[R-gregmisc-commits] r2110 - in pkg/gplots: . inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 25 19:48:39 CET 2016
Author: warnes
Date: 2016-03-25 19:48:39 +0100 (Fri, 25 Mar 2016)
New Revision: 2110
Modified:
pkg/gplots/DESCRIPTION
pkg/gplots/inst/ChangeLog
pkg/gplots/inst/NEWS
Log:
Update files for gplots 2.18.0
Modified: pkg/gplots/DESCRIPTION
===================================================================
--- pkg/gplots/DESCRIPTION 2016-03-25 18:48:24 UTC (rev 2109)
+++ pkg/gplots/DESCRIPTION 2016-03-25 18:48:39 UTC (rev 2110)
@@ -1,7 +1,7 @@
Package: gplots
Title: Various R Programming Tools for Plotting Data
Description: Various R programming tools for plotting data, including:
- - calculating and plotting locally smoothed summary functionas
+ - calculating and plotting locally smoothed summary function as
('bandplot', 'wapply'),
- enhanced versions of standard plots ('barplot2', 'boxplot2',
'heatmap.2', 'smartlegend'),
@@ -15,7 +15,7 @@
- plotting a matrix where each cell contains a dot whose size
reflects the relative magnitude of the elements ('balloonplot'),
- plotting venn diagrams ('venn'),
- - displaying Open-Office syle plots ('ooplot'),
+ - displaying Open-Office style plots ('ooplot'),
- plotting multiple datasets on same region, with separate axes
('overplot'),
- plotting means and cofidence intervals ('plotCI', 'plotmeans'),
@@ -23,8 +23,8 @@
Depends: R (>= 3.0)
Imports: gtools, gdata, stats, caTools, KernSmooth
Suggests: grid, MASS
-Version: 2.17.0
-Date: 2015-05-01
+Version: 2.18.0
+Date: 2016-03-25
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: pkg/gplots/inst/ChangeLog
===================================================================
--- pkg/gplots/inst/ChangeLog 2016-03-25 18:48:24 UTC (rev 2109)
+++ pkg/gplots/inst/ChangeLog 2016-03-25 18:48:39 UTC (rev 2110)
@@ -1,59 +1,145 @@
+2016-03-25 warnes
+
+ * [r2106] R/plot.venn.R: Warning message didn't have spaces between
+ words. Minor code reformatting.
+ * [r2105] R/lowess.R: Remove obsolete function to add '...' to
+ argument list for stats::lowess().
+ * [r2104] man/lowess.Rd, man/venn.Rd: Fix errors identified by R
+ CMD check
+ * [r2103] R/heatmap.2.R: Fix error when Rowv=FALSE or Colv=FALSE
+ * [r2102] man/gplots-defunct.Rd, man/gplots-deprecated.Rd: Fix
+ documenation issues identified by 'R CMD check'
+ * [r2101] man/venn.Rd: Correct discrepencies in man page
+ * [r2100] man/venn.Rd: Correct discrepencies in man page
+ * [r2099] man/lowess.Rd: Correct differences between calls on man
+ page and in code
+ * [r2098] R/lmplot2.R: Fix name of replacement functon in defuct
+ message generated by plot.lm2
+ * [r2097] man/lowess.Rd: Improve lowess() man page
+ * [r2096] NAMESPACE: Add plotLowess() and plot.lowess() to the
+ NAMESPACE
+ * [r2095] R/plot.lowess.R: Ensure lowess plot methods (invisibly)
+ return the lowess object.
+ * [r2094] man/lowess.Rd: Update man page for lowess to reflect new
+ lowess method for plot().
+ * [r2093] R/plot.lowess.R: Ensure extra arguments are properly
+ passed to the plot call.
+ * [r2092] R/heatmap.2.R: Corrected a bug causing "Error in
+ plot.new() : figure margins too large" to occur when 'key=FALSE'.
+ (Reported and patch provided by Sveinung Gundersen.)
+
+2016-03-24 warnes
+
+ * [r2091] R/lowess.R, R/plot.lowess.R: Rename plot.lowess to
+ plotLowess to avoid confusions with plot() method for class
+ 'lowess', create a plot() method for class 'lowess' and modify
+ the lowess.default() and lowess.formula() to add the 'lowess'
+ class to the returned object, along with a 'call' list element.
+ * [r2090] R/venn.R, R/vennMembers.R, man/venn.Rd: The
+ 'intersections' attribute returned from venn() has been improved
+ to use set names instead of indicators, and is ordered from
+ simplest to most complex set interactions.
+ * [r2089] R/smartlegend.R, man/gplots-defunct.Rd,
+ man/gplots-deprecated.Rd: The smartlegend() function has been
+ made defunct and is no longer available.
+ * [r2088] R/lmplot2.R: Indentation changes
+ * [r2087] man/heatmap.2.Rd: Update heatmap.2() man page to reflect
+ addition of to the returned object.
+ * [r2086] R/lowess.R: Remove observations with missing values when
+ lowess is called using the formula interface.
+ * [r2085] R/heatmap.2.R: Add layout infromation to object returned
+ from heatmap.2() (patch provided by Jenny Drnevich).
+ * [r2084] DESCRIPTION: Correct spelling
+
+2016-03-08 warnes
+
+ * [r2083] R/plot.lowess.R: Add function to plot points and lowess
+ using formula interface.
+ * [r2082] R/lowess.R: Remove old code for S-Plus and modernize
+ formula handling code.
+ * [r2081] R/heatmap.2.R: Set srtCol default if missing and colCol
+ is set
+
+2016-02-26 warnes
+
+ * [r2080] R/venn.R: venn() now support matrix arguments.
+ * [r2079] R/angleAxis.R, man/angleAxis.Rd: New angleAxis() function
+ to create axis labels with rotated text.
+ * [r2078] R/heatmap.2.R: - heatmap.2() can now be used to plot
+ subsets of a previous heatmap.
+ - Remove stray 'browser()' debuggint statement from heatmap.2()
+ code.
+ - Decrease the granularity of the carpet in heatmap.2()'s color
+ key to
+ avoid visual artifacts.
+
+2015-11-23 warnes
+
+ * [r2070] R/heatmap.2.R: Remove debugging print() statement.
+
+2015-07-22 warnes
+
+ * [r2062] DESCRIPTION, R/heatmap.2.R, R/layout_set.R: Renamed
+ 'test' directory to 'tests', commented out tests for lme4 which
+ has a changed API
+
+2015-06-02 warnes
+
+ * [r2052] R/boxplot2.R: Defunct message for boxplot.n was
+ recommending the wrong function
+
+2015-05-02 warnes
+
+ * [r2018] Rename 'trunk' to 'pkg' for compatibility with R-forge
+
2015-05-01 warnes
- * [r2013] inst/ChangeLog: Update ChangeLog (again)
- * [r2012] man/gplots-defunct.Rd: Summary: Correct man page name
- * [r2011] man/gplots-deprecated.Rd: Summary: Forgot to add \alias
- for smartlegend.
- * [r2010] man/lmplot2.Rd: Remove leftover alias
- * [r2009] inst/ChangeLog: Commit ChangeLog
- * [r2008] NAMESPACE, inst/NEWS: Update NEWS again.
- * [r2007] man/gplots-defunct.Rd, man/gplots-deprecated.Rd,
- man/lmplot2.Rd, man/smartlegend.Rd: Mark boxplot.n and()
- plot.lm2() as defunct.
- * [r2006] R/boxplot2.R, R/lmplot2.R: Make ballonplot.n() and
- plot.lm2() 'defunct'.
- * [r2005] inst/ChangeLog, inst/NEWS: Update NEWS and ChangeLog
- again.
- * [r2004] man/sinkplot.Rd: Summary: Punctuation.
- * [r2003] NAMESPACE: Correct URLs in man pages.
- * [r2002] man/heatmap.2.Rd, man/sinkplot.Rd: Correct URLs in man
- pages.
- * [r2001] inst/NEWS: Update NEWS again.
- * [r2000] DESCRIPTION: Improve package description.
- * [r1999] man/smartlegend.Rd: Mark 'smartlegend' as deprecated
- * [r1998] R/smartlegend.R: Summary: Mark smartlegend() as
- deprecated.
- * [r1997] man/venn.Rd: Summary: venn example used 'F' instead of
- 'FALSE'.
- * [r1996] DESCRIPTION, inst/ChangeLog, inst/NEWS: Update
- DESCRIPTION, NEWS, and ChangeLog again for gplots 2.17.0.
- * [r1995] R/heatmap.2.R: - heatmap.2: row traces could be plotted
- in the wrong order.
- * [r1994] R/heatmap.2.R, man/heatmap.2.Rd: - heatmap.2: column
- traces could be plotted in the wrong order.
+ * [r2014] Again...
+ * [r2013] Update ChangeLog (again)
+ * [r2012] Summary: Correct man page name
+ * [r2011] Summary: Forgot to add \alias for smartlegend.
+ * [r2010] Remove leftover alias
+ * [r2009] Commit ChangeLog
+ * [r2008] Update NEWS again.
+ * [r2007] Mark boxplot.n and() plot.lm2() as defunct.
+ * [r2006] Make ballonplot.n() and plot.lm2() 'defunct'.
+ * [r2005] Update NEWS and ChangeLog again.
+ * [r2004] Summary: Punctuation.
+ * [r2003] Correct URLs in man pages.
+ * [r2002] Correct URLs in man pages.
+ * [r2001] Update NEWS again.
+ * [r2000] Improve package description.
+ * [r1999] Mark 'smartlegend' as deprecated
+ * [r1998] Summary: Mark smartlegend() as deprecated.
+ * [r1997] Summary: venn example used 'F' instead of 'FALSE'.
+ * [r1996] Update DESCRIPTION, NEWS, and ChangeLog again for gplots
+ 2.17.0.
+ * [r1995] - heatmap.2: row traces could be plotted in the wrong
+ order.
+ * [r1994] - heatmap.2: column traces could be plotted in the wrong
+ order.
- heatmap.2: add support for plotting sub-clusters of the full
row and
column dendrograms
2015-04-23 warnes
- * [r1955] inst/ChangeLog, inst/NEWS: Update NEWS and ChangeLog
- * [r1954] DESCRIPTION, R/heatmap.2.R, inst/ChangeLog, inst/NEWS: In
- heatmap.2(), the color key now properly handles color breaks that
+ * [r1955] Update NEWS and ChangeLog
+ * [r1954] In heatmap.2(), the color key now properly handles color
+ breaks that
are not equally spaced. (Issue reported by Tim Richter-Heitmann.)
- * [r1948] R/plotCI.R: - plotCI() was not properly respecting the
- 'type=' argument. This has
+ * [r1948] - plotCI() was not properly respecting the 'type='
+ argument. This has
been corrected.
- * [r1947] R/overplot.R: - Remove stray browser() call from
- overplot()
- * [r1943] man/balloonplot.Rd: Explicitly specify argument to
- gplots:::reorder.factor to prevent error.
- * [r1942] R/venn.R, man/venn.Rd: - The returned object from venn()
- now includes a 'interesection'
+ * [r1947] - Remove stray browser() call from overplot()
+ * [r1943] Explicitly specify argument to gplots:::reorder.factor to
+ prevent error.
+ * [r1942] - The returned object from venn() now includes a
+ 'interesection'
attribution containing a list of which items are in each set
intersection. This can be turned off by settting
'intersection=FALSE'.
- * [r1941] R/heatmap.2.R: Patch submitted by Ilia Kats:
+ * [r1941] Patch submitted by Ilia Kats:
- easily extract and plot subclusters from a big heatmap using
the
same colorkey, by passing a dendgrogram of the subcluster
@@ -65,92 +151,83 @@
paper, but maintain consistent color coding.
- Improves the behavior of the color key axis labels, as they now
honor par("cex") and par("cex.lab").
- * [r1940] R/heatmap.2.R: In heatmap.2() split calls to distfun()
- and hclustfun() into separate steps to make debugging easier
+ * [r1940] In heatmap.2() split calls to distfun() and hclustfun()
+ into separate steps to make debugging easier
2015-04-22 warnes
- * [r1931] DESCRIPTION, inst/ChangeLog, inst/NEWS: Update
- DESCRIPTION, ChangeLog, and NEWS for gplots 2.17.0
- * [r1930] R/heatmap.2.R, man/heatmap.2.Rd: heatmap.2: add new
- 'colRow' and 'colCol' arguments to control the color of row and
- column text labels
+ * [r1931] Update DESCRIPTION, ChangeLog, and NEWS for gplots 2.17.0
+ * [r1930] heatmap.2: add new 'colRow' and 'colCol' arguments to
+ control the color of row and column text labels
2015-04-06 warnes
- * [r1916] inst/ChangeLog: Add ChangeLog files to repository
+ * [r1916] Add ChangeLog files to repository
2015-01-02 warnes
- * [r1913] DESCRIPTION, inst/NEWS: Update for gplots release 2.16.0.
- * [r1912] R/plotmeans.R: Change default group count lable back to
- 'n='.
- * [r1911] R/plotmeans.R, man/plotmeans.Rd: - plotmeans: Pass
- optional graphical arguments captured in '...' axis function
+ * [r1913] Update for gplots release 2.16.0.
+ * [r1912] Change default group count lable back to 'n='.
+ * [r1911] - 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.
- * [r1910] R/plotmeans.R: - Remove S-Plus-specific code
+ * [r1910] - Remove S-Plus-specific code
- Simplify model frame code
2014-12-03 warnes
- * [r1909] tests/heatmap2Test.Rout.save: Update stored test output
- to account for new startup message from KernSmooth package
- * [r1908] DESCRIPTION: Fix package title capitalization.
+ * [r1909] Update stored test output to account for new startup
+ message from KernSmooth package
+ * [r1908] Fix package title capitalization.
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.
+ * [r1907] Add descrioption of node stack overflow issue and
+ work-around.
+ * [r1906] Move '...' argument to bandplot.formula to match man
+ page.
+ * [r1905] plot.dendrogram isn't exported by gplots, so it must be
+ referenced using the ':::' notation.
+ * [r1904] Man page fixes.
+ * [r1903] Add exports of new bandplot methods to NAMESPACE file.
+ * [r1902] Code cleanup.
+ * [r1901] 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
+ * [r1900] Update for 2.15.0
+ * [r1899] Convert bandplot to S3-method dispatch and add method for
+ class formula.
+ * [r1898] 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
+ * [r1895] Minor reformatting.
+ * [r1894] Explicitly reset namespace for dendrogram functions
+ copied from stats.
+ * [r1893] Update DESCRIPTION and NEWS for gplots 2.14.2
+ * [r1892] 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.
+ * [r1891] Add test case for exceeding recursion limits when
+ plotting deeply nested dendrograms
+ * [r1890] heatmap.2 was not properly handling integer vectors for
+ Rowv and Colv.
+ * [r1889] 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'.
+ * [r1888] Add plotNode code to allow modificaiton of algorithm from
+ recursive to iterative for the purpose of avoiding node stack
+ overflow.
+ * [r1887] - 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
@@ -160,222 +237,187 @@
2014-06-30 warnes
- * [r1823] R/heatmap.2.R: Fix typo in dendrogram size checking code.
+ * [r1823] 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
+ * [r1822] Fix typo 'ColInd' --> 'colInd'.
+ * [r1821] 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',
+ * [r1820] - 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
+ * [r1819] 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.
+ * [r1818] 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.
+ * [r1817] 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.
+ * [r1812] Add see also to r2d2::freq2d.
+ * [r1811] Add reference to r2d2::conf2d.
2014-04-09 warnes
- * [r1802] R/heatmap.2.R: Add padj=0.5 to better align margin
- labels.
+ * [r1802] 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
+ * [r1781] Update NEWS
+ * [r1780] 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.
+ * [r1779] Update for gplots 2.13.0
+ * [r1778] 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
+ * [r1744] Handle 'ask' argument in lmplot2 function proper, rather
+ than in (depreciated) plot.lm2 wrapper.
+ * [r1743] Correct release number
+ * [r1742] Handle 'ask' argument in lmplot2 function proper, rather
+ than in (depreciated) plot.lm2 wrapper.
+ * [r1741] 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
+ * [r1740] Add boxplot2 and lmplot2 to NAMESPACE
+ * [r1739] Update for gplots release 2.12.1
+ * [r1738] Rename boxplot.n to boxplt2 and plot.lm2 to lmplot2
+ * [r1737] Make lmplot2 manual page from plot.lm.2 manual page.
+ * [r1736] Make boxplot2 manual page from boxplot.n manual page.
+ * [r1735] 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.
+ * [r1734] Update NEWS with latest changes
+ * [r1733] 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.
+ * [r1732] Allow standard S3 method handling to locate the correct
+ function.
+ * [r1731] Fix error when a subgroup contains no finite values
+ * [r1730] Update test output
+ * [r1729] Move several packages from Depends to Imports, Suggests
+ * [r1728] Use gdata::nobs in example
+ * [r1727] caTools and KernSmooth now have namespaces, so import
+ from them.
+ * [r1726] Update files for gplots 2.12.0
+ * [r1725] Update files for gplots 2.12.0
+ * [r1724] Add parameters to control row and column label
+ positioning, rotation, justification, and offset.
+ * [r1723] 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
+ * [r1680] 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.
+ * [r1679] Update for gplots 2.11.3
+ * [r1678] Update for release 2.11.3
+ * [r1677] Update with tests for only 1 row/column separator
+ * [r1676] Fix typo
+ * [r1675] Add test for one row/column separator
+ * [r1674] Add more in-line comments
+ * [r1673] 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
+ * [r1647] Update news for release 2.11.2
+ * [r1646] Add ci.width argument to barplot2() to allow varying the
+ length of the 't' at the end of confidence interval bars.
+ * [r1642] Update for release 2.11.2
+ * [r1641] 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
+ * [r1631] Fix typo: warn() instead of warning().
+ * [r1630] Fix syntax of VignetteIndexEntry in venn.Rnw.
+ * [r1629] Add generated vignette pdf.
+ * [r1628] Add required VignetteIndexEntry metadata to venn vignette
+ code.
+ * [r1627] Update DESCRIPTION and NEWS for release 2.11.1.
+ * [r1626] Improve venn() to work with PDF and Sweave/pdflatex.
+ Provide a vignette for venn().
+ * [r1625] Fix error in processing the colsep argument to heatmap.2.
+ * [r1624] 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.
+ * [r1623] 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.
+ * [r1558] Update NEWS for 2.11.0 release.
+ * [r1557] Fix R CMD check warnings.
+ * [r1556] 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:
+ * [r1555] 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
+ * [r1554] 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()
+ * [r1553] Add default value for lwd argument to plotmeans()
2012-05-31 warnes
- * [r1533] man/qqnorm.aov.Rd: Properly mark up S3 method.
+ * [r1533] Properly mark up S3 method.
2011-12-09 warnes
- * [r1519] R/plotmeans.R, man/plotmeans.Rd: Add 'lwd' (linewidth) to
- arguments handled by plotmeans.
+ * [r1519] 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'
+ * [r1505] Update NEWS for release 2.10.1.
+ * [r1504] Increment version counter.
+ * [r1503] 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
+ * [r1502] Fix naming error
+ * [r1501] Provide print() methods for 'hist2d' and 'ci2d' objects.
+ * [r1498] 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
+ * [r1491] - Correct issues in ci2d() man page.
+ * [r1490] - 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():
+ * [r1489] - Update NEWS file and correct version number
+ * [r1488] - Depend on KernSmooth package. Increment version number.
+ * [r1487] - Depend on KernSmooth package and import 'bkdeD2' and
+ 'dpik'.
+ * [r1486] Improvements to ci2d():
- Add option to utilize KernDensity::bkde2D to estimate the 2-d
density (now the default).
@@ -388,63 +430,53 @@
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.
+ * [r1485] 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
+ * [r1478] Update NEWS for 2.10.0 release
+ * [r1477] Add dependency on R>= 2.10 to handle compressed Rda data
+ file.
+ * [r1476] Compress rtPCR example data set to make distributed
+ package smaller.
+ * [r1475] 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.
+ * [r1474] - 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).
+ * [r1473] Update DESCRIPTION file for 2.8.1.
+ * [r1472] Add 'alpha' argument to rich.colors() to control
+ transparency.
+ * [r1471] 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()
+ * [r1470] 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
+ * [r1463] 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
+ * [r1446] Fix errors detected by R CMD check
+ * [r1445] Fix errors detected by R CMD check
+ * [r1444] Use 'TRUE' instead of 'T' for true in venn man page
+ * [r1443] Update for gplots 2.8.0
+ * [r1442] Moved baseOf() into a separate file
+ * [r1441] Update Greg's email address
+ * [r1440] - 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
@@ -453,482 +485,386 @@
2010-02-17 warnes
- * [r1420] DESCRIPTION, R/hist2d.R, inst/NEWS: Improve performance
- of hist2d thanks to suggestion by Joerg van den Hoff.
+ * [r1420] 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
+ * [r1372] Renamed files rich.color.* to rich.colors.* and renamed
+ rich.colors args
2009-11-16 arnima
- * [r1367] R/rich.color.R: Minor reformatting only.
+ * [r1367] 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'.
+ * [r1365] 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
+ * [r1364] Fixed typo in bug fix.
+ * [r1363] Update NEWS and DESCRIPTION for gplots 2.7.3
+ * [r1362] Fix transposed display of data (but not labels) in
+ heatmap.2 when symm=TRUE
2009-10-12 warnes
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/r-gregmisc -r 2110
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