r-gregmisc-users Mailing List for R gregmisc package (Page 27)
Brought to you by:
warnes
Menu
▾
▴
r-gregmisc-users — Discussion list for R gregmisc packages (gplot, gmodels, gdata, gtools)
You can subscribe to this list here.
| 2006 |
Jan
|
Feb
|
Mar
(12) |
Apr
(5) |
May
(3) |
Jun
(5) |
Jul
(2) |
Aug
(5) |
Sep
(7) |
Oct
(15) |
Nov
(34) |
Dec
(3) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2007 |
Jan
(3) |
Feb
(16) |
Mar
(28) |
Apr
(5) |
May
|
Jun
(5) |
Jul
(9) |
Aug
(50) |
Sep
(29) |
Oct
(9) |
Nov
(25) |
Dec
(7) |
| 2008 |
Jan
(6) |
Feb
(4) |
Mar
(5) |
Apr
(8) |
May
(26) |
Jun
(11) |
Jul
|
Aug
(2) |
Sep
|
Oct
|
Nov
|
Dec
(9) |
| 2009 |
Jan
|
Feb
(1) |
Mar
|
Apr
(2) |
May
(26) |
Jun
|
Jul
(10) |
Aug
(6) |
Sep
|
Oct
(7) |
Nov
(3) |
Dec
(2) |
| 2010 |
Jan
(45) |
Feb
(11) |
Mar
|
Apr
(1) |
May
(8) |
Jun
(7) |
Jul
(3) |
Aug
(1) |
Sep
|
Oct
(1) |
Nov
(9) |
Dec
(1) |
| 2011 |
Jan
(2) |
Feb
|
Mar
|
Apr
(3) |
May
(1) |
Jun
|
Jul
|
Aug
(14) |
Sep
(29) |
Oct
(3) |
Nov
|
Dec
(3) |
| 2012 |
Jan
|
Feb
|
Mar
|
Apr
(7) |
May
(6) |
Jun
(59) |
Jul
|
Aug
(8) |
Sep
(21) |
Oct
|
Nov
|
Dec
|
| 2013 |
Jan
(1) |
Feb
|
Mar
(10) |
Apr
|
May
(18) |
Jun
(25) |
Jul
(18) |
Aug
(1) |
Sep
(6) |
Oct
(28) |
Nov
(4) |
Dec
(13) |
| 2014 |
Jan
(7) |
Feb
(5) |
Mar
(4) |
Apr
(36) |
May
(3) |
Jun
(7) |
Jul
(46) |
Aug
(14) |
Sep
(12) |
Oct
(2) |
Nov
|
Dec
(12) |
| 2015 |
Jan
(4) |
Feb
|
Mar
|
Apr
(80) |
May
(36) |
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: <wa...@us...> - 2009-07-17 22:01:17
|
Revision: 1351
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1351&view=rev
Author: warnes
Date: 2009-07-17 22:01:07 +0000 (Fri, 17 Jul 2009)
Log Message:
-----------
Add NAMESPACE file, update version number to 1.2.3
Modified Paths:
--------------
trunk/fork/DESCRIPTION
trunk/fork/inst/NEWS
Added Paths:
-----------
trunk/fork/NAMESPACE
Modified: trunk/fork/DESCRIPTION
===================================================================
--- trunk/fork/DESCRIPTION 2009-07-16 10:55:53 UTC (rev 1350)
+++ trunk/fork/DESCRIPTION 2009-07-17 22:01:07 UTC (rev 1351)
@@ -1,7 +1,7 @@
Package: fork
Title: R functions for handling multiple processes.
-Version: 1.2.2
-Date: 2009-05-09
+Version: 1.2.3
+Date: 2009-07-17
Author: Gregory R. Warnes <gr...@ra...>. Financial
support for some aspects of this package provided by Metrum Research Group,
LLC <http://www.metrumrg.com>.
Added: trunk/fork/NAMESPACE
===================================================================
--- trunk/fork/NAMESPACE (rev 0)
+++ trunk/fork/NAMESPACE 2009-07-17 22:01:07 UTC (rev 1351)
@@ -0,0 +1,14 @@
+export(
+ exit,
+ fork,
+ getpid,
+ handleSIGCLD,
+ kill,
+ killall,
+ restoreSIGCLD,
+ signal,
+ signame,
+ sigval,
+ siglist,
+ wait
+)
Modified: trunk/fork/inst/NEWS
===================================================================
--- trunk/fork/inst/NEWS 2009-07-16 10:55:53 UTC (rev 1350)
+++ trunk/fork/inst/NEWS 2009-07-17 22:01:07 UTC (rev 1351)
@@ -1,12 +1,27 @@
+Version 1.2.3 - 2009-07-17
+==========================
+- Add NAMESPACE file
+
+Version 1.2.2 - 2009-05-09
+===========================
+
+- Correct Greg's email address
+- Fix syntax error in man page for wait()
+
+Version 1.2.1 - 2007-10-22
+===========================
+
+- Clarify GPL version
+
Version: 1.2.0 - 2007-03-22
===========================
- - Added new function handleSIGCLD/restoreSIGCLD for setting
- up/removing a SIGCLD handler so that fork'ed processes can safely be
- ignored without becoming zombies. See ?handleSIGCLD for details.
+- Added new function handleSIGCLD/restoreSIGCLD for setting
+ up/removing a SIGCLD handler so that fork'ed processes can safely be
+ ignored without becoming zombies. See ?handleSIGCLD for details.
- - Added regression tests for SysV and BSD style signal handling that
- checks for zombie process creation & tests that signal("SIGCHLD","ignore")
- and/or handleSIGCLD() prevents zombie process creation.
+- Added regression tests for SysV and BSD style signal handling that
+ checks for zombie process creation & tests that signal("SIGCHLD","ignore")
+ and/or handleSIGCLD() prevents zombie process creation.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gg...@us...> - 2009-07-16 10:56:07
|
Revision: 1350
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1350&view=rev
Author: ggorjan
Date: 2009-07-16 10:55:53 +0000 (Thu, 16 Jul 2009)
Log Message:
-----------
Reverting recent change and clarifying the meaning.
Modified Paths:
--------------
trunk/gdata/man/write.fwf.Rd
Modified: trunk/gdata/man/write.fwf.Rd
===================================================================
--- trunk/gdata/man/write.fwf.Rd 2009-07-16 03:23:06 UTC (rev 1349)
+++ trunk/gdata/man/write.fwf.Rd 2009-07-16 10:55:53 UTC (rev 1350)
@@ -75,13 +75,13 @@
data back into \R. Check examples. Do read the details about
\code{quoteInfo} argument.
-Use only *true* character, i.e., avoid use of "T" or similar separators
-for \code{sep}. Width of the separator is taken as number of characters
-in \code{sep} as evaluated via \code{\link{nchar}}.
+Use only *true* character, i.e., avoid use of tabs, i.e., "\\t", or similar
+separators via argument \code{sep}. Width of the separator is taken as
+the number of characters evaluated via \code{\link{nchar}(sep)}.
-Use \code{NA} to convert missing/unknown values. Only single value can
-be specified in \code{na}. Use \code{\link{NAToUnknown}} prior to export
-if you need greater flexibility.
+Use argument \code{na} to convert missing/unknown values. Only single value
+can be specified. Use \code{\link{NAToUnknown}} prior to export if you need
+greater flexibility.
If \code{rowCol} is not \code{NULL} and \code{rownames=TRUE}, rownames
will also have column name with \code{rowCol} value. This is mainly for
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-07-16 03:23:11
|
Revision: 1349
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1349&view=rev
Author: warnes
Date: 2009-07-16 03:23:06 +0000 (Thu, 16 Jul 2009)
Log Message:
-----------
Add contents of \value section for resample() man page
Modified Paths:
--------------
trunk/gdata/inst/doc/mapLevels.pdf
trunk/gdata/inst/doc/unknown.pdf
trunk/gdata/man/resample.Rd
Modified: trunk/gdata/inst/doc/mapLevels.pdf
===================================================================
(Binary files differ)
Modified: trunk/gdata/inst/doc/unknown.pdf
===================================================================
(Binary files differ)
Modified: trunk/gdata/man/resample.Rd
===================================================================
--- trunk/gdata/man/resample.Rd 2009-07-16 03:15:58 UTC (rev 1348)
+++ trunk/gdata/man/resample.Rd 2009-07-16 03:23:06 UTC (rev 1349)
@@ -25,7 +25,7 @@
have identical behavior.
}
\value{
-
+ Vector of the same length as the input, with the elements permuted.
}
\author{Gregory R. Warnes \email{gr...@ra...} }
\seealso{ \code{\link{sample}} }
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-07-16 03:15:59
|
Revision: 1348
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1348&view=rev
Author: warnes
Date: 2009-07-16 03:15:58 +0000 (Thu, 16 Jul 2009)
Log Message:
-----------
Update test output to remove R CMD check warning
Modified Paths:
--------------
trunk/gdata/tests/tests.write.fwf.Rout.save
Modified: trunk/gdata/tests/tests.write.fwf.Rout.save
===================================================================
--- trunk/gdata/tests/tests.write.fwf.Rout.save 2009-07-16 03:10:52 UTC (rev 1347)
+++ trunk/gdata/tests/tests.write.fwf.Rout.save 2009-07-16 03:15:58 UTC (rev 1348)
@@ -1,14 +1,12 @@
-R version 2.7.1 (2008-06-23)
-Copyright (C) 2008 The R Foundation for Statistical Computing
+R version 2.9.0 (2009-04-17)
+Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
- Natural language support but running in an English locale
-
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
@@ -17,7 +15,6 @@
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
-Loading required package: gtools
> ### tests.write.fwf.R
> ###------------------------------------------------------------------------
> ### What: Tests for write.fwf
@@ -26,6 +23,14 @@
> ###------------------------------------------------------------------------
>
> library(gdata)
+
+Attaching package: 'gdata'
+
+
+ The following object(s) are masked from package:utils :
+
+ object.size
+
>
> ## --- Test data ---
>
@@ -218,6 +223,3 @@
> ###------------------------------------------------------------------------
> ### tests.write.fwf.R ends
>
-> proc.time()
- user system elapsed
- 2.120 0.060 2.226
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-07-16 03:11:18
|
Revision: 1347
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1347&view=rev
Author: warnes
Date: 2009-07-16 03:10:52 +0000 (Thu, 16 Jul 2009)
Log Message:
-----------
Update ChangeLog and NEWS for gdata 2.6.0 release
Modified Paths:
--------------
trunk/gdata/inst/NEWS
Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS 2009-07-16 02:56:35 UTC (rev 1346)
+++ trunk/gdata/inst/NEWS 2009-07-16 03:10:52 UTC (rev 1347)
@@ -1,6 +1,47 @@
-CHANGES IN 2.5.0 (2009-??-??)
+CHANGES IN 2.6.0 (2009-07-15)
-----------------------------
+Bug Fixes
+
+- Correct minor typos & issues in man pages for write.fwf(),
+ resample() (Greg Warnes)
+
+- Correct calculation of object sizes in env() and ll() (Gregor Gorjanc)
+
+New Features
+
+- Add support for using tab for field separator during translation
+ from xls format in read.xls (Greg Warnes)
+
+- 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).
+ (Gregor Gorjanc)
+
+- New function wideByFactor that reshapes given dataset by a given
+ factor - it creates a "multivariate" data.frame. (Gregor Gorjanc)
+
+- New function nPairs that gives the number of variable pairs in a
+ data.frame or a matrix. (Gregor Gorjanc)
+
+- New functions getYear, getMonth, getDay, getHour, getMin, and getSec
+ for extracting the date/time parts from objects of a date/time
+ class. (Gregor Gorjanc)
+
+- New function bindData that binds two data frames into a multivariate
+ data frame in a different way than merge. (Gregor Gorjanc)
+
+Other Changes
+
+- Correct Greg's email address
+
+
+CHANGES IN 2.5.0
+----------------
+
- New function .runRUnitTestsGdata that enables run of all RUnit tests during
the R CMD check as well as directly from within R.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-07-16 02:56:38
|
Revision: 1346
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1346&view=rev
Author: warnes
Date: 2009-07-16 02:56:35 +0000 (Thu, 16 Jul 2009)
Log Message:
-----------
Update DESCRIPTION file for gdata 2.6.0
Modified Paths:
--------------
trunk/gdata/DESCRIPTION
Modified: trunk/gdata/DESCRIPTION
===================================================================
--- trunk/gdata/DESCRIPTION 2009-07-16 02:55:27 UTC (rev 1345)
+++ trunk/gdata/DESCRIPTION 2009-07-16 02:56:35 UTC (rev 1346)
@@ -3,9 +3,9 @@
Description: Various R programming tools for data manipulation
Depends: R (>= 2.6.0)
Imports: gtools
-Version: 2.5.0
-Date: 2008-08-05
+Version: 2.6.0
+Date: 2009-07-15
Author: Gregory R. Warnes and Gregor Gorjanc. Includes R source code
and/or documentation contributed by Ben Bolker and Thomas Lumley.
-Maintainer: Gregory Warnes <gre...@ur...>
+Maintainer: Gregory Warnes <gr...@ra...>
License: GPL-2
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-07-16 02:55:32
|
Revision: 1345
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1345&view=rev
Author: warnes
Date: 2009-07-16 02:55:27 +0000 (Thu, 16 Jul 2009)
Log Message:
-----------
Correct Greg's email address
Modified Paths:
--------------
trunk/gdata/inst/doc/gregmisc.tex
trunk/gdata/inst/doc/mapLevels.pdf
trunk/gdata/inst/doc/unknown.pdf
trunk/gdata/man/ConvertMedUnits.Rd
trunk/gdata/man/aggregate.table.Rd
trunk/gdata/man/combine.Rd
trunk/gdata/man/interleave.Rd
trunk/gdata/man/matchcols.Rd
trunk/gdata/man/nobs.Rd
trunk/gdata/man/rename.vars.Rd
trunk/gdata/man/reorder.Rd
trunk/gdata/man/trim.Rd
trunk/gdata/man/unmatrix.Rd
trunk/gdata/man/upperTriangle.Rd
Modified: trunk/gdata/inst/doc/gregmisc.tex
===================================================================
--- trunk/gdata/inst/doc/gregmisc.tex 2009-07-16 02:52:07 UTC (rev 1344)
+++ trunk/gdata/inst/doc/gregmisc.tex 2009-07-16 02:55:27 UTC (rev 1345)
@@ -95,8 +95,8 @@
\address{Gregory R. Warnes \\
- Pfizer Global Research and Development \\
- \emph{wa...@bs...} } %%!!!%%
+ Random Technologies LLC. \\
+ \emph{gr...@ra...} } %%!!!%%
\end{multicols} %%!!!%%
Modified: trunk/gdata/inst/doc/mapLevels.pdf
===================================================================
(Binary files differ)
Modified: trunk/gdata/inst/doc/unknown.pdf
===================================================================
(Binary files differ)
Modified: trunk/gdata/man/ConvertMedUnits.Rd
===================================================================
--- trunk/gdata/man/ConvertMedUnits.Rd 2009-07-16 02:52:07 UTC (rev 1344)
+++ trunk/gdata/man/ConvertMedUnits.Rd 2009-07-16 02:55:27 UTC (rev 1345)
@@ -46,7 +46,7 @@
\references{
\url{http://www.globalrph.com/conv_si.htm}
}
-\author{ Gregory R. Warnes \email{wa...@bs...} }
+\author{ Gregory R. Warnes \email{gr...@ra...} }
\examples{
data(MedUnits)
Modified: trunk/gdata/man/aggregate.table.Rd
===================================================================
--- trunk/gdata/man/aggregate.table.Rd 2009-07-16 02:52:07 UTC (rev 1344)
+++ trunk/gdata/man/aggregate.table.Rd 2009-07-16 02:55:27 UTC (rev 1345)
@@ -49,7 +49,7 @@
Returns a matrix with one element for each combination of \code{by1}
and \code{by2}.
}
-\author{ Gregory R. Warnes \email{wa...@bs...}}
+\author{ Gregory R. Warnes \email{gr...@ra...}}
\seealso{ \code{\link{aggregate}}, \code{\link{tapply}},
\code{\link{interleave}} }
Modified: trunk/gdata/man/combine.Rd
===================================================================
--- trunk/gdata/man/combine.Rd 2009-07-16 02:52:07 UTC (rev 1344)
+++ trunk/gdata/man/combine.Rd 2009-07-16 02:55:27 UTC (rev 1345)
@@ -59,7 +59,7 @@
% ...
% }
%\references{ ~put references to the literature/web site here ~ }
-\author{Gregory R. Warnes \email{wa...@bs...}}
+\author{Gregory R. Warnes \email{gr...@ra...}}
%\note{ ~~further notes~~ }
\seealso{ \code{\link{rbind}}, \code{\link{merge}}}
Modified: trunk/gdata/man/interleave.Rd
===================================================================
--- trunk/gdata/man/interleave.Rd 2009-07-16 02:52:07 UTC (rev 1344)
+++ trunk/gdata/man/interleave.Rd 2009-07-16 02:55:27 UTC (rev 1345)
@@ -66,7 +66,7 @@
\value{
Matrix containing the interleaved rows of the function arguments.
}
-\author{ Gregory R. Warnes \email{wa...@bs...}
+\author{ Gregory R. Warnes \email{gr...@ra...}
}
\seealso{ \code{\link{cbind}}, \code{\link{rbind}}, \code{\link{combine}} }
Modified: trunk/gdata/man/matchcols.Rd
===================================================================
--- trunk/gdata/man/matchcols.Rd 2009-07-16 02:52:07 UTC (rev 1344)
+++ trunk/gdata/man/matchcols.Rd 2009-07-16 02:55:27 UTC (rev 1345)
@@ -20,7 +20,7 @@
none of the patterns specified in \code{without}.
}
-\author{Gregory R. Warnes \email{wa...@bs...}}
+\author{Gregory R. Warnes \email{gr...@ra...}}
\seealso{ \code{\link[base]{grep}} }
\examples{
Modified: trunk/gdata/man/nobs.Rd
===================================================================
--- trunk/gdata/man/nobs.Rd 2009-07-16 02:52:07 UTC (rev 1344)
+++ trunk/gdata/man/nobs.Rd 2009-07-16 02:55:27 UTC (rev 1345)
@@ -58,7 +58,7 @@
A single numeric value or a vector of values (for data.frames) giving
the number of non-missing values.
}
-\author{ Gregory R. Warnes \email{wa...@bs...} }
+\author{ Gregory R. Warnes \email{gr...@ra...} }
\seealso{ \code{\link{is.na}}, \code{\link{length}} }
Modified: trunk/gdata/man/rename.vars.Rd
===================================================================
--- trunk/gdata/man/rename.vars.Rd 2009-07-16 02:52:07 UTC (rev 1344)
+++ trunk/gdata/man/rename.vars.Rd 2009-07-16 02:55:27 UTC (rev 1345)
@@ -49,7 +49,7 @@
}
\author{Code by Don MacQueen \email{macq\@llnl.gov}.
Documentation by Gregory R. Warnes
- \email{wa...@bs...} }
+ \email{gr...@ra...} }
\seealso{ \code{\link{names}},
\code{\link{colnames}},
\code{\link{data.frame}}
Modified: trunk/gdata/man/reorder.Rd
===================================================================
--- trunk/gdata/man/reorder.Rd 2009-07-16 02:52:07 UTC (rev 1344)
+++ trunk/gdata/man/reorder.Rd 2009-07-16 02:55:27 UTC (rev 1345)
@@ -56,7 +56,7 @@
A new factor with reordered levels
}
-\author{Gregory R. Warnes \email{wa...@bs...}}
+\author{Gregory R. Warnes \email{gr...@ra...}}
\seealso{\code{\link{factor}} and \code{\link[stats]{reorder}}}
Modified: trunk/gdata/man/trim.Rd
===================================================================
--- trunk/gdata/man/trim.Rd 2009-07-16 02:52:07 UTC (rev 1344)
+++ trunk/gdata/man/trim.Rd 2009-07-16 02:55:27 UTC (rev 1345)
@@ -32,7 +32,7 @@
\value{
\code{s} with all leading and trailing spaces removed in its elements.
}
-\author{Gregory R. Warnes \email{wa...@bs...} with
+\author{Gregory R. Warnes \email{gr...@ra...} with
contributions by Gregor Gorjanc}
\seealso{ \code{\link[base]{sub}}, \code{\link[base]{gsub}} as well as
argument \code{strip.white} in \code{\link{read.table}} and
Modified: trunk/gdata/man/unmatrix.Rd
===================================================================
--- trunk/gdata/man/unmatrix.Rd 2009-07-16 02:52:07 UTC (rev 1344)
+++ trunk/gdata/man/unmatrix.Rd 2009-07-16 02:55:27 UTC (rev 1345)
@@ -19,7 +19,7 @@
matrix. If the the row or column names are missing, ('r1', 'r2', ..,) or
('c1', 'c2', ..) will be used as appropriate.
}
-\author{Gregory R. Warnes \email{wa...@bs...} }
+\author{Gregory R. Warnes \email{gr...@ra...} }
\seealso{ \code{\link[base]{as.vector}} }
\examples{
# simple, useless example
Modified: trunk/gdata/man/upperTriangle.Rd
===================================================================
--- trunk/gdata/man/upperTriangle.Rd 2009-07-16 02:52:07 UTC (rev 1344)
+++ trunk/gdata/man/upperTriangle.Rd 2009-07-16 02:55:27 UTC (rev 1345)
@@ -16,7 +16,7 @@
%- maybe also 'usage' for other objects documented here.
\arguments{
\item{x}{Matrix}
- \item{diag}{Logical. If code{TRUE}, include the matrix diagonal.}
+ \item{diag}{Logical. If \code{TRUE}, include the matrix diagonal.}
\item{value}{Either a single value or a vector of length equal to that
of the current upper/lower triangular. Should be of a mode which
can be coerced to that of \code{x}.}
@@ -28,7 +28,7 @@
replace the upper or lower traingular area of the
matrix with the provided value(s).
}
-\author{Gregory R. Warnes \email{wa...@bs...}}
+\author{Gregory R. Warnes \email{gr...@ra...}}
\seealso{ \code{\link[base]{diag}} }
\examples{
x <- matrix( 1:25, nrow=5, ncol=5)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-07-16 02:52:08
|
Revision: 1344
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1344&view=rev
Author: warnes
Date: 2009-07-16 02:52:07 +0000 (Thu, 16 Jul 2009)
Log Message:
-----------
Correct minor typos in write.fwf() man page
Modified Paths:
--------------
trunk/gdata/man/write.fwf.Rd
Modified: trunk/gdata/man/write.fwf.Rd
===================================================================
--- trunk/gdata/man/write.fwf.Rd 2009-07-16 02:50:52 UTC (rev 1343)
+++ trunk/gdata/man/write.fwf.Rd 2009-07-16 02:52:07 UTC (rev 1344)
@@ -75,11 +75,11 @@
data back into \R. Check examples. Do read the details about
\code{quoteInfo} argument.
-Use only *true* character, i.e., avoid use of "\t" or similar separators
+Use only *true* character, i.e., avoid use of "T" or similar separators
for \code{sep}. Width of the separator is taken as number of characters
in \code{sep} as evaluated via \code{\link{nchar}}.
-Use \code{na} to convert missing/unknown values. Only single value can
+Use \code{NA} to convert missing/unknown values. Only single value can
be specified in \code{na}. Use \code{\link{NAToUnknown}} prior to export
if you need greater flexibility.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-07-16 02:50:54
|
Revision: 1343
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1343&view=rev
Author: warnes
Date: 2009-07-16 02:50:52 +0000 (Thu, 16 Jul 2009)
Log Message:
-----------
Correct page for resample()
Modified Paths:
--------------
trunk/gdata/man/resample.Rd
Modified: trunk/gdata/man/resample.Rd
===================================================================
--- trunk/gdata/man/resample.Rd 2009-07-16 02:49:11 UTC (rev 1342)
+++ trunk/gdata/man/resample.Rd 2009-07-16 02:50:52 UTC (rev 1343)
@@ -25,36 +25,19 @@
have identical behavior.
}
\value{
- ~Describe the value returned
- If it is a LIST, use
- \item{comp1 }{Description of 'comp1'}
- \item{comp2 }{Description of 'comp2'}
- ...
-}
-\references{ ~put references to the literature/web site here ~ }
-\author{ ~~who you are~~ }
-\note{ ~~further notes~~
- ~Make other sections like Warning with \section{Warning }{....} ~
}
-\seealso{ ~~objects to See Also as \code{\link{help}}, ~~~ }
+\author{Gregory R. Warnes \email{gr...@ra...} }
+\seealso{ \code{\link{sample}} }
\examples{
-##---- Should be DIRECTLY executable !! ----
-##-- ==> Define data, use random,
-##-- or do help(data=index) for the standard data sets.
-## The function is currently defined as
-function(x, n, ...)
- {
- if(length(x)==1)
- {
- if(n==1)
- x
- else
- stop("Requested sample of size ", n, " from list of length 1")
- }
- else
- sample(x, n, ...)
- }
+## sample behavior differs if first argument is scalar vs vector
+sample( c(10) )
+sample( c(10,10) )
+
+## resample has the consistent behavior for both cases
+resample( c(10) )
+resample( c(10,10) )
+
}
-\keyword{misc}% at least one, from doc/KEYWORDS
+\keyword{misc}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-07-16 02:49:24
|
Revision: 1342
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1342&view=rev
Author: warnes
Date: 2009-07-16 02:49:11 +0000 (Thu, 16 Jul 2009)
Log Message:
-----------
Add support for using tab for field separator during translation from xls format in read.xls
Modified Paths:
--------------
trunk/gdata/NAMESPACE
trunk/gdata/R/read.xls.R
trunk/gdata/man/read.xls.Rd
Added Paths:
-----------
trunk/gdata/inst/perl/xls2tab.pl
Modified: trunk/gdata/NAMESPACE
===================================================================
--- trunk/gdata/NAMESPACE 2009-05-09 05:45:13 UTC (rev 1341)
+++ trunk/gdata/NAMESPACE 2009-07-16 02:49:11 UTC (rev 1342)
@@ -32,6 +32,8 @@
wideByFactor,
write.fwf,
xls2csv,
+ xls2tab,
+ xls2sep,
## Object size stuff
object.size, as.object_size, is.object_size, humanReadable,
Modified: trunk/gdata/R/read.xls.R
===================================================================
--- trunk/gdata/R/read.xls.R 2009-05-09 05:45:13 UTC (rev 1341)
+++ trunk/gdata/R/read.xls.R 2009-07-16 02:49:11 UTC (rev 1342)
@@ -4,126 +4,170 @@
dQuote.ascii <- function(x) paste('"',x,'"',sep='')
-xls2csv <- function(xls, sheet = 1, verbose=FALSE, ..., perl="perl")
- {
+xls2csv <- function(xls, sheet=1, verbose=FALSE, ..., perl="perl")
+ xls2sep(xls=xls, sheet=sheet, verbose=verbose, ..., method="csv",
+ perl="perl")
+xls2tab <- function(xls, sheet=1, verbose=FALSE, ..., perl="perl")
+ xls2sep(xls=xls, sheet=sheet, verbose=verbose, ..., method="tab",
+ perl="perl")
- ###
- # directories
- package.dir <- .path.package('gdata')
- perl.dir <- file.path(package.dir,'perl')
- #
- ###
+xls2sep <- function(xls, sheet = 1, verbose=FALSE, ...,
+ method=c("csv","tab"), perl="perl")
+ {
+
+ method <- match.arg(method)
+
+ ##
+ ## directories
+ package.dir <- .path.package('gdata')
+ perl.dir <- file.path(package.dir,'perl')
+ ##
- ###
- # files
+ ##
+ ## files
+ tf <- NULL
+ if (substring(xls, 1, 7) == "http://") {
+ tf <- paste(tempfile(), "xls", sep = ".")
+ if(verbose)
+ cat("Downloading",
+ dQuote.ascii(xls), " to ",
+ dQuote.ascii(tf), "...\n")
+ else
+ cat("Downloading...\n")
+ download.file(xls, tf, mode = "wb")
+ cat("Done.\n")
+ xls <- tf
+ }
- tf <- NULL
- if (substring(xls, 1, 7) == "http://") {
- tf <- paste(tempfile(), "xls", sep = ".")
- if(verbose)
- cat("Downloading",
- dQuote.ascii(xls), " to ",
- dQuote.ascii(tf), "...\n")
- else
- cat("Downloading...\n")
- download.file(xls, tf, mode = "wb")
- cat("Done.\n")
- xls <- tf
- }
+ if(file.access(xls, 4)!=0)
+ stop("Unable to read xls file '", xls, "'." )
- if(file.access(xls, 4)!=0)
- stop("Unable to read xls file '", xls, "'." )
+ if(method=="csv")
+ {
+ script <- file.path(perl.dir,'xls2csv.pl')
+ targetFile <- paste(tempfile(), "csv", sep = ".")
+ }
+ else if(method=="tab")
+ {
+ script <- file.path(perl.dir,'xls2tab.pl')
+ targetFile <- paste(tempfile(), "tab", sep = ".")
+ }
+ else
+ {
+ stop("Unknown method", method)
+ }
+
+ ##
+ ##
- xls2csv <- file.path(perl.dir,'xls2csv.pl')
- csv <- paste(tempfile(), "csv", sep = ".")
- #
- ###
+ ##
+ ## execution command
+ cmd <- paste(perl, script, dQuote.ascii(xls), dQuote.ascii(targetFile),
+ sheet, sep=" ")
+ ##
+ ##
- ###
- # execution command
- cmd <- paste(perl, xls2csv, dQuote.ascii(xls), dQuote.ascii(csv),
- sheet, sep=" ")
- #
- ###
-
if(verbose)
{
cat("\n")
cat("Converting xls file\n")
cat(" ", dQuote.ascii(xls), "\n")
- cat("to csv file \n")
- cat(" ", dQuote.ascii(csv), "\n")
+ cat("to", method, " file \n")
+ cat(" ", dQuote.ascii(targetFile), "\n")
cat("... \n\n")
}
- else
- cat("Converting xls file to csv file... ")
+ else
+ cat("Converting xls file to", method, "file... ")
- ###
- # do the translation
- if(verbose) cat("Executing ", cmd, "... \n\n")
- #
- results <- system(cmd, intern=!verbose)
- #
- if (verbose) cat("Done.\n\n")
- #
- ###
+ ##
+ ## do the translation
+ if(verbose) cat("Executing ", cmd, "... \n\n")
+ #
+ results <- system(cmd, intern=!verbose)
+ #
+ if (verbose) cat("Done.\n\n")
+ #
+ ##
- if(file.access(csv, 4)!=0)
- stop("Unable to read translated csv file '", csv, "'." )
+ if(file.access(targetFile, 4)!=0)
+ stop("Unable to read translated", method, "file '", targetFile, "'." )
- cat("Done.\n")
+ cat("Done.\n")
- # prepare for cleanup now, in case of error reading file
- file(csv)
-}
+ ## prepare for cleanup now, in case of error reading file
+ file(targetFile)
+ }
-read.xls <- function(xls, sheet = 1, verbose=FALSE, pattern, ..., perl="perl") {
- con <- tfn <- NULL
- on.exit({
- if (inherits(con, "connection") && isOpen(con)) close(con)
- if (file.exists(tfn)) file.remove(tfn)
- })
+read.xls <- function(xls, sheet = 1, verbose=FALSE, pattern, ...,
+ method=c("csv","tab"), perl="perl")
+{
+ con <- tfn <- NULL
+ on.exit({
+ if (inherits(con, "connection") && isOpen(con)) close(con)
+ if (file.exists(tfn)) file.remove(tfn)
+ })
- ## expand file path, translating ~ to user's home directory, etc.
- xls <- path.expand(xls)
+ method <- match.arg(method)
+
+ ## expand file path, translating ~ to user's home directory, etc.
+ xls <- path.expand(xls)
- ## translate from xls to csv format (returns csv file name)
- con <- xls2csv(xls, sheet, verbose=verbose, ..., perl = perl)
+ ## translate from xls to csv/tab format (returns csv file name)
+ if(method=="csv")
+ con <- xls2csv(xls, sheet, verbose=verbose, ..., perl = perl)
+ else if(method=="tab")
+ con <- xls2tab(xls, sheet, verbose=verbose, ..., perl = perl)
+ else
+ stop("Unknown method", method)
- ## load the csv file
- open(con)
- tfn <- summary(con)$description
- if (missing(pattern))
- {
- if(verbose)
- cat("Reading csv file ", dQuote.ascii(tfn), "...\n")
- else
- cat("Reading csv file... ")
- retval <- read.csv(con, ...)
- cat("Done.\n")
- }
- else {
- cat("Searching for lines containing pattern ", pattern, "... ")
- idx <- grep(pattern, readLines(con))
- if (length(idx) == 0) {
- warning("pattern not found")
- return(NULL)
- }
- cat("Done.\n")
-
- seek(con, 0)
+ ## load the csv file
+ open(con)
+ tfn <- summary(con)$description
+ if (missing(pattern))
+ {
+ if(verbose)
+ cat("Reading", method, "file ", dQuote.ascii(tfn), "...\n")
+ else
+ cat("Reading", method, "file... ")
+
+ if(method=="csv")
+ retval <- read.csv(con, ...)
+ else if (method=="tab")
+ retval <- read.delim(con, ...)
+ else
+ stop("Unknown method", method)
+
+ cat("Done.\n")
+ }
+ else {
+ cat("Searching for lines containing pattern ", pattern, "... ")
+ idx <- grep(pattern, readLines(con))
+ if (length(idx) == 0) {
+ warning("pattern not found")
+ return(NULL)
+ }
+ cat("Done.\n")
+
+ seek(con, 0)
- if(verbose)
- cat("Reading csv file ", dQuote.ascii(tfn), "...\n")
- else
- cat("Reading csv file... ")
- retval <- read.csv(con, skip = idx[1]-1, ...)
- cat("Done.\n")
- }
- retval
+ if(verbose)
+ cat("Reading", method, "file ", dQuote.ascii(tfn), "...\n")
+ else
+ cat("Reading", method, "file... ")
+
+ if(method=="csv")
+ retval <- read.csv(con, skip = idx[1]-1, ...)
+ else if (method=="tab")
+ retval <- read.delim(con, skip = idx[1]-1, ...)
+ else
+ stop("Unknown method", method)
+
+ cat("Done.\n")
+ }
+ retval
}
Copied: trunk/gdata/inst/perl/xls2tab.pl (from rev 1341, trunk/gdata/inst/perl/xls2csv.pl)
===================================================================
--- trunk/gdata/inst/perl/xls2tab.pl (rev 0)
+++ trunk/gdata/inst/perl/xls2tab.pl 2009-07-16 02:49:11 UTC (rev 1342)
@@ -0,0 +1,166 @@
+#!/bin/env perl
+
+BEGIN {
+use File::Basename;
+unshift(@INC, dirname $0);
+}
+
+use strict;
+use Spreadsheet::ParseExcel;
+
+# declare some varibles local
+my($row, $col, $sheet, $cell, $usage, $basename, $sheetnumber, $filename);
+
+##
+## Usage information
+##
+$usage = <<EOF;
+
+xls2tab.pl <excel file> [<output file>] [<worksheet number>]
+
+Translate the Microsoft Excel spreadsheet file contained in
+<excel file> into tab separated value format (TAB) and store
+in <output file>.
+
+If <output file> is not specified, the output file will have the
+same name as the input file with '.xls' or '.XLS' (if any)
+removed and '.tab' appended.
+
+If no worksheet number is given, each worksheet will be written to
+a separate file with the name '<output file>_<worksheet name>.tab'.
+
+EOF
+
+##
+## parse arguments
+##
+
+if(!defined($ARGV[0]))
+ {
+ print $usage;
+ exit 1;
+ }
+
+$basename = $ARGV[1];
+$basename =~ s/.tab//;
+if ($basename eq "")
+ {
+ my @path;
+ @path = split(/[\/\\]/, $ARGV[0]); # split on file separator
+ $basename = $path[$#path];
+ $basename =~ s/.xls//i;
+ }
+
+if(defined($ARGV[2]) )
+ {
+ $sheetnumber = $ARGV[2];
+ die "Sheetnumber must be an integer larger than 0." if $sheetnumber < 1;
+ }
+
+##
+## open spreadsheet
+##
+
+my $oExcel = new Spreadsheet::ParseExcel;
+
+print "Loading $ARGV[0] ...\n";
+
+open(FH, "<$ARGV[0]") or die "Unable to open file '$ARGV[0]'.\n";
+close(FH);
+
+my $oBook = $oExcel->Parse($ARGV[0]);
+
+print "\n";
+print "Orignal Filename :", $oBook->{File} , "\n";
+print "Number of Sheets :", $oBook->{SheetCount} , "\n";
+print "Author :", $oBook->{Author} , "\n";
+print "\n";
+
+my @sheetlist = (@{$oBook->{Worksheet}});
+if (defined($sheetnumber))
+ {
+ @sheetlist=($sheetlist[$sheetnumber-1]);
+ }
+
+##
+## iterate across each worksheet, writing out a separat tab file
+##
+
+my $i=0;
+foreach my $sheet (@sheetlist)
+{
+ $i++;
+
+ my $sheetname = $sheet->{Name};
+ if(defined($sheetnumber))
+ {
+ $filename = "${basename}.tab";
+ }
+ else
+ {
+ $filename = "${basename}_${sheetname}.tab";
+ }
+
+ print "Writing Sheet number $i ('$sheetname') to file '$filename'\n";
+
+ open(OutFile,">$filename");
+
+ my $cumulativeBlankLines=0;
+
+ my $minrow = $sheet->{MinRow};
+ my $maxrow = $sheet->{MaxRow};
+ my $mincol = $sheet->{MinCol};
+ my $maxcol = $sheet->{MaxCol};
+
+ print "Minrow=$minrow Maxrow=$maxrow Mincol=$mincol Maxcol=$maxcol\n";
+
+ for(my $row = $minrow; $row <= $maxrow; $row++)
+ {
+ my $outputLine = "";
+
+ for(my $col = $mincol; $col <= $maxcol; $col++)
+ {
+ my $cell = $sheet->{Cells}[$row][$col];
+ if( defined($cell) )
+ {
+ $_=$cell->Value; #{Val};
+
+ # convert '#NUM!' strings to missing (empty) values
+ s/#NUM!//;
+
+ # escape double-quote characters in the data since
+ # they are used as field delimiters
+ s/\"/\\\"/g;
+ }
+ else
+ {
+ $_ = '';
+ }
+
+ $outputLine .= "\"" . $_ . "\"" if(length($_)>0);
+
+ # separate cells with tabs
+ $outputLine .= "\t" if( $col != $maxcol) ;
+
+ }
+
+ #$outputLine =~ s/[\t ]+$//g; ## strip off trailing blanks and tabs
+
+ # skip blank/empty lines
+ if( $outputLine =~ /^[\t ]*$/ )
+ {
+ $cumulativeBlankLines++
+ }
+ else
+ {
+ print OutFile "$outputLine \n"
+ }
+ }
+
+ close OutFile;
+
+ print " (Ignored $cumulativeBlankLines blank lines.)\n"
+ if ($cumulativeBlankLines);
+ print "\n";
+}
+
Property changes on: trunk/gdata/inst/perl/xls2tab.pl
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:keywords
+ Author Date Id Revision
Added: svn:mergeinfo
+
Added: svn:eol-style
+ native
Modified: trunk/gdata/man/read.xls.Rd
===================================================================
--- trunk/gdata/man/read.xls.Rd 2009-05-09 05:45:13 UTC (rev 1341)
+++ trunk/gdata/man/read.xls.Rd 2009-07-16 02:49:11 UTC (rev 1342)
@@ -1,41 +1,53 @@
\name{read.xls}
\alias{read.xls}
\alias{xls2csv}
+\alias{xls2tab}
+\alias{xls2sep}
\title{Read Excel files}
\description{Reads a Microsoft Excel file into a data frame}
\usage{
-read.xls(xls, sheet=1, verbose=FALSE, pattern, ..., perl="perl")
+read.xls(xls, sheet=1, verbose=FALSE, pattern, ...,
+ method=c("csv","tab"), perl="perl")
+
xls2csv(xls, sheet=1, verbose=FALSE, ..., perl="perl")
+xls2tab(xls, sheet=1, verbose=FALSE, ..., perl="perl")
+xls2sep(xls, sheet=1, verbose=FALSE, ..., method=c("csv","tab"),
+ perl="perl")
}
\arguments{
- \item{xls}{name of the Microsoft Excel file. If on internet it
- should begin with code{"http://"}.}
- \item{sheet}{number of sheet within the Excel file from which data are
- to be read}
+ \item{xls}{path to the Microsoft Excel file. To access a file on the
+ internet, start the path with "http://".}
+ \item{sheet}{number of the sheet within the Excel file from which data
+ are to be read}
\item{verbose}{logical flag indicating whether details should be
printed as the file is processed.}
\item{pattern}{if specified, them skip all lines before the first
- containing this string}
+ containing this string}
\item{perl}{name of the perl executable to be called.}
+ \item{method}{intermediate file format, "csv" for comma-separated and
+ "tab" for tab-separated}
\item{...}{additional arguments to read.table. The defaults of
read.csv are used.}
}
\value{
- \code{"read.xls"} returns a data frame. \code{"xls2csv"} returns a
- connection to a temporary file in csv format.
+ \code{"read.xls"} returns a data frame.
+
+ \code{"xls2sep"} returns a temporary file in the specified format.
+ \code{"xls2csv"} and \code{"xls2tab"} are simply wrappers for
+ \code{"xls2sep"} specifying method as "csv" or "tab", respectively.
}
\details{
This function works translating the named Microsoft Excel file into a
- temporary .csv file, using Greg Warnes' xls2csv Perl script (installed
- as part of the gregmisc package).
+ temporary .csv or .tab file, using the xls2csv or xls2tab
+ Perl script installed as part of this (gdata) package.
Caution: In the conversion to csv, strings will be quoted. This can be
problem if you are trying to use the \code{comment.char} option of
\code{read.table} since the first character of all lines (including
comment lines) will be "\"" after conversion.
- Caution: With \code{"xls2csv"} it is the responsibility of the user
- to close and delete the file after using it.
+ Caution: If you call \code{"xls2csv"} directly, is your responsibility
+ to close and delete the file after using it.
}
\references{http://www.analytics.washington.edu/statcomp/downloads/xls2csv}
\note{ Either a working version of Perl must be present in the executable
@@ -48,9 +60,22 @@
xlsfile <- file.path(.path.package('gdata'),'xls','iris.xls')
xlsfile
- iris <- read.xls(xlsfile)
+ iris <- read.xls(xlsfile) # defaults to csv format
+ iris <- read.xls(xlsfile,method="csv") # specify csv format
+ iris <- read.xls(xlsfile,method="tab") # specify tab format
+
head(iris) # look at the top few rows
+ \dontshow{
+ iris.1 <- read.xls(xlsfile) # defaults to csv format
+ iris.2 <- read.xls(xlsfile,method="csv") # specify csv format
+ iris.3 <- read.xls(xlsfile,method="tab") # specify tab format
+
+ stopifnot(all.equal(iris.1, iris.2))
+ stopifnot(all.equal(iris.1, iris.3))
+ }
+
+
\dontrun{
# Example specifying exact Perl path for default MS-Windows install of
# ActiveState perl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 05:45:20
|
Revision: 1341
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1341&view=rev
Author: warnes
Date: 2009-05-09 05:45:13 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Update for 1.2.1
Modified Paths:
--------------
trunk/fork/DESCRIPTION
Modified: trunk/fork/DESCRIPTION
===================================================================
--- trunk/fork/DESCRIPTION 2009-05-09 05:44:57 UTC (rev 1340)
+++ trunk/fork/DESCRIPTION 2009-05-09 05:45:13 UTC (rev 1341)
@@ -1,7 +1,7 @@
Package: fork
Title: R functions for handling multiple processes.
-Version: 1.2.1
-Date: 2007-03-24
+Version: 1.2.2
+Date: 2009-05-09
Author: Gregory R. Warnes <gr...@ra...>. Financial
support for some aspects of this package provided by Metrum Research Group,
LLC <http://www.metrumrg.com>.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 05:45:10
|
Revision: 1340
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1340&view=rev
Author: warnes
Date: 2009-05-09 05:44:57 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Add convenience links to NEWS and ChangeLog at top level
Added Paths:
-----------
trunk/fork/ChangeLog
trunk/fork/NEWS
Added: trunk/fork/ChangeLog
===================================================================
--- trunk/fork/ChangeLog (rev 0)
+++ trunk/fork/ChangeLog 2009-05-09 05:44:57 UTC (rev 1340)
@@ -0,0 +1 @@
+link inst/ChangeLog
\ No newline at end of file
Property changes on: trunk/fork/ChangeLog
___________________________________________________________________
Added: svn:special
+ *
Added: trunk/fork/NEWS
===================================================================
--- trunk/fork/NEWS (rev 0)
+++ trunk/fork/NEWS 2009-05-09 05:44:57 UTC (rev 1340)
@@ -0,0 +1 @@
+link inst/NEWS
\ No newline at end of file
Property changes on: trunk/fork/NEWS
___________________________________________________________________
Added: svn:special
+ *
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 05:43:25
|
Revision: 1339
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1339&view=rev
Author: warnes
Date: 2009-05-09 05:43:24 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Move NEWS to inst subdir.
Added Paths:
-----------
trunk/fork/inst/
trunk/fork/inst/NEWS
Removed Paths:
-------------
trunk/fork/NEWS
Deleted: trunk/fork/NEWS
===================================================================
--- trunk/fork/NEWS 2009-05-09 05:42:05 UTC (rev 1338)
+++ trunk/fork/NEWS 2009-05-09 05:43:24 UTC (rev 1339)
@@ -1,12 +0,0 @@
-
-Version: 1.2.0 - 2007-03-22
-===========================
-
- - Added new function handleSIGCLD/restoreSIGCLD for setting
- up/removing a SIGCLD handler so that fork'ed processes can safely be
- ignored without becoming zombies. See ?handleSIGCLD for details.
-
- - Added regression tests for SysV and BSD style signal handling that
- checks for zombie process creation & tests that signal("SIGCHLD","ignore")
- and/or handleSIGCLD() prevents zombie process creation.
-
Copied: trunk/fork/inst/NEWS (from rev 1099, trunk/fork/NEWS)
===================================================================
--- trunk/fork/inst/NEWS (rev 0)
+++ trunk/fork/inst/NEWS 2009-05-09 05:43:24 UTC (rev 1339)
@@ -0,0 +1,12 @@
+
+Version: 1.2.0 - 2007-03-22
+===========================
+
+ - Added new function handleSIGCLD/restoreSIGCLD for setting
+ up/removing a SIGCLD handler so that fork'ed processes can safely be
+ ignored without becoming zombies. See ?handleSIGCLD for details.
+
+ - Added regression tests for SysV and BSD style signal handling that
+ checks for zombie process creation & tests that signal("SIGCHLD","ignore")
+ and/or handleSIGCLD() prevents zombie process creation.
+
Property changes on: trunk/fork/inst/NEWS
___________________________________________________________________
Added: svn:mergeinfo
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 05:42:13
|
Revision: 1338
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1338&view=rev
Author: warnes
Date: 2009-05-09 05:42:05 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Fix .Rd syntax error and update mailing address
Modified Paths:
--------------
trunk/fork/man/wait.Rd
Modified: trunk/fork/man/wait.Rd
===================================================================
--- trunk/fork/man/wait.Rd 2009-05-09 05:29:53 UTC (rev 1337)
+++ trunk/fork/man/wait.Rd 2009-05-09 05:42:05 UTC (rev 1338)
@@ -2,8 +2,9 @@
\name{wait}
\alias{wait}
\title{Wait for child process(es) to stop or terminate.}
-\description{Wait for child process(es) created using 'fork' command to
- stop or terminate.}
+\description{
+ Wait for child process(es) created using 'fork' command to
+ stop or terminate.
}
\usage{
wait(pid, nohang=FALSE, untraced=FALSE)
@@ -33,7 +34,7 @@
and the meanings of the status indicator.
}
\references{"wait" and "waitpid" man pages}
-\author{ Gregory R. Warnes \email{warnes\@bst.rochester.edu}}
+\author{ Gregory R. Warnes \email{gr...@ra...}}
\seealso{\code{\link{fork}}, \code{\link{exit}}, \code{\link{getpid}},
\code{\link{kill}}, \code{\link{killall}}}
\examples{
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 05:29:59
|
Revision: 1337
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1337&view=rev
Author: warnes
Date: 2009-05-09 05:29:53 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Add tests for lme4 'mer' objects
Added Paths:
-----------
trunk/gmodels/test/
trunk/gmodels/test/lme-test.R
Added: trunk/gmodels/test/lme-test.R
===================================================================
--- trunk/gmodels/test/lme-test.R (rev 0)
+++ trunk/gmodels/test/lme-test.R 2009-05-09 05:29:53 UTC (rev 1337)
@@ -0,0 +1,23 @@
+library(gmodels)
+library(lme4)
+
+sleepstudy$dayGroup <- cut(sleepstudy$Days, seq(-1,9,by=2), include=T)
+
+# ci example
+fm2 <- lmer(Reaction ~ dayGroup + (1|Subject) + (0+Days|Subject), sleepstudy)
+ci(fm2)
+
+
+# estimable examples
+estimable(fm2, c( 0, -1, 1, 0, 0 ) ) # list all terms
+estimable(fm2, c("dayGroup(1,3]"=-1, "dayGroup(3,5]"=1)) # just the nonzero terms
+estimable(fm2, c("dayGroup(1,3]"=-1, "dayGroup(3,5]"=1), n.sim=5000 ) # more simulations...
+
+
+# fit.contrast example
+fit.contrast( fm2, "dayGroup",
+ rbind("0-1 vs 3-4"=c(-1,0,1,0,0),
+ "3-4 vs 5-6"=c(0,0,-1,1,0)
+ ),
+ conf=0.95 )
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 05:04:09
|
Revision: 1336
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1336&view=rev
Author: warnes
Date: 2009-05-09 05:04:07 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Update for 2.15.0
Modified Paths:
--------------
trunk/gmodels/inst/NEWS
Modified: trunk/gmodels/inst/NEWS
===================================================================
--- trunk/gmodels/inst/NEWS 2009-05-09 05:02:46 UTC (rev 1335)
+++ trunk/gmodels/inst/NEWS 2009-05-09 05:04:07 UTC (rev 1336)
@@ -1,3 +1,17 @@
+Version 2.15.0
+--------------
+
+New features:
+
+- Add support for 'mer' model from lme4.
+
+Bug fixes:
+
+- Correct several minor .Rd syntax errors
+
+- Move extra copyright text to Author field instead of License field.
+
+
Version 2.14.1
--------------
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 05:02:48
|
Revision: 1335
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1335&view=rev
Author: warnes
Date: 2009-05-09 05:02:46 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Update description for 2.15.0
Modified Paths:
--------------
trunk/gmodels/DESCRIPTION
Modified: trunk/gmodels/DESCRIPTION
===================================================================
--- trunk/gmodels/DESCRIPTION 2009-05-09 05:01:47 UTC (rev 1334)
+++ trunk/gmodels/DESCRIPTION 2009-05-09 05:02:46 UTC (rev 1335)
@@ -1,19 +1,18 @@
Package: gmodels
-Version: 2.14.1
+Version: 2.15.0
Title: Various R programming tools for model fitting
Author: Gregory R. Warnes. Includes R source code and/or documentation
- contributed by Ben Bolker, Thomas Lumley, and Randall C Johnson.
+ contributed by Ben Bolker, Thomas Lumley, and Randall C
+ Johnson. Contributions from Randall C. Johnson are Copyright
+ (2005) SAIC-Frederick, Inc. Funded by the Intramural Research
+ Program, of the NIH, National Cancer Institute, Center for
+ Cancer Research under NCI Contract NO1-CO-12400.
Maintainer: Gregory R. Warnes <gr...@ra...>
Description: Various R programming tools for model fitting
Depends: R (>= 1.9.0)
Suggests: gplots, Matrix, nlme, lme4
Imports: MASS, gdata
-License: GPL-2. Contributions from Randall C. Johnson are
- Copyright (2005) SAIC-Frederick, Inc. Funded by
- the Intramural Research Program, of the NIH, National
- Cancer Institute, Center for Cancer Research under NCI
- Contract NO1-CO-12400.
+License: GPL-2
URL: http://cran.r-project.org/src/contrib/PACKAGES.html
http://www.sf.net/projects/r-gregmisc
-Date: 2007-07-24
-Packaged: Fri Dec 7 17:22:36 2007; warnes
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 05:01:51
|
Revision: 1334
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1334&view=rev
Author: warnes
Date: 2009-05-09 05:01:47 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Add support for lme4's 'mer' objects
Added Paths:
-----------
trunk/gmodels/R/est.mer.R
Added: trunk/gmodels/R/est.mer.R
===================================================================
--- trunk/gmodels/R/est.mer.R (rev 0)
+++ trunk/gmodels/R/est.mer.R 2009-05-09 05:01:47 UTC (rev 1334)
@@ -0,0 +1,70 @@
+# est.mer.R
+# generate estimable output for mer objects using mcmcsamp()
+# Randall Johnson
+# Laboratory of Genomic Diversity at NCI Frederick
+# SAIC Frederick, Inc
+# Created April 25, 2006
+
+est.mer <- function(obj, cm, beta0, conf.int, show.beta0, n.sim)
+{
+## if(!require(coda, quietly=TRUE))
+## stop("coda package required when sim.mer == TRUE")
+
+ samp <- mcmcsamp(obj, n.sim)
+## samp.summ <- summary(samp)
+
+ if(is.null(dim(cm)))
+ n <- length(cm)
+ else
+ n <- dim(cm)[2]
+ # drop extra information on end
+ samp.cm <- as.matrix(samp)[, 1:n] %*% t(cm)
+
+ # calculate requested statistics
+ est <- apply(samp.cm, 2, mean)
+ stderr <- sd(samp.cm)
+
+ pval <- sapply(1:length(beta0),
+ function(i){percentile(beta0[i], samp.cm[,i])})
+ pval <- ifelse(pval <= .5, 2*pval, 2*(1-pval))
+
+ if(is.null(conf.int))
+ {
+ lower.ci <- NULL
+ upper.ci <- NULL
+ }else{
+ alpha <- 1-conf.int
+ samp.ci <- sapply(1:length(beta0),
+ function(i)
+ {
+ quantile(samp.cm[,i], probs=c(alpha/2, 1-alpha/2))
+ }
+ )
+
+ lower.ci <- samp.ci[1,]
+ upper.ci <- samp.ci[2,]
+ }
+
+ # return results
+ if(!show.beta0)
+ beta0 <- NULL
+
+ samp.stats <- cbind('beta0' = beta0,
+ 'Estimate' = est,
+ 'Std. Error' = stderr,
+ 'p value' = pval,
+ 'Lower.CI' = lower.ci,
+ 'Upper.CI' = upper.ci)
+
+ row.names(samp.stats) <- paste('(', apply(cm, 1, paste, collapse=" "),
+ ')', sep='')
+
+ return(samp.stats)
+}
+
+percentile <- function(x, distn)
+{
+ n <- length(distn)
+
+ return(findInterval(x, distn[order(distn)]) / n)
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 05:00:52
|
Revision: 1333
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1333&view=rev
Author: warnes
Date: 2009-05-09 05:00:47 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Add support for lme4's 'mer' objects
Modified Paths:
--------------
trunk/gmodels/NAMESPACE
trunk/gmodels/R/ci.R
trunk/gmodels/R/est.lmer.R
trunk/gmodels/R/estimable.R
trunk/gmodels/R/fit.contrast.R
trunk/gmodels/R/to.est.R
Modified: trunk/gmodels/NAMESPACE
===================================================================
--- trunk/gmodels/NAMESPACE 2009-05-09 04:53:47 UTC (rev 1332)
+++ trunk/gmodels/NAMESPACE 2009-05-09 05:00:47 UTC (rev 1333)
@@ -18,14 +18,14 @@
S3method(ci, binom)
S3method(ci, lm)
S3method(ci, lme)
-S3method(ci, lmer)
+S3method(ci, mer)
S3method(fit.contrast, lm)
S3method(fit.contrast, lme)
-S3method(fit.contrast, lmer)
+S3method(fit.contrast, mer)
S3method(estimable, default)
-S3method(estimable, lmer)
+S3method(estimable, mer)
S3method(estimable, mlm)
S3method(print, glh.test)
Modified: trunk/gmodels/R/ci.R
===================================================================
--- trunk/gmodels/R/ci.R 2009-05-09 04:53:47 UTC (rev 1332)
+++ trunk/gmodels/R/ci.R 2009-05-09 05:00:47 UTC (rev 1333)
@@ -68,21 +68,21 @@
retval
}
-ci.lmer <- function(x,
+ci.mer <- function(x,
confidence=0.95,
alpha=1-confidence,
- sim.lmer=TRUE,
+ sim.mer=TRUE,
n.sim=1000,
...
)
{
- if(!(require(coda, quietly=TRUE) & require(Matrix, quietly=TRUE)))
- stop("coda and Matrix packages required for ci.lmer")
+## if(!(require(coda, quietly=TRUE) & require(Matrix, quietly=TRUE)))
+## stop("coda and Matrix packages required for ci.mer")
x.effects <- fixef(x)
n <- length(x.effects)
- retval <- est.lmer(obj = x, cm = diag(n), beta0 = rep(0, n),
+ retval <- est.mer(obj = x, cm = diag(n), beta0 = rep(0, n),
conf.int = confidence, show.beta0 = FALSE,
n.sim = n.sim)[,c("Estimate", "Lower.CI", "Upper.CI",
"Std. Error", "p value")]
Modified: trunk/gmodels/R/est.lmer.R
===================================================================
--- trunk/gmodels/R/est.lmer.R 2009-05-09 04:53:47 UTC (rev 1332)
+++ trunk/gmodels/R/est.lmer.R 2009-05-09 05:00:47 UTC (rev 1333)
@@ -7,8 +7,8 @@
est.lmer <- function(obj, cm, beta0, conf.int, show.beta0, n.sim)
{
- if(!require(coda, quietly=TRUE))
- stop("coda package required when sim.lmer == TRUE")
+## if(!require(coda, quietly=TRUE))
+## stop("coda package required when sim.lmer == TRUE")
samp <- mcmcsamp(obj, n.sim)
samp.summ <- summary(samp)
Modified: trunk/gmodels/R/estimable.R
===================================================================
--- trunk/gmodels/R/estimable.R 2009-05-09 04:53:47 UTC (rev 1332)
+++ trunk/gmodels/R/estimable.R 2009-05-09 05:00:47 UTC (rev 1333)
@@ -1,4 +1,4 @@
-# $Id$
+## $Id$
estimable <- function (obj, cm, beta0, conf.int=NULL, show.beta0, ...)
{
UseMethod("estimable")
@@ -163,53 +163,53 @@
if(!show.beta0) retval$beta0 <- NULL
return(retval)
}
- }
+}
.wald <- function (obj, cm,
beta0=rep(0, ifelse(is.null(nrow(cm)), 1, nrow(cm))))
{
- if (!is.matrix(cm) && !is.data.frame(cm))
- cm <- matrix(cm, nrow=1)
- df <- nrow(cm)
- if ("geese" %in% class(obj))
- {
- cf <- obj$beta
- vcv <- obj$vbeta
- }
- else if ("gee" %in% class(obj))
- {
- cf <- summary(obj)$coef
- vcv <- obj$robust.variance
- }
- else if ("lm" %in% class(obj))
- {
- cf <- summary.lm(obj)$coefficients[, 1]
- if ("glm" %in% class(obj))
- vcv <- summary(obj)$cov.scaled
- else
- vcv <- summary.lm(obj)$cov.unscaled * summary.lm(obj)$sigma^2
- }
- else if ("lme" %in% class(obj))
- {
- s.o <- summary(obj)
- cf <- s.o$tTable[,1]
- se <- s.o$tTable[, 2]
- rho <- s.o$cor
- vcv <- rho * outer(se, se)
- }
- else
- stop("obj must be of class 'lm', 'glm', 'aov', 'gee', 'geese', or 'lme'.")
- u <- (cm %*% cf)-beta0
- vcv.u <- cm %*% vcv %*% t(cm)
- W <- t(u) %*% solve(vcv.u) %*% u
- prob <- 1 - pchisq(W, df=df)
- retval <- as.data.frame(cbind(W, df, prob))
- names(retval) <- c("X2.stat", "DF", "Pr(>|X^2|)")
- print(as.data.frame(retval))
+ if (!is.matrix(cm) && !is.data.frame(cm))
+ cm <- matrix(cm, nrow=1)
+ df <- nrow(cm)
+ if ("geese" %in% class(obj))
+ {
+ cf <- obj$beta
+ vcv <- obj$vbeta
+ }
+ else if ("gee" %in% class(obj))
+ {
+ cf <- summary(obj)$coef
+ vcv <- obj$robust.variance
+ }
+ else if ("lm" %in% class(obj))
+ {
+ cf <- summary.lm(obj)$coefficients[, 1]
+ if ("glm" %in% class(obj))
+ vcv <- summary(obj)$cov.scaled
+ else
+ vcv <- summary.lm(obj)$cov.unscaled * summary.lm(obj)$sigma^2
+ }
+ else if ("lme" %in% class(obj))
+ {
+ s.o <- summary(obj)
+ cf <- s.o$tTable[,1]
+ se <- s.o$tTable[, 2]
+ rho <- s.o$cor
+ vcv <- rho * outer(se, se)
+ }
+ else
+ stop("obj must be of class 'lm', 'glm', 'aov', 'gee', 'geese', or 'lme'.")
+ u <- (cm %*% cf)-beta0
+ vcv.u <- cm %*% vcv %*% t(cm)
+ W <- t(u) %*% solve(vcv.u) %*% u
+ prob <- 1 - pchisq(W, df=df)
+ retval <- as.data.frame(cbind(W, df, prob))
+ names(retval) <- c("X2.stat", "DF", "Pr(>|X^2|)")
+ print(as.data.frame(retval))
}
-estimable.lmer <- function (obj, cm, beta0, conf.int=NULL, show.beta0,
- sim.lmer=TRUE, n.sim=1000, ...)
+estimable.mer <- function (obj, cm, beta0, conf.int=NULL, show.beta0,
+ sim.mer=TRUE, n.sim=1000, ...)
{
if (is.matrix(cm) || is.data.frame(cm))
{
@@ -225,7 +225,7 @@
}
else
{
- stop("`cm' argument must be of type vector, list, or matrix.")
+ stop("'cm' argument must be of type vector, list, or matrix.")
}
if(missing(show.beta0))
@@ -243,30 +243,36 @@
}
- if ("lmer" %in% class(obj)) {
- if(!require(Matrix, quietly=TRUE))
- stop("Matrix package required for lmer objects")
-
- if(sim.lmer)
- return(est.lmer(obj=obj, cm=cm, beta0=beta0, conf.int=conf.int,
- show.beta0=show.beta0, n.sim=n.sim))
-
- stat.name <- "lmer"
- cf <- as.matrix(fixef(obj))
- vcv <- as.matrix(vcov(obj))
- df <- NA
- }
- else {
- stop("obj is not of class lmer")
- }
+ if ("mer" %in% class(obj)) {
+ if(sim.mer)
+ return(est.mer(obj=obj, cm=cm, beta0=beta0, conf.int=conf.int,
+ show.beta0=show.beta0, n.sim=n.sim))
+
+ stat.name <- "mer"
+ cf <- as.matrix(fixef(obj))
+ vcv <- as.matrix(vcov(obj))
+ df <- NA
+ }
+ else {
+ stop("obj is not of class mer")
+ }
- retval <- cbind(hyp=beta0, est=ct, stderr=vc, "t value"=ct.diff/vc)
- dimnames(retval) <- list(rn, c("beta0", "Estimate", "Std. Error",
- "t value"))
+ if (is.null(rownames(cm)))
+ rn <- paste("(", apply(cm, 1, paste, collapse=" "),
+ ")", sep="")
+ else rn <- rownames(cm)
+
+ ct <- cm %*% cf[, 1]
+ ct.diff <- cm %*% cf[, 1] - beta0
+ vc <- sqrt(diag(cm %*% vcv %*% t(cm)))
+
+ retval <- cbind(hyp=beta0, est=ct, stderr=vc, "t value"=ct.diff/vc)
+ dimnames(retval) <- list(rn, c("beta0", "Estimate", "Std. Error",
+ "t value"))
- rownames(retval) <- make.unique(rownames(retval))
- retval <- as.data.frame(retval)
- if(!show.beta0) retval$beta0 <- NULL
- return(retval)
+ rownames(retval) <- make.unique(rownames(retval))
+ retval <- as.data.frame(retval)
+ if(!show.beta0) retval$beta0 <- NULL
+ return(retval)
}
Modified: trunk/gmodels/R/fit.contrast.R
===================================================================
--- trunk/gmodels/R/fit.contrast.R 2009-05-09 04:53:47 UTC (rev 1332)
+++ trunk/gmodels/R/fit.contrast.R 2009-05-09 05:00:47 UTC (rev 1333)
@@ -4,9 +4,9 @@
conf.int=NULL, df=FALSE, ...)
{
# check class of model
- if( !(any(class(model) %in% c("lm", "aov", "lme") ) )) ######
- stop("contrast.lm can only be applied to objects inheriting from 'lm'", ###### took lmer out of here
- "and 'lme' (eg: lm,glm,aov,lme).") ######
+ if( !(any(class(model) %in% c("lm", "aov", "lme") ) ))
+ stop("contrast.lm can only be applied to objects inheriting from 'lm'",
+ "and 'lme' (eg: lm,glm,aov,lme).")
# make sure we have the NAME of the variable
if(!is.character(varname))
@@ -34,7 +34,7 @@
colnames(cmat) <- cn
# recall fitting method with the specified contrast
- m <- model$call ###### deleted lmer specific/S4 portion
+ m <- model$call
if(is.null(m$contrasts))
m$contrasts <- list()
@@ -46,7 +46,7 @@
r <- eval(m)
# now return the correct elements ....
- if( 'lme' %in% class(model) ) ####### took out lmer section
+ if( 'lme' %in% class(model) )
{
est <- r$coefficients$fixed
se <- sqrt(diag(r$varFix))
@@ -81,7 +81,7 @@
}
else
{
- rn <- paste(varname,rownames(coeff),sep="") ####### removed lmer portion
+ rn <- paste(varname,rownames(coeff),sep="")
ind <- match(rn,rownames(retval))
retval <- retval[ind,,drop=FALSE]
}
@@ -104,8 +104,8 @@
return(retval)
}
-# fit.contrast.lme and fit.contrast.lmer are necessary because
-# 'lme' and 'lmer' objects do not inherit from 'lm'.
+# fit.contrast.lme and fit.contrast.mer are necessary because
+# 'lme' and 'mer' objects do not inherit from 'lm'.
#
# **Make sure that the argument list *exactly* matches the one
# for fit.contrast.lm() above.**
@@ -117,10 +117,10 @@
fit.contrast.lm(model, varname, coeff, showall, conf.int, df)
}
-# I made rather dramatic changes here and do all calculations in fit.contrast.lmer rather than
-# fit.contrast.lm because of the simulation extras ... added sim.lmer and n.sim to the parameter list
-fit.contrast.lmer <- function(model, varname, coeff, showall=FALSE,
- conf.int=NULL, sim.lmer=TRUE, n.sim=1000, ...)
+# I made rather dramatic changes here and do all calculations in fit.contrast.mer rather than
+# fit.contrast.lm because of the simulation extras ... added sim.mer and n.sim to the parameter list
+fit.contrast.mer <- function(model, varname, coeff, showall=FALSE,
+ conf.int=NULL, sim.mer=TRUE, n.sim=1000, ...)
{
require(lme4)
@@ -163,15 +163,15 @@
r.effects <- fixef(r)
n <- length(r.effects)
- if(sim.lmer)
+ if(sim.mer)
{
- retval <- est.lmer(obj = r, cm = diag(n), beta0 = rep(0, n),
+ retval <- est.mer(obj = r, cm = diag(n), beta0 = rep(0, n),
conf.int = conf.int, show.beta0 = FALSE,
n.sim=n.sim)
rownames(retval) <- names(r.effects)
}else{
if(!is.null(conf.int))
- warning("Confidence interval calculation for lmer objects requires simulation -- use sim.lmer = TRUE")
+ warning("Confidence interval calculation for mer objects requires simulation -- use sim.mer = TRUE")
est <- fixef(r)
se <- sqrt(diag(as.matrix(vcov(r))))
Modified: trunk/gmodels/R/to.est.R
===================================================================
--- trunk/gmodels/R/to.est.R 2009-05-09 04:53:47 UTC (rev 1332)
+++ trunk/gmodels/R/to.est.R 2009-05-09 05:00:47 UTC (rev 1333)
@@ -5,7 +5,7 @@
.to.est <- function(obj, params)
{
- if('lme' %in% class(obj) | 'lmer' %in% class(obj))
+ if('lme' %in% class(obj) | 'mer' %in% class(obj))
{
eff.obj <- fixef(obj)
}
@@ -30,7 +30,7 @@
if(length(params)==length(est))
names(params) <- names(est)
else
- stop("`param' has no names and does not match number of coefficients of model. Unable to construct coefficient vector")
+ stop("'param' has no names and does not match number of coefficients of model. Unable to construct coefficient vector")
else
{
matches <- names(params) %in% names(est)
@@ -45,10 +45,10 @@
)
}
- if(is.list(params)) #####################
- est[names(params)] <- unlist(params) ##################### changed
- else #####################
- est[names(params)] <- params #####################
+ if(is.list(params))
+ est[names(params)] <- unlist(params)
+ else
+ est[names(params)] <- params
}
return(est)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 04:53:48
|
Revision: 1332
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1332&view=rev
Author: warnes
Date: 2009-05-09 04:53:47 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Fix .Rd syntax error
Modified Paths:
--------------
trunk/gmodels/man/glh.test.Rd
Modified: trunk/gmodels/man/glh.test.Rd
===================================================================
--- trunk/gmodels/man/glh.test.Rd 2009-05-09 04:37:01 UTC (rev 1331)
+++ trunk/gmodels/man/glh.test.Rd 2009-05-09 04:53:47 UTC (rev 1332)
@@ -4,12 +4,10 @@
\alias{glh.test}
\alias{print.glh.test}
\alias{summary.glh.test}
-
\title{ Test a General Linear Hypothesis for a Regression Model }
\description{
-Test, print, or summarize a general linear hypothesis for a regression model }
+ Test, print, or summarize a general linear hypothesis for a regression model
}
-
\usage{
glh.test(reg, cm, d=rep(0, nrow(cm)) )
print.glh.test(x, digits=4,...)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 04:37:18
|
Revision: 1331
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1331&view=rev
Author: warnes
Date: 2009-05-09 04:37:01 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Add softlinks for ChangeLog and NEWS to top level dir for convenience
Added Paths:
-----------
trunk/gmodels/NEWS
Added: trunk/gmodels/NEWS
===================================================================
--- trunk/gmodels/NEWS (rev 0)
+++ trunk/gmodels/NEWS 2009-05-09 04:37:01 UTC (rev 1331)
@@ -0,0 +1 @@
+link inst/NEWS
\ No newline at end of file
Property changes on: trunk/gmodels/NEWS
___________________________________________________________________
Added: svn:special
+ *
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 04:36:16
|
Revision: 1330
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1330&view=rev
Author: warnes
Date: 2009-05-09 04:36:13 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Move ChangeLog and NEWS files into inst directory
Added Paths:
-----------
trunk/gmodels/ChangeLog
trunk/gmodels/inst/
trunk/gmodels/inst/NEWS
Removed Paths:
-------------
trunk/gmodels/NEWS
Added: trunk/gmodels/ChangeLog
===================================================================
--- trunk/gmodels/ChangeLog (rev 0)
+++ trunk/gmodels/ChangeLog 2009-05-09 04:36:13 UTC (rev 1330)
@@ -0,0 +1 @@
+link inst/ChangeLog
\ No newline at end of file
Property changes on: trunk/gmodels/ChangeLog
___________________________________________________________________
Added: svn:special
+ *
Deleted: trunk/gmodels/NEWS
===================================================================
--- trunk/gmodels/NEWS 2009-05-09 04:00:15 UTC (rev 1329)
+++ trunk/gmodels/NEWS 2009-05-09 04:36:13 UTC (rev 1330)
@@ -1,80 +0,0 @@
-Version 2.14.1
---------------
-
-New features:
-
-- Add support for 'lme' objects to estimable().
-
-Other:
-
-- Fix minor typos in manual page for estimable().
-
-Version 2.14.0
---------------
-
-New Features:
-
-- Add support for 'mlm' objects to estimable
-
-
-Version 2.13.2
---------------
-
-Bug Fixes:
-
-- Lower and upper end of confidence interval for lmer objects were
- reversed in est.lmer().
-
-- Correct Greg's email address in two help files.
-
-
-Version 2.13.1
---------------
-
-Bug Fixes:
-
-- Problem: R CMD check errors under development version of R 2.5.0
- Solution:
- - Add additional packages to 'Suggests' list in DESCRIPTION
- - Remove extra trailing comma in function calls
- - fix various code/doc inconsistencies
-
-- Problem: estimable() was failing for lmer objects.
- Solution:
- - Create a generic estimable()
- - Move old function to estimable.default()
- - Add estimable.lmer() to the exported methods list in NAMESPACE
-
-
-Version 2.13.0
---------------
-
-
-Version 2.12.0
---------------
-
-- Updated Greg's email address.
-
-- Add support for lmer (lme version 4) objects to ci(), estimable(),
- and fit.contrast() via code contributed by Randall C Johnson.
-
-- Add simplfied coefficient specification to 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.
-
-Version 2.1.0
--------------
-
-Version 2.0.8
--------------
-
- - Added DESCRIPTION and removed DESCRIPTION.in
-
- - Updated CrossTable.R
-
- - Updated NAMESPACE file
-
Copied: trunk/gmodels/inst/NEWS (from rev 1232, trunk/gmodels/NEWS)
===================================================================
--- trunk/gmodels/inst/NEWS (rev 0)
+++ trunk/gmodels/inst/NEWS 2009-05-09 04:36:13 UTC (rev 1330)
@@ -0,0 +1,80 @@
+Version 2.14.1
+--------------
+
+New features:
+
+- Add support for 'lme' objects to estimable().
+
+Other:
+
+- Fix minor typos in manual page for estimable().
+
+Version 2.14.0
+--------------
+
+New Features:
+
+- Add support for 'mlm' objects to estimable
+
+
+Version 2.13.2
+--------------
+
+Bug Fixes:
+
+- Lower and upper end of confidence interval for lmer objects were
+ reversed in est.lmer().
+
+- Correct Greg's email address in two help files.
+
+
+Version 2.13.1
+--------------
+
+Bug Fixes:
+
+- Problem: R CMD check errors under development version of R 2.5.0
+ Solution:
+ - Add additional packages to 'Suggests' list in DESCRIPTION
+ - Remove extra trailing comma in function calls
+ - fix various code/doc inconsistencies
+
+- Problem: estimable() was failing for lmer objects.
+ Solution:
+ - Create a generic estimable()
+ - Move old function to estimable.default()
+ - Add estimable.lmer() to the exported methods list in NAMESPACE
+
+
+Version 2.13.0
+--------------
+
+
+Version 2.12.0
+--------------
+
+- Updated Greg's email address.
+
+- Add support for lmer (lme version 4) objects to ci(), estimable(),
+ and fit.contrast() via code contributed by Randall C Johnson.
+
+- Add simplfied coefficient specification to 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.
+
+Version 2.1.0
+-------------
+
+Version 2.0.8
+-------------
+
+ - Added DESCRIPTION and removed DESCRIPTION.in
+
+ - Updated CrossTable.R
+
+ - Updated NAMESPACE file
+
Property changes on: trunk/gmodels/inst/NEWS
___________________________________________________________________
Added: svn:keywords
+ Author Date Id Revision
Added: svn:mergeinfo
+
Added: svn:eol-style
+ native
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 04:00:24
|
Revision: 1329
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1329&view=rev
Author: warnes
Date: 2009-05-09 04:00:15 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Update Greg's email address
Modified Paths:
--------------
trunk/gmodels/DESCRIPTION
trunk/gmodels/man/ci.Rd
trunk/gmodels/man/estimable.Rd
trunk/gmodels/man/fast.prcomp.Rd
trunk/gmodels/man/fit.contrast.Rd
trunk/gmodels/man/glh.test.Rd
trunk/gmodels/man/make.contrasts.Rd
Modified: trunk/gmodels/DESCRIPTION
===================================================================
--- trunk/gmodels/DESCRIPTION 2009-05-09 03:35:14 UTC (rev 1328)
+++ trunk/gmodels/DESCRIPTION 2009-05-09 04:00:15 UTC (rev 1329)
@@ -3,16 +3,17 @@
Title: Various R programming tools for model fitting
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker, Thomas Lumley, and Randall C Johnson.
- Contributions from Randall C. Johnson are Copyright (2005)
- SAIC-Frederick, Inc. Funded by the Intramural Research Program,
- of the NIH, National Cancer Institute, Center for Cancer Research
- under NCI Contract NO1-CO-12400.
-Maintainer: Gregory R. Warnes <wa...@bs...>
+Maintainer: Gregory R. Warnes <gr...@ra...>
Description: Various R programming tools for model fitting
Depends: R (>= 1.9.0)
-Suggests: gplots, Matrix, nlme, lme4, coda
+Suggests: gplots, Matrix, nlme, lme4
Imports: MASS, gdata
-License: GPL-2.
+License: GPL-2. Contributions from Randall C. Johnson are
+ Copyright (2005) SAIC-Frederick, Inc. Funded by
+ the Intramural Research Program, of the NIH, National
+ Cancer Institute, Center for Cancer Research under NCI
+ Contract NO1-CO-12400.
URL: http://cran.r-project.org/src/contrib/PACKAGES.html
http://www.sf.net/projects/r-gregmisc
Date: 2007-07-24
+Packaged: Fri Dec 7 17:22:36 2007; warnes
Modified: trunk/gmodels/man/ci.Rd
===================================================================
--- trunk/gmodels/man/ci.Rd 2009-05-09 03:35:14 UTC (rev 1328)
+++ trunk/gmodels/man/ci.Rd 2009-05-09 04:00:15 UTC (rev 1329)
@@ -6,20 +6,21 @@
\alias{ci.binom}
\alias{ci.lm}
\alias{ci.lme}
-\alias{ci.lmer}
+\alias{ci.mer}
\title{Compute Confidence Intervals}
\description{ Compute and display confidence intervals for model
estimates. Methods are provided for the mean of a numeric vector
\code{ci.default}, the probability of a binomial vector
- \code{ci.binom}, and for \code{lm}, \code{lme}, and \code{lmer} objects. }
+ \code{ci.binom}, and for \code{lm}, \code{lme}, and \code{mer} objects are
+ provided. }
\synopsis{
ci(x, confidence = 0.95, alpha = 1 - confidence,...)
\method{ci}{default}(x, confidence = 0.95, alpha = 1 - confidence, na.rm=FALSE)...)
\method{ci}{binom}(x, confidence = 0.95, alpha = 1 - confidence,...)
\method{ci}{lm}(x, confidence = 0.95, alpha = 1 - confidence,...)
\method{ci}{lme}(x, confidence = 0.95, alpha = 1 - confidence,...)
- \method{ci}{lmer}(x, confidence = 0.95, alpha = 1 - confidence,
- sim.lmer=TRUE, n.sim=1000, ...)
+ \method{ci}{mer}(x, confidence = 0.95, alpha = 1 - confidence,
+ sim.mer=TRUE, n.sim=1000, ...)
}
\arguments{
\item{x}{ object from which to compute confidence intervals. }
@@ -28,8 +29,8 @@
\item{na.rm}{boolean indicating whether missing values should be
removed. Defaults to \code{FALSE}.}
\item{\dots}{Arguments for methods}
- \item{sim.lmer}{Logical value. If TRUE confidence
- intervals will be estimated using \code{\Link[Matrix]{mcmcsamp}}. This option only takes effect for lmer
+ \item{sim.mer}{Logical value. If TRUE confidence
+ intervals will be estimated using \code{\Link[Matrix]{mcmcsamp}}. This option only takes effect for mer
objects.}
\item{n.sim}{Number of samples to take in \code{\Link[Matrix]{mcmcsamp}}.}
}
@@ -41,7 +42,7 @@
\code{Estimate}, \code{CI lower}, \code{CI upper}, \code{Std. Error},
\code{DF} (for lme objects only), and \code{p-value}.
}
-\author{ Gregory R. Warnes \email{wa...@bs...}
+\author{ Gregory R. Warnes \email{gr...@ra...}
}
\seealso{
\code{\link[stats]{confint}},
@@ -66,7 +67,7 @@
ci(reg)
\dontrun{
-# lmer example
+# mer example
library(lme4)
fm2 <- lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy)
ci(fm2)
Modified: trunk/gmodels/man/estimable.Rd
===================================================================
--- trunk/gmodels/man/estimable.Rd 2009-05-09 03:35:14 UTC (rev 1328)
+++ trunk/gmodels/man/estimable.Rd 2009-05-09 04:00:15 UTC (rev 1329)
@@ -3,27 +3,27 @@
\name{estimable}
\alias{estimable}
\alias{estimable.default}
-\alias{estimable.lmer}
+\alias{estimable.mer}
\alias{estimable.mlm}
%\alias{.wald}
%\alias{.to.est}
\title{Contrasts and estimable linear functions of model coefficients}
\description{
Compute and test contrasts and other estimable linear
- functions of model coefficients for for lm, glm, lme, lmer, and geese
+ functions of model coefficients for for lm, glm, lme, mer, and geese
objects
}
\usage{
estimable(obj, cm, beta0, conf.int=NULL, show.beta0, ...)
\method{estimable}{default} (obj, cm, beta0, conf.int=NULL, show.beta0, joint.test=FALSE, ...)
-\method{estimable}{lmer}(obj, cm, beta0, conf.int=NULL,
- show.beta0, sim.lmer=TRUE, n.sim=1000, ...)
+\method{estimable}{mer}(obj, cm, beta0, conf.int=NULL,
+ show.beta0, sim.mer=TRUE, n.sim=1000, ...)
\method{estimable}{mlm}(obj, cm, beta0, conf.int=NULL, show.beta0, ...)
%.wald(obj, cm,beta0=rep(0, ifelse(is.null(nrow(cm)), 1, nrow(cm))))
%.to.est(obj, params)
}
\arguments{
- \item{obj}{Regression (lm, glm, lme, lmer, mlm) object. }
+ \item{obj}{Regression (lm, glm, lme, mer, mlm) object. }
\item{cm}{Vector, List, or Matrix specifying estimable linear functions or
contrasts. See below for details.}
\item{beta0}{Vector of null hypothesis values}
@@ -37,7 +37,7 @@
\item{show.beta0}{Logical value. If TRUE a column for beta0 will be
included in the output table. Defaults to TRUE when beta0 is
specified, FALSE otherwise.}
- \item{sim.lmer}{Logical value. If TRUE p-values and confidence
+ \item{sim.mer}{Logical value. If TRUE p-values and confidence
intervals will be estimated using \code{\Link[Matrix]{mcmcsamp}}.
}
\item{n.sim}{Number of MCMC samples to take in
@@ -95,7 +95,7 @@
}
\author{
BXC (Bendix Carstensen) \email{bxc\@novonordisk.com},
- Gregory R. Warnes \email{wa...@bs...},
+ Gregory R. Warnes \email{gr...@ra...},
Soren Hojsgaard \email{so...@ag...}, and
Randall C Johnson \email{rjo...@nc...}
}
Modified: trunk/gmodels/man/fast.prcomp.Rd
===================================================================
--- trunk/gmodels/man/fast.prcomp.Rd 2009-05-09 03:35:14 UTC (rev 1328)
+++ trunk/gmodels/man/fast.prcomp.Rd 2009-05-09 04:00:15 UTC (rev 1329)
@@ -69,7 +69,7 @@
\code{\link{svd}} .
}
\author{Modifications by Gregory R. Warnes
- \email{wa...@bs...} }
+ \email{gr...@ra...} }
\seealso{
\code{\link[stats]{prcomp}}, \code{\link{svd}}, \code{\link{La.svd}}
Modified: trunk/gmodels/man/fit.contrast.Rd
===================================================================
--- trunk/gmodels/man/fit.contrast.Rd 2009-05-09 03:35:14 UTC (rev 1328)
+++ trunk/gmodels/man/fit.contrast.Rd 2009-05-09 04:00:15 UTC (rev 1329)
@@ -4,7 +4,7 @@
\alias{fit.contrast}
\alias{fit.contrast.lm}
\alias{fit.contrast.lme}
-\alias{fit.contrast.lmer}
+\alias{fit.contrast.mer}
\title{Compute and test arbitrary contrasts for regression objects}
\description{
Compute and test arbitrary contrasts for regression objects.
@@ -15,8 +15,8 @@
conf.int=NULL, df=FALSE, ...)
\method{fit.contrast}{lme}(model, varname, coeff, showall=FALSE,
conf.int=NULL, df=FALSE, ...)
-\method{fit.contrast}{lmer}(model, varname, coeff, showall=FALSE,
- conf.int=NULL, sim.lmer = TRUE, n.sim = 1000, ...)
+\method{fit.contrast}{mer}(model, varname, coeff, showall=FALSE,
+ conf.int=NULL, sim.mer = TRUE, n.sim = 1000, ...)
}
\arguments{
\item{model}{regression (lm,glm,aov,lme) object for which the
@@ -34,8 +34,8 @@
\item{df}{boolean indicating whether to return a column containing the
degrees of freedom.}
\item{\dots}{optional arguments provided by methods.}
- \item{sim.lmer}{Logical value. If TRUE p-values and confidence
- intervals will be estimated using \code{\Link[Matrix]{mcmcsamp}}. This option only takes effect for lmer
+ \item{sim.mer}{Logical value. If TRUE p-values and confidence
+ intervals will be estimated using \code{\Link[Matrix]{mcmcsamp}}. This option only takes effect for mer
objects.}
\item{n.sim}{Number of samples to use in \code{\Link[Matrix]{mcmcsamp}}.}
}
@@ -52,7 +52,7 @@
specified lower and upper confidence limits are also returned.}
\references{Venables & Ripley, Section 6.2}
-\author{ Gregory R. Warnes \email{wa...@bs...}}
+\author{ Gregory R. Warnes \email{gr...@ra...}}
\seealso{ \code{\link{lm}}, \code{\link{contrasts}},
\code{\link{contr.treatment}}, \code{\link{contr.poly}},
Modified: trunk/gmodels/man/glh.test.Rd
===================================================================
--- trunk/gmodels/man/glh.test.Rd 2009-05-09 03:35:14 UTC (rev 1328)
+++ trunk/gmodels/man/glh.test.Rd 2009-05-09 04:00:15 UTC (rev 1329)
@@ -67,7 +67,7 @@
}
\references{ R.H. Myers, Classical and Modern Regression with
Applications, 2nd Ed, 1990, p. 105}
-\author{Gregory R. Warnes \email{wa...@bs...} }
+\author{Gregory R. Warnes \email{gr...@ra...} }
\seealso{\code{\link{fit.contrast}}, \code{\link{estimable}},
\code{\link{contrasts}} }
\examples{
Modified: trunk/gmodels/man/make.contrasts.Rd
===================================================================
--- trunk/gmodels/man/make.contrasts.Rd 2009-05-09 03:35:14 UTC (rev 1328)
+++ trunk/gmodels/man/make.contrasts.Rd 2009-05-09 04:00:15 UTC (rev 1329)
@@ -31,7 +31,7 @@
\code{\link{contrasts}} or to the \code{contrasts} argument of model
functions (eg, \code{\link{lm}}).
}
-\author{ Gregory R. Warnes \email{wa...@bs...}}
+\author{ Gregory R. Warnes \email{gr...@ra...}}
\seealso{ \code{\link{lm}}, \code{\link{contrasts}},
\code{\link{contr.treatment}}, \code{\link{contr.poly}},
Computation and testing of General Linear Hypothesis:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 03:35:23
|
Revision: 1328
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1328&view=rev
Author: warnes
Date: 2009-05-09 03:35:14 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Escape $ in .Rd file to avoid latex issues
Modified Paths:
--------------
trunk/gtools/man/keywords.Rd
Modified: trunk/gtools/man/keywords.Rd
===================================================================
--- trunk/gtools/man/keywords.Rd 2009-05-09 03:26:19 UTC (rev 1327)
+++ trunk/gtools/man/keywords.Rd 2009-05-09 03:35:14 UTC (rev 1328)
@@ -11,7 +11,7 @@
\item{\dots}{Optional argumenst to pass to show.file()}
}
\details{
- This function simply determines the path $RHOME/doc/KEYWORDS and calls
+ This function simply determines the path \$RHOME/doc/KEYWORDS and calls
show.file() to display it.
}
\value{
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2009-05-09 03:26:35
|
Revision: 1327
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1327&view=rev
Author: warnes
Date: 2009-05-09 03:26:19 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Update NEWS and create softlinks for NEWS and ChangeLog in top level directory
Modified Paths:
--------------
trunk/gtools/inst/NEWS
Added Paths:
-----------
trunk/gtools/ChangeLog
trunk/gtools/NEWS
Added: trunk/gtools/ChangeLog
===================================================================
--- trunk/gtools/ChangeLog (rev 0)
+++ trunk/gtools/ChangeLog 2009-05-09 03:26:19 UTC (rev 1327)
@@ -0,0 +1 @@
+link inst/ChangeLog
\ No newline at end of file
Property changes on: trunk/gtools/ChangeLog
___________________________________________________________________
Added: svn:special
+ *
Added: trunk/gtools/NEWS
===================================================================
--- trunk/gtools/NEWS (rev 0)
+++ trunk/gtools/NEWS 2009-05-09 03:26:19 UTC (rev 1327)
@@ -0,0 +1 @@
+link inst/NEWS
\ No newline at end of file
Property changes on: trunk/gtools/NEWS
___________________________________________________________________
Added: svn:special
+ *
Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS 2009-05-09 03:15:10 UTC (rev 1326)
+++ trunk/gtools/inst/NEWS 2009-05-09 03:26:19 UTC (rev 1327)
@@ -1,3 +1,21 @@
+
+gtools 2.6.1
+------------
+
+New features:
+
+- Add newVersionAvailable() function to compare running and latest
+ available R versions.
+
+- Add keywords() function to show $RHOME/doc/KEYWORDS file
+
+Bug fixes:
+
+- Correct windows make flags as suggested by Brian Ripley.
+
+- Update Greg's email address and fix Rd syntax errors
+
+
gtools 2.5.0
------------
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
3 messages has been excluded from this view by a project administrator.
