0 - 2015-04-06
-------------------------
New features:
@@ -9,7 +9,11 @@
- New functions left() and right() to return the leftmost or
rightmost n (default to 6) columns of a matrix or dataframe.
+Bug fixes:
+- Modify keywords() to work properly in R 3.4.X and later.
+
+
gtools 3.4.1 - 2014-05-27
-------------------------
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|
|
From: <wa...@us...> - 2015-04-06 21:52:15
|
Revision: 1916
http://sourceforge.net/p/r-gregmisc/code/1916
Author: warnes
Date: 2015-04-06 21:52:12 +0000 (Mon, 06 Apr 2015)
Log Message:
-----------
Add ChangeLog files to repository
Added Paths:
-----------
trunk/gmodels/inst/ChangeLog
trunk/gplots/inst/ChangeLog
trunk/gtools/inst/ChangeLog
Added: trunk/gmodels/inst/ChangeLog
===================================================================
--- trunk/gmodels/inst/ChangeLog (rev 0)
+++ trunk/gmodels/inst/ChangeLog 2015-04-06 21:52:12 UTC (rev 1916)
@@ -0,0 +1,614 @@
+2014-07-24 warnes
+
+ * [r1868] DESCRIPTION, NAMESPACE, R/ci.R, R/estimable.R, man/ci.Rd,
+ man/estimable.Rd: - Estimable now adds the class 'estimable' to
+ returned objects.
+ - New ci() method for estimable objects.
+ - Minor improvemets to man page formatting.
+
+2013-07-18 warnes
+
+ * [r1710] DESCRIPTION, inst/NEWS: Looks like Brian Ripley
+ repackaged for R 3.0.0 and bumped version number, so change it to
+ 2.15.5
+ * [r1709] DESCRIPTION, inst/NEWS: Update for gmodels 2.15.4
+ * [r1708] man/ci.Rd: Update to current Rd syntax
+ * [r1707] R/estimable.mlm.R, test/test_estimable_mlm.R: Correct bug
+ in estimable.mlm
+
+2013-07-15 warnes
+
+ * [r1706] R/ci.R, man/ci.Rd: Remove unused argument to ci.mer
+
+2012-06-28 warnes
+
+ * [r1577] DESCRIPTION, inst/NEWS: Update for gmodels version
+ 2.15.3.
+ * [r1576] R/percentile.R: Move percentile() function to a separate
+ file.
+ * [r1575] R/est.lmer.R, R/est.mer.R: Update est.mer() to support
+ new S4 "mer" class.
+ * [r1574] man/ci.Rd: Make lme4 example executable.
+
+2012-06-27 warnes
+
+ * [r1573] test/lme-test.R: Add test code submitted by
+ Ari...@or....
+
+2012-04-19 warnes
+
+ * [r1528] inst/NEWS: Update for release 2.15.2
+ * [r1527] DESCRIPTION: Update version and date.
+ * [r1526] man/estimable.Rd: The 'Design' package has been replaced
+ my 'rms', so update man page references.
+ * [r1525] R/ci.R, R/est.mer.R: More fixes for support of S4 'mer'
+ class from lme4 package.
+ * [r1524] man/coefFrame.Rd: Split long line.
+ * [r1523] man/ci.Rd, man/glh.test.Rd: Changes to pass R CMD check
+
+2011-12-14 warnes
+
+ * [r1521] R/ci.R: Improve formatting of ci.mer().
+ * [r1520] R/est.mer.R: Modify est.mer to work with recent lme4
+ 'mer' S4 objects.
+
+2011-01-16 warnes
+
+ * [r1466] DESCRIPTION, inst/NEWS, man/ci.Rd, man/estimable.Rd,
+ man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd,
+ man/make.contrasts.Rd: Fix warnings reported by R CMD check.
+ Update version number to 2.15.1.
+
+2009-05-09 warnes
+
+ * [r1337] test, test/lme-test.R: Add tests for lme4 'mer' objects
+ * [r1336] inst/NEWS: Update for 2.15.0
+ * [r1335] DESCRIPTION: Update description for 2.15.0
+ * [r1334] R/est.mer.R: Add support for lme4's 'mer' objects
+ * [r1333] NAMESPACE, R/ci.R, R/est.lmer.R, R/estimable.R,
+ R/fit.contrast.R, R/to.est.R: Add support for lme4's 'mer'
+ objects
+ * [r1332] man/glh.test.Rd: Fix .Rd syntax error
+ * [r1331] NEWS: Add softlinks for ChangeLog and NEWS to top level
+ dir for convenience
+ * [r1330] ChangeLog, NEWS, inst, inst/NEWS: Move ChangeLog and NEWS
+ files into inst directory
+ * [r1329] DESCRIPTION, man/ci.Rd, man/estimable.Rd,
+ man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd,
+ man/make.contrasts.Rd: Update Greg's email address
+
+2008-04-10 warnes
+
+ * [r1255] man/ci.Rd: Improve languages a bit
+
+2008-01-02 warnes
+
+ * [r1236] man/CrossTable.Rd: Update Marc's email address
+
+2007-12-12 warnes
+
+ * [r1233] DESCRIPTION: Move copyright notice for Randall's
+ contributions from License section to Author section of the
+ DESCRIPTION file.
+
+2007-12-07 warnes
+
+ * [r1232] DESCRIPTION, NEWS: Update DESCRIPTION and NEWS for
+ release 2.14.1
+ * [r1231] man/estimable.Rd: Correct minor typos in man page for
+ estimable()
+ * [r1230] R/estimable.R: Add support for lme models to estimable()
+ * [r1229] man/estimable.Rd: Replace non-ascii characters in Soren's
+ name with (equivalent?) ascii character to avoid character
+ encoding issues.
+
+2007-10-22 warnes
+
+ * [r1196] DESCRIPTION: Clarify GPL version
+
+2007-07-26 warnes
+
+ * [r1105] DESCRIPTION, NAMESPACE, NEWS, R/estimable.mlm.R,
+ man/estimable.Rd: Add support for mlm to estimable().
+ * [r1104] R/estimable.R, R/estimable.mlm.R: Add estimable method
+ for mlm objects
+
+2007-03-09 warnes
+
+ * [r1079] R/ci.R: Remove stray character
+ * [r1078] NEWS: Update NEWS file.
+ * [r1077] DESCRIPTION: Update version number
+ * [r1076] R/ci.R: Minor code formatting changes
+ * [r1075] R/est.lmer.R, man/ci.Rd: Flip lower and upper interval in
+ ci.lmer(). Add example to man page.
+ * [r1074] man/ci.Rd, man/estimable.Rd: Fix some old email
+ addressses that got missed
+
+2006-11-29 warnes
+
+ * [r1029] NEWS: Update for 2.13.1
+ * [r1028] NAMESPACE: Correct declartion of S3 methods for
+ estimable()
+ * [r1027] DESCRIPTION: Add additional suggested packages
+ * [r1026] R/estimable.R, man/estimable.Rd: - Add generic
+ - Fix code vs. doc inconsistiencies
+
+2006-11-28 warnes
+
+ * [r1025] R/ci.R, R/estimable.R, R/fast.prcomp.R: Remove extraneous
+ comma that causes errors in R 2.5.0
+
+2006-11-27 warnes
+
+ * [r1016] DESCRIPTION, NEWS: Update for 2.13.1
+ * [r1015] DESCRIPTION, NAMESPACE: Add missing export of methods for
+ estimable()
+
+2006-11-14 ggorjan
+
+ * [r1012] R/ci.R, R/fast.prcomp.R, man/ci.Rd: Removed executable
+ property
+
+2006-08-02 warnes
+
+ * [r977] man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd,
+ man/make.contrasts.Rd: Update my email address
+
+2006-06-06 nj7w
+
+ * [r966] man/ci.Rd, man/estimable.Rd, man/fit.contrast.Rd: Updated
+ ci, estimable and fit.contrast as per Randall Johnson
+
+2006-06-05 nj7w
+
+ * [r965] DESCRIPTION: Additions as per Randall C Johnson
+ * [r964] R/ci.R, R/estimable.R, R/fit.contrast.R, R/to.est.R:
+ Additions as per Randall C Johnson
+ * [r963] R/est.lmer.R: - New function to estimate CI's and p-values
+ using mcmcsamp() from the
+ Matrix package
+
+2006-05-05 nj7w
+
+ * [r959] R/CrossTable.R, man/CrossTable.Rd: Fixed an error:
+ According to Marc Schwartz - there was an error when a matrix
+ without dimnames(or names(dimnames)) was passed as x argument
+
+2005-12-13 nj7w
+
+ * [r808] ChangeLog: Removed ChangeLog
+ * [r807] NEWS: Updated NEWS
+
+2005-12-12 nj7w
+
+ * [r796] DESCRIPTION: Updated version number for CRAN
+
+2005-12-04 warnes
+
+ * [r781] NEWS: Update for 2.11.0
+ * [r780] DESCRIPTION, NAMESPACE, R/ci.R, R/estimable.R,
+ R/fit.contrast.R, R/to.est.R, man/ci.Rd, man/estimable.Rd:
+ Integration of code changes suggested by Randall C Johnson to add
+ support for lmer (lme version 4) objects to ci(), estimable(),
+ and
+ fit.contrast().
+
+ Addition of simplified coefficient specificaiton for estimable()
+ based on a function provided by Randall C Johnson. It is now
+ possible to do things like:
+ estimable(reg, c("xB"=1,"xD"=-1) )
+ instead of:
+ estimable(reg, c( 0, 1, 0, -1) )
+ which should make estimable much easier to use for large models.
+
+2005-12-01 nj7w
+
+ * [r776] man/ci.Rd, man/coefFrame.Rd, man/estimable.Rd,
+ man/fit.contrast.Rd, man/make.contrasts.Rd: Updated Greg's email
+ address
+
+2005-10-27 warnes
+
+ * [r709] DESCRIPTION: Update version number. Bump minor version
+ since we added functionality.
+ * [r708] DESCRIPTION, NAMESPACE: Add ci.binom() to NAMESPACE, bump
+ version
+
+2005-10-26 warnes
+
+ * [r707] R/ci.R, man/ci.Rd: Add ci.binom
+
+2005-10-25 warnes
+
+ * [r706] NAMESPACE: Add gdata::nobs to import list. Needed by ci()
+
+2005-09-12 nj7w
+
+ * [r671] man/fast.prcomp.Rd, man/glh.test.Rd: Updated Greg's email
+
+2005-09-07 nj7w
+
+ * [r667] man/CrossTable.Rd: Fixed man page
+
+2005-09-06 nj7w
+
+ * [r664] DESCRIPTION: Updated DESCRIPTION
+ * [r663] NEWS: Added NEWS
+ * [r662] DESCRIPTION: Fixed the Package name
+
+2005-09-02 nj7w
+
+ * [r655] ChangeLog: Added ChangeLog
+
+2005-08-31 nj7w
+
+ * [r644] DESCRIPTION: Added DESCRIPTION file
+ * [r643] DESCRIPTION.in: removed DESCRIPTION.in
+
+2005-07-11 nj7w
+
+ * [r627] R/CrossTable.R, man/CrossTable.Rd: Revision based on Marc
+ Schwartz's suggestions:
+ 1) Added 'dnn' argument to enable specification of dimnames as
+ per table()
+ 2) Corrected bug in SPSS output for 1d table, where proportions
+ were being printed and not percentages ('%' output)
+
+2005-06-09 nj7w
+
+ * [r625] R/ci.R, R/coefFrame.R, R/estimable.R, R/fast.prcomp.R,
+ R/fit.contrast.R, R/glh.test.R, R/make.contrasts.R,
+ man/CrossTable.Rd, man/ci.Rd, man/coefFrame.Rd, man/estimable.Rd,
+ man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd,
+ man/make.contrasts.Rd: Updating the version number, and various
+ help files to synchronize splitting of gregmisc bundle in 4
+ individual components.
+ * [r623] R/CrossTable.R: Updates by Marc Schwartz:
+ CrossTable:
+
+ # Revision 2.0 2005/04/27
+ # Added 'format = "d"' to all table count output
+ # so that large integers do not print in
+ # scientific notation
+
+2005-05-13 nj7w
+
+ * [r621] man/CrossTable.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.
+
+2005-05-11 warnes
+
+ * [r620] DESCRIPTION.in, NAMESPACE: Add dependency on
+ gdata::frameApply.
+
+2005-03-31 warnes
+
+ * [r593] NAMESPACE: Add ceofFrame function to NAMESPACE
+ * [r592] man/coefFrame.Rd: coefFrame example needs to properly load
+ ELISA data from gtools package
+ * [r588] R/CrossTable.R, man/CrossTable.Rd, man/ci.Rd,
+ man/estimable.Rd, man/fast.prcomp.Rd, man/fit.contrast.Rd,
+ man/glh.test.Rd, man/make.contrasts.Rd: Ensure that each file has
+ $Id$ header, and no $Log$
+ * [r587] R/coefFrame.R, man/coefFrame.Rd: Add coefFrame() function
+ contributed by Jim Rogers
+
+2005-01-18 warnes
+
+ * [r521] R/CrossTable.R: Removed Windows Line Endings
+
+2005-01-14 nj7w
+
+ * [r518] man/CrossTable.Rd: Updated the manual to reflect
+ prop.chisq change in its R file.
+
+2005-01-14 warnes
+
+ * [r517] R/CrossTable.R: Nitin added display of the Chisquare
+ contribution of each cell, as suggested
+ by Greg Snow.
+
+2005-01-12 warnes
+
+ * [r515] DESCRIPTION.in: Add dependency on R 1.9.0+ to prevent
+ poeple from installing on old
+ versions of R which don't support namespaces.
+
+2004-12-23 nj7w
+
+ * [r507] R/CrossTable.R, man/CrossTable.Rd: Split the function
+ print.CrossTable.vector in two parts - for SAS behaiour and SPSS
+ behaviour. Also put the code of printing statistics in a function
+ 'print.statistics'
+
+2004-12-21 warnes
+
+ * [r502] R/CrossTable.R: Added & extended changes made by Nitin to
+ implement 'SPSS' format, as suggested by
+ Dirk Enzmann <dir...@ju...>.
+
+2004-09-30 warneg
+
+ * [r464] man/glh.test.Rd: Fix typos.
+
+2004-09-27 warneg
+
+ * [r461] DESCRIPTION, DESCRIPTION.in: Updated to pass R CMD check.
+
+2004-09-03 warneg
+
+ * [r450] man/fit.contrast.Rd: Add explicit package to call to
+ quantcut in example.
+ * [r446] DESCRIPTION, NAMESPACE, R/CrossTable.R, R/ci.R,
+ R/estimable.R, R/fast.prcomp.R, R/fit.contrast.R, R/glh.test.R,
+ R/make.contrasts.R, man/estimable.Rd, man/fit.contrast.Rd,
+ man/glh.test.Rd, man/make.contrasts.Rd: initial bundle checkin
+
+2004-09-02 warneg
+
+ * [r442] DESCRIPTION, DESCRIPTION.in, NAMESPACE: Initial revision
+
+2004-05-25 warnes
+
+ * [r327] R/CrossTable.R, man/CrossTable.Rd: Updates from Mark
+ Schwartz.
+
+2004-04-13 warnes
+
+ * [r314] man/estimable.Rd: Fix latex warning: it doesn't like
+ double subscripts.
+
+2004-03-26 warnes
+
+ * [r306] man/fast.prcomp.Rd: Reflect movement of code from 'mva'
+ package to 'stats' in R 1.9.0.
+
+2004-03-25 warnes
+
+ * [r296] R/estimable.R, man/estimable.Rd: - Estimable was reporting
+ sqrt(X^2) rather than X^2 in the output.
+ - Provide latex math markup for linear algebra expressions in
+ help text.
+ - Other clarifications in help text
+ * [r295] R/estimable.R, man/estimable.Rd: Add enhancements to
+ estimable() provided by S�ren H�jsgaard
+ \email{so...@ag...}:
+
+ I have made a modified version of the function [..] which
+ 1) also works on geese and gee objects and
+ 2) can test hypotheses af the forb L * beta = beta0 both as a
+ single Wald test and row-wise for each row in L.
+
+2003-11-17 warnes
+
+ * [r221] R/fit.contrast.R: - Fix incorrect handling of glm objects
+ by fit.contrast, as reported
+ by Ulrich Halekoh, Phd <ulr...@ag...>.
+
+ - Add regression test code to for this bug.
+
+2003-08-07 warnes
+
+ * [r217] R/ci.R: - Fixed incorrect denominator in standard error
+ for mean in ci.default.
+
+2003-04-22 warnes
+
+ * [r190] R/fit.contrast.R: - the variable 'df' was used within the
+ lme code section overwriting
+ the argument 'df'.
+
+2003-03-12 warnes
+
+ * [r173] man/fit.contrast.Rd: - Fixed a typo in the example
+ - Added to lme example
+
+2003-03-07 warnes
+
+ * [r168] R/fast.prcomp.R: - Minor changes to code to allow the
+ package to be provided as an
+ S-Plus chapter.
+
+2003-01-30 warnes
+
+ * [r160] R/fit.contrast.R, man/fit.contrast.Rd: - Renamed
+ 'contrast.lm' to 'fit.contrast'. This new name is more
+ descriptive and makes it easier to create and use methods for
+ other
+ classes, eg lme.
+
+ - Enabled fit.contrast for lme object now that Doug Bates has
+ provided
+ the necessary support for contrasts in the nlme package.
+
+ - New contrast.lm function which generates a 'depreciated'
+ warning and
+ calls fit.contrast
+
+ - Updated help text to match changes.
+ * [r158] R/CrossTable.R, man/CrossTable.Rd: - Removed argument
+ 'correct' and now print separate corrected values
+ for 2 x 2 tables.
+ - Added arguments 'prop.r', 'prop.c' and 'prop.t' to toggle
+ printing
+ of row, col and table percentages. Default is TRUE.
+ - Added argument 'fisher' to toggle fisher exact test. Default is
+ FALSE.
+ - Added McNemar test to statistics and argument 'mcnemar' to
+ toggle
+ test. Default is FALSE.
+ - Added code to generate an invisible return list containing
+ table
+ counts, proportions and the results of the appropriate
+ statistical tests.
+ * [r157] R/make.contrasts.R: - Added explicit check to ensure that
+ the number of specified
+ contrasts is less than or equal to the ncol - 1. Previously, this
+ failed with an obtuse error message when the contrast matrix had
+ row
+ names, and silently dropped contrasts over ncol-1.
+
+2002-11-04 warnes
+
+ * [r142] R/CrossTable.R: - Moved fisher.test() to after table is
+ printed, so that table is
+ still printed in the event that fisher.test() results in errors.
+
+2002-10-29 warnes
+
+ * [r138] R/fast.prcomp.R, man/fast.prcomp.Rd: - Fixes to fast.svd
+ to make it actually work.
+ - Updates to man page to fix mistmatches between code and docs
+ and to
+ fix warnings.
+ * [r137] R/make.contrasts.R, man/make.contrasts.Rd: - Moved
+ make.contrasts to a separate file.
+ - Enhanced make contrasts to better label contrast matrix, to
+ give
+ how.many a default value, and to coerce vectors into row
+ matrixes.
+ - Added help page for make.contrasts.
+ - Added link from contrasts.lm seealso to make.contrasts.
+ * [r136] R/fast.prcomp.R, man/fast.prcomp.Rd: Initial checkin for
+ fast.prcomp() and fast.svd().
+
+2002-09-26 warnes
+
+ * [r127] man/glh.test.Rd: - Added note and example code to
+ illustrate how to properly compute
+ contrasts for the first factor in the model.
+
+2002-09-24 warnes
+
+ * [r124] R/glh.test.R: - Fixed a typo.
+
+2002-09-23 warnes
+
+ * [r119] man/CrossTable.Rd, man/glh.test.Rd: - Fixed syntax errors
+ in barplot2.Rd and CrossTable.Rd
+ - Fixed incorrect translation of 'F' (distribution) to 'FALSE' in
+ glh.test.Rd
+ * [r117] R/ci.R, man/estimable.Rd, man/glh.test.Rd: - Modified all
+ files to include CVS Id and Log tags.
+ * [r116] R/CrossTable.R, man/CrossTable.Rd: - Added CrossTable()
+ and barplot2() code and docs contributed by Marc Schwartz.
+ - Permit combinations() to be used when r>n provided
+ repeat.allowed=TRUE
+ - Bumped up version number
+
+2002-08-01 warnes
+
+ * [r114] R/ci.R, man/ci.Rd, man/estimable.Rd, man/glh.test.Rd: -
+ Corrected documentation mismatch for ci, ci.default.
+
+ - Replaced all occurences of '_' for assignment with '<-'.
+
+ - Replaced all occurences of 'T' or 'F' for 'TRUE' and 'FALSE'
+ with
+ the spelled out version.
+
+ - Updaded version number and date.
+
+2002-04-09 warneg
+
+ * [r109] R/ci.R, R/estimable.R, R/glh.test.R, man/glh.test.Rd:
+ Checkin for version 0.5.3
+
+2002-03-26 warneg
+
+ * [r104] R/ci.R, R/glh.test.R, man/ci.Rd, man/glh.test.Rd: -
+ Changed methods to include '...' to match the generic.
+ - Updated for version 0.5.1
+ * [r99] man/glh.test.Rd: Removed incorrect link to 'contrast' from
+ seealso.
+
+2002-02-20 warneg
+
+ * [r81] man/ci.Rd, man/estimable.Rd, man/glh.test.Rd: Minor
+ changes, typo and formatting fixes.
+
+2002-01-17 warneg
+
+ * [r70] man/estimable.Rd: - Fixed errror in last example by adding
+ 'conf.int' parameter to
+ 'estimable' call.
+ * [r69] R/glh.test.R: - Fixed typo in code that resulted in an
+ syntax error.
+
+2002-01-10 warneg
+
+ * [r68] R/glh.test.R: - print.glh.test() was using cat() to
+ printing the call. This didn't work and
+ generated an error.
+
+2001-12-19 warneg
+
+ * [r66] man/glh.test.Rd: - Fixed display of formulae.
+ - Added description of return value
+ * [r65] R/glh.test.R: - Removed extra element of return object.
+
+2001-12-18 warneg
+
+ * [r64] man/estimable.Rd: - Updated documentation to reflect change
+ of parameters from 'alpha'
+ to 'conf.int', including the new optional status of the
+ confidence
+ intervals.
+ * [r63] R/estimable.R: - Modified to make confidence intervals
+ optional. Changed 'alpha'
+ parameter giving significance level to 'conf.int' giving
+ confidence
+ level.
+ * [r62] man/glh.test.Rd: - Added summary.glh.test to alias, usage,
+ and example sections.
+ * [r61] R/glh.test.R: - Modified to work correctly when obj is of
+ class 'aov' by specifying
+ summary.lm instead of summary. This ensures that the summary
+ object
+ has the fields we need.
+
+ - Moved detailed reporting of results from 'print' to 'summary'
+ function and added a simpler report to 'print'
+ * [r60] R/estimable.R: - Modified to work correctly when obj is of
+ class 'aov' by specifying
+ summary.lm instead of summary. This ensures that the summary
+ object
+ has the fields we need.
+ * [r59] R/glh.test.R, man/glh.test.Rd: Initial checkin.
+
+2001-12-17 warneg
+
+ * [r56] man/estimable.Rd: - Fixed spelling errors.
+ * [r55] man/estimable.Rd: - Fixed the link to contrasts.lm.
+ - Rephrased title/description to be more clear.
+
+2001-12-10 warneg
+
+ * [r49] man/estimable.Rd: Renamed 'contrsts.coeff.Rd' to
+ 'estimable.Rd' corresponding to function rename.
+ * [r48] R/estimable.R: renamed from contrast.coeff.R to estimable.R
+ (incorrectly via contrast.lm.R)
+
+2001-12-07 warneg
+
+ * [r37] man/ci.Rd: - Added text noting that lme is now supported.
+ * [r36] R/ci.R: - Fixed typo: DF column was being filled in with
+ p-value.
+ * [r35] R/ci.R: - Added ci.lme method to handle lme objects.
+
+2001-10-16 warneg
+
+ * [r27] man/ci.Rd: Fixed unbalanced brace.
+
+2001-08-25 warneg
+
+ * [r12] man/ci.Rd: - Added CVS header.
+ - Added my email address.
+
+2001-05-30 warneg
+
+ * [r2] ., R, R/ci.R, man, man/ci.Rd: Initial revision
+
Added: trunk/gplots/inst/ChangeLog
===================================================================
--- trunk/gplots/inst/ChangeLog (rev 0)
+++ trunk/gplots/inst/ChangeLog 2015-04-06 21:52:12 UTC (rev 1916)
@@ -0,0 +1,1561 @@
+2014-12-02 warnes
+
+ * [r1907] inst/NEWS: Add descrioption of node stack overflow issue
+ and work-around.
+ * [r1906] R/bandplot.R: Move '...' argument to bandplot.formula to
+ match man page.
+ * [r1905] tests/test_plottingDeepDendrogram.R: plot.dendrogram
+ isn't exported by gplots, so it must be referenced using the
+ ':::' notation.
+ * [r1904] man/bandplot.Rd: Man page fixes.
+ * [r1903] NAMESPACE: Add exports of new bandplot methods to
+ NAMESPACE file.
+ * [r1902] R/bandplot.R: Code cleanup.
+ * [r1901] R/bandplot.R: Simplify model.frame code for
+ bandplot.formula.
+
+2014-12-01 warnes
+
+ * [r1900] inst/NEWS: Update for 2.15.0
+ * [r1899] DESCRIPTION, R/bandplot.R, man/bandplot.Rd: Convert
+ bandplot to S3-method dispatch and add method for class formula.
+ * [r1898] NAMESPACE: Improve whitespace
+
+2014-09-17 warnes
+
+ * [r1895] NAMESPACE: Minor reformatting.
+ * [r1894] R/plotNode.R: Explicitly reset namespace for dendrogram
+ functions copied from stats.
+ * [r1893] DESCRIPTION, inst/NEWS: Update DESCRIPTION and NEWS for
+ gplots 2.14.2
+ * [r1892] R/heatmap.2.R, R/plotNode.R: To work around recursion
+ limit issues triggered by deeply nested
+ dendrograms, (1) create a local *intepreted* copy of
+ stats:::plotNode(), (2) detect recursion limit error message
+ within
+ heatmap.2() and generate a more user-friendly message.
+ * [r1891] tests/dat.csv, tests/test_plottingDeepDendrogram.R: Add
+ test case for exceeding recursion limits when plotting deeply
+ nested dendrograms
+ * [r1890] R/heatmap.2.R: heatmap.2 was not properly handling
+ integer vectors for Rowv and Colv.
+ * [r1889] R/heatmap.2.R: key.title=NA was not being honored when
+ density.info=NA.
+
+2014-09-16 warnes
+
+ * [r1888] R/plotNode.R: Add plotNode code to allow modificaiton of
+ algorithm from recursive to iterative for the purpose of avoiding
+ node stack overflow.
+ * [r1887] R/heatmap.2.R, man/heatmap.2.Rd: - Correct statement of
+ default color for 'notecol' argumemt to 'heatmap.2'.
+ - Modify default arguments to 'symbreaks' and 'symkey' to make
+ the
+ logic more evident by replacing min() with any(). (The previous
+ code executed properly, but relied on implicit coercion of
+ logicals
+ to numeric, obscuring the intent.)
+
+2014-06-30 warnes
+
+ * [r1823] R/heatmap.2.R: Fix typo in dendrogram size checking code.
+
+2014-06-19 warnes
+
+ * [r1822] R/heatmap.2.R: Fix typo 'ColInd' --> 'colInd'.
+ * [r1821] DESCRIPTION, inst/NEWS: Update for gplots 2.14.0
+
+2014-06-17 warnes
+
+ * [r1820] man/heatmap.2.Rd: - Document new 'key.title', 'key.xlab',
+ 'key.ylab', 'key.xtickfun',
+ 'key.ytickfun', 'key.par' arguments to heatmap.2 (belated
+ commit).
+ - Document new 'reorderfun' argument to heatmap.2.
+ * [r1819] R/heatmap.2.R: Allow user to specify function used to
+ reorder based on the dendogram
+ via a new 'reorderfun' argument. Suggested by Yuanhua Liu.
+ * [r1818] R/heatmap.2.R: Fix typo in heatmap.2() reported by
+ Yuanhua Liu.
+
+2014-06-05 warnes
+
+ * [r1817] R/heatmap.2.R: Check size of Rowv and Colv dendogram
+ objects to ensure they matches data.
+
+2014-04-17 warnes
+
+ * [r1812] man/hist2d.Rd: Add see also to r2d2::freq2d.
+ * [r1811] man/ci2d.Rd: Add reference to r2d2::conf2d.
+
+2014-04-09 warnes
+
+ * [r1802] R/heatmap.2.R: Add padj=0.5 to better align margin
+ labels.
+
+2014-04-05 warnes
+
+ * [r1781] inst/NEWS: Update NEWS
+ * [r1780] R/heatmap.2.R, man/heatmap.2.Rd: Add 'extrafun' argument
+ to heatmap.2 to allow the user to perform
+ additional customization by providing a function to be called
+ before
+ heatmap.2 exits.
+
+2014-04-04 warnes
+
+ * [r1779] DESCRIPTION, inst/NEWS: Update for gplots 2.13.0
+ * [r1778] R/heatmap.2.R: Fix handling of row trace (hline). Bug
+ report and patch provided by Ilia Kats.
+
+2013-10-21 warnes
+
+ * [r1744] man/gplots-deprecated.Rd: Handle 'ask' argument in
+ lmplot2 function proper, rather than in (depreciated) plot.lm2
+ wrapper.
+ * [r1743] inst/NEWS: Correct release number
+ * [r1742] R/lmplot2.R: Handle 'ask' argument in lmplot2 function
+ proper, rather than in (depreciated) plot.lm2 wrapper.
+ * [r1741] man/lmplot2.Rd: Fix typo
+
+2013-10-15 warnes
+
+ * [r1740] NAMESPACE: Add boxplot2 and lmplot2 to NAMESPACE
+ * [r1739] DESCRIPTION, inst/NEWS: Update for gplots release 2.12.1
+ * [r1738] R/boxplot.n.R, R/boxplot2.R, R/lmplot2.R, R/plot.lm.R,
+ man/boxplot.n.Rd, man/boxplot2.Rd, man/gplots-deprecated.Rd,
+ man/lmplot2.Rd, man/plot.lm2.Rd: Rename boxplot.n to boxplt2 and
+ plot.lm2 to lmplot2
+ * [r1737] man/lmplot2.Rd: Make lmplot2 manual page from plot.lm.2
+ manual page.
+ * [r1736] man/boxplot2.Rd: Make boxplot2 manual page from boxplot.n
+ manual page.
+ * [r1735] man/gplots-deprecated.Rd: Create deprecated man page from
+ boxplot.n man page
+
+2013-10-12 warnes
+
+ * [r1734] inst/NEWS: Update NEWS with latest changes
+ * [r1733] man/ci2d.Rd: Mark one example dontrun to avoid --as-cran
+ warning.
+
+2013-10-11 warnes
+
+ * [r1732] R/overplot.R: Allow standard S3 method handling to locate
+ the correct function.
+ * [r1731] R/overplot.R: Fix error when a subgroup contains no
+ finite values
+ * [r1730] tests/heatmap2Test.Rout.save: Update test output
+ * [r1729] DESCRIPTION: Move several packages from Depends to
+ Imports, Suggests
+ * [r1728] man/ci2d.Rd: Use gdata::nobs in example
+ * [r1727] NAMESPACE: caTools and KernSmooth now have namespaces, so
+ import from them.
+ * [r1726] inst/NEWS: Update files for gplots 2.12.0
+ * [r1725] DESCRIPTION, inst/NEWS: Update files for gplots 2.12.0
+ * [r1724] R/heatmap.2.R, man/heatmap.2.Rd: Add parameters to
+ control row and column label positioning, rotation,
+ justification, and offset.
+ * [r1723] R/venn.R: Fix bug in getVennCounts.data.frame when number
+ of TRUE cases in each variable are equal.
+
+2013-06-28 warnes
+
+ * [r1680] inst/doc/BalloonPlot.pdf: Update PDF file, including new
+ email addresses
+
+2013-06-27 warnes
+
+ * [r1679] inst/NEWS: Update for gplots 2.11.3
+ * [r1678] DESCRIPTION: Update for release 2.11.3
+ * [r1677] tests/heatmap2Test.Rout.save: Update with tests for only
+ 1 row/column separator
+ * [r1676] man/plotmeans.Rd: Fix typo
+ * [r1675] tests/heatmap2Test.R: Add test for one row/column
+ separator
+ * [r1674] R/baseOf.R: Add more in-line comments
+ * [r1673] R/sinkplot.R, man/sinkplot.Rd: Modify sinkplot to use a
+ local environement to store its information instead of the global
+ environment.
+
+2013-03-24 warnes
+
+ * [r1647] inst/NEWS: Update news for release 2.11.2
+ * [r1646] R/barplot2.R, man/barplot2.Rd: Add ci.width argument to
+ barplot2() to allow varying the length of the 't' at the end of
+ confidence interval bars.
+ * [r1642] DESCRIPTION: Update for release 2.11.2
+ * [r1641] man/lowess.Rd: Update manual page for lowess.default() to
+ match changed argument list for lowess() in R 3.0.0
+
+2012-12-14 warnes
+
+ * [r1631] R/plot.venn.R: Fix typo: warn() instead of warning().
+ * [r1630] vignettes/venn.Rnw: Fix syntax of VignetteIndexEntry in
+ venn.Rnw.
+ * [r1629] vignettes/venn.Rnw, vignettes/venn.pdf: Add generated
+ vignette pdf.
+ * [r1628] vignettes/venn.Rnw: Add required VignetteIndexEntry
+ metadata to venn vignette code.
+ * [r1627] DESCRIPTION, inst/NEWS: Update DESCRIPTION and NEWS for
+ release 2.11.1.
+ * [r1626] R/baseOf.R, R/plot.venn.R, R/venn.R, vignettes,
+ vignettes/venn.Rnw: Improve venn() to work with PDF and
+ Sweave/pdflatex. Provide a vignette for venn().
+ * [r1625] R/heatmap.2.R: Fix error in processing the colsep
+ argument to heatmap.2.
+ * [r1624] man/plotmeans.Rd: Clarify that plotmeans is intended for
+ a *continuous* outcome based on
+ a *factor* grouping level.
+ * [r1623] inst/doc/BalloonPlot.pdf: Replace corrupted
+ BalloonPlot.pdf file and remove svn properties that were causing
+ it to be corrupted.
+
+2012-06-08 warnes
+
+ * [r1558] inst/NEWS: Update NEWS for 2.11.0 release.
+ * [r1557] DESCRIPTION, R/barplot2.R, R/ooplot.R, R/plotCI.R,
+ R/sinkplot.R, man/qqnorm.aov.Rd, tests/heatmap2Test.Rout.save:
+ Fix R CMD check warnings.
+ * [r1556] man/hist2d.Rd: Move incorrectly placed closing brace.
+
+2012-06-07 warnes
+
+ * [r1555] R/ci2d.R, R/hist2d.R, R/print.hist2d.R, man/hist2d.Rd:
+ Object returned by hist2d() has been changed:
+ - $x and $y now contain the n midpoints of the bins in each
+ direction
+ - $x.breaks, $y.breaks now contain the n+1 limits of the bins in
+ each direction
+ The function print.hist2d() has been updated appropriately.
+ * [r1554] R/hist2d.R: Correct error in handling binning:
+ (N+1)x(N+1) bins were being created
+ instead of NxN bins, and the highest row/column in each direction
+ was
+ being omitted from the results and plot.
+ * [r1553] R/plotmeans.R, man/plotmeans.Rd: Add default value for
+ lwd argument to plotmeans()
+
+2012-05-31 warnes
+
+ * [r1533] man/qqnorm.aov.Rd: Properly mark up S3 method.
+
+2011-12-09 warnes
+
+ * [r1519] R/plotmeans.R, man/plotmeans.Rd: Add 'lwd' (linewidth) to
+ arguments handled by plotmeans.
+
+2011-09-02 warnes
+
+ * [r1505] inst/NEWS: Update NEWS for release 2.10.1.
+ * [r1504] DESCRIPTION: Increment version counter.
+ * [r1503] man/ci2d.Rd, man/hist2d.Rd: Add necessary alias statment
+ to man files for for 'hist2d' and 'ci2d'
+ print methods.
+ * [r1502] R/print.hist2d, R/print.hist2d.R: Fix naming error
+ * [r1501] NAMESPACE, R/ci2d.R, R/hist2d.R, R/print.ci2d.R,
+ R/print.hist2d, man/ci2d.Rd, man/hist2d.Rd: Provide print()
+ methods for 'hist2d' and 'ci2d' objects.
+ * [r1498] DESCRIPTION: Correct dependence on R >= 2.10
+
+2011-09-01 warnes
+
+ * [r1491] NAMESPACE, man/ci2d.Rd: - Correct issues in ci2d() man
+ page.
+ * [r1490] DESCRIPTION, NAMESPACE, tests/heatmap2Test.Rout.save: -
+ Comment out import from KernSmooth in NAMESPACES, since
+ KernSmooth
+ doesn't provide a namespace.
+ - Update a test output.
+ * [r1489] DESCRIPTION, inst/NEWS: - Update NEWS file and correct
+ version number
+ * [r1488] DESCRIPTION: - Depend on KernSmooth package. Increment
+ version number.
+ * [r1487] NAMESPACE: - Depend on KernSmooth package and import
+ 'bkdeD2' and 'dpik'.
+ * [r1486] R/ci2d.R, man/ci2d.Rd: Improvements to ci2d():
+
+ - Add option to utilize KernDensity::bkde2D to estimate the 2-d
+ density (now the default).
+
+ - Add option to display points for original data on generated
+ plots
+
+ - Name elements of returned contour list according to the
+ significance
+ level to make it easier to select desired contours.
+
+ - Improve handling of x and y labels
+ * [r1485] man/hist2d.Rd: Remove log tag and comments from top of
+ the file.
+
+2011-08-26 warnes
+
+ * [r1478] inst/NEWS: Update NEWS for 2.10.0 release
+ * [r1477] DESCRIPTION: Add dependency on R>= 2.10 to handle
+ compressed Rda data file.
+ * [r1476] data/rtPCR.rda: Compress rtPCR example data set to make
+ distributed package smaller.
+ * [r1475] R/ci2d.R: Remove '1.0' confidence line from
+ ci2d(..,show="contour").
+
+2011-08-25 warnes
+
+ * [r1474] DESCRIPTION, NAMESPACE, R/ci2d.R, man/ci2d.Rd,
+ man/rich.colors.Rd: - Add 'ci2d()' to compute 2-dimensional
+ emipirical confidence interval.
+ - Fix parse error in help page for 'rich.colors()'.
+
+2011-08-16 warnes
+
+ * [r1473] DESCRIPTION: Update DESCRIPTION file for 2.8.1.
+ * [r1472] R/rich.colors.R, man/rich.colors.Rd: Add 'alpha' argument
+ to rich.colors() to control transparency.
+ * [r1471] R/hist2d.R, man/hist2d.Rd: Accellerate hist2d by
+ replacing for() loop with tapply(), and allow user to specify
+ summary function applied, per suggestion by Peter Hagedorn (PHA
+ -at- santaris -dot- com).
+
+2011-05-02 arnima
+
+ * [r1470] R/rich.colors.R, man/rich.colors.Rd: Added argument
+ 'alpha' and removed argument 'rgb' in rich.colors()
+
+2010-12-13 warnes
+
+ * [r1463] R/heatmap.2.R: Correct error that arises when data
+ includes NA values, identified by Melissa Key
+
+2010-06-11 warnes
+
+ * [r1446] man/venn.Rd: Fix errors detected by R CMD check
+ * [r1445] man/venn.Rd: Fix errors detected by R CMD check
+ * [r1444] man/venn.Rd: Use 'TRUE' instead of 'T' for true in venn
+ man page
+ * [r1443] DESCRIPTION, NAMESPACE, inst/NEWS: Update for gplots
+ 2.8.0
+ * [r1442] R/baseOf.R: Moved baseOf() into a separate file
+ * [r1441] man/balloonplot.Rd, man/bandplot.Rd, man/boxplot.n.Rd,
+ man/colorpanel.Rd, man/hist2d.Rd, man/ooplot.Rd, man/overplot.Rd,
+ man/plot.lm2.Rd, man/plotCI.Rd, man/plotmeans.Rd,
+ man/residplot.Rd, man/sinkplot.Rd, man/smartlegend.Rd,
+ man/space.Rd, man/textplot.Rd, man/wapply.Rd: Update Greg's email
+ address
+ * [r1440] R/plot.venn.R, R/venn.R, man/venn.Rd: - venn() now
+ returns an object of class venn() and a plot method for
+ this class is provided.
+
+ - Manual page for venn has been improved, based on contributions
+ by
+ Steffen Moeller
+
+2010-02-17 warnes
+
+ * [r1420] DESCRIPTION, R/hist2d.R, inst/NEWS: Improve performance
+ of hist2d thanks to suggestion by Joerg van den Hoff.
+
+2010-01-22 arnima
+
+ * [r1372] R/rich.color.R, R/rich.colors.R, man/rich.color.Rd,
+ man/rich.colors.Rd: Renamed files rich.color.* to rich.colors.*
+ and renamed rich.colors args
+
+2009-11-16 arnima
+
+ * [r1367] R/rich.color.R: Minor reformatting only.
+
+2009-11-12 warnes
+
+ * [r1365] DESCRIPTION, R/plotmeans.R, inst/NEWS,
+ tests/plotmeans_nobars.R: Correct bug reported by Alan Yong:
+ plotmeans() crashed when 'bars=FALSE'.
+
+2009-10-22 warnes
+
+ * [r1364] R/heatmap.2.R: Fixed typo in bug fix.
+ * [r1363] DESCRIPTION, inst/NEWS: Update NEWS and DESCRIPTION for
+ gplots 2.7.3
+ * [r1362] R/heatmap.2.R: Fix transposed display of data (but not
+ labels) in heatmap.2 when symm=TRUE
+
+2009-10-12 warnes
+
+ * [r1361] DESCRIPTION, inst/NEWS: Update version number to 2.7.2,
+ 2.7.1 was already up but apparently DESCRIPTION wasn't commited
+ with change.
+
+2009-10-10 warnes
+
+ * [r1360] R/col2hex.R, man/colorpanel.Rd, man/lowess.Rd,
+ man/ooplot.Rd, man/overplot.Rd, man/smartlegend.Rd, man/space.Rd,
+ tests/heatmap2Test.Rout.save: Various minor changes to remove new
+ R CMD CHECK warnings.
+ * [r1359] DESCRIPTION, inst/NEWS: Update DESCRIPTION and NEWS file
+ for 2.7.1
+ * [r1358] R/col2hex.R: Fix bug reported by Ken Lo: col2hex had blue
+ and green components swapped.
+
+2009-05-08 warnes
+
+ * [r1324] tests/heatmap_to_heatmap.2_test.R: Add test of using a
+ dendrogram created by heatmap() with heatmap.2()
+ * [r1323] R/heatmap.2.R: heatmap.2: handle NA for RowV or ColV the
+ same way as NULL
+ * [r1322] man/plotCI.Rd: Fix typo
+ * [r1321] inst/NEWS: Update NEWS for release 2.7.0
+ * [r1320] inst/ChangeLog: We don't want the Changelog in svn, since
+ it is autogenerated from svn logs!
+ * [r1319] man/balloonplot.Rd, man/bandplot.Rd, man/boxplot.n.Rd,
+ man/colorpanel.Rd, man/hist2d.Rd, man/ooplot.Rd, man/overplot.Rd,
+ man/plot.lm2.Rd, man/plotCI.Rd, man/plotmeans.Rd,
+ man/residplot.Rd, man/sinkplot.Rd, man/smartlegend.Rd,
+ man/space.Rd, man/textplot.Rd, man/wapply.Rd: Update Greg's email
+ address to 'gr...@ra...'
+ * [r1318] R/plotCI.R, man/plotCI.Rd: plotCI now properly handles
+ 'NULL' and 'NA' values for ui, li, uiw, and liw.
+ * [r1317] R/heatmap.2.R, man/heatmap.2.Rd,
+ tests/heatmap2Test.Rout.save: heatmap.2: Add option to create
+ breakpoints symmetric around 0, provide additional information in
+ the return value
+ * [r1316] man/space.Rd: Fix Rd syntax error
+
+2009-04-22 warnes
+
+ * [r1315] man/barplot2.Rd, man/ooplot.Rd: VADeaths data set has
+ move to dataset package
+
+2008-08-14 warnes
+
+ * [r1302] R/balloonplot.R: balloonpot() was incorrectly displaying
+ warning about z values below 0 when scale.method="relative".
+ Fixed.
+
+2008-08-07 warnes
+
+ * [r1301] DESCRIPTION, NAMESPACE, inst/ChangeLog, inst/NEWS: Update
+ DESCRIPTION NAMESPACE and NEWS for 2.7.0 release
+
+2008-06-16 warnes
+
+ * [r1296] TODO, inst/TODO: Add TODO list to gplots
+
+2008-05-20 warnes
+
+ * [r1274] DESCRIPTION, man/plot.lm2.Rd: Update man page to match
+ recent changes to plot.lm2()
+ * [r1273] man/venn.Rd: More work on documentation for venn()
+ * [r1272] R/bandplot.R, man/bandplot.Rd: Fix code/doc mismatch due
+ to recent changes to bandplot()
+ * [r1271] DESCRIPTION, NAMESPACE, R/venn.R, man/venn.Rd: Add Venn
+ Diagram plot submitted by Steffen Moeller
+
+2008-05-07 warnes
+
+ * [r1264] DESCRIPTION, R/bandplot.R: Improve performance of
+ bandplot by calculating running standard deviation using
+ caTools::runsd() instead of (ver slow) window() call. In addtion,
+ the standard deviations are now only calculated once, rather than
+ once for each band.
+ * [r1263] R/plot.lm.R: Improve performance of plot.lm for large lm
+ objects by using fitted() instead of predict() to get y-hat
+
+2008-05-05 warnes
+
+ * [r1262] DESCRIPTION, R/bandplot.R: Use caTools's runsd in
+ bandplot for a dramatic speedup for large data
+ * [r1261] NAMESPACE: Add import of gtools::reorder.factor for
+ ballonplot man page
+ * [r1260] R/balloonplot.R, man/balloonplot.Rd: balloonplot: Add
+ option to scale balloons so [min,max]->[0,1] (relative) or so
+ [0,max] <- [0,1] (absolute)
+
+2008-04-07 warnes
+
+ * [r1254] man/barplot2.Rd: Fix typo in barplot2() man page
+ * [r1253] DESCRIPTION, inst/ChangeLog, inst/NEWS: Updates for
+ gplots 2.6.0
+ * [r1252] R/heatmap.2.R, man/heatmap.2.Rd: Add ability to control
+ location of individual heatmap.2 components
+
+2008-03-27 warnes
+
+ * [r1251] R/heatmap.2.R: Fix bug in handling rowsep, per suggestion
+ by Steven Paugh
+
+2008-01-04 warnes
+
+ * [r1238] man/overplot.Rd: Fix examples for overplot()
+
+2008-01-02 warnes
+
+ * [r1237] man/barplot2.Rd: Update Marc's email address
+
+2007-12-20 warnes
+
+ * [r1235] man/heatmap.2.Rd: Two letter clarification of help text
+ for heatmap.2()
+ * [r1234] man/ooplot.Rd: Restore plot layout at end of ooplot()
+ example
+
+2007-11-06 warnes
+
+ * [r1222] man/hist2d.Rd: Remove extraneous closing brace in the
+ hist2d documentation file
+
+2007-11-05 warnes
+
+ * [r1221] inst/NEWS: Fix typo in NEWS: col2hex() is the new
+ function, not col2rgb() which is part of grDevices
+
+2007-11-02 warnes
+
+ * [r1219] DESCRIPTION, NAMESPACE, inst/ChangeLog, inst/NEWS:
+ Updates for gplots 2.5.0
+ * [r1218] tests/heatmap2Test.Rout.save: Update saved test output
+ due to changes in how R reports warnings
+ * [r1217] ChangeLog, NEWS: Create soft links of gmodels/ChangeLog
+ -> gmodels/inst/ChangeLog, and gmodels/NEWS -> gmodels/inst/NEWS
+ for my convenience
+ * [r1216] ChangeLog, NEWS, inst/ChangeLog, inst/NEWS: Move actual
+ ChangeLog and NEWS files to gmodels/inst so they will be copied
+ into the installed R package area
+ * [r1215] man/bandplot.Rd, man/textplot.Rd: Fix code/doc mismatches
+ * [r1214] R/plot.lm.R: Update plot.lm2 to match changes made to
+ bandplot
+
+2007-11-01 warnes
+
+ * [r1213] ChangeLog, DESCRIPTION, R/replaceTabs.R, R/textplot.R: in
+ textplot(), convert tab characters to spaces before processing to
+ avoid problems with computing height and width of text including
+ tabs when using pdf()
+ * [r1212] R/overplot.R, man/overplot.Rd: Minor reformatting of
+ overplot code and docs
+
+2007-10-22 warnes
+
+ * [r1196] DESCRIPTION: Clarify GPL version
+
+2007-08-14 warnes
+
+ * [r1141] R/balloonplot.R: Correct error in balloonplot when z
+ contains NA values.
+ * [r1140] R/balloonplot.R, man/balloonplot.Rd: Augment
+ balloonplot() with control of character size and color for text
+ and label items
+ * [r1139] R/balloonplot.R: Correct balloonplot.default to properly
+ show specified x and y axis labels when explicitly provided
+
+2007-03-09 ggorjan
+
+ * [r1073] man/ooplot.Rd: use of \method in Rd markup - issues a
+ warning with _R_CHECK_RD_STYLE_=TRUE env. variable with R 2.5.0
+
+2007-02-08 warnes
+
+ * [r1052] DESCRIPTION: Bump version number
+ * [r1051] man/textplot.Rd: Update documentation for textplot()
+ * [r1050] R/col2hex.R, man/col2hex.Rd: Add col2rgb() function to
+ convert color names to rgb hex codes
+ * [r1049] R/textplot.R: Add paramaeters 'col.data', 'col.rows', and
+ 'col.columns' to
+ textplot.matrix to allow specification of the color of the matrix
+ data, rows, and columns.
+ * [r1048] R/bandplot.R: Add parameters to control line width and
+ line type.
+
+2006-11-14 ggorjan
+
+ * [r1012] R/bandplot.R, R/boxplot.n.R, R/lowess.R, R/plot.lm.R,
+ R/plotCI.R, R/plotmeans.R, R/residplot.R, R/wapply.R,
+ man/boxplot.n.Rd, man/plotCI.Rd, man/plotmeans.Rd: Removed
+ executable property
+
+2006-11-14 warnes
+
+ * [r1010] tests/heatmap2Test.Rout.save: Update output file to match
+ (trivial) changes in the test code.
+ * [r1008] ChangeLog, NEWS: Update ChangeLog and NEWS files for
+ release 2.3.2.
+ * [r1007] DESCRIPTION: Update version number
+ * [r1006] DESCRIPTION: Update version number and maintainer
+ * [r1005] man/heatmap.2.Rd: Correct problem with labeled
+ correlation matrix example. Thanks to Jean Vidal for reporting
+ the error..
+
+2006-08-02 warnes
+
+ * [r977] inst/doc/BalloonPlot.pdf, man/balloonplot.Rd,
+ man/bandplot.Rd, man/boxplot.n.Rd, man/colorpanel.Rd,
+ man/hist2d.Rd, man/ooplot.Rd, man/overplot.Rd, man/plot.lm2.Rd,
+ man/plotCI.Rd, man/plotmeans.Rd, man/residplot.Rd,
+ man/sinkplot.Rd, man/smartlegend.Rd, man/space.Rd,
+ man/textplot.Rd, man/wapply.Rd: Update my email address
+
+2006-06-26 nj7w
+
+ * [r967] R/heatmap.2.R: Fixed a bug which displayed warnings when
+ Rowv and Colv were specified as dendrograms
+
+2006-03-10 warnes
+
+ * [r937] tests/heatmap2Test.R: Remove code that added a local path
+
+2006-03-09 nj7w
+
+ * [r935] tests/heatmap2Test.R, tests/heatmap2Test.Rout.save: Added
+ the correct library path where gplots is installed locally and
+ corresponding .save file
+ * [r934] tests/heatmap2Test.R: Updated the tests file
+ * [r933] R/heatmap.2.R: Removed the condition Colv != Rowv as it
+ has already been taken care of
+ * [r932] rtPCR.rda: Deleted rtPCR.rda from the main directory
+ * [r931] ChangeLog: Added ChangeLog
+
+2006-03-07 nj7w
+
+ * [r919] DESCRIPTION, NEWS: Updated ChangeLog and NEWS
+ * [r918] tests, tests/heatmap2Test.R, tests/heatmap2Test.Rout.save:
+ Added the tests and fixed corrupted files
+ * [r917] data/rtPCR.rda: Replaced the corrupted rtPCR.rda file in
+ data directory
+ * [r916] tests: Removed the corrputed tests directory
+ * [r915] data/rtPCR.rda, rtPCR.rda: Replaced the corrupted
+ rtPCR.rda file in data directory
+
+2006-03-03 nj7w
+
+ * [r914] R/heatmap.2.R, man/heatmap.2.Rd: Updated the code and man
+ page to make sure the Rowv and Colv values are properly handled
+
+2006-03-02 warnes
+
+ * [r908] R/balloonplot.R: Adjust row total placement to adjust for
+ width of the totals
+ * [r907] DESCRIPTION, R/balloonplot.R, man/1: Row totals in
+ ballonplot were in reverse order. Fixed.
+
+2006-02-23 nj7w
+
+ * [r899] R/heatmap.2.R, tests/heatmap2Test.R: Add ability to scale
+ the color key using the new 'keysize' argument.
+ * [r898] tests, tests/heatmap2Test.R, tests/heatmap2Test.Rout.save:
+ Add tests for heatmap.2
+ * [r897] inst/doc/Figure1.eps, inst/doc/Table.eps,
+ inst/doc/bka.bst, inst/doc/heatmap2.R, inst/doc/heatmap2.tex,
+ inst/doc/regression_rank_image.Rda,
+ inst/doc/regression_rank_image_II.Rda: Move heatmap and
+ ballonplot paper source materials to their respective cvs modules
+ * [r896] inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex,
+ inst/doc/Figure1.pdf, inst/doc/Figure2.pdf, inst/doc/Figure3.pdf,
+ inst/doc/Figure4.pdf, inst/doc/Rnews.sty,
+ inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
+ inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Moved
+ balloonplot paper materials to BallonPlotPaper cvs module
+ * [r891] inst/doc/colSeparator.pdf, inst/doc/logData.pdf,
+ inst/doc/logDataColDendrogram.pdf, inst/doc/logDataColOrd.pdf,
+ inst/doc/logDataColOrdNo.pdf, inst/doc/logDataRowDendrogram.pdf,
+ inst/doc/origScale.pdf, inst/doc/rowSeparator.pdf,
+ inst/doc/scaled.pdf: Remove heatmap paper files and move them to
+ the HeatmapPaper cvs module.
+ * [r888] inst/doc/colSeparator.pdf, inst/doc/logData.pdf,
+ inst/doc/logDataColDendrogram.pdf, inst/doc/logDataColOrd.pdf,
+ inst/doc/logDataColOrdNo.pdf, inst/doc/logDataRowDendrogram.pdf,
+ inst/doc/origScale.pdf, inst/doc/rowSeparator.pdf,
+ inst/doc/scaled.pdf: Added figures for heatmap2 paper
+ * [r887] inst/doc/regression_rank_image.Rda,
+ inst/doc/regression_rank_image_II.Rda: Added the .Rda files for
+ the heatmap2 paper
+ * [r886] inst/doc/heatmap2.tex: Added the source - (tex file) of
+ the heatmap paper
+ * [r885] inst/doc/heatmap2.R: Added the code for the figures of
+ heatmap paper
+
+2006-02-21 nj7w
+
+ * [r884] R/heatmap.2.R, man/heatmap.2.Rd: Minor updates to
+ heatmap.2 - fixed Rowv, Colv and dendrogram behaviour. Now
+ Rowv=NULL or FALSE both imply no dendrogram computation.
+
+2006-01-12 warnes
+
+ * [r844] inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.pdf,
+ inst/doc/BalloonPlot.tex, inst/doc/Figure1.pdf,
+ inst/doc/Figure2.pdf, inst/doc/Figure3.pdf, inst/doc/Figure4.pdf:
+ more updates
+ * [r843] inst/doc/bka.bst: Add Biometrica bibliography style file
+ * [r842] inst/doc/BalloonPlot.tex: A little more.
+ * [r841] inst/doc/BalloonPlot.tex: Updates to respond to referee.
+
+2006-01-12 nj7w
+
+ * [r840] inst/doc/BalloonPlot.tex: Added references
+
+2005-12-13 nj7w
+
+ * [r811] inst/doc/BalloonPlot.tex: Fixed Nitin's company name
+ * [r809] ChangeLog, NEWS: Updated NEWS and removed ChangeLog
+
+2005-12-12 nj7w
+
+ * [r802] R/plotmeans.R: Fixed bug in plotmeans - based on Stefano
+ Calza's suggestion
+
+2005-12-07 nj7w
+
+ * [r787] DESCRIPTION: Updated version number
+ * [r786] NAMESPACE, R/plot.lm.R, man/plot.lm2.Rd: Added plot.lm
+ * [r785] man/barplot2.Rd: Changed the default grey colors to heat
+ colors, if height is matrix
+ * [r784] R/barplot2.R: Changed the default greay colors to heat
+ colors, if height is matrix
+
+2005-12-06 nj7w
+
+ * [r783] man/barplot2.Rd: Fixed minor error in documentation of
+ barplot2
+
+2005-12-02 warnes
+
+ * [r777] R/plot.lm.R: Remove .Alias calls, since .Alias is defunct.
+
+2005-12-01 nj7w
+
+ * [r776] man/balloonplot.Rd, man/bandplot.Rd, man/boxplot.n.Rd,
+ man/colorpanel.Rd, man/overplot.Rd, man/plotmeans.Rd,
+ man/textplot.Rd, man/wapply.Rd: Updated Greg's email address
+
+2005-11-23 nj7w
+
+ * [r764] inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.pdf,
+ inst/doc/BalloonPlot.tex, inst/doc/Figure2.pdf: Updated Figure 2
+ colors
+
+2005-11-18 warnes
+
+ * [r743] inst/doc/BalloonPlot.pdf, inst/doc/Figure1.pdf,
+ inst/doc/Figure2.pdf, inst/doc/Figure3.pdf, inst/doc/Figure4.pdf:
+ Latest version of the pdf files
+ * [r742] inst/doc/BalloonPlot.tex: Nitin works for the Cambrige
+ Group, not Pfizer.
+ * [r741] inst/doc/BalloonPlot.tex: Minor text rewording.
+ * [r740] inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex: More
+ edits.
+ * [r739] R/balloonplot.R: Recent changes to align row totals with
+ the overall total broke how
+ the marginal cumulative fractions were displayed. This patch
+ fixes
+ the problem.
+ * [r737] DESCRIPTION, R/balloonplot.R, R/plot.lm.R,
+ inst/doc/BalloonPlot.pdf, man/balloonplot.Rd: - Update
+ documentation for balloonplot to match the latest code.
+ - Correct spelling of 'show.zeroes' to 'show.zeros'
+ * [r736] R/colorpanel.R: More changes: colorpanel now allows only 2
+ colors to be specified if
+ no 'middle' color is desired.
+
+2005-11-17 warnes
+
+ * [r735] R/balloonplot.R: Allow user to control removal of
+ duplicate entries in balloonplot.
+ * [r734] R/colorpanel.R, man/colorpanel.Rd: Extend colorpanel to
+ handle just two-colors in addition to three.
+
+2005-11-09 nj7w
+
+ * [r733] inst/doc/BalloonPlot.pdf: Updated the pdf file
+ * [r732] inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex: Updated
+ the changes
+ * [r731] inst/doc/Figure4.pdf: Modified figure 4
+ * [r730] inst/doc/BalloonPlot.R: Updated code
+ * [r729] inst/doc/Figure3.pdf: Modified figure 3
+ * [r728] inst/doc/Figure2.pdf: Modified figure 2
+ * [r727] inst/doc/Figure1.pdf: Modified figure 1
+
+2005-11-08 nj7w
+
+ * [r726] man/plotCI.Rd: Updated Greg's email
+
+2005-11-07 nj7w
+
+ * [r725] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Minor
+ modifications to fit the code properly on pdf
+
+2005-11-07 warnes
+
+ * [r724] inst/doc/BalloonPlot.R: Add R code that generates plots
+ * [r723] inst/doc/Figure2.pdf, inst/doc/Figure3.pdf,
+ inst/doc/Figure4.pdf: Add figures to CVS
+ * [r722] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex,
+ inst/doc/Figure1.pdf: Text changes
+
+2005-11-04 warnes
+
+ * [r721] R/balloonplot.R: Fix some alignment issues.
+ * [r720] inst/doc/BalloonPlot.pdf, inst/doc/Table.pdf: Remove
+ Table.pdf since it is no longer needed
+ * [r719] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex,
+ inst/doc/Figure1.pdf: Nitin's Changes
+ * [r718] inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
+ inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Add figure
+ plots
+ * [r717] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Fix
+ paths
+
+2005-10-20 nj7w
+
+ * [r705] inst/doc/Figure1.eps, inst/doc/Table.eps: added the eps
+ version of figures
+ * [r704] inst/doc/BalloonPlot.pdf: Updated BallonPlot.pdf
+ * [r703] inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
+ inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Removed Old
+ Figure
+ * [r702] inst/doc/Figure1.pdf, inst/doc/Table.pdf: Added the new
+ figure - for total popluation - Balloonplot
+ * [r701] inst/doc/BalloonPlot.tex: Modified the BallonPlot article
+ * [r700] inst/doc/BalloonPlot.tex: Added references
+
+2005-10-19 arnima
+
+ * [r697] man/rich.color.Rd: The last example now displays the
+ correct heat.colors.
+ Default 'palette' argument is now a single string, not a vector.
+ * [r696] R/rich.color.R: Default 'palette' argument is now a single
+ string, not a vector.
+
+2005-10-14 warnes
+
+ * [r694] DESCRIPTION, R/balloonplot.R, man/balloonplot.Rd:
+ Formatting fixes:
+ - Handle multiple row or column category variables
+ - Separate rows/columns of category labels by lines
+ - Fix handling of 'cumsum' plots on row/column labels
+ - Improve display of row/column sums
+
+2005-10-13 warnes
+
+ * [r693] man/balloonplot.Rd: Add example using Titanic data that
+ exercises the multi-factor
+ display.
+
+2005-10-11 warnes
+
+ * [r692] R/balloonplot.R: Initial changes to allow multiple x and y
+ factor variables. Yet to
+ be done: 1) remove extra 'boxes'. 2) omit duplicated values
+
+2005-10-04 warnes
+
+ * [r691] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: more
+ minor fixes
+ * [r690] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: fix
+ spacing
+ * [r689] inst/doc/Rnews.sty: Inlcude Rnews.sty
+ * [r688] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Some
+ textual edits.
+
+2005-10-03 nj7w
+
+ * [r687] inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
+ inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Added figures
+ for the R-News Article
+
+2005-09-29 nj7w
+
+ * [r680] inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex:
+ Updated the documentation - added the name of the person who
+ asked the question
+ * [r679] inst, inst/doc, inst/doc/BalloonPlot.pdf,
+ inst/doc/BalloonPlot.tex: Added R-news article
+
+2005-09-12 nj7w
+
+ * [r671] man/hist2d.Rd, man/ooplot.Rd, man/residplot.Rd,
+ man/sinkplot.Rd, man/smartlegend.Rd, man/space.Rd: Updated Greg's
+ email
+ * [r670] R/balloonplot.R: Updated version of balloonplot - by
+ Romain Francois <fra...@fr...>
+
+2005-09-09 nj7w
+
+ * [r669] ChangeLog, DESCRIPTION: Updated the version and ChangeLog
+ * [r668] R/balloonplot.R, man/balloonplot.Rd: Changes in ballon
+ plot based on Romain Francois (fra...@fr...)
+ suggestions
+
+2005-09-06 nj7w
+
+ * [r666] DESCRIPTION: Updated package dependencies
+ * [r665] NEWS: Added NEWS
+
+2005-09-02 nj7w
+
+ * [r655] ChangeLog: Added ChangeLog
+
+2005-08-31 nj7w
+
+ * [r644] DESCRIPTION: Added DESCRIPTION file
+ * [r643] DESCRIPTION.in: removed DESCRIPTION.in
+
+2005-06-09 nj7w
+
+ * [r625] R/balloonplot.R, R/bandplot.R, R/boxplot.n.R,
+ R/colorpanel.R, R/heatmap.2.R, R/hist2d.R, R/lowess.R,
+ R/ooplot.R, R/overplot.R, R/plotCI.R, R/plotmeans.R,
+ R/qqnorm.aov.R, R/residplot.R, R/rich.color.R, R/sinkplot.R,
+ R/smartlegend.R, R/space.R, R/textplot.R, R/wapply.R, man/1,
+ man/bandplot.Rd, man/barplot2.Rd, man/boxplot.n.Rd,
+ man/hist2d.Rd, man/lowess.Rd, man/plotCI.Rd, man/plotmeans.Rd,
+ man/residplot.Rd, man/space.Rd, man/wapply.Rd: Updating the
+ version number, and various help files to synchronize splitting
+ of gregmisc bundle in 4 individual components.
+ * [r624] R/barplot2.R: Changes based on Marc Schwartz's suggestions
+ to handel 0's and NA's appropriately.
+
+2005-05-13 nj7w
+
+ * [r621] man/heatmap.2.Rd: 1) Using dQuote.ascii function in
+ read.xls as the new version of dQuote doesn't work proprly with
+ UTF-8 locale.
+ 2) Modified CrossTable.Rd usage in gmodels
+ 3) Modified heatmap.2 usage in gplots.
+
+2005-04-04 warnes
+
+ * [r603] R/overplot.R: Explicitly reference package containing
+ lowess.formula in
+ panel.overplot(). This should fix the error reported by Troels
+ Ring
+ <tr...@gv...>.
+
+2005-02-26 nj7w
+
+ * [r565] R/heatmap.2.R, man/heatmap.2.Rd, man/rich.color.Rd,
+ man/sinkplot.Rd, man/textplot.Rd: *** empty log message ***
+
+2005-02-25 warnes
+
+ * [r563] man/rich.color.Rd: Integrate changes submitted by Arni
+ Magnusson
+ * [r559] NAMESPACE: Add dependency imports from 'stats' package.
+
+2005-02-22 warnes
+
+ * [r555] R/bandplot.R: Fix problem in passing graphical parameters
+ (xlim,etc).@
+
+2005-02-08 warnes
+
+ * [r541] DESCRIPTION.in: Improve package title.
+ * [r540] R/heatmap.2.R: Ignore missing values when computing
+ symmetric range.
+
+2005-02-02 warnes
+
+ * [r530] man/plotmeans.Rd: Add more extensive example.
+
+2005-01-14 warnes
+
+ * [r516] R/textplot.R: Code can be simplified because R now
+ supports selecting a fixed width font.
+
+2005-01-12 warnes
+
+ * [r515] DESCRIPTION.in: Add dependency on R 1.9.0+ to prevent
+ poeple from installing on old
+ versions of R which don't support namespaces.
+
+2004-11-30 warnes
+
+ * [r495] R/heatmap.2.R, man/heatmap.2.Rd: 1. Add new parameters for
+ controlling color key:
+ - If `symkey==TRUE', the color key will be made symmetric about
+ 0.
+ - The `densadj' parameter can be used to modify the smoother
+ width
+ (see the `adjust' parameter under `help(density)') for the
+ density
+ plotted in the key.
+
+ 2. Fix handling of rowsep/colsep.
+
+ 3. Vector of length 2 giving the width (colsep) or height
+ (rowsep) the separator box
+ drawn by colsep and rowsep as a function of the width (colsep) or
+ height (rowsep) of a cell.
+
+ 4. Appropriate changes to the corresponding help page, plus some
+ minor formatting changes.
+
+2004-11-03 warnes
+
+ * [r474] R/heatmap.2.R: Fix bugs in layout of cell notes. They were
+ being plotted top down
+ rather than bottom up. Further reordering of the x matrix didn't
+ also reorder the notes. Both issues should now be resolved.
+
+2004-09-27 warneg
+
+ * [r461] DESCRIPTION, DESCRIPTION.in, man/sinkplot.Rd,
+ man/textplot.Rd: Updated to pass R CMD check.
+
+2004-09-03 warneg
+
+ * [r453] man/textplot.Rd: Provide explicit package for call to
+ nobs.
+ * [r452] man/heatmap.2.Rd: Fix typos.
+ * [r446] DESCRIPTION, NAMESPACE, R/balloonplot.R, R/bandplot.R,
+ R/barplot2.R, R/boxplot.n.R, R/colorpanel.R, R/heatmap.2.R,
+ R/hist2d.R, R/lowess.R, R/ooplot.R, R/overplot.R, R/plotCI.R,
+ R/plotmeans.R, R/qqnorm.aov.R, R/residplot.R, R/rich.color.R,
+ R/sinkplot.R, R/smartlegend.R, R/space.R, R/textplot.R,
+ R/wapply.R: initial bundle checkin
+
+2004-09-02 warneg
+
+ * [r442] DESCRIPTION, DESCRIPTION.in, NAMESPACE, man/1,
+ man/residplot.Rd: Initial revision
+
+2004-07-29 warnes
+
+ * [r426] R/plotCI.R, man/plotCI.Rd: Integrate changes from the
+ version of plotCI maintained by Martin Maechler.
+
+2004-06-30 warnes
+
+ * [r393] R/textplot.R: Remove commented-out code.
+ * [r392] R/textplot.R: Fixed text size calculations
+
+2004-06-28 warnes
+
+ * [r391] R/barplot2.R, man/barplot2.Rd: - Default 2-d color set to
+ grey as in (v2.0.0) r-devel
+ - The default (v1.9.1) barplot method now handles vectors and 1-d
+ arrays
+ (e.g., obtained by table()) the same, and uses grey instead of
+ heat color palettes in these cases. (Also fixes PR#6776.)
+ - Updated to reflect the addition of 'offset' argument in base
+ - Fix bug in stacked barplots, which would not be plotted
+ properly
+
+2004-06-24 warnes
+
+ * [r385] R/heatmap.2.R, man/heatmap.2.Rd: Add ability to specify
+ color of NA cells.
+
+2004-05-27 warnes
+
+ * [r349] man/plotCI.Rd: Fix spelling error.
+
+2004-05-26 warnes
+
+ * [r347] R/overplot.R: One more fix to get it right.
+ * [r346] R/overplot.R: Use triple-colon operator ':::' to access
+ plot.formula from the graphics package.
+ * [r344] man/rich.color.Rd: Replace 'F' by 'FALSE' to pass R CMD
+ check.
+
+2004-05-25 warnes
+
+ * [r338] R/overplot.R: Work around bug in R 1.9.X due to
+ plot.formula() not having the same
+ arguments as plot().
+ * [r336] R/rich.color.R, man/rich.color.Rd: Add rich.colors()
+ submitted by Arni Magnusson <arnima@u.washington.edu>.
+ * [r328] R/ooplot.R, man/ooplot.Rd: ??
+
+2004-05-24 warnes
+
+ * [r324] R/plotCI.R, R/plotmeans.R: Modified to use invalid() to
+ check arguments instead of missing().
+ This fixes some build errors under R-1.9.0-Patched.
+
+2004-04-22 warnes
+
+ * [r319] R/ooplot.R, man/ooplot.Rd: Integrate changes from Lodewijk
+ Bonebakker <bon...@co...>
+
+2004-04-13 warnes
+
+ * [r318] R/space.R, man/space.Rd: Add ability to space points along
+ 'y' direction.
+
+2004-04-02 warnes
+
+ * [r313] R/smartlegend.R: Fixed smartlegend() positioning when x
+ and/or y axis are log-scale.
+
+2004-03-30 warnes
+
+ * [r311] R/textplot.R: - Fix bug in textplot() reported by Wright,
+ Kevin <kev...@pi...>.
+
+2004-03-26 warnes
+
+ * [r305] man/textplot.Rd: Update to match changes in textplot()
+ code.
+ * [r304] man/ooplot.Rd: Remove Windows EOL characters.
+ * [r302] man/barplot2.Rd: - Remove some commented-out code.
+ - Remove cvs log tag.
+ * [r300] R/textplot.R: Misc changes.
+
+2004-02-17 warnes
+
+ * [r290] man/ooplot.Rd: Minor fix to ooplot documentation.
+ * [r289] R/ooplot.R, man/ooplot.Rd: Integrate ooplot updates
+ provided by Lodewijk Bonebakker
+ <bon...@co...>
+
+2004-02-02 warnes
+
+ * [r287] R/colorpanel.R, man/colorpanel.Rd: - Add colorpanel
+ function, which generates a smoothly varying band of
+ colors over a three color range (lo, mid, high).
+
+2004-01-21 warnes
+
+ * [r283] man/textplot.Rd: - Correct arguments to halign to match
+ code.
+ * [r281] R/lowess.R: Track R 1.9.0's move of 'lowess' from the base
+ package to the (new)
+ stats package.
+ * [r279] man/sinkplot.Rd: - Fix sinkplot() example by replacing 'T'
+ with 'TRUE'.
+ * [r278] man/ooplot.Rd: - Add some more details to the ooplot()
+ documentation. The
+ documentation is *not* complete.
+ * [r277] R/textplot.R: - Mark sprint() as depreciated.
+ - Replace references to sprint with capture.output()
+ - Use match.arg for halign and valign arguments to
+ textplot.default.
+ - Fix textplot.character so that a vector of characters is
+ properly
+ displayed. Previouslt, character vectors were plotted on top of
+ each
+ other.
+
+2004-01-19 warnes
+
+ * [r276] R/sinkplot.R, man/sinkplot.Rd: New function sinkplot(), as
+ requested on R-devel by Kevin Wright
+ <kw...@es...> in
+ https://www.stat.math.ethz.ch/pipermail/r-devel/2004-January/028483.html.
+
+2004-01-15 warnes
+
+ * [r...
[truncated message content] |
|
From: <wa...@us...> - 2015-04-06 21:44:09
|
Revision: 1915
http://sourceforge.net/p/r-gregmisc/code/1915
Author: warnes
Date: 2015-04-06 21:44:02 +0000 (Mon, 06 Apr 2015)
Log Message:
-----------
Implement fix to keywords() needed for R-3.4.1, as suggested by Kurt
Hornik.
Modified Paths:
--------------
trunk/gtools/R/keywords.R
Modified: trunk/gtools/R/keywords.R
===================================================================
--- trunk/gtools/R/keywords.R 2015-04-06 21:40:03 UTC (rev 1914)
+++ trunk/gtools/R/keywords.R 2015-04-06 21:44:02 UTC (rev 1915)
@@ -32,7 +32,11 @@
item <- paste("^",topic,"$", sep="")
- topics <- function(k) help.search(keyword=k)$matches[,"topic"]
+ topics <- function(k)
+ {
+ matches <- help.search(keyword=k)$matches
+ matches[ , match("topic", tolower(colnames(matches)))]
+ }
matches <- lapply(kw, topics)
names(matches) <- kw
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2015-04-06 21:40:05
|
Revision: 1914
http://sourceforge.net/p/r-gregmisc/code/1914
Author: warnes
Date: 2015-04-06 21:40:03 +0000 (Mon, 06 Apr 2015)
Log Message:
-----------
- Export S3 methods for first(), last(), left() and right().
- Ensure code matches man page for first(), last(), left(), and right().
Modified Paths:
--------------
trunk/gtools/NAMESPACE
trunk/gtools/R/first.R
Modified: trunk/gtools/NAMESPACE
===================================================================
--- trunk/gtools/NAMESPACE 2015-01-02 20:20:05 UTC (rev 1913)
+++ trunk/gtools/NAMESPACE 2015-04-06 21:40:03 UTC (rev 1914)
@@ -40,3 +40,16 @@
stars.pval,
strmacro
)
+
+S3method(first, default)
+S3method(first, list )
+
+S3method(last, default)
+S3method(last, list )
+
+S3method(left, data.frame)
+S3method(left, matrix)
+
+S3method(right, data.frame)
+S3method(right, matrix)
+
Modified: trunk/gtools/R/first.R
===================================================================
--- trunk/gtools/R/first.R 2015-01-02 20:20:05 UTC (rev 1913)
+++ trunk/gtools/R/first.R 2015-04-06 21:40:03 UTC (rev 1914)
@@ -1,15 +1,18 @@
first <- function(x) UseMethod("first")
last <- function(x) UseMethod("last")
-left <- function(x, n) UseMethod("left")
-right <- function(x, n) UseMethod("left")
+left <- function(x, n=6) UseMethod("left")
+right <- function(x, n=6) UseMethod("left")
+
+
first.default <- function(x) x[1]
last.default <- function(x) x[length(x)]
-first.list <- function(x, ...) x[[1]]
-last.list <- function(x, ...) x[[length(x)]]
+first.list <- function(x) x[[1]]
+last.list <- function(x) x[[length(x)]]
+
left.data.frame <- function(x, n=6)
{
n <- min(n, ncol(x))
@@ -17,6 +20,7 @@
}
left.matrix <- left.data.frame
+
right.data.frame <- function(x, n=6)
{
n <- min(n, ncol(x))
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2015-01-02 20:20:13
|
Revision: 1913
http://sourceforge.net/p/r-gregmisc/code/1913
Author: warnes
Date: 2015-01-02 20:20:05 +0000 (Fri, 02 Jan 2015)
Log Message:
-----------
Update for gplots release 2.16.0.
Modified Paths:
--------------
trunk/gplots/DESCRIPTION
trunk/gplots/inst/NEWS
Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION 2015-01-02 20:10:21 UTC (rev 1912)
+++ trunk/gplots/DESCRIPTION 2015-01-02 20:20:05 UTC (rev 1913)
@@ -4,8 +4,8 @@
Depends: R (>= 3.0)
Imports: gtools, gdata, stats, caTools, KernSmooth
Suggests: grid, MASS
-Version: 2.15.0
-Date: 2014-12-01
+Version: 2.16.0
+Date: 2015-01-02
Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert
Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin
Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2015-01-02 20:10:21 UTC (rev 1912)
+++ trunk/gplots/inst/NEWS 2015-01-02 20:20:05 UTC (rev 1913)
@@ -1,3 +1,17 @@
+Release 2.16.0 - 2015-01-02
+---------------------------
+
+New Features:
+
+- plotmeans() has a new argument, 'text.n.label' which specifies the
+ text used for labeling the number of elements in a group.
+
+Bug Fixes:
+
+- plotmeans() now respects (optional) graphical arguments captured in
+ '...' when drawing the x axis.
+
+
Release 2.15.0 - 2014-12-01
---------------------------
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2015-01-02 20:10:24
|
Revision: 1912
http://sourceforge.net/p/r-gregmisc/code/1912
Author: warnes
Date: 2015-01-02 20:10:21 +0000 (Fri, 02 Jan 2015)
Log Message:
-----------
Change default group count lable back to 'n='.
Modified Paths:
--------------
trunk/gplots/R/plotmeans.R
Modified: trunk/gplots/R/plotmeans.R
===================================================================
--- trunk/gplots/R/plotmeans.R 2015-01-02 20:06:35 UTC (rev 1911)
+++ trunk/gplots/R/plotmeans.R 2015-01-02 20:10:21 UTC (rev 1912)
@@ -7,7 +7,7 @@
mean.labels=FALSE,
ci.label=FALSE,
n.label=TRUE,
- text.n.label="N=",
+ text.n.label="n=",
digits=getOption("digits"), col="black",
barwidth=1,
barcol="blue",
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2015-01-02 20:06:42
|
Revision: 1911
http://sourceforge.net/p/r-gregmisc/code/1911
Author: warnes
Date: 2015-01-02 20:06:35 +0000 (Fri, 02 Jan 2015)
Log Message:
-----------
- plotmeans: Pass optional graphical arguments captured in '...' axis function
used to draw the x axis.
- plotmeans: Add an new argument 'text.n.label' to specify the text
used for labelingthe number of elements in a group.
Modified Paths:
--------------
trunk/gplots/R/plotmeans.R
trunk/gplots/man/plotmeans.Rd
Modified: trunk/gplots/R/plotmeans.R
===================================================================
--- trunk/gplots/R/plotmeans.R 2015-01-02 19:50:10 UTC (rev 1910)
+++ trunk/gplots/R/plotmeans.R 2015-01-02 20:06:35 UTC (rev 1911)
@@ -7,6 +7,7 @@
mean.labels=FALSE,
ci.label=FALSE,
n.label=TRUE,
+ text.n.label="N=",
digits=getOption("digits"), col="black",
barwidth=1,
barcol="blue",
@@ -78,7 +79,7 @@
xlab=xlab, ylab=ylab, labels=mean.labels, col=col, xlim=xlim,
lwd=barwidth, barcol=barcol, minbar=minbar, maxbar=maxbar, ... )
if(invalid(xaxt) || xaxt!="n")
- axis(1, at = 1:length(means), labels = legends)
+ axis(1, at = 1:length(means), labels = legends, ...)
if(ci.label)
{
@@ -103,8 +104,12 @@
if(n.label)
- text(x=1:length(means),y=par("usr")[3],
- labels=paste("n=",ns,"\n",sep=""))
+ {
+ text(x=1:length(means),
+ y=par("usr")[3],
+ labels=paste(text.n.label, ns, "\n", sep="")
+ )
+ }
if(!invalid(connect) & !identical(connect,FALSE))
{
@@ -120,6 +125,5 @@
lines(means, ..., lwd=lwd, col=ccol)
}
-
}
Modified: trunk/gplots/man/plotmeans.Rd
===================================================================
--- trunk/gplots/man/plotmeans.Rd 2015-01-02 19:50:10 UTC (rev 1910)
+++ trunk/gplots/man/plotmeans.Rd 2015-01-02 20:06:35 UTC (rev 1911)
@@ -1,24 +1,17 @@
-% $Id$
-
\name{plotmeans}
\alias{plotmeans}
\title{Plot Group Means and Confidence Intervals}
\description{Plot group means and confidence intervals.}
-%\synopsis{
\usage{
plotmeans(formula, data=NULL, subset, na.action,
bars=TRUE, p=0.95, minsd=0, minbar, maxbar,
xlab=names(mf)[2], ylab=names(mf)[1], mean.labels=FALSE,
- ci.label=FALSE, n.label=TRUE, digits=getOption("digits"),
- col="black", barwidth=1, barcol="blue",
- connect=TRUE, ccol=col, legends=names(means), xaxt,
- use.t=TRUE, lwd=par("lwd"), ...)
+ ci.label=FALSE, n.label=TRUE, text.n.label="n=",
+ digits=getOption("digits"), col="black", barwidth=1,
+ barcol="blue", connect=TRUE, ccol=
+ col, legends=names(means), xaxt, use.t=TRUE,
+ lwd=par("lwd"), ...)
}
-%
-%\usage{
-% plotmeans( outcome ~ treatment)
-%}
-
\arguments{
\item{formula}{symbolic expression specifying the outcome (continuous)
and grouping variable (factor). See lm() for details.}
@@ -42,12 +35,12 @@
\item{minbar}{minumum allowed value for bar ends. If specified,
values smaller than \code{minbar} will be replaced with
- \code{minbar}. }
-
+ \code{minbar}. }
+
\item{maxbar}{maximum allowed value for bar ends. If specified,
values larger than \code{maxbar} will be replaced with
\code{maxbar}. }
-
+
\item{xlab}{x-axis label.}
\item{ylab}{y-axis label.}
@@ -63,6 +56,9 @@
\item{n.label}{ a logical value indicating whether text giving the number of
observations in each group should should be added to the plot. }
+ \item{text.n.label}{Prefix text for labeling observation counts.
+ Defaults to "n=". }
+
\item{digits}{ number of significant digits to use when displaying
mean or confidince limit values.}
@@ -86,22 +82,22 @@
\item{xaxt}{A character which specifies the axis type. Specifying `"n"'
causes an axis to be set up, but not plotted.}
-
+
\item{use.t}{ a logical value indicating whether the t distribution
should be used to compute confidence intervals. If \code{TRUE}, the
default, a t distribution will the correct number of degrees of
freedom for each group be used. If \code{FALSE}, the a normal
distribution will be used.}
-
+
\item{lwd}{Width of connecting lines }
-
+
\item{\dots}{ optional plotting parameters. }
}
-%\details{
-%
-%
+%\details{
+%
+%
%}
@@ -109,7 +105,7 @@
# show comparison with boxplot
data(state)
- plotmeans(state.area ~ state.region)
+ plotmeans(state.area ~ state.region)
# show some color and mean labels
plotmeans(state.area ~ state.region,
@@ -121,12 +117,12 @@
ccol="red", pch=7 )
# more complicated example showing how to show an interaction
- data(esoph)
+ data(esoph)
par(las=2, # use perpendicular axis labels
mar=c(10.1,4.1,4.1,2.1), # create enough space for long x labels
mgp=c(8,1,0) # move x axis legend down to avoid overlap
)
- plotmeans(ncases/ncontrols ~ interaction(agegp , alcgp, sep =" "),
+ plotmeans(ncases/ncontrols ~ interaction(agegp , alcgp, sep =" "),
connect=list(1:6,7:12,13:18,19:24),
barwidth=2,
col="dark green",
@@ -137,7 +133,7 @@
"Ile-et-Vilaine Esophageal Cancer Study")
)
abline(v=c(6.5, 12.5, 18.5), lty=2)
-
+
}
\author{Gregory R. Warnes \email{gr...@wa...}}
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|
|
From: <wa...@us...> - 2015-01-02 19:50:17
|
Revision: 1910
http://sourceforge.net/p/r-gregmisc/code/1910
Author: warnes
Date: 2015-01-02 19:50:10 +0000 (Fri, 02 Jan 2015)
Log Message:
-----------
- Remove S-Plus-specific code
- Simplify model frame code
Modified Paths:
--------------
trunk/gplots/R/plotmeans.R
Modified: trunk/gplots/R/plotmeans.R
===================================================================
--- trunk/gplots/R/plotmeans.R 2014-12-03 15:28:55 UTC (rev 1909)
+++ trunk/gplots/R/plotmeans.R 2015-01-02 19:50:10 UTC (rev 1910)
@@ -4,7 +4,9 @@
bars=TRUE, p=0.95,
minsd=0, minbar=NULL, maxbar=NULL,
xlab=names(mf)[2], ylab=names(mf)[1],
- mean.labels=FALSE, ci.label=FALSE, n.label=TRUE,
+ mean.labels=FALSE,
+ ci.label=FALSE,
+ n.label=TRUE,
digits=getOption("digits"), col="black",
barwidth=1,
barcol="blue",
@@ -16,56 +18,36 @@
lwd=par("lwd"),
...)
{
- is.R <- get("is.R")
- if(is.null(is.R)) is.R <- function(x) FALSE
-
- if(!is.R())
- {
- if(col=="black")
- col <- 1
- if(barcol=="blue")
- barcol <- 2
- }
-
if (invalid(formula) || (length(formula) != 3))
stop("formula missing or incorrect")
if (invalid(na.action))
na.action <- options("na.action")
- m <- match.call(expand.dots = FALSE)
- if(is.R())
- {
- if (is.matrix(eval(m$data, parent.frame())))
- m$data <- as.data.frame(data)
- }
- else
- {
- if (is.matrix(eval(m$data, FALSE)))
- m$data <- as.data.frame(data)
- }
- m$... <- m$bars <- m$barcol <- m$p <- NULL
- m$minsd <- m$minbar <- m$maxbar <- NULL
- m$xlab <- m$ylab <- NULL
- m$col <- m$barwidth <- NULL
- m$digits <- m$mean.labels <- m$ci.label <- m$n.label <- NULL
- m$connect <- m$ccol <- m$legends <- m$labels<- NULL
- m$xaxt <- m$use.t <- m$lwd <- NULL
- m[[1]] <- as.name("model.frame")
- mf <- eval(m, parent.frame())
+
+ mf <- match.call(expand.dots = FALSE)
+ if (is.matrix(eval(mf$data, parent.frame())))
+ mf$data <- as.data.frame(data)
+
+ m <- match(c("formula", "data", "subset", "na.action"), names(mf), 0L)
+
+ mf <- mf[c(1L, m)]
+
+ mf[[1L]] <- quote(stats::model.frame)
+ mf <- eval(mf, parent.frame())
response <- attr(attr(mf, "terms"), "response")
## drop unused levels in factors!!!
-
+
wFact <- which(attr(attr(mf, "terms"),"dataClasses") == "factor")
for(i in wFact)
mf[,i] <- factor(mf[,i])
-
+
means <- sapply(split(mf[[response]], mf[[-response]]), mean, na.rm=TRUE)
ns <- sapply(sapply(split(mf[[response]], mf[[-response]]), na.omit,
simplify=FALSE), length )
xlim <- c(0.5, length(means)+0.5)
-
+
if(!bars)
{
plot( means, ..., col=col, xlim=xlim)
@@ -121,15 +103,8 @@
if(n.label)
- if(is.R())
text(x=1:length(means),y=par("usr")[3],
labels=paste("n=",ns,"\n",sep=""))
- else
- {
- axisadj <- (par("usr")[4] - (par("usr")[3]) )/75
- text(x=1:length(means),y=par("usr")[3] + axisadj,
- labels=paste("n=",ns,"\n",sep=""))
- }
if(!invalid(connect) & !identical(connect,FALSE))
{
@@ -146,6 +121,5 @@
}
-
}
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|
|
From: <wa...@us...> - 2014-12-03 15:28:58
|
Revision: 1909
http://sourceforge.net/p/r-gregmisc/code/1909
Author: warnes
Date: 2014-12-03 15:28:55 +0000 (Wed, 03 Dec 2014)
Log Message:
-----------
Update stored test output to account for new startup message from KernSmooth package
Modified Paths:
--------------
trunk/gplots/tests/heatmap2Test.Rout.save
Modified: trunk/gplots/tests/heatmap2Test.Rout.save
===================================================================
--- trunk/gplots/tests/heatmap2Test.Rout.save 2014-12-03 15:00:58 UTC (rev 1908)
+++ trunk/gplots/tests/heatmap2Test.Rout.save 2014-12-03 15:28:55 UTC (rev 1909)
@@ -1,7 +1,7 @@
-R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
-Copyright (C) 2013 The R Foundation for Statistical Computing
-Platform: i686-pc-linux-gnu (32-bit)
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-apple-darwin13.1.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -16,8 +16,6 @@
Type 'q()' to quit R.
> library(gplots)
-KernSmooth 2.23 loaded
-Copyright M. P. Wand 1997-2009
Attaching package: 'gplots'
@@ -224,4 +222,4 @@
>
> proc.time()
user system elapsed
- 4.852 0.372 5.389
+ 1.485 0.094 2.015
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|
From: <wa...@us...> - 2014-12-03 15:01:09
|
Revision: 1908
http://sourceforge.net/p/r-gregmisc/code/1908
Author: warnes
Date: 2014-12-03 15:00:58 +0000 (Wed, 03 Dec 2014)
Log Message:
-----------
Fix package title capitalization.
Modified Paths:
--------------
trunk/gplots/DESCRIPTION
Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION 2014-12-02 15:55:07 UTC (rev 1907)
+++ trunk/gplots/DESCRIPTION 2014-12-03 15:00:58 UTC (rev 1908)
@@ -1,5 +1,5 @@
Package: gplots
-Title: Various R programming tools for plotting data
+Title: Various R Programming Tools for Plotting Data
Description: Various R programming tools for plotting data
Depends: R (>= 3.0)
Imports: gtools, gdata, stats, caTools, KernSmooth
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|
From: <wa...@us...> - 2014-12-02 15:55:14
|
Revision: 1907
http://sourceforge.net/p/r-gregmisc/code/1907
Author: warnes
Date: 2014-12-02 15:55:07 +0000 (Tue, 02 Dec 2014)
Log Message:
-----------
Add descrioption of node stack overflow issue and work-around.
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2014-12-02 01:46:35 UTC (rev 1906)
+++ trunk/gplots/inst/NEWS 2014-12-02 15:55:07 UTC (rev 1907)
@@ -3,10 +3,22 @@
New features:
-- Convert bandplot() to S3-method dispatch and add method for class formula, so that
- 'bandplot( y ~ x, data=dataframe )' now works as expected.
+- Convert bandplot() to S3-method dispatch and add method for class
+ formula, so that 'bandplot( y ~ x, data=dataframe )' now works as
+ expected.
+Other changes:
+- heatmap.2() now uses a local *non-byte-compiled* copy of
+ plot.dengrogram, because the byte-compiled stats:::plot.dendrogram
+ uses a recursive algorithm that generates a 'node stack overflow'
+ error for deeply nested dendrograms and the node stack size cannot
+ be changed at execution time. Instead, tne local non-byte-compiled
+ gplots:::plot.dendrogram will trigger a recursion limit for such
+ dengrograms. heatmap.2() will detect this error and recommend that
+ the user increase the recursion limit (via,
+ e.g. 'options("expressions"=20000)' ) and rerun.
+
Release 2.14.2 - 2014-09-17
---------------------------
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|
|
From: <wa...@us...> - 2014-12-02 01:46:38
|
Revision: 1906
http://sourceforge.net/p/r-gregmisc/code/1906
Author: warnes
Date: 2014-12-02 01:46:35 +0000 (Tue, 02 Dec 2014)
Log Message:
-----------
Move '...' argument to bandplot.formula to match man page.
Modified Paths:
--------------
trunk/gplots/R/bandplot.R
Modified: trunk/gplots/R/bandplot.R
===================================================================
--- trunk/gplots/R/bandplot.R 2014-12-02 01:39:19 UTC (rev 1905)
+++ trunk/gplots/R/bandplot.R 2014-12-02 01:46:35 UTC (rev 1906)
@@ -62,9 +62,9 @@
data,
subset,
na.action,
+ ...,
xlab=NULL,
ylab=NULL,
- ...,
add=FALSE,
sd=c(-2:2),
sd.col=c("magenta","blue","red",
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|
From: <wa...@us...> - 2014-12-02 01:39:26
|
Revision: 1905
http://sourceforge.net/p/r-gregmisc/code/1905
Author: warnes
Date: 2014-12-02 01:39:19 +0000 (Tue, 02 Dec 2014)
Log Message:
-----------
plot.dendrogram isn't exported by gplots, so it must be referenced using the ':::' notation.
Modified Paths:
--------------
trunk/gplots/tests/test_plottingDeepDendrogram.R
Modified: trunk/gplots/tests/test_plottingDeepDendrogram.R
===================================================================
--- trunk/gplots/tests/test_plottingDeepDendrogram.R 2014-12-02 01:38:01 UTC (rev 1904)
+++ trunk/gplots/tests/test_plottingDeepDendrogram.R 2014-12-02 01:39:19 UTC (rev 1905)
@@ -10,10 +10,10 @@
dend <- as.dendrogram(cluster)
## R's default recursion limits will be exceeded when plotting this dendrogram
-try( plot.dendrogram(dend) )
+try( gplots:::plot.dendrogram(dend) )
try( heatmap.2(dat, Rowv=dend) )
## Increase them and try again
options("expressions"=20000)
-plot.dendrogram(dend)
+gplots:::plot.dendrogram(dend)
heatmap.2(dat, Rowv=dend)
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