Thread: [R-gregmisc-users] SF.net SVN: r-gregmisc:[1321] trunk/gplots/inst/NEWS
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From: <wa...@us...> - 2009-05-08 22:32:36
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Revision: 1321
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1321&view=rev
Author: warnes
Date: 2009-05-08 22:32:28 +0000 (Fri, 08 May 2009)
Log Message:
-----------
Update NEWS for release 2.7.0
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2009-05-08 22:30:55 UTC (rev 1320)
+++ trunk/gplots/inst/NEWS 2009-05-08 22:32:28 UTC (rev 1321)
@@ -1,8 +1,31 @@
-Release 2.7.0 - 2008-08-05
+Release 2.7.0 - 2009-05-08
--------------------------
New Features:
+
+- Enhancements to heatmap.2()
+
+ - New arguments 'lmat', 'lhei', and 'lwid' that allow controlling
+ component plot layout. Users can now resize and rearrange plot
+ components.
+
+ - heatmap.2() will now compute color breakpoints that are
+ symmetric about 0 when the new 'symbreak' parameter is TRUE. This
+ parameter, as well as the symkey parameter now default to TRUE
+ whenever negative values of x are present, and to FALSE othewise.
+
+ - the heatmap.2() return value now includes additional useful
+ information, including: call, rowMeans, rowSDs, colMeans,
+ colSDs, carpet (reordered and scaled 'x' values), rowDendrogram,
+ colDendrogram, breaks, col, vline, hline, and colorTable. Of
+ these, the most useful are breaks, col, and colorTable. The
+ latter is a three-column data frame providing the lower and
+ upper bound and color for each bin.
+
+ See the manual page for complete details and examples.
+
+
- New function venn(), contributed by Steffen Moeller (Thanks
Steffen!) to generate Venn diagrams for up to 5 sets. See ?venn for
details.
@@ -15,10 +38,6 @@
using the new bandplot() and by using fitted() instead of predict()
to obtain y-hat.
-- New arguments for heatmap.2 ('lmat', 'lhei', and 'lwid') that allow
- controlling component plot layout. This allows the user to both
- resize and rearrange plot components.
-
- Add 'scale.range' argument to balloonplot(), option to scale
balloons so [min,max]->[0,1] ('relative') or [0,max] -> [0,1]
('absolute').
@@ -29,9 +48,14 @@
- balloonplot() now properly handles dimension labels provided by
'xlab' and 'ylab'
+- plotCI now properly handles 'NULL' and 'NA' values for ui, li, uiw,
+ and liw.
+
- Corrections of minor typos in man pages
+- Update Greg's email address to 'gr...@ra...'
+
Release 2.6.0 - 2008-04-07
--------------------------
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From: <wa...@us...> - 2011-08-26 20:38:19
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Revision: 1478
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1478&view=rev
Author: warnes
Date: 2011-08-26 20:38:12 +0000 (Fri, 26 Aug 2011)
Log Message:
-----------
Update NEWS for 2.10.0 release
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2011-08-26 20:29:58 UTC (rev 1477)
+++ trunk/gplots/inst/NEWS 2011-08-26 20:38:12 UTC (rev 1478)
@@ -1,3 +1,25 @@
+Release 2.10.0 - 2011-08-26
+---------------------------
+
+New Features:
+
+- New ci2d() function to create 2-dimensional empirical confidence
+ intervals utilizing hist2d(). See ?ci2d for details.
+
+- Add 'alpha' argument to rich.colors() to control transparency.
+
+Improvements:
+
+- Accellerate hist2d by replacing for() loop with tapply(), and allow
+ user to specify summary function applied (per suggestion by Peter
+ Hagedorn).
+
+Bug Fixes:
+
+- Correct error in heatmap.2() that arises when data includes NA values
+ (identified by Melissa Key).
+
+
Release 2.8.0 - 2010-06-10
--------------------------
@@ -15,7 +37,7 @@
Improvements:
-- Performance of 'hist2d' improved thanks to a suggestion from i
+- Performance of 'hist2d' improved thanks to a suggestion from
Joerg van den Hoff.
Release 2.7.4 - 2009-11-12
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From: <wa...@us...> - 2011-09-02 18:26:03
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Revision: 1505
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1505&view=rev
Author: warnes
Date: 2011-09-02 18:25:57 +0000 (Fri, 02 Sep 2011)
Log Message:
-----------
Update NEWS for release 2.10.1.
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2011-09-02 18:23:33 UTC (rev 1504)
+++ trunk/gplots/inst/NEWS 2011-09-02 18:25:57 UTC (rev 1505)
@@ -1,3 +1,11 @@
+Release 2.10.1 - 2011-09-02
+---------------------------
+
+New features:
+
+- Make results of hist2d() and ci2d() into objects, and add print()
+ methods to display them.
+
Release 2.10.0 - 2011-08-26
---------------------------
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From: <wa...@us...> - 2012-06-08 18:30:57
|
Revision: 1558
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1558&view=rev
Author: warnes
Date: 2012-06-08 18:30:51 +0000 (Fri, 08 Jun 2012)
Log Message:
-----------
Update NEWS for 2.11.0 release.
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2012-06-08 17:56:37 UTC (rev 1557)
+++ trunk/gplots/inst/NEWS 2012-06-08 18:30:51 UTC (rev 1558)
@@ -1,3 +1,24 @@
+Release 2.11.0 - 2011-06-08
+---------------------------
+
+New Features:
+
+- Objects returned by hist2d() have been changed:
+ 1) $x and $y now contain the n midpoints of the bins in each direction
+ 2) $x.breaks, $y.breaks now contain the n+1 limits of the bins in
+ each direction.
+
+- Add lwd argument to plotmeans().
+
+Bug Fixes:
+
+- Correct error in handling binning in hist2d(): (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.
+
+- Changes to fix R CMD check warnings
+
+
Release 2.10.1 - 2011-09-02
---------------------------
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From: <wa...@us...> - 2013-03-24 05:21:33
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Revision: 1647
http://sourceforge.net/p/r-gregmisc/code/1647
Author: warnes
Date: 2013-03-24 05:21:31 +0000 (Sun, 24 Mar 2013)
Log Message:
-----------
Update news for release 2.11.2
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2013-03-24 05:19:04 UTC (rev 1646)
+++ trunk/gplots/inst/NEWS 2013-03-24 05:21:31 UTC (rev 1647)
@@ -1,3 +1,17 @@
+Release 2.11.2 - 2013-03-24
+---------------------------
+
+Enhancements:
+
+- Add ci.width argument to barplot2() to allow varying the length of
+ the 't' at the end of confidence interval bars.
+
+Updates:
+
+- Update manual page for lowess.default() to
+ match changed argument list for lowess() in R 3.0.0
+
+
Release 2.11.1 - 2012-12-14
---------------------------
@@ -41,7 +55,7 @@
New Features:
- New ci2d() function to create 2-dimensional empirical confidence
- intervals utilizing KernSmooth:bkde2D and gplots::hist2d().
+ intervals utilizing KernSmooth:bkde2D and gplots::hist2d().
See ?ci2d for details.
- Add 'alpha' argument to rich.colors() to control transparency.
@@ -66,7 +80,7 @@
- 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
+- Manual page for venn has been improved, based on contributions by
Steffen Moeller
@@ -75,7 +89,7 @@
Improvements:
-- Performance of 'hist2d' improved thanks to a suggestion from
+- Performance of 'hist2d' improved thanks to a suggestion from
Joerg van den Hoff.
Release 2.7.4 - 2009-11-12
@@ -126,14 +140,14 @@
colDendrogram, breaks, col, vline, hline, and colorTable. Of
these, the most useful are breaks, col, and colorTable. The
latter is a three-column data frame providing the lower and
- upper bound and color for each bin.
+ upper bound and color for each bin.
See the manual page for complete details and examples.
- New function venn(), contributed by Steffen Moeller (Thanks
Steffen!) to generate Venn diagrams for up to 5 sets. See ?venn for
- details.
+ details.
- Performance of bandplot() has been dramatically improved, in part by
using runsd() and runmean() from the caTools package. As a
@@ -151,10 +165,10 @@
Bug Fixes:
- balloonplot() now properly handles dimension labels provided by
- 'xlab' and 'ylab'
+ 'xlab' and 'ylab'
- plotCI now properly handles 'NULL' and 'NA' values for ui, li, uiw,
- and liw.
+ and liw.
- Corrections of minor typos in man pages
@@ -164,7 +178,7 @@
Release 2.6.0 - 2008-04-07
--------------------------
-New Features:
+New Features:
- heatmap() now allows control of the location of individual plot components
(e.g. color key)
@@ -179,7 +193,7 @@
- Restore plot layout settings to default state at end of ooplot() example
-- Various typo fixes
+- Various typo fixes
Release 2.5.0 - 2007-11-02
--------------------------
@@ -187,7 +201,7 @@
New Features:
- textplot() now converts tab characters to spaces before processing to
- avoid problems with computing height and width of text that includes
+ avoid problems with computing height and width of text that includes
tabs.
- Add col2hex() function to convert color names to rgb hex codes
@@ -195,7 +209,7 @@
Bug Fixes:
- Correct balloonplot.default to properly show specified x and y axis
- labels when explicitly provided
+ labels when explicitly provided
- R/balloonplot.R: Correct error in balloonplot when z contains NA values.
@@ -204,7 +218,7 @@
Other:
- Clarify GPL version
-
+
Release 2.4.0 - 2007-02-08
--------------------------
@@ -218,7 +232,7 @@
Bug Fixes:
-Other:
+Other:
Release 2.3.2 - 2006-11-14
@@ -254,9 +268,9 @@
-------------
- plotmeans.R: Fixed bug in plotmeans - based on Stefano Calza's
- suggestion (the function didn't account for factors
+ suggestion (the function didn't account for factors
unused levels, returning an error.)
-
+
- exported plot.lm to NAMESPACE, Remove .Alias calls in plot.lm.R
since .Alias is defunct.
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From: <wa...@us...> - 2013-06-27 21:23:43
|
Revision: 1679
http://sourceforge.net/p/r-gregmisc/code/1679
Author: warnes
Date: 2013-06-27 21:23:40 +0000 (Thu, 27 Jun 2013)
Log Message:
-----------
Update for gplots 2.11.3
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2013-06-27 21:16:38 UTC (rev 1678)
+++ trunk/gplots/inst/NEWS 2013-06-27 21:23:40 UTC (rev 1679)
@@ -1,3 +1,18 @@
+Release 2.11.3 - 2013-06-27
+---------------------------
+
+Enhancements:
+
+- Modify sinkplot() to use a local environment rather than the global
+ environment, to conform to CRAN policies.
+
+Bug Fixes:
+
+- Fixed typo/spelling error in plotmeans() man page.
+
+Other changes
+
+
Release 2.11.2 - 2013-03-24
---------------------------
@@ -6,6 +21,10 @@
- Add ci.width argument to barplot2() to allow varying the length of
the 't' at the end of confidence interval bars.
+Bug Fixes:
+
+- Fix error in heatmap.2 when colsep argument had length 1.
+
Updates:
- Update manual page for lowess.default() to
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From: <wa...@us...> - 2013-10-11 20:25:00
|
Revision: 1726
http://sourceforge.net/p/r-gregmisc/code/1726
Author: warnes
Date: 2013-10-11 20:24:57 +0000 (Fri, 11 Oct 2013)
Log Message:
-----------
Update files for gplots 2.12.0
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2013-10-11 20:24:34 UTC (rev 1725)
+++ trunk/gplots/inst/NEWS 2013-10-11 20:24:57 UTC (rev 1726)
@@ -1,4 +1,4 @@
-Release 2.11.4 - 2013-10-11
+Release 2.12.0 - 2013-10-11
---------------------------
Enhancements:
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From: <wa...@us...> - 2013-10-12 00:14:42
|
Revision: 1734
http://sourceforge.net/p/r-gregmisc/code/1734
Author: warnes
Date: 2013-10-12 00:14:37 +0000 (Sat, 12 Oct 2013)
Log Message:
-----------
Update NEWS with latest changes
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2013-10-12 00:09:52 UTC (rev 1733)
+++ trunk/gplots/inst/NEWS 2013-10-12 00:14:37 UTC (rev 1734)
@@ -9,10 +9,24 @@
Bug Fixes:
-- Fix bug in venn diagram code when number of TRUE cases in each
- variable are equal.
+- Fix error in in venn() when all groups contained the same number of TRUE cases.
+- Correct error in overplot() when that occured when a group-category contained no
+ finite values.
+Other Changes:
+
+- Changes to overplot() to avoid warnings from upcoming enhancements to R CMD check.
+
+- Move several packages from Depends to Imports or Suggests.
+
+- Packages caTools and KernSmooth now have namespaces, so import
+ needed functions in NAMESPACE.
+
+- Mark one example in manual page for ci2d 'dontrun' to avoid timing
+ warning in R CMD check.
+
+
Release 2.11.3 - 2013-06-27
---------------------------
@@ -25,9 +39,7 @@
- Fixed typo/spelling error in plotmeans() man page.
-Other changes
-
Release 2.11.2 - 2013-03-24
---------------------------
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From: <wa...@us...> - 2013-10-21 23:32:59
|
Revision: 1743
http://sourceforge.net/p/r-gregmisc/code/1743
Author: warnes
Date: 2013-10-21 23:32:57 +0000 (Mon, 21 Oct 2013)
Log Message:
-----------
Correct release number
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2013-10-21 23:32:26 UTC (rev 1742)
+++ trunk/gplots/inst/NEWS 2013-10-21 23:32:57 UTC (rev 1743)
@@ -1,4 +1,4 @@
-Release 2.12.0 - 2013-10-14
+Release 2.12.1 - 2013-10-14
---------------------------
API Changes:
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From: <wa...@us...> - 2014-04-05 00:14:28
|
Revision: 1781
http://sourceforge.net/p/r-gregmisc/code/1781
Author: warnes
Date: 2014-04-05 00:14:24 +0000 (Sat, 05 Apr 2014)
Log Message:
-----------
Update NEWS
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2014-04-05 00:10:13 UTC (rev 1780)
+++ trunk/gplots/inst/NEWS 2014-04-05 00:14:24 UTC (rev 1781)
@@ -8,9 +8,12 @@
Enhancements:
-- When the row or column trace is enabled, show the corresponding
- reference line in the color key.
+- In heatmap.2, when the row or column trace is enabled, show the
+ corresponding reference line in the color key.
+- In heatmap.2, a new 'extrafun' argument is provided that allows the
+ user to specify a function to be called before the function returns.
+ This allows the user to add additional plots to the page.
Release 2.12.1 - 2013-10-14
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From: <wa...@us...> - 2014-12-01 22:55:43
|
Revision: 1900
http://sourceforge.net/p/r-gregmisc/code/1900
Author: warnes
Date: 2014-12-01 22:55:41 +0000 (Mon, 01 Dec 2014)
Log Message:
-----------
Update for 2.15.0
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2014-12-01 22:52:47 UTC (rev 1899)
+++ trunk/gplots/inst/NEWS 2014-12-01 22:55:41 UTC (rev 1900)
@@ -1,3 +1,12 @@
+Release 2.15.0 - 2014-12-01
+---------------------------
+
+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.
+
+
Release 2.14.2 - 2014-09-17
---------------------------
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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...> - 2015-05-01 16:34:21
|
Revision: 2001
http://sourceforge.net/p/r-gregmisc/code/2001
Author: warnes
Date: 2015-05-01 16:34:19 +0000 (Fri, 01 May 2015)
Log Message:
-----------
Update NEWS again.
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2015-05-01 16:34:02 UTC (rev 2000)
+++ trunk/gplots/inst/NEWS 2015-05-01 16:34:19 UTC (rev 2001)
@@ -1,4 +1,4 @@
-Release 2.17.0 - 2015-04-23
+Release 2.17.0 - 2015-04-28
---------------------------
New Features:
@@ -33,6 +33,13 @@
- In the balloonplot() examples, explicitly specify the 'neworder'
argument to gplots:::reorder.factor to prevent errors.
+Other Changes:
+
+- smartlegend() is now marked as deprecated, since the relative
+ positioning feature ('top', 'right') has been added to
+ graphics::legend()
+
+
Release 2.16.0 - 2015-01-02
---------------------------
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