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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:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2013-10-11 20:24:37
|
Revision: 1725
http://sourceforge.net/p/r-gregmisc/code/1725
Author: warnes
Date: 2013-10-11 20:24:34 +0000 (Fri, 11 Oct 2013)
Log Message:
-----------
Update files for gplots 2.12.0
Modified Paths:
--------------
trunk/gplots/DESCRIPTION
trunk/gplots/inst/NEWS
Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION 2013-10-11 20:19:22 UTC (rev 1724)
+++ trunk/gplots/DESCRIPTION 2013-10-11 20:24:34 UTC (rev 1725)
@@ -3,13 +3,13 @@
Description: Various R programming tools for plotting data
Depends: R (>= 3.0), gtools, gdata, stats, caTools, grid, KernSmooth,
MASS, datasets
-Recommends: grid
-Suggests: gtools
-Version: 2.11.3
-Date: 2013-06-27
+Suggests: gtools, grid
+Version: 2.12.0
+Date: 2013-10-11
Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert
Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin
Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill
Venables
Maintainer: Gregory R. Warnes <gr...@wa...>
License: GPL-2
+NeedsCompilation: No
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2013-10-11 20:19:22 UTC (rev 1724)
+++ trunk/gplots/inst/NEWS 2013-10-11 20:24:34 UTC (rev 1725)
@@ -1,3 +1,18 @@
+Release 2.11.4 - 2013-10-11
+---------------------------
+
+Enhancements:
+
+- Add heatmap.2() parameters to control row and column label rotation
+ ('srtRow', 'srtCol'), justification ('adjRow', 'adjCol'), and space
+ from plot edge ('offsetRow', 'offsetCol').
+
+Bug Fixes:
+
+- Fix bug in venn diagram code when number of TRUE cases in each
+ variable are equal.
+
+
Release 2.11.3 - 2013-06-27
---------------------------
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|
|
From: <wa...@us...> - 2013-10-11 20:19:25
|
Revision: 1724
http://sourceforge.net/p/r-gregmisc/code/1724
Author: warnes
Date: 2013-10-11 20:19:22 +0000 (Fri, 11 Oct 2013)
Log Message:
-----------
Add parameters to control row and column label positioning, rotation, justification, and offset.
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
trunk/gplots/man/heatmap.2.Rd
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2013-10-11 17:15:54 UTC (rev 1723)
+++ trunk/gplots/R/heatmap.2.R 2013-10-11 20:19:22 UTC (rev 1724)
@@ -52,6 +52,12 @@
cexCol = 0.2 + 1/log10(nc),
labRow = NULL,
labCol = NULL,
+ srtRow = NULL,
+ srtCol = NULL,
+ adjRow = c(0,NA),
+ adjCol = c(NA,0),
+ offsetRow = 0.5,
+ offsetCol = 0.5,
## color key + density info
key = TRUE,
@@ -389,10 +395,79 @@
col=na.color, add=TRUE)
}
- ## add labels
- axis(1, 1:nc, labels= labCol, las= 2, line= -0.5, tick= 0, cex.axis= cexCol)
+ ## add column labels
+ if(is.null(srtCol))
+ axis(1,
+ 1:nc,
+ labels= labCol,
+ las= 2,
+ line= -0.5 + offsetCol,
+ tick= 0,
+ cex.axis= cexCol,
+ hadj=adjCol[1],
+ padj=adjCol[2]
+ )
+ else
+ {
+ if(is.numeric(srtCol))
+ {
+ if(missing(adjCol) || is.null(adjCol))
+ adjCol=c(1,NA)
+
+ xpd.orig <- par("xpd")
+ par(xpd=NA)
+ xpos <- axis(1, 1:nc, labels=rep("", nc), las=2, tick=0)
+ text(x=xpos,
+ y=par("usr")[3] - (1.0 + offsetCol) * strheight("M"),
+ labels=labCol,
+ ##pos=1,
+ adj=adjCol,
+ cex=cexCol,
+ srt=srtCol)
+ par(xpd=xpd.orig)
+ }
+ else
+ warning("Invalid value for srtCol ignored.")
+ }
+
+ ## add row labels
+ if(is.null(srtRow))
+ {
+ axis(4,
+ iy,
+ labels=labRow,
+ las=2,
+ line=-0.5+offsetRow,
+ tick=0,
+ cex.axis=cexRow,
+ hadj=adjRow[1],
+ padj=adjRow[2]
+ )
+ }
+ else
+ {
+ if(is.numeric(srtRow))
+ {
+ xpd.orig <- par("xpd")
+ par(xpd=NA)
+ ypos <- axis(4, iy, labels=rep("", nr), las=2, line= -0.5, tick=0)
+ text(x=par("usr")[2] + (1.0 + offsetRow) * strwidth("M"),
+ y=ypos,
+ labels=labRow,
+ adj=adjRow,
+ cex=cexRow,
+ srt=srtRow
+ )
+ par(xpd=xpd.orig)
+ }
+ else
+ warning("Invalid value for srtRow ignored.")
+ }
+
+
+
+ ## add row and column headings (xlab, ylab)
if(!is.null(xlab)) mtext(xlab, side = 1, line = margins[1] - 1.25)
- axis(4, iy, labels= labRow, las= 2, line= -0.5, tick= 0, cex.axis= cexRow)
if(!is.null(ylab)) mtext(ylab, side = 4, line = margins[2] - 1.25)
## perform user-specified function
Modified: trunk/gplots/man/heatmap.2.Rd
===================================================================
--- trunk/gplots/man/heatmap.2.Rd 2013-10-11 17:15:54 UTC (rev 1723)
+++ trunk/gplots/man/heatmap.2.Rd 2013-10-11 20:19:22 UTC (rev 1724)
@@ -64,6 +64,12 @@
cexCol = 0.2 + 1/log10(nc),
labRow = NULL,
labCol = NULL,
+ srtRow = NULL,
+ srtCol = NULL,
+ adjRow = c(0,NA),
+ adjCol = c(NA,0),
+ offsetRow = 0.5,
+ offsetCol = 0.5,
# color key + density info
key = TRUE,
@@ -178,6 +184,12 @@
\item{labRow, labCol}{character vectors with row and column labels to
use; these default to \code{rownames(x)} or \code{colnames(x)},
respectively.}
+ \item{srtRow, srtCol}{angle of row/column labels, in degrees from horizontal}
+ \item{adjRow, adjCol}{2-element vector giving the (left-right,
+ top-bottom) justification of row/column labels (relative to the text
+ orientation).}
+ \item{offsetRow, offsetCol}{Number of character-width spaces to place
+ between row/column labels and the edge of the plotting region.}
% Color key and density info
\item{key}{logical indicating whether a color-key should be shown.}
\item{keysize}{numeric value indicating the size of the key}
@@ -302,6 +314,33 @@
heatmap.2(x, Rowv=NULL, dendrogram="both") ## generate warning!
heatmap.2(x, Colv=FALSE, dendrogram="both") ## generate warning!
+ ## Show effect of row and column label rotation
+ heatmap.2(x, srtCol=NULL)
+ heatmap.2(x, srtCol=0, adjCol = c(0.5,1) )
+ heatmap.2(x, srtCol=45, adjCol = c(1,1) )
+ heatmap.2(x, srtCol=135, adjCol = c(1,0) )
+ heatmap.2(x, srtCol=180, adjCol = c(0.5,0) )
+ heatmap.2(x, srtCol=225, adjCol = c(0,0) ) ## not very useful
+ heatmap.2(x, srtCol=270, adjCol = c(0,0.5) )
+ heatmap.2(x, srtCol=315, adjCol = c(0,1) )
+ heatmap.2(x, srtCol=360, adjCol = c(0.5,1) )
+
+ heatmap.2(x, srtRow=45, adjRow=c(0, 1) )
+ heatmap.2(x, srtRow=45, adjRow=c(0, 1), srtCol=45, adjCol=c(1,1) )
+ heatmap.2(x, srtRow=45, adjRow=c(0, 1), srtCol=270, adjCol=c(0,0.5) )
+
+ ## Show effect of offsetRow/offsetCol (only works when srtRow/srtCol is
+ ## not also present)
+ heatmap.2(x, offsetRow=0, offsetCol=0)
+ heatmap.2(x, offsetRow=1, offsetCol=1)
+ heatmap.2(x, offsetRow=2, offsetCol=2)
+ heatmap.2(x, offsetRow=-1, offsetCol=-1)
+
+ heatmap.2(x, srtRow=0, srtCol=90, offsetRow=0, offsetCol=0)
+ heatmap.2(x, srtRow=0, srtCol=90, offsetRow=1, offsetCol=1)
+ heatmap.2(x, srtRow=0, srtCol=90, offsetRow=2, offsetCol=2)
+ heatmap.2(x, srtRow=0, srtCol=90, offsetRow=-1, offsetCol=-1)
+
##
## Show effect of z-score scaling within columns, blue-red color scale
##
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|
|
From: <wa...@us...> - 2013-10-11 17:15:58
|
Revision: 1723
http://sourceforge.net/p/r-gregmisc/code/1723
Author: warnes
Date: 2013-10-11 17:15:54 +0000 (Fri, 11 Oct 2013)
Log Message:
-----------
Fix bug in getVennCounts.data.frame when number of TRUE cases in each variable are equal.
Modified Paths:
--------------
trunk/gplots/R/venn.R
Modified: trunk/gplots/R/venn.R
===================================================================
--- trunk/gplots/R/venn.R 2013-10-09 18:39:35 UTC (rev 1722)
+++ trunk/gplots/R/venn.R 2013-10-11 17:15:54 UTC (rev 1723)
@@ -22,7 +22,7 @@
if( !all(unique(unlist(l)) %in% c(0,1)) )
stop("Only indicator columns permitted")
- l <- sapply( l, function(x) which(as.logical(x)))
+ l <- lapply( l, function(x) which(as.logical(x)))
getVennCounts.list(l)
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2013-10-09 18:39:39
|
Revision: 1722
http://sourceforge.net/p/r-gregmisc/code/1722
Author: warnes
Date: 2013-10-09 18:39:35 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
Remove duplicate Imports field
Modified Paths:
--------------
trunk/SASxport/DESCRIPTION
Modified: trunk/SASxport/DESCRIPTION
===================================================================
--- trunk/SASxport/DESCRIPTION 2013-10-09 18:25:07 UTC (rev 1721)
+++ trunk/SASxport/DESCRIPTION 2013-10-09 18:39:35 UTC (rev 1722)
@@ -39,5 +39,4 @@
Maintainer: Gregory R. Warnes <gr...@wa...>
License: GPL-2
Depends: R (>= 2.4.0), chron
-Imports: chron
URL: http://www.warnes.net, http://metruminstitute.org
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2013-10-09 18:25:10
|
Revision: 1721
http://sourceforge.net/p/r-gregmisc/code/1721
Author: warnes
Date: 2013-10-09 18:25:07 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
Update examples
Modified Paths:
--------------
trunk/SASxport/tests/Alfalfa_Test.Rout.save
trunk/SASxport/tests/Theoph.Rout.save
trunk/SASxport/tests/cars.Rout.save
trunk/SASxport/tests/testDates.Rout.save
trunk/SASxport/tests/testDuplicateNames.Rout.save
trunk/SASxport/tests/testEmpty.Rout.save
trunk/SASxport/tests/testManyNames.Rout.save
trunk/SASxport/tests/testNegative.Rout.save
trunk/SASxport/tests/testNumeric.Rout.save
trunk/SASxport/tests/testUnnamedComponents.Rout.save
trunk/SASxport/tests/test_as_is.Rout.save
trunk/SASxport/tests/test_fields.Rout.save
trunk/SASxport/tests/xport.Rout.save
trunk/SASxport/tests/xxx.Rout.save
Modified: trunk/SASxport/tests/Alfalfa_Test.Rout.save
===================================================================
--- trunk/SASxport/tests/Alfalfa_Test.Rout.save 2013-10-09 18:20:23 UTC (rev 1720)
+++ trunk/SASxport/tests/Alfalfa_Test.Rout.save 2013-10-09 18:25:07 UTC (rev 1721)
@@ -19,8 +19,9 @@
> ## existing SAS xport file "Alfalfa.xpt"
>
> library(SASxport)
+Loading required package: chron
-Loaded SASxport version 1.3.5 (2013-06-14).
+Loaded SASxport version 1.3.6 (2013-10-09).
Type `?SASxport' for usage information.
@@ -47,4 +48,4 @@
>
> proc.time()
user system elapsed
- 0.956 0.092 1.147
+ 0.972 0.072 1.031
Modified: trunk/SASxport/tests/Theoph.Rout.save
===================================================================
--- trunk/SASxport/tests/Theoph.Rout.save 2013-10-09 18:20:23 UTC (rev 1720)
+++ trunk/SASxport/tests/Theoph.Rout.save 2013-10-09 18:25:07 UTC (rev 1721)
@@ -21,8 +21,9 @@
> ####
>
> library(SASxport)
+Loading required package: chron
-Loaded SASxport version 1.3.5 (2013-06-14).
+Loaded SASxport version 1.3.6 (2013-10-09).
Type `?SASxport' for usage information.
@@ -43,4 +44,4 @@
>
> proc.time()
user system elapsed
- 1.740 0.136 2.578
+ 1.656 0.112 1.878
Modified: trunk/SASxport/tests/cars.Rout.save
===================================================================
--- trunk/SASxport/tests/cars.Rout.save 2013-10-09 18:20:23 UTC (rev 1720)
+++ trunk/SASxport/tests/cars.Rout.save 2013-10-09 18:25:07 UTC (rev 1721)
@@ -16,8 +16,9 @@
Type 'q()' to quit R.
> library(SASxport)
+Loading required package: chron
-Loaded SASxport version 1.3.5 (2013-06-14).
+Loaded SASxport version 1.3.6 (2013-10-09).
Type `?SASxport' for usage information.
@@ -64,4 +65,4 @@
>
> proc.time()
user system elapsed
- 1.016 0.092 1.399
+ 0.972 0.084 1.074
Modified: trunk/SASxport/tests/testDates.Rout.save
===================================================================
--- trunk/SASxport/tests/testDates.Rout.save 2013-10-09 18:20:23 UTC (rev 1720)
+++ trunk/SASxport/tests/testDates.Rout.save 2013-10-09 18:25:07 UTC (rev 1721)
@@ -16,8 +16,9 @@
Type 'q()' to quit R.
> library(SASxport)
+Loading required package: chron
-Loaded SASxport version 1.3.5 (2013-06-14).
+Loaded SASxport version 1.3.6 (2013-10-09).
Type `?SASxport' for usage information.
@@ -62,4 +63,4 @@
>
> proc.time()
user system elapsed
- 1.176 0.080 1.532
+ 1.168 0.116 1.716
Modified: trunk/SASxport/tests/testDuplicateNames.Rout.save
===================================================================
--- trunk/SASxport/tests/testDuplicateNames.Rout.save 2013-10-09 18:20:23 UTC (rev 1720)
+++ trunk/SASxport/tests/testDuplicateNames.Rout.save 2013-10-09 18:25:07 UTC (rev 1721)
@@ -16,8 +16,9 @@
Type 'q()' to quit R.
> library(SASxport)
+Loading required package: chron
-Loaded SASxport version 1.3.5 (2013-06-14).
+Loaded SASxport version 1.3.6 (2013-10-09).
Type `?SASxport' for usage information.
@@ -26,79 +27,143 @@
> ##tests
> example(read.xport)
-rd.xpr> # -------
-rd.xpr> # SAS code to generate test dataset:
-rd.xpr> # -------
-rd.xpr> # libname y SASV5XPT "test2.xpt";
-rd.xpr> #
-rd.xpr> # PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;
-rd.xpr> # PROC FORMAT CNTLOUT=format;RUN; * Name, e.g. 'format', unimportant;
-rd.xpr> # data test;
-rd.xpr> # LENGTH race 3 age 4;
-rd.xpr> # age=30; label age="Age at Beginning of Study";
-rd.xpr> # race=2;
-rd.xpr> # d1='3mar2002'd ;
-rd.xpr> # dt1='3mar2002 9:31:02'dt;
-rd.xpr> # t1='11:13:45't;
-rd.xpr> # output;
-rd.xpr> #
-rd.xpr> # age=31;
-rd.xpr> # race=4;
-rd.xpr> # d1='3jun2002'd ;
-rd.xpr> # dt1='3jun2002 9:42:07'dt;
-rd.xpr> # t1='11:14:13't;
-rd.xpr> # output;
-rd.xpr> # format d1 mmddyy10. dt1 datetime. t1 time. race race.;
-rd.xpr> # run;
-rd.xpr> # data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;
-rd.xpr> # DO i=1 TO 100;
-rd.xpr> # x3=ranuni(3);
-rd.xpr> # x4=ranuni(5);
-rd.xpr> # x5=ranuni(7);
-rd.xpr> # x6=ranuni(9);
-rd.xpr> # x7=ranuni(11);
-rd.xpr> # x8=ranuni(13);
-rd.xpr> # output;
-rd.xpr> # END;
-rd.xpr> # DROP i;
-rd.xpr> # RUN;
-rd.xpr> # PROC MEANS; RUN;
-rd.xpr> # PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;
-rd.xpr> # ------
+rd.xpr> ## -------
+rd.xpr> ## SAS code to generate test dataset:
+rd.xpr> ## -------
+rd.xpr> ## libname y SASV5XPT "test2.xpt";
+rd.xpr> ##
+rd.xpr> ## PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;
+rd.xpr> ## PROC FORMAT CNTLOUT=format;RUN; * Name, e.g. 'format', unimportant;
+rd.xpr> ## data test;
+rd.xpr> ## LENGTH race 3 age 4;
+rd.xpr> ## age=30; label age="Age at Beginning of Study";
+rd.xpr> ## race=2;
+rd.xpr> ## d1='3mar2002'd ;
+rd.xpr> ## dt1='3mar2002 9:31:02'dt;
+rd.xpr> ## t1='11:13:45't;
+rd.xpr> ## output;
+rd.xpr> ##
+rd.xpr> ## age=31;
+rd.xpr> ## race=4;
+rd.xpr> ## d1='3jun2002'd ;
+rd.xpr> ## dt1='3jun2002 9:42:07'dt;
+rd.xpr> ## t1='11:14:13't;
+rd.xpr> ## output;
+rd.xpr> ## format d1 mmddyy10. dt1 datetime. t1 time. race race.;
+rd.xpr> ## run;
+rd.xpr> ## data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;
+rd.xpr> ## DO i=1 TO 100;
+rd.xpr> ## x3=ranuni(3);
+rd.xpr> ## x4=ranuni(5);
+rd.xpr> ## x5=ranuni(7);
+rd.xpr> ## x6=ranuni(9);
+rd.xpr> ## x7=ranuni(11);
+rd.xpr> ## x8=ranuni(13);
+rd.xpr> ## output;
+rd.xpr> ## END;
+rd.xpr> ## DROP i;
+rd.xpr> ## RUN;
+rd.xpr> ## PROC MEANS; RUN;
+rd.xpr> ## PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;
+rd.xpr> ## ------
rd.xpr>
-rd.xpr> # Read this dataset from a local file:
+rd.xpr> ## Read this dataset from a local file:
+rd.xpr> testFile <- system.file('extdata', 'test2.xpt', package="SASxport")
+
+rd.xpr> w <- read.xport(testFile)
+
+rd.xpr> class(w)
+[1] "list"
+
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
+
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
+
+
rd.xpr> ## Not run:
-rd.xpr> ##D w <- read.xport('test2.xpt')
+rd.xpr> ##D ## Or read a copy of test2.xpt available on the web:
+rd.xpr> ##D url <- 'http://biostat.mc.vanderbilt.edu/wiki/pub/Main/Hmisc/test2.xpt'
+rd.xpr> ##D w <- read.xport(url)
rd.xpr> ## End(Not run)
rd.xpr>
-rd.xpr> # Or read a copy of test2.xpt available on the web:
-rd.xpr> host <- 'http://biostat.mc.vanderbilt.edu'
+rd.xpr> ## We can also get the dataset wrapped in a list
+rd.xpr> w <- read.xport(testFile, as.list=TRUE)
-rd.xpr> path <- '/cgi-bin/viewvc.cgi/*checkout*/Hmisc/trunk/tests/test2.xpt'
+rd.xpr> class(w)
+[1] "list"
-rd.xpr> url <- paste(host,path,sep="")
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
-rd.xpr> w <- read.xport(url)
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
-rd.xpr> # We can also get the dataset wrapped in a list
-rd.xpr> w <- read.xport(url, as.list=TRUE)
-rd.xpr> # And we can ask for the format information to be included as well.
-rd.xpr> w <- read.xport(url, as.list=TRUE, include.formats=TRUE)
+rd.xpr> ## And we can ask for the format information to be included as well.
+rd.xpr> w <- read.xport(testFile, as.list=TRUE, include.formats=TRUE)
+rd.xpr> class(w)
+[1] "list"
+
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
+
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
+
+$FORMATS
+ FMTNAME START END LABEL MIN MAX DEFAULT LENGTH FUZZ
+1 RACE 1 1 green 1 40 6 6 1e-12
+2 RACE 2 2 blue 1 40 6 6 1e-12
+3 RACE 3 3 purple 1 40 6 6 1e-12
+ PREFIX MULT FILL NOEDIT TYPE SEXCL EEXCL HLO DECSEP DIG3SEP DATATYPE LANGUAGE
+1 0 0 N N N
+2 0 0 N N N
+3 0 0 N N N
+
+
rd.xpr> ## Don't show:
-rd.xpr> SASxport:::assert( is.data.frame(w)==FALSE && is.list(w)==TRUE )
+rd.xpr> stopifnot( is.data.frame(w)==FALSE && is.list(w)==TRUE )
rd.xpr> ## End Don't show
rd.xpr>
rd.xpr>
rd.xpr> ## Not run:
-rd.xpr> ##D ## The Hmisc library provides many useful functions for interacting with
-rd.xpr> ##D ## data imported from SAS via read.xport()
+rd.xpr> ##D #### The Hmisc library provides many useful functions for interacting with
+rd.xpr> ##D #### data imported from SAS via read.xport()
rd.xpr> ##D library(Hmisc)
rd.xpr> ##D
rd.xpr> ##D describe(w$test) # see labels, format names for dataset test
-rd.xpr> ##D lapply(w, describe)# see descriptive stats in more detaiil for each variable
+rd.xpr> ##D lapply(w, describe)# see descriptive stats in more detail for each variable
rd.xpr> ##D
rd.xpr> ##D contents(w$test) # another way to see variable attributes
rd.xpr> ##D lapply(w, contents)# show contents of individual items in more detail
@@ -155,4 +220,4 @@
>
> proc.time()
user system elapsed
- 1.392 0.152 3.531
+ 1.480 0.176 1.791
Modified: trunk/SASxport/tests/testEmpty.Rout.save
===================================================================
--- trunk/SASxport/tests/testEmpty.Rout.save 2013-10-09 18:20:23 UTC (rev 1720)
+++ trunk/SASxport/tests/testEmpty.Rout.save 2013-10-09 18:25:07 UTC (rev 1721)
@@ -16,8 +16,9 @@
Type 'q()' to quit R.
> library(SASxport)
+Loading required package: chron
-Loaded SASxport version 1.3.5 (2013-06-14).
+Loaded SASxport version 1.3.6 (2013-10-09).
Type `?SASxport' for usage information.
@@ -70,4 +71,4 @@
>
> proc.time()
user system elapsed
- 1.344 0.120 1.715
+ 1.332 0.136 1.949
Modified: trunk/SASxport/tests/testManyNames.Rout.save
===================================================================
--- trunk/SASxport/tests/testManyNames.Rout.save 2013-10-09 18:20:23 UTC (rev 1720)
+++ trunk/SASxport/tests/testManyNames.Rout.save 2013-10-09 18:25:07 UTC (rev 1721)
@@ -16,8 +16,9 @@
Type 'q()' to quit R.
> library(SASxport)
+Loading required package: chron
-Loaded SASxport version 1.3.5 (2013-06-14).
+Loaded SASxport version 1.3.6 (2013-10-09).
Type `?SASxport' for usage information.
@@ -95,4 +96,4 @@
>
> proc.time()
user system elapsed
- 19.368 0.216 20.394
+ 19.200 0.208 19.802
Modified: trunk/SASxport/tests/testNegative.Rout.save
===================================================================
--- trunk/SASxport/tests/testNegative.Rout.save 2013-10-09 18:20:23 UTC (rev 1720)
+++ trunk/SASxport/tests/testNegative.Rout.save 2013-10-09 18:25:07 UTC (rev 1721)
@@ -16,8 +16,9 @@
Type 'q()' to quit R.
> library(SASxport)
+Loading required package: chron
-Loaded SASxport version 1.3.5 (2013-06-14).
+Loaded SASxport version 1.3.6 (2013-10-09).
Type `?SASxport' for usage information.
@@ -48,4 +49,4 @@
>
> proc.time()
user system elapsed
- 1.312 0.044 1.360
+ 1.300 0.128 1.982
Modified: trunk/SASxport/tests/testNumeric.Rout.save
===================================================================
--- trunk/SASxport/tests/testNumeric.Rout.save 2013-10-09 18:20:23 UTC (rev 1720)
+++ trunk/SASxport/tests/testNumeric.Rout.save 2013-10-09 18:25:07 UTC (rev 1721)
@@ -16,8 +16,9 @@
Type 'q()' to quit R.
> library(SASxport)
+Loading required package: chron
-Loaded SASxport version 1.3.5 (2013-06-14).
+Loaded SASxport version 1.3.6 (2013-10-09).
Type `?SASxport' for usage information.
@@ -87,4 +88,4 @@
>
> proc.time()
user system elapsed
- 1.572 0.104 1.713
+ 1.636 0.104 1.856
Modified: trunk/SASxport/tests/testUnnamedComponents.Rout.save
===================================================================
--- trunk/SASxport/tests/testUnnamedComponents.Rout.save 2013-10-09 18:20:23 UTC (rev 1720)
+++ trunk/SASxport/tests/testUnnamedComponents.Rout.save 2013-10-09 18:25:07 UTC (rev 1721)
@@ -16,8 +16,9 @@
Type 'q()' to quit R.
> library(SASxport)
+Loading required package: chron
-Loaded SASxport version 1.3.5 (2013-06-14).
+Loaded SASxport version 1.3.6 (2013-10-09).
Type `?SASxport' for usage information.
@@ -26,79 +27,143 @@
> ##tests
> example(read.xport)
-rd.xpr> # -------
-rd.xpr> # SAS code to generate test dataset:
-rd.xpr> # -------
-rd.xpr> # libname y SASV5XPT "test2.xpt";
-rd.xpr> #
-rd.xpr> # PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;
-rd.xpr> # PROC FORMAT CNTLOUT=format;RUN; * Name, e.g. 'format', unimportant;
-rd.xpr> # data test;
-rd.xpr> # LENGTH race 3 age 4;
-rd.xpr> # age=30; label age="Age at Beginning of Study";
-rd.xpr> # race=2;
-rd.xpr> # d1='3mar2002'd ;
-rd.xpr> # dt1='3mar2002 9:31:02'dt;
-rd.xpr> # t1='11:13:45't;
-rd.xpr> # output;
-rd.xpr> #
-rd.xpr> # age=31;
-rd.xpr> # race=4;
-rd.xpr> # d1='3jun2002'd ;
-rd.xpr> # dt1='3jun2002 9:42:07'dt;
-rd.xpr> # t1='11:14:13't;
-rd.xpr> # output;
-rd.xpr> # format d1 mmddyy10. dt1 datetime. t1 time. race race.;
-rd.xpr> # run;
-rd.xpr> # data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;
-rd.xpr> # DO i=1 TO 100;
-rd.xpr> # x3=ranuni(3);
-rd.xpr> # x4=ranuni(5);
-rd.xpr> # x5=ranuni(7);
-rd.xpr> # x6=ranuni(9);
-rd.xpr> # x7=ranuni(11);
-rd.xpr> # x8=ranuni(13);
-rd.xpr> # output;
-rd.xpr> # END;
-rd.xpr> # DROP i;
-rd.xpr> # RUN;
-rd.xpr> # PROC MEANS; RUN;
-rd.xpr> # PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;
-rd.xpr> # ------
+rd.xpr> ## -------
+rd.xpr> ## SAS code to generate test dataset:
+rd.xpr> ## -------
+rd.xpr> ## libname y SASV5XPT "test2.xpt";
+rd.xpr> ##
+rd.xpr> ## PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;
+rd.xpr> ## PROC FORMAT CNTLOUT=format;RUN; * Name, e.g. 'format', unimportant;
+rd.xpr> ## data test;
+rd.xpr> ## LENGTH race 3 age 4;
+rd.xpr> ## age=30; label age="Age at Beginning of Study";
+rd.xpr> ## race=2;
+rd.xpr> ## d1='3mar2002'd ;
+rd.xpr> ## dt1='3mar2002 9:31:02'dt;
+rd.xpr> ## t1='11:13:45't;
+rd.xpr> ## output;
+rd.xpr> ##
+rd.xpr> ## age=31;
+rd.xpr> ## race=4;
+rd.xpr> ## d1='3jun2002'd ;
+rd.xpr> ## dt1='3jun2002 9:42:07'dt;
+rd.xpr> ## t1='11:14:13't;
+rd.xpr> ## output;
+rd.xpr> ## format d1 mmddyy10. dt1 datetime. t1 time. race race.;
+rd.xpr> ## run;
+rd.xpr> ## data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;
+rd.xpr> ## DO i=1 TO 100;
+rd.xpr> ## x3=ranuni(3);
+rd.xpr> ## x4=ranuni(5);
+rd.xpr> ## x5=ranuni(7);
+rd.xpr> ## x6=ranuni(9);
+rd.xpr> ## x7=ranuni(11);
+rd.xpr> ## x8=ranuni(13);
+rd.xpr> ## output;
+rd.xpr> ## END;
+rd.xpr> ## DROP i;
+rd.xpr> ## RUN;
+rd.xpr> ## PROC MEANS; RUN;
+rd.xpr> ## PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;
+rd.xpr> ## ------
rd.xpr>
-rd.xpr> # Read this dataset from a local file:
+rd.xpr> ## Read this dataset from a local file:
+rd.xpr> testFile <- system.file('extdata', 'test2.xpt', package="SASxport")
+
+rd.xpr> w <- read.xport(testFile)
+
+rd.xpr> class(w)
+[1] "list"
+
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
+
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
+
+
rd.xpr> ## Not run:
-rd.xpr> ##D w <- read.xport('test2.xpt')
+rd.xpr> ##D ## Or read a copy of test2.xpt available on the web:
+rd.xpr> ##D url <- 'http://biostat.mc.vanderbilt.edu/wiki/pub/Main/Hmisc/test2.xpt'
+rd.xpr> ##D w <- read.xport(url)
rd.xpr> ## End(Not run)
rd.xpr>
-rd.xpr> # Or read a copy of test2.xpt available on the web:
-rd.xpr> host <- 'http://biostat.mc.vanderbilt.edu'
+rd.xpr> ## We can also get the dataset wrapped in a list
+rd.xpr> w <- read.xport(testFile, as.list=TRUE)
-rd.xpr> path <- '/cgi-bin/viewvc.cgi/*checkout*/Hmisc/trunk/tests/test2.xpt'
+rd.xpr> class(w)
+[1] "list"
-rd.xpr> url <- paste(host,path,sep="")
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
-rd.xpr> w <- read.xport(url)
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
-rd.xpr> # We can also get the dataset wrapped in a list
-rd.xpr> w <- read.xport(url, as.list=TRUE)
-rd.xpr> # And we can ask for the format information to be included as well.
-rd.xpr> w <- read.xport(url, as.list=TRUE, include.formats=TRUE)
+rd.xpr> ## And we can ask for the format information to be included as well.
+rd.xpr> w <- read.xport(testFile, as.list=TRUE, include.formats=TRUE)
+rd.xpr> class(w)
+[1] "list"
+
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
+
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
+
+$FORMATS
+ FMTNAME START END LABEL MIN MAX DEFAULT LENGTH FUZZ
+1 RACE 1 1 green 1 40 6 6 1e-12
+2 RACE 2 2 blue 1 40 6 6 1e-12
+3 RACE 3 3 purple 1 40 6 6 1e-12
+ PREFIX MULT FILL NOEDIT TYPE SEXCL EEXCL HLO DECSEP DIG3SEP DATATYPE LANGUAGE
+1 0 0 N N N
+2 0 0 N N N
+3 0 0 N N N
+
+
rd.xpr> ## Don't show:
-rd.xpr> SASxport:::assert( is.data.frame(w)==FALSE && is.list(w)==TRUE )
+rd.xpr> stopifnot( is.data.frame(w)==FALSE && is.list(w)==TRUE )
rd.xpr> ## End Don't show
rd.xpr>
rd.xpr>
rd.xpr> ## Not run:
-rd.xpr> ##D ## The Hmisc library provides many useful functions for interacting with
-rd.xpr> ##D ## data imported from SAS via read.xport()
+rd.xpr> ##D #### The Hmisc library provides many useful functions for interacting with
+rd.xpr> ##D #### data imported from SAS via read.xport()
rd.xpr> ##D library(Hmisc)
rd.xpr> ##D
rd.xpr> ##D describe(w$test) # see labels, format names for dataset test
-rd.xpr> ##D lapply(w, describe)# see descriptive stats in more detaiil for each variable
+rd.xpr> ##D lapply(w, describe)# see descriptive stats in more detail for each variable
rd.xpr> ##D
rd.xpr> ##D contents(w$test) # another way to see variable attributes
rd.xpr> ##D lapply(w, contents)# show contents of individual items in more detail
@@ -1401,79 +1466,143 @@
> # Check with different list construction function *name*
> example(read.xport)
-rd.xpr> # -------
-rd.xpr> # SAS code to generate test dataset:
-rd.xpr> # -------
-rd.xpr> # libname y SASV5XPT "test2.xpt";
-rd.xpr> #
-rd.xpr> # PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;
-rd.xpr> # PROC FORMAT CNTLOUT=format;RUN; * Name, e.g. 'format', unimportant;
-rd.xpr> # data test;
-rd.xpr> # LENGTH race 3 age 4;
-rd.xpr> # age=30; label age="Age at Beginning of Study";
-rd.xpr> # race=2;
-rd.xpr> # d1='3mar2002'd ;
-rd.xpr> # dt1='3mar2002 9:31:02'dt;
-rd.xpr> # t1='11:13:45't;
-rd.xpr> # output;
-rd.xpr> #
-rd.xpr> # age=31;
-rd.xpr> # race=4;
-rd.xpr> # d1='3jun2002'd ;
-rd.xpr> # dt1='3jun2002 9:42:07'dt;
-rd.xpr> # t1='11:14:13't;
-rd.xpr> # output;
-rd.xpr> # format d1 mmddyy10. dt1 datetime. t1 time. race race.;
-rd.xpr> # run;
-rd.xpr> # data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;
-rd.xpr> # DO i=1 TO 100;
-rd.xpr> # x3=ranuni(3);
-rd.xpr> # x4=ranuni(5);
-rd.xpr> # x5=ranuni(7);
-rd.xpr> # x6=ranuni(9);
-rd.xpr> # x7=ranuni(11);
-rd.xpr> # x8=ranuni(13);
-rd.xpr> # output;
-rd.xpr> # END;
-rd.xpr> # DROP i;
-rd.xpr> # RUN;
-rd.xpr> # PROC MEANS; RUN;
-rd.xpr> # PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;
-rd.xpr> # ------
+rd.xpr> ## -------
+rd.xpr> ## SAS code to generate test dataset:
+rd.xpr> ## -------
+rd.xpr> ## libname y SASV5XPT "test2.xpt";
+rd.xpr> ##
+rd.xpr> ## PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;
+rd.xpr> ## PROC FORMAT CNTLOUT=format;RUN; * Name, e.g. 'format', unimportant;
+rd.xpr> ## data test;
+rd.xpr> ## LENGTH race 3 age 4;
+rd.xpr> ## age=30; label age="Age at Beginning of Study";
+rd.xpr> ## race=2;
+rd.xpr> ## d1='3mar2002'd ;
+rd.xpr> ## dt1='3mar2002 9:31:02'dt;
+rd.xpr> ## t1='11:13:45't;
+rd.xpr> ## output;
+rd.xpr> ##
+rd.xpr> ## age=31;
+rd.xpr> ## race=4;
+rd.xpr> ## d1='3jun2002'd ;
+rd.xpr> ## dt1='3jun2002 9:42:07'dt;
+rd.xpr> ## t1='11:14:13't;
+rd.xpr> ## output;
+rd.xpr> ## format d1 mmddyy10. dt1 datetime. t1 time. race race.;
+rd.xpr> ## run;
+rd.xpr> ## data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;
+rd.xpr> ## DO i=1 TO 100;
+rd.xpr> ## x3=ranuni(3);
+rd.xpr> ## x4=ranuni(5);
+rd.xpr> ## x5=ranuni(7);
+rd.xpr> ## x6=ranuni(9);
+rd.xpr> ## x7=ranuni(11);
+rd.xpr> ## x8=ranuni(13);
+rd.xpr> ## output;
+rd.xpr> ## END;
+rd.xpr> ## DROP i;
+rd.xpr> ## RUN;
+rd.xpr> ## PROC MEANS; RUN;
+rd.xpr> ## PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;
+rd.xpr> ## ------
rd.xpr>
-rd.xpr> # Read this dataset from a local file:
+rd.xpr> ## Read this dataset from a local file:
+rd.xpr> testFile <- system.file('extdata', 'test2.xpt', package="SASxport")
+
+rd.xpr> w <- read.xport(testFile)
+
+rd.xpr> class(w)
+[1] "list"
+
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
+
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
+
+
rd.xpr> ## Not run:
-rd.xpr> ##D w <- read.xport('test2.xpt')
+rd.xpr> ##D ## Or read a copy of test2.xpt available on the web:
+rd.xpr> ##D url <- 'http://biostat.mc.vanderbilt.edu/wiki/pub/Main/Hmisc/test2.xpt'
+rd.xpr> ##D w <- read.xport(url)
rd.xpr> ## End(Not run)
rd.xpr>
-rd.xpr> # Or read a copy of test2.xpt available on the web:
-rd.xpr> host <- 'http://biostat.mc.vanderbilt.edu'
+rd.xpr> ## We can also get the dataset wrapped in a list
+rd.xpr> w <- read.xport(testFile, as.list=TRUE)
-rd.xpr> path <- '/cgi-bin/viewvc.cgi/*checkout*/Hmisc/trunk/tests/test2.xpt'
+rd.xpr> class(w)
+[1] "list"
-rd.xpr> url <- paste(host,path,sep="")
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
-rd.xpr> w <- read.xport(url)
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
-rd.xpr> # We can also get the dataset wrapped in a list
-rd.xpr> w <- read.xport(url, as.list=TRUE)
-rd.xpr> # And we can ask for the format information to be included as well.
-rd.xpr> w <- read.xport(url, as.list=TRUE, include.formats=TRUE)
+rd.xpr> ## And we can ask for the format information to be included as well.
+rd.xpr> w <- read.xport(testFile, as.list=TRUE, include.formats=TRUE)
+rd.xpr> class(w)
+[1] "list"
+
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
+
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
+
+$FORMATS
+ FMTNAME START END LABEL MIN MAX DEFAULT LENGTH FUZZ
+1 RACE 1 1 green 1 40 6 6 1e-12
+2 RACE 2 2 blue 1 40 6 6 1e-12
+3 RACE 3 3 purple 1 40 6 6 1e-12
+ PREFIX MULT FILL NOEDIT TYPE SEXCL EEXCL HLO DECSEP DIG3SEP DATATYPE LANGUAGE
+1 0 0 N N N
+2 0 0 N N N
+3 0 0 N N N
+
+
rd.xpr> ## Don't show:
-rd.xpr> SASxport:::assert( is.data.frame(w)==FALSE && is.list(w)==TRUE )
+rd.xpr> stopifnot( is.data.frame(w)==FALSE && is.list(w)==TRUE )
rd.xpr> ## End Don't show
rd.xpr>
rd.xpr>
rd.xpr> ## Not run:
-rd.xpr> ##D ## The Hmisc library provides many useful functions for interacting with
-rd.xpr> ##D ## data imported from SAS via read.xport()
+rd.xpr> ##D #### The Hmisc library provides many useful functions for interacting with
+rd.xpr> ##D #### data imported from SAS via read.xport()
rd.xpr> ##D library(Hmisc)
rd.xpr> ##D
rd.xpr> ##D describe(w$test) # see labels, format names for dataset test
-rd.xpr> ##D lapply(w, describe)# see descriptive stats in more detaiil for each variable
+rd.xpr> ##D lapply(w, describe)# see descriptive stats in more detail for each variable
rd.xpr> ##D
rd.xpr> ##D contents(w$test) # another way to see variable attributes
rd.xpr> ##D lapply(w, contents)# show contents of individual items in more detail
@@ -1639,79 +1768,143 @@
> # remove names
> example(read.xport)
-rd.xpr> # -------
-rd.xpr> # SAS code to generate test dataset:
-rd.xpr> # -------
-rd.xpr> # libname y SASV5XPT "test2.xpt";
-rd.xpr> #
-rd.xpr> # PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;
-rd.xpr> # PROC FORMAT CNTLOUT=format;RUN; * Name, e.g. 'format', unimportant;
-rd.xpr> # data test;
-rd.xpr> # LENGTH race 3 age 4;
-rd.xpr> # age=30; label age="Age at Beginning of Study";
-rd.xpr> # race=2;
-rd.xpr> # d1='3mar2002'd ;
-rd.xpr> # dt1='3mar2002 9:31:02'dt;
-rd.xpr> # t1='11:13:45't;
-rd.xpr> # output;
-rd.xpr> #
-rd.xpr> # age=31;
-rd.xpr> # race=4;
-rd.xpr> # d1='3jun2002'd ;
-rd.xpr> # dt1='3jun2002 9:42:07'dt;
-rd.xpr> # t1='11:14:13't;
-rd.xpr> # output;
-rd.xpr> # format d1 mmddyy10. dt1 datetime. t1 time. race race.;
-rd.xpr> # run;
-rd.xpr> # data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;
-rd.xpr> # DO i=1 TO 100;
-rd.xpr> # x3=ranuni(3);
-rd.xpr> # x4=ranuni(5);
-rd.xpr> # x5=ranuni(7);
-rd.xpr> # x6=ranuni(9);
-rd.xpr> # x7=ranuni(11);
-rd.xpr> # x8=ranuni(13);
-rd.xpr> # output;
-rd.xpr> # END;
-rd.xpr> # DROP i;
-rd.xpr> # RUN;
-rd.xpr> # PROC MEANS; RUN;
-rd.xpr> # PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;
-rd.xpr> # ------
+rd.xpr> ## -------
+rd.xpr> ## SAS code to generate test dataset:
+rd.xpr> ## -------
+rd.xpr> ## libname y SASV5XPT "test2.xpt";
+rd.xpr> ##
+rd.xpr> ## PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;
+rd.xpr> ## PROC FORMAT CNTLOUT=format;RUN; * Name, e.g. 'format', unimportant;
+rd.xpr> ## data test;
+rd.xpr> ## LENGTH race 3 age 4;
+rd.xpr> ## age=30; label age="Age at Beginning of Study";
+rd.xpr> ## race=2;
+rd.xpr> ## d1='3mar2002'd ;
+rd.xpr> ## dt1='3mar2002 9:31:02'dt;
+rd.xpr> ## t1='11:13:45't;
+rd.xpr> ## output;
+rd.xpr> ##
+rd.xpr> ## age=31;
+rd.xpr> ## race=4;
+rd.xpr> ## d1='3jun2002'd ;
+rd.xpr> ## dt1='3jun2002 9:42:07'dt;
+rd.xpr> ## t1='11:14:13't;
+rd.xpr> ## output;
+rd.xpr> ## format d1 mmddyy10. dt1 datetime. t1 time. race race.;
+rd.xpr> ## run;
+rd.xpr> ## data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;
+rd.xpr> ## DO i=1 TO 100;
+rd.xpr> ## x3=ranuni(3);
+rd.xpr> ## x4=ranuni(5);
+rd.xpr> ## x5=ranuni(7);
+rd.xpr> ## x6=ranuni(9);
+rd.xpr> ## x7=ranuni(11);
+rd.xpr> ## x8=ranuni(13);
+rd.xpr> ## output;
+rd.xpr> ## END;
+rd.xpr> ## DROP i;
+rd.xpr> ## RUN;
+rd.xpr> ## PROC MEANS; RUN;
+rd.xpr> ## PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;
+rd.xpr> ## ------
rd.xpr>
-rd.xpr> # Read this dataset from a local file:
+rd.xpr> ## Read this dataset from a local file:
+rd.xpr> testFile <- system.file('extdata', 'test2.xpt', package="SASxport")
+
+rd.xpr> w <- read.xport(testFile)
+
+rd.xpr> class(w)
+[1] "list"
+
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
+
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
+
+
rd.xpr> ## Not run:
-rd.xpr> ##D w <- read.xport('test2.xpt')
+rd.xpr> ##D ## Or read a copy of test2.xpt available on the web:
+rd.xpr> ##D url <- 'http://biostat.mc.vanderbilt.edu/wiki/pub/Main/Hmisc/test2.xpt'
+rd.xpr> ##D w <- read.xport(url)
rd.xpr> ## End(Not run)
rd.xpr>
-rd.xpr> # Or read a copy of test2.xpt available on the web:
-rd.xpr> host <- 'http://biostat.mc.vanderbilt.edu'
+rd.xpr> ## We can also get the dataset wrapped in a list
+rd.xpr> w <- read.xport(testFile, as.list=TRUE)
-rd.xpr> path <- '/cgi-bin/viewvc.cgi/*checkout*/Hmisc/trunk/tests/test2.xpt'
+rd.xpr> class(w)
+[1] "list"
-rd.xpr> url <- paste(host,path,sep="")
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
-rd.xpr> w <- read.xport(url)
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
-rd.xpr> # We can also get the dataset wrapped in a list
-rd.xpr> w <- read.xport(url, as.list=TRUE)
-rd.xpr> # And we can ask for the format information to be included as well.
-rd.xpr> w <- read.xport(url, as.list=TRUE, include.formats=TRUE)
+rd.xpr> ## And we can ask for the format information to be included as well.
+rd.xpr> w <- read.xport(testFile, as.list=TRUE, include.formats=TRUE)
+rd.xpr> class(w)
+[1] "list"
+
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
+
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
+
+$FORMATS
+ FMTNAME START END LABEL MIN MAX DEFAULT LENGTH FUZZ
+1 RACE 1 1 green 1 40 6 6 1e-12
+2 RACE 2 2 blue 1 40 6 6 1e-12
+3 RACE 3 3 purple 1 40 6 6 1e-12
+ PREFIX MULT FILL NOEDIT TYPE SEXCL EEXCL HLO DECSEP DIG3SEP DATATYPE LANGUAGE
+1 0 0 N N N
+2 0 0 N N N
+3 0 0 N N N
+
+
rd.xpr> ## Don't show:
-rd.xpr> SASxport:::assert( is.data.frame(w)==FALSE && is.list(w)==TRUE )
+rd.xpr> stopifnot( is.data.frame(w)==FALSE && is.list(w)==TRUE )
rd.xpr> ## End Don't show
rd.xpr>
rd.xpr>
rd.xpr> ## Not run:
-rd.xpr> ##D ## The Hmisc library provides many useful functions for interacting with
-rd.xpr> ##D ## data imported from SAS via read.xport()
+rd.xpr> ##D #### The Hmisc library provides many useful functions for interacting with
+rd.xpr> ##D #### data imported from SAS via read.xport()
rd.xpr> ##D library(Hmisc)
rd.xpr> ##D
rd.xpr> ##D describe(w$test) # see labels, format names for dataset test
-rd.xpr> ##D lapply(w, describe)# see descriptive stats in more detaiil for each variable
+rd.xpr> ##D lapply(w, describe)# see descriptive stats in more detail for each variable
rd.xpr> ##D
rd.xpr> ##D contents(w$test) # another way to see variable attributes
rd.xpr> ##D lapply(w, contents)# show contents of individual items in more detail
@@ -1879,79 +2072,143 @@
> # remove variable names
> example(read.xport)
-rd.xpr> # -------
-rd.xpr> # SAS code to generate test dataset:
-rd.xpr> # -------
-rd.xpr> # libname y SASV5XPT "test2.xpt";
-rd.xpr> #
-rd.xpr> # PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;
-rd.xpr> # PROC FORMAT CNTLOUT=format;RUN; * Name, e.g. 'format', unimportant;
-rd.xpr> # data test;
-rd.xpr> # LENGTH race 3 age 4;
-rd.xpr> # age=30; label age="Age at Beginning of Study";
-rd.xpr> # race=2;
-rd.xpr> # d1='3mar2002'd ;
-rd.xpr> # dt1='3mar2002 9:31:02'dt;
-rd.xpr> # t1='11:13:45't;
-rd.xpr> # output;
-rd.xpr> #
-rd.xpr> # age=31;
-rd.xpr> # race=4;
-rd.xpr> # d1='3jun2002'd ;
-rd.xpr> # dt1='3jun2002 9:42:07'dt;
-rd.xpr> # t1='11:14:13't;
-rd.xpr> # output;
-rd.xpr> # format d1 mmddyy10. dt1 datetime. t1 time. race race.;
-rd.xpr> # run;
-rd.xpr> # data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;
-rd.xpr> # DO i=1 TO 100;
-rd.xpr> # x3=ranuni(3);
-rd.xpr> # x4=ranuni(5);
-rd.xpr> # x5=ranuni(7);
-rd.xpr> # x6=ranuni(9);
-rd.xpr> # x7=ranuni(11);
-rd.xpr> # x8=ranuni(13);
-rd.xpr> # output;
-rd.xpr> # END;
-rd.xpr> # DROP i;
-rd.xpr> # RUN;
-rd.xpr> # PROC MEANS; RUN;
-rd.xpr> # PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;
-rd.xpr> # ------
+rd.xpr> ## -------
+rd.xpr> ## SAS code to generate test dataset:
+rd.xpr> ## -------
+rd.xpr> ## libname y SASV5XPT "test2.xpt";
+rd.xpr> ##
+rd.xpr> ## PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;
+rd.xpr> ## PROC FORMAT CNTLOUT=format;RUN; * Name, e.g. 'format', unimportant;
+rd.xpr> ## data test;
+rd.xpr> ## LENGTH race 3 age 4;
+rd.xpr> ## age=30; label age="Age at Beginning of Study";
+rd.xpr> ## race=2;
+rd.xpr> ## d1='3mar2002'd ;
+rd.xpr> ## dt1='3mar2002 9:31:02'dt;
+rd.xpr> ## t1='11:13:45't;
+rd.xpr> ## output;
+rd.xpr> ##
+rd.xpr> ## age=31;
+rd.xpr> ## race=4;
+rd.xpr> ## d1='3jun2002'd ;
+rd.xpr> ## dt1='3jun2002 9:42:07'dt;
+rd.xpr> ## t1='11:14:13't;
+rd.xpr> ## output;
+rd.xpr> ## format d1 mmddyy10. dt1 datetime. t1 time. race race.;
+rd.xpr> ## run;
+rd.xpr> ## data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;
+rd.xpr> ## DO i=1 TO 100;
+rd.xpr> ## x3=ranuni(3);
+rd.xpr> ## x4=ranuni(5);
+rd.xpr> ## x5=ranuni(7);
+rd.xpr> ## x6=ranuni(9);
+rd.xpr> ## x7=ranuni(11);
+rd.xpr> ## x8=ranuni(13);
+rd.xpr> ## output;
+rd.xpr> ## END;
+rd.xpr> ## DROP i;
+rd.xpr> ## RUN;
+rd.xpr> ## PROC MEANS; RUN;
+rd.xpr> ## PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;
+rd.xpr> ## ------
rd.xpr>
-rd.xpr> # Read this dataset from a local file:
+rd.xpr> ## Read this dataset from a local file:
+rd.xpr> testFile <- system.file('extdata', 'test2.xpt', package="SASxport")
+
+rd.xpr> w <- read.xport(testFile)
+
+rd.xpr> class(w)
+[1] "list"
+
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
+
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
+
+
rd.xpr> ## Not run:
-rd.xpr> ##D w <- read.xport('test2.xpt')
+rd.xpr> ##D ## Or read a copy of test2.xpt available on the web:
+rd.xpr> ##D url <- 'http://biostat.mc.vanderbilt.edu/wiki/pub/Main/Hmisc/test2.xpt'
+rd.xpr> ##D w <- read.xport(url)
rd.xpr> ## End(Not run)
rd.xpr>
-rd.xpr> # Or read a copy of test2.xpt available on the web:
-rd.xpr> host <- 'http://biostat.mc.vanderbilt.edu'
+rd.xpr> ## We can also get the dataset wrapped in a list
+rd.xpr> w <- read.xport(testFile, as.list=TRUE)
-rd.xpr> path <- '/cgi-bin/viewvc.cgi/*checkout*/Hmisc/trunk/tests/test2.xpt'
+rd.xpr> class(w)
+[1] "list"
-rd.xpr> url <- paste(host,path,sep="")
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
-rd.xpr> w <- read.xport(url)
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
-rd.xpr> # We can also get the dataset wrapped in a list
-rd.xpr> w <- read.xport(url, as.list=TRUE)
-rd.xpr> # And we can ask for the format information to be included as well.
-rd.xpr> w <- read.xport(url, as.list=TRUE, include.formats=TRUE)
+rd.xpr> ## And we can ask for the format information to be included as well.
+rd.xpr> w <- read.xport(testFile, as.list=TRUE, include.formats=TRUE)
+rd.xpr> class(w)
+[1] "list"
+
+rd.xpr> sapply(w, head)
+$test
+ RACE AGE D1 DT1 T1
+1 blue 30 2002-03-03 (03 Mar 2002 09:31:02) 11:13:45
+2 <NA> 31 2002-06-03 (03 Jun 2002 09:42:07) 11:14:13
+
+$z
+ X3 X4 X5 X6 X7 X8
+1 0.5548096 0.9102659 0.19947292 0.7781959 0.7648077 0.90783205
+2 0.6289062 0.5950751 0.14938208 0.1996997 0.4579557 0.57161156
+3 0.5601807 0.2015537 0.87107157 0.8915819 0.8178354 0.06978889
+4 0.9301758 0.6795225 0.06470965 0.2382916 0.6756623 0.86167683
+5 0.4273071 0.5349607 0.90357235 0.7710940 0.7477446 0.13104011
+6 0.1850586 0.5198102 0.79364078 0.7873601 0.7689810 0.89166854
+
+$FORMATS
+ FMTNAME START END LABEL MIN MAX DEFAULT LENGTH FUZZ
+1 RACE 1 1 green 1 40 6 6 1e-12
+2 RACE 2 2 blue 1 40 6 6 1e-12
+3 RACE 3 3 purple 1 40 6 6 1e-12
+ PREFIX MULT FILL NOEDIT TYPE SEXCL EEXCL HLO DECSEP DIG3SEP DATATYPE LANGUAGE
+1 0 0 N N N
+2 0 0 N N N
+3 0 0 N N N
+
+
rd.xpr> ## Don't show:
-rd.xpr> SASxport:::assert( is.data.frame(w)==FALSE && is.list(w)==TRUE )
+rd.xpr> stopifnot( is.data.frame(w)==FALSE && is.list(w)==TRUE )
rd.xpr> ## End Don't show
rd.xpr>
rd.xpr>
rd.xpr> ## Not run:
-rd.xpr> ##D ## The Hmisc library provides many useful functions for interacting with
-rd.xpr> ##D ## data imported from SAS via read.xport()
+rd.xpr> ##D #### The Hmisc library provides many useful functions for interacting with
+rd.xpr> ##D #### data imported from SAS via read.xport()
rd.xpr> ##D library(Hmisc)
rd.xpr> ##D
rd.xpr> ##D describe(w$test) # see labels, format names for dataset test
-rd.xpr> ##D lapply(w, describe)# see descriptive stats in more detaiil for each variable
+rd.xpr> ##D lapply(w, describe)# see descriptive stats in more detail for each variable
rd.xpr> ##D
rd.xpr> ##D contents(w$test) # another way to see variable attributes
rd.xpr> ##D lapply(w, contents)# show contents of individual items in more detail
@@ -2163,4 +2420,4 @@
>
> proc.time()
user system elapsed
- 6.192 1.760 17.901
+ 6.172 1.968 9.155
Modified: trunk/SASxport/tests/test_as_is.Rout.save
===================================================================
--- trunk/SASxport/tests/test_as_is.Rout.save 2013-10-09 18:20:23 UTC (rev 1720)
+++ trunk/SASxport/tests/test_as_is.Rout.save 2013-10-09 18:25:07 UTC (rev 1721)
@@ -16,8 +16,9 @@
Type 'q()' to quit R.
> library(SASxport)
+Loading required package: chron
-Loaded SASxport version 1.3.5 (2013-06-14).
+Loaded SASxport version 1.3.6 (2013-10-09).
Type `?SASxport' for usage information.
@@ -71,4 +72,4 @@
>
> proc.time()
user system elapsed
- 0.884 0.076 0.963
+ 0.924 0.104 1.071
Modified: trunk/SASxport/tests/test_fields.Rout.save
===================================================================
--- trunk/SASxport/tests/test_fields.Rout.save 2013-10-09 18:20:23 UTC (rev 1720)
+++ trunk/SASxport/tests/test_fields.Rout.save 2013-10-09 18:25:07 UTC (rev 1721)
@@ -16,8 +16,9 @@
Type 'q()' to quit R.
> library(SASxport)
+Loading required package: chron
-Loaded SASxport version 1.3.5 (2013-06-14).
+Loaded SASxport version 1.3.6 (2013-10-09).
Type `?SASxport' for usage information.
@@ -32,4 +33,4 @@
>
> proc.time()
user system elapsed
- 0.756 0.048 0.824
+ 0.824 0.056 0.908
Modified: trunk/SASxport/tests/xport.Rout.save
===================================================================
--- trunk/SASxport/tests/xport.Rout.save 2013-10-09 18:20:23 UTC (rev 1720)
+++ trunk/SASxport/tests/xport.Rout.save 2013-10-09 18:25:07 UTC (rev 1721)
@@ -16,8 +16,9 @@
Type 'q()' to quit R.
> library(SASxport)
+Loading required package: chron
-Loaded SASxport version 1.3.5 (2013-06-14).
+Loaded SASxport version 1.3.6 (2013-10-09).
Type `?SASxport' for usage information.
@@ -106,4 +107,4 @@
> q()
> proc.time()
user system elapsed
- 0.904 0.100 1.013
+ 0.932 0.152 1.164
Modified: trunk/SASxport/tests/xxx.Rout.save
===================================================================
--- trunk/SASxport/tests/xxx.Rout.save 2013-10-09 18:20:23 UTC (rev 1720)
+++ trunk/SASxport/tests/xxx.Rout.save 2013-10-09 18:25:07 UTC (rev 1721)
@@ -16,8 +16,9 @@
Type 'q()' to quit R.
> library(SASxport)
+Loading required package: chron
-Loaded SASxport version 1.3.5 (2013-06-14).
+Loaded SASxport version 1.3.6 (2013-10-09).
Type `?SASxport' for usage information.
@@ -79,4 +80,4 @@
>
> proc.time()
user system elapsed
- 0.912 0.112 1.021
+ 0.948 0.100 1.147
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|
|
From: <wa...@us...> - 2013-10-09 18:20:26
|
Revision: 1720
http://sourceforge.net/p/r-gregmisc/code/1720
Author: warnes
Date: 2013-10-09 18:20:23 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
Change to camelcase
Modified Paths:
--------------
trunk/SASxport/man/read.xport.Rd
Modified: trunk/SASxport/man/read.xport.Rd
===================================================================
--- trunk/SASxport/man/read.xport.Rd 2013-10-09 18:18:08 UTC (rev 1719)
+++ trunk/SASxport/man/read.xport.Rd 2013-10-09 18:20:23 UTC (rev 1720)
@@ -181,12 +181,12 @@
}
## We can also get the dataset wrapped in a list
-w <- read.xport(testfile, as.list=TRUE)
+w <- read.xport(testFile, as.list=TRUE)
class(w)
sapply(w, head)
## And we can ask for the format information to be included as well.
-w <- read.xport(testfile, as.list=TRUE, include.formats=TRUE)
+w <- read.xport(testFile, as.list=TRUE, include.formats=TRUE)
class(w)
sapply(w, head)
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|
From: <wa...@us...> - 2013-10-09 18:18:11
|
Revision: 1719
http://sourceforge.net/p/r-gregmisc/code/1719
Author: warnes
Date: 2013-10-09 18:18:08 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
Update for SASxport 1.3.6 release
Modified Paths:
--------------
trunk/SASxport/DESCRIPTION
trunk/SASxport/inst/NEWS
Modified: trunk/SASxport/DESCRIPTION
===================================================================
--- trunk/SASxport/DESCRIPTION 2013-10-09 18:15:08 UTC (rev 1718)
+++ trunk/SASxport/DESCRIPTION 2013-10-09 18:18:08 UTC (rev 1719)
@@ -1,8 +1,8 @@
Package: SASxport
Type: Package
Title: Read and Write SAS XPORT Files
-Version: 1.3.5
-Date: 2013-06-14
+Version: 1.3.6
+Date: 2013-10-09
Description: This package provides functions for reading, listing
the contents of, and writing SAS xport format files.
The functions support reading and writing of either
@@ -38,6 +38,6 @@
<http://metruminstitute.org>.
Maintainer: Gregory R. Warnes <gr...@wa...>
License: GPL-2
-Depends: R (>= 2.4.0)
+Depends: R (>= 2.4.0), chron
Imports: chron
URL: http://www.warnes.net, http://metruminstitute.org
Modified: trunk/SASxport/inst/NEWS
===================================================================
--- trunk/SASxport/inst/NEWS 2013-10-09 18:15:08 UTC (rev 1718)
+++ trunk/SASxport/inst/NEWS 2013-10-09 18:18:08 UTC (rev 1719)
@@ -1,3 +1,11 @@
+Version 1.3.6 2013-10-09
+------------------------
+
+Bug fixes:
+
+- In manual pages for read.xport() and lookup.xporT(): Update URL for
+ 'test2.xpt', and use a local copy for executed example code.
+
Version 1.3.5 2013-06-14
------------------------
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|
|
From: <wa...@us...> - 2013-10-09 18:15:11
|
Revision: 1718
http://sourceforge.net/p/r-gregmisc/code/1718
Author: warnes
Date: 2013-10-09 18:15:08 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
Issue: URL test2.xpt file has moved. Solution: (1) Use local copy of file for executed examples, (2) update URL for displayed examples.
Modified Paths:
--------------
trunk/SASxport/man/lookup.xport.Rd
trunk/SASxport/man/read.xport.Rd
Modified: trunk/SASxport/man/lookup.xport.Rd
===================================================================
--- trunk/SASxport/man/lookup.xport.Rd 2013-10-09 17:19:31 UTC (rev 1717)
+++ trunk/SASxport/man/lookup.xport.Rd 2013-10-09 18:15:08 UTC (rev 1718)
@@ -44,21 +44,21 @@
for \code{\link[foreign]{lookup.xport}}.
}
\examples{
-\dontshow{
-setwd(system.file("extdata", package="SASxport"))
-}
-## Get information on a local file
-lookup.xport("Alfalfa.xpt")
+## Get information about a local file
+alfFile <- system.file('extdata', 'Alfalfa.xpt', package='SASxport')
+lookup.xport(alfFile)
-## Or read a copy of test2.xpt available on the web:
+## Read a copy of test2.xpt available on the web:
\dontrun{
-host <- 'http://biostat.mc.vanderbilt.edu'
-path <- '/cgi-bin/viewvc.cgi/*checkout*/Hmisc/trunk/tests/test2.xpt'
-url <- paste(host,path,sep="")
-
+url <- 'http://biostat.mc.vanderbilt.edu/wiki/pub/Main/Hmisc/test2.xpt'
w <- lookup.xport(url)
+}
+## Or use the local copy...
+testFile <- system.file('extdata', 'test2.xpt', package="SASxport")
+w <- lookup.xport(testFile)
+
# display the information (calls 'print.lookup.xport')
w
@@ -74,7 +74,6 @@
# variable names within all data sets
wS$name
-}
}
\keyword{file}
Modified: trunk/SASxport/man/read.xport.Rd
===================================================================
--- trunk/SASxport/man/read.xport.Rd 2013-10-09 17:19:31 UTC (rev 1717)
+++ trunk/SASxport/man/read.xport.Rd 2013-10-09 18:15:08 UTC (rev 1718)
@@ -128,77 +128,80 @@
}
\examples{
-# -------
-# SAS code to generate test dataset:
-# -------
-# libname y SASV5XPT "test2.xpt";
-#
-# PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;
-# PROC FORMAT CNTLOUT=format;RUN; * Name, e.g. 'format', unimportant;
-# data test;
-# LENGTH race 3 age 4;
-# age=30; label age="Age at Beginning of Study";
-# race=2;
-# d1='3mar2002'd ;
-# dt1='3mar2002 9:31:02'dt;
-# t1='11:13:45't;
-# output;
-#
-# age=31;
-# race=4;
-# d1='3jun2002'd ;
-# dt1='3jun2002 9:42:07'dt;
-# t1='11:14:13't;
-# output;
-# format d1 mmddyy10. dt1 datetime. t1 time. race race.;
-# run;
-# data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;
-# DO i=1 TO 100;
-# x3=ranuni(3);
-# x4=ranuni(5);
-# x5=ranuni(7);
-# x6=ranuni(9);
-# x7=ranuni(11);
-# x8=ranuni(13);
-# output;
-# END;
-# DROP i;
-# RUN;
-# PROC MEANS; RUN;
-# PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;
-# ------
+## -------
+## SAS code to generate test dataset:
+## -------
+## libname y SASV5XPT "test2.xpt";
+##
+## PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;
+## PROC FORMAT CNTLOUT=format;RUN; * Name, e.g. 'format', unimportant;
+## data test;
+## LENGTH race 3 age 4;
+## age=30; label age="Age at Beginning of Study";
+## race=2;
+## d1='3mar2002'd ;
+## dt1='3mar2002 9:31:02'dt;
+## t1='11:13:45't;
+## output;
+##
+## age=31;
+## race=4;
+## d1='3jun2002'd ;
+## dt1='3jun2002 9:42:07'dt;
+## t1='11:14:13't;
+## output;
+## format d1 mmddyy10. dt1 datetime. t1 time. race race.;
+## run;
+## data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;
+## DO i=1 TO 100;
+## x3=ranuni(3);
+## x4=ranuni(5);
+## x5=ranuni(7);
+## x6=ranuni(9);
+## x7=ranuni(11);
+## x8=ranuni(13);
+## output;
+## END;
+## DROP i;
+## RUN;
+## PROC MEANS; RUN;
+## PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;
+## ------
-# Read this dataset from a local file:
+## Read this dataset from a local file:
+testFile <- system.file('extdata', 'test2.xpt', package="SASxport")
+w <- read.xport(testFile)
+class(w)
+sapply(w, head)
+
\dontrun{
-w <- read.xport('test2.xpt')
+## Or read a copy of test2.xpt available on the web:
+url <- 'http://biostat.mc.vanderbilt.edu/wiki/pub/Main/Hmisc/test2.xpt'
+w <- read.xport(url)
}
-# Or read a copy of test2.xpt available on the web:
-host <- 'http://biostat.mc.vanderbilt.edu'
-path <- '/cgi-bin/viewvc.cgi/*checkout*/Hmisc/trunk/tests/test2.xpt'
-url <- paste(host,path,sep="")
+## We can also get the dataset wrapped in a list
+w <- read.xport(testfile, as.list=TRUE)
+class(w)
+sapply(w, head)
-w <- read.xport(url)
+## And we can ask for the format information to be included as well.
+w <- read.xport(testfile, as.list=TRUE, include.formats=TRUE)
+class(w)
+sapply(w, head)
-
-# We can also get the dataset wrapped in a list
-w <- read.xport(url, as.list=TRUE)
-
-# And we can ask for the format information to be included as well.
-w <- read.xport(url, as.list=TRUE, include.formats=TRUE)
-
\dontshow{
-SASxport:::assert( is.data.frame(w)==FALSE && is.list(w)==TRUE )
+stopifnot( is.data.frame(w)==FALSE && is.list(w)==TRUE )
}
\dontrun{
-## The Hmisc library provides many useful functions for interacting with
-## data imported from SAS via read.xport()
+#### The Hmisc library provides many useful functions for interacting with
+#### data imported from SAS via read.xport()
library(Hmisc)
describe(w$test) # see labels, format names for dataset test
-lapply(w, describe)# see descriptive stats in more detaiil for each variable
+lapply(w, describe)# see descriptive stats in more detail for each variable
contents(w$test) # another way to see variable attributes
lapply(w, contents)# show contents of individual items in more detail
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From: <wa...@us...> - 2013-10-09 17:19:34
|
Revision: 1717
http://sourceforge.net/p/r-gregmisc/code/1717
Author: warnes
Date: 2013-10-09 17:19:31 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
Add local copy of test2.xpt SAS file
Added Paths:
-----------
trunk/SASxport/inst/extdata/test2.xpt
Added: trunk/SASxport/inst/extdata/test2.xpt
===================================================================
(Binary files differ)
Index: trunk/SASxport/inst/extdata/test2.xpt
===================================================================
--- trunk/SASxport/inst/extdata/test2.xpt 2013-09-23 15:46:43 UTC (rev 1716)
+++ trunk/SASxport/inst/extdata/test2.xpt 2013-10-09 17:19:31 UTC (rev 1717)
Property changes on: trunk/SASxport/inst/extdata/test2.xpt
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
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|
|
From: <wa...@us...> - 2013-09-23 15:46:47
|
Revision: 1716
http://sourceforge.net/p/r-gregmisc/code/1716
Author: warnes
Date: 2013-09-23 15:46:43 +0000 (Mon, 23 Sep 2013)
Log Message:
-----------
Comment out empty sections in gtools-deprecated.Rd
Modified Paths:
--------------
trunk/gtools/man/gtools-deprecated.Rd
Modified: trunk/gtools/man/gtools-deprecated.Rd
===================================================================
--- trunk/gtools/man/gtools-deprecated.Rd 2013-09-23 15:41:36 UTC (rev 1715)
+++ trunk/gtools/man/gtools-deprecated.Rd 2013-09-23 15:46:43 UTC (rev 1716)
@@ -5,10 +5,10 @@
These functions are provided for compatibility with older versions of
gtools, and may be defunct as soon as the next release.
}
-\usage{
-}
-\arguments{
-}
+%\usage{
+%}
+%\arguments{
+%}
\details{
gtools currently contains no deprecated functions.
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|
From: <wa...@us...> - 2013-09-23 15:41:40
|
Revision: 1715
http://sourceforge.net/p/r-gregmisc/code/1715
Author: warnes
Date: 2013-09-23 15:41:36 +0000 (Mon, 23 Sep 2013)
Log Message:
-----------
Update files for gtools 3.1.0 release
Modified Paths:
--------------
trunk/gtools/DESCRIPTION
trunk/gtools/inst/NEWS
Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION 2013-09-23 15:37:21 UTC (rev 1714)
+++ trunk/gtools/DESCRIPTION 2013-09-23 15:41:36 UTC (rev 1715)
@@ -1,7 +1,7 @@
Package: gtools
Title: Various R programming tools
Description: Various R programming tools
-Version: 3.0.1
+Version: 3.1.0
Date: 2013-09-22
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes <gr...@wa...>
Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS 2013-09-23 15:37:21 UTC (rev 1714)
+++ trunk/gtools/inst/NEWS 2013-09-23 15:41:36 UTC (rev 1715)
@@ -1,6 +1,11 @@
-gtools 3.0.1 - 2013-09-22
+gtools 3.1.0 - 2013-09-22
-------------------------
+Major changes:
+
+- The function 'addLast()' (deprecated since gtools 3.0.0) is no
+ longer available, and has been marked defunct.
+
Bug fixes:
- Modified 'mixedorder()' to use Use 'suppressWarnings() instead of
@@ -8,6 +13,7 @@
called from within a nested environment, such as when run from
within 'knitr'
+
gtools 3.0.0 - 2013-07-06
-------------------------
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From: <wa...@us...> - 2013-09-23 15:37:24
|
Revision: 1714
http://sourceforge.net/p/r-gregmisc/code/1714
Author: warnes
Date: 2013-09-23 15:37:21 +0000 (Mon, 23 Sep 2013)
Log Message:
-----------
Make 'addLast()' defunct.
Modified Paths:
--------------
trunk/gtools/man/gtools-defunct.Rd
trunk/gtools/man/gtools-deprecated.Rd
trunk/gtools/man/lastAdd.Rd
Removed Paths:
-------------
trunk/gtools/man/addLast-deprecated.Rd
Deleted: trunk/gtools/man/addLast-deprecated.Rd
===================================================================
--- trunk/gtools/man/addLast-deprecated.Rd 2013-09-23 15:29:26 UTC (rev 1713)
+++ trunk/gtools/man/addLast-deprecated.Rd 2013-09-23 15:37:21 UTC (rev 1714)
@@ -1,78 +0,0 @@
-\name{addLast-deprecated}
-\alias{addLast-deprecated}
-\title{Add a function to be executed when R exits.}
-\description{
- Add a function to be executed when R exits.
-}
-\usage{
-addLast(fun)
-}
-\arguments{
- \item{fun}{Function to be called.}
-}
-\details{
- \code{addLast} defines the \code{.Last} function in the global
- environment (if not already present) or redifines it so that the
- function \code{fun} will be called when R exits. The latter is
- accomplished by saving the current definition of \code{.Last} and
- creating a new \code{.Last} function that calls \code{fun} and then
- the original \code{.Last} function.
-}
-\value{
- None.
-}
-\note{This function has been deprecated in favor of \code{lastAdd}
- because it creates/modifies the definition of '.Last' in the
- global environment, which is expressly disallowed by the CRAN
- policies. }
-\author{Gregory R. Warnes \email{gr...@wa...}}
-\seealso{
- \code{\link[base]{.Last}},
- \code{\link[gtools]{lastAdd}}
-}
-\examples{
-
-## Print a couple of cute messages when R exits.
-helloWorld <- function() cat("\nHello World!\n")
-byeWorld <- function() cat("\nGoodbye World!\n")
-
-addLast(byeWorld)
-addLast(helloWorld)
-
-\dontrun{
-q("no")
-
-## Should yield:
-##
-## Save workspace image? [y/n/c]: n
-##
-## Hello World!
-##
-## Goodbye World!
-##
-## Process R finished at Tue Nov 22 10:28:55 2005
-}
-
-## Unix-flavour example: send Rplots.ps to printer on exit.
-myLast <- function()
-{
- cat("Now sending PostScript graphics to the printer:\n")
- system("lpr Rplots.ps")
- cat("bye bye...\n")
-}
-addLast(myLast)
-\dontrun{
-quit("yes")
-
-## Should yield:
-##
-## Now sending PostScript graphics to the printer:
-## lpr: job 1341 queued
-## bye bye...
-##
-## Process R finished at Tue Nov 22 10:28:55 2005
-}
-
-}
-\keyword{programming}
-
Modified: trunk/gtools/man/gtools-defunct.Rd
===================================================================
--- trunk/gtools/man/gtools-defunct.Rd 2013-09-23 15:29:26 UTC (rev 1713)
+++ trunk/gtools/man/gtools-defunct.Rd 2013-09-23 15:37:21 UTC (rev 1714)
@@ -1,20 +1,30 @@
\name{gtools-defunct}
\alias{gtools-defunct}
\alias{assert}
+\alias{addLast}
\title{Deprecated Functions in the gtools package}
\description{
These functions are no longer available in gtools.
}
\usage{
assert(FLAG)
+addLast(fun)
}
\arguments{
\item{FLAG}{ Expression that should evaluate to a boolean vector}
+ \item{fun}{Function to be called.}
}
\details{
- \code{assert} is a defunct synonym for \code{\link[base]{stopifnot}}.
+ \itemize{
+ \item{ \code{assert} is a defunct synonym for
+ \code{\link[base]{stopifnot}}. }
+ \item{ \code{addLast} has been replaced by \code{lastAdd}, which has
+ the same purpose but appled using different syntax. }
+ }
}
\seealso{
- \code{\link{Defunct}}
+ \code{\link[base]{Defunct}}
+ \code{\link[base]{stopifnot}}
+ \code{\link[gtools]{lastAdd}}
}
\keyword{misc}
Modified: trunk/gtools/man/gtools-deprecated.Rd
===================================================================
--- trunk/gtools/man/gtools-deprecated.Rd 2013-09-23 15:29:26 UTC (rev 1713)
+++ trunk/gtools/man/gtools-deprecated.Rd 2013-09-23 15:37:21 UTC (rev 1714)
@@ -1,29 +1,26 @@
\name{gtools-deprecated}
\alias{gtools-deprecated}
-\alias{addLast}
\title{Deprecated Functions in the gtools package}
\description{
These functions are provided for compatibility with older versions of
gtools, and may be defunct as soon as the next release.
}
\usage{
-addLast(fun)
}
\arguments{
- \item{fun}{Function to be called.}
}
\details{
- The original help page for these functions is often
- available at \code{help("oldName-deprecated")} (note the quotes).
-
- \itemize{
- \item{ \code{addLast} has been replaced by \code{lastAdd}, which has
- the same purpose but appled using different syntax. }
- }
+ gtools currently contains no deprecated functions.
+
+% The original help page for these functions is often
+% available at \code{help("oldName-deprecated")} (note the quotes).
+%
+% \itemize{
+% \item{}
+% }
}
\seealso{
\code{\link{Deprecated}}
- \code{\link[gtools]{lastAdd}}
}
\keyword{misc}
Modified: trunk/gtools/man/lastAdd.Rd
===================================================================
--- trunk/gtools/man/lastAdd.Rd 2013-09-23 15:29:26 UTC (rev 1713)
+++ trunk/gtools/man/lastAdd.Rd 2013-09-23 15:37:21 UTC (rev 1714)
@@ -25,7 +25,7 @@
}
\note{
- This function replaces the (now deprecated) \code{addLast} function.
+ This function replaces the (now defunct) \code{addLast} function.
}
\value{
A new function to be used for \code{.Last}.
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|
From: <wa...@us...> - 2013-09-23 15:29:29
|
Revision: 1713
http://sourceforge.net/p/r-gregmisc/code/1713
Author: warnes
Date: 2013-09-23 15:29:26 +0000 (Mon, 23 Sep 2013)
Log Message:
-----------
Mark 'addLast()' as defunct and move 'lastAdd()' function to a separate file.
Modified Paths:
--------------
trunk/gtools/R/addLast.R
Added Paths:
-----------
trunk/gtools/R/lastAdd.R
Modified: trunk/gtools/R/addLast.R
===================================================================
--- trunk/gtools/R/addLast.R 2013-09-23 15:23:34 UTC (rev 1712)
+++ trunk/gtools/R/addLast.R 2013-09-23 15:29:26 UTC (rev 1713)
@@ -1,39 +1,4 @@
addLast <- function( fun )
- {
- .Deprecated(new=paste(".Last <- lastAdd(", deparse(substitute(fun)), ")", sep=''),
- package='gtools'
- )
-
- if (!is.function(fun)) stop("fun must be a function")
- if (!exists(".Last", envir = .GlobalEnv))
- assign(".Last", fun, envir = .GlobalEnv)
- else
- {
- Last <- get(".Last", envir = .GlobalEnv)
- newfun <- function(...) {
- fun()
- Last()
- }
- assign(".Last", newfun, envir = .GlobalEnv)
- }
- }
-
-lastAdd <- function( fun )
- {
- if (!is.function(fun)) stop("fun must be a function")
- if(!exists(".Last", envir=.GlobalEnv))
- {
- return(fun)
- }
- else
- {
- Last <- get(".Last", envir=.GlobalEnv)
- newfun <- function(...)
- {
- fun()
- Last()
- }
- return(newfun)
- }
- }
-
+ .Defunct(new=paste(".Last <- lastAdd(", deparse(substitute(fun)), ")", sep=''),
+ package='gtools'
+ )
Added: trunk/gtools/R/lastAdd.R
===================================================================
--- trunk/gtools/R/lastAdd.R (rev 0)
+++ trunk/gtools/R/lastAdd.R 2013-09-23 15:29:26 UTC (rev 1713)
@@ -0,0 +1,22 @@
+##
+## Replaces the (defunct) addLast() function.
+##
+lastAdd <- function( fun )
+ {
+ if (!is.function(fun)) stop("fun must be a function")
+ if(!exists(".Last", envir=.GlobalEnv))
+ {
+ return(fun)
+ }
+ else
+ {
+ Last <- get(".Last", envir=.GlobalEnv)
+ newfun <- function(...)
+ {
+ fun()
+ Last()
+ }
+ return(newfun)
+ }
+ }
+
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|
From: <wa...@us...> - 2013-09-23 15:23:37
|
Revision: 1712
http://sourceforge.net/p/r-gregmisc/code/1712
Author: warnes
Date: 2013-09-23 15:23:34 +0000 (Mon, 23 Sep 2013)
Log Message:
-----------
Update for gtools 3.0.1 release
Modified Paths:
--------------
trunk/gtools/DESCRIPTION
trunk/gtools/inst/NEWS
Modified: trunk/gtools/DESCRIPTION
===================================================================
--- trunk/gtools/DESCRIPTION 2013-09-23 15:19:06 UTC (rev 1711)
+++ trunk/gtools/DESCRIPTION 2013-09-23 15:23:34 UTC (rev 1712)
@@ -1,8 +1,8 @@
Package: gtools
Title: Various R programming tools
Description: Various R programming tools
-Version: 3.0.0
-Date: 2013-07-06
+Version: 3.0.1
+Date: 2013-09-22
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes <gr...@wa...>
License: LGPL-2.1
Modified: trunk/gtools/inst/NEWS
===================================================================
--- trunk/gtools/inst/NEWS 2013-09-23 15:19:06 UTC (rev 1711)
+++ trunk/gtools/inst/NEWS 2013-09-23 15:23:34 UTC (rev 1712)
@@ -1,3 +1,13 @@
+gtools 3.0.1 - 2013-09-22
+-------------------------
+
+Bug fixes:
+
+- Modified 'mixedorder()' to use Use 'suppressWarnings() instead of
+ 'options(warn=-1)'. This will avoid egregious warning messages when
+ called from within a nested environment, such as when run from
+ within 'knitr'
+
gtools 3.0.0 - 2013-07-06
-------------------------
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|
From: <wa...@us...> - 2013-09-23 15:19:09
|
Revision: 1711
http://sourceforge.net/p/r-gregmisc/code/1711
Author: warnes
Date: 2013-09-23 15:19:06 +0000 (Mon, 23 Sep 2013)
Log Message:
-----------
Use 'suppressWarnings() instead of 'options(warn=-1)' in 'mixedorder()'.
Modified Paths:
--------------
trunk/gtools/R/mixedsort.R
Modified: trunk/gtools/R/mixedsort.R
===================================================================
--- trunk/gtools/R/mixedsort.R 2013-07-18 14:09:14 UTC (rev 1710)
+++ trunk/gtools/R/mixedsort.R 2013-09-23 15:19:06 UTC (rev 1711)
@@ -13,19 +13,12 @@
numeric <- function(x)
{
- optwarn = options("warn")
- on.exit( options(optwarn) )
- options(warn=-1)
- as.numeric(x)
+ suppressWarnings( as.numeric(x) )
}
nonnumeric <- function(x)
{
- optwarn = options("warn")
- on.exit( options(optwarn) )
- options(warn=-1)
-
- ifelse(is.na(as.numeric(x)), toupper(x), NA)
+ suppressWarnings( ifelse(is.na(as.numeric(x)), toupper(x), NA) )
}
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|
From: Charles S. <cst...@ch...> - 2013-08-03 03:58:04
|
Hello,
So I want to prettify my crosstables output a bit.
I tried to create an object that holds the table itself:
ct <- CrossTable(es$Q4_fac, mydata$time, prop.t = FALSE, prop.r = TRUE,
prop.c = FALSE, prop.chisq = FALSE) #, format = c("SPSS"))
..thinking that I could change the attributes and then print, but when I
try to display the table:
>ct
I don't get the table.
Thanks in advance.
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|
From: <wa...@us...> - 2013-07-18 14:09:17
|
Revision: 1710
http://sourceforge.net/p/r-gregmisc/code/1710
Author: warnes
Date: 2013-07-18 14:09:14 +0000 (Thu, 18 Jul 2013)
Log Message:
-----------
Looks like Brian Ripley repackaged for R 3.0.0 and bumped version number, so change it to 2.15.5
Modified Paths:
--------------
trunk/gmodels/DESCRIPTION
trunk/gmodels/inst/NEWS
Modified: trunk/gmodels/DESCRIPTION
===================================================================
--- trunk/gmodels/DESCRIPTION 2013-07-18 13:57:26 UTC (rev 1709)
+++ trunk/gmodels/DESCRIPTION 2013-07-18 14:09:14 UTC (rev 1710)
@@ -1,5 +1,5 @@
Package: gmodels
-Version: 2.15.4
+Version: 2.15.5
Date: 2013-07-18
Title: Various R programming tools for model fitting
Author: Gregory R. Warnes, Ben Bolker, Thomas Lumley, and Randall C
@@ -13,6 +13,5 @@
Suggests: gplots, gtools, Matrix, nlme, lme4 (>= 0.999999-0)
Imports: MASS, gdata
License: GPL-2
-URL: http://cran.r-project.org/src/contrib/PACKAGES.html
- http://www.sf.net/projects/r-gregmisc
-
+URL: http://www.sf.net/projects/r-gregmisc
+NeedsCompilation: no
Modified: trunk/gmodels/inst/NEWS
===================================================================
--- trunk/gmodels/inst/NEWS 2013-07-18 13:57:26 UTC (rev 1709)
+++ trunk/gmodels/inst/NEWS 2013-07-18 14:09:14 UTC (rev 1710)
@@ -1,4 +1,4 @@
-Version 2.15.4 - 2013-07-18
+Version 2.15.5 - 2013-07-18
---------------------------
Bug fixes:
@@ -9,8 +9,8 @@
Other Changes:
- Update man page file for ci() to current Rd syntax.
+- Remove unused argument to ci.mer()
-
Version 2.15.3 - 2012-06-27
---------------------------
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|
From: <wa...@us...> - 2013-07-18 13:57:29
|
Revision: 1709
http://sourceforge.net/p/r-gregmisc/code/1709
Author: warnes
Date: 2013-07-18 13:57:26 +0000 (Thu, 18 Jul 2013)
Log Message:
-----------
Update for gmodels 2.15.4
Modified Paths:
--------------
trunk/gmodels/DESCRIPTION
trunk/gmodels/inst/NEWS
Modified: trunk/gmodels/DESCRIPTION
===================================================================
--- trunk/gmodels/DESCRIPTION 2013-07-18 13:54:31 UTC (rev 1708)
+++ trunk/gmodels/DESCRIPTION 2013-07-18 13:57:26 UTC (rev 1709)
@@ -1,9 +1,8 @@
Package: gmodels
-Version: 2.15.3
-Date: 2012-06-27
+Version: 2.15.4
+Date: 2013-07-18
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
+Author: Gregory R. Warnes, 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
Modified: trunk/gmodels/inst/NEWS
===================================================================
--- trunk/gmodels/inst/NEWS 2013-07-18 13:54:31 UTC (rev 1708)
+++ trunk/gmodels/inst/NEWS 2013-07-18 13:57:26 UTC (rev 1709)
@@ -1,3 +1,16 @@
+Version 2.15.4 - 2013-07-18
+---------------------------
+
+Bug fixes:
+
+- Correct error in estimable.mlm() that caused it to always fail. Added
+ test code to prevent future issues.
+
+Other Changes:
+
+- Update man page file for ci() to current Rd syntax.
+
+
Version 2.15.3 - 2012-06-27
---------------------------
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|
From: <wa...@us...> - 2013-07-18 13:54:35
|
Revision: 1708
http://sourceforge.net/p/r-gregmisc/code/1708
Author: warnes
Date: 2013-07-18 13:54:31 +0000 (Thu, 18 Jul 2013)
Log Message:
-----------
Update to current Rd syntax
Modified Paths:
--------------
trunk/gmodels/man/ci.Rd
Modified: trunk/gmodels/man/ci.Rd
===================================================================
--- trunk/gmodels/man/ci.Rd 2013-07-18 13:46:00 UTC (rev 1707)
+++ trunk/gmodels/man/ci.Rd 2013-07-18 13:54:31 UTC (rev 1708)
@@ -13,9 +13,9 @@
\code{ci.default}, the probability of a binomial vector
\code{ci.binom}, and for \code{lm}, \code{lme}, and \code{mer} objects are
provided. }
-\synopsis{
+\usage{
ci(x, confidence = 0.95, alpha = 1 - confidence,...)
- \method{ci}{default}(x, confidence = 0.95, alpha = 1 - confidence, na.rm=FALSE)...)
+ \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,...)
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|
From: <wa...@us...> - 2013-07-18 13:46:04
|
Revision: 1707
http://sourceforge.net/p/r-gregmisc/code/1707
Author: warnes
Date: 2013-07-18 13:46:00 +0000 (Thu, 18 Jul 2013)
Log Message:
-----------
Correct bug in estimable.mlm
Modified Paths:
--------------
trunk/gmodels/R/estimable.mlm.R
Added Paths:
-----------
trunk/gmodels/test/test_estimable_mlm.R
Modified: trunk/gmodels/R/estimable.mlm.R
===================================================================
--- trunk/gmodels/R/estimable.mlm.R 2013-07-15 18:13:11 UTC (rev 1706)
+++ trunk/gmodels/R/estimable.mlm.R 2013-07-18 13:46:00 UTC (rev 1707)
@@ -1,28 +1,28 @@
`estimable.mlm` <-
function (obj, cm, beta0, conf.int=NULL, show.beta0, ...)
{
- coef <- coef(object)
+ coef <- coef(obj)
ny <- ncol(coef)
- effects <- object$effects
- resid <- object$residuals
- fitted <- object$fitted
+ effects <- obj$effects
+ resid <- obj$residuals
+ fitted <- obj$fitted
ynames <- colnames(coef)
if (is.null(ynames)) {
- lhs <- object$terms[[2]]
+ lhs <- obj$terms[[2]]
if (mode(lhs) == "call" && lhs[[1]] == "cbind")
ynames <- as.character(lhs)[-1]
else ynames <- paste("Y", seq(ny), sep = "")
}
value <- vector("list", ny)
names(value) <- paste("Response", ynames)
- cl <- oldClass(object)
- class(object) <- cl[match("mlm", cl):length(cl)][-1]
+ cl <- oldClass(obj)
+ class(obj) <- cl[match("mlm", cl):length(cl)][-1]
for (i in seq(ny)) {
- object$coefficients <- coef[, i]
- object$residuals <- resid[, i]
- object$fitted.values <- fitted[, i]
- object$effects <- effects[, i]
- object$call$formula[[2]] <- object$terms[[2]] <- as.name(ynames[i])
+ obj$coefficients <- coef[, i]
+ obj$residuals <- resid[, i]
+ obj$fitted.values <- fitted[, i]
+ obj$effects <- effects[, i]
+ obj$call$formula[[2]] <- obj$terms[[2]] <- as.name(ynames[i])
value[[i]] <- estimable(obj, cm, beta0, conf.int=NULL, show.beta0, ...)
}
class(value) <- "listof"
Added: trunk/gmodels/test/test_estimable_mlm.R
===================================================================
--- trunk/gmodels/test/test_estimable_mlm.R (rev 0)
+++ trunk/gmodels/test/test_estimable_mlm.R 2013-07-18 13:46:00 UTC (rev 1707)
@@ -0,0 +1,15 @@
+library(gmodels)
+
+y <- cbind(rnorm(100), rnorm(100))
+
+x1 <- rnorm(100)
+x2 <- rnorm(100)
+
+cm <- t(matrix(c(0, 1,-1)))
+lm.1 <- lm(y ~ x1 + x2)
+
+estimable(lm.1, cm)
+
+## >> Error in coef(object) : object 'object' not found
+
+gmodels:::estimable.mlm(lm.1, cm)
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|
From: <wa...@us...> - 2013-07-15 18:13:15
|
Revision: 1706
http://sourceforge.net/p/r-gregmisc/code/1706
Author: warnes
Date: 2013-07-15 18:13:11 +0000 (Mon, 15 Jul 2013)
Log Message:
-----------
Remove unused argument to ci.mer
Modified Paths:
--------------
trunk/gmodels/R/ci.R
trunk/gmodels/man/ci.Rd
Modified: trunk/gmodels/R/ci.R
===================================================================
--- trunk/gmodels/R/ci.R 2013-07-07 00:11:06 UTC (rev 1705)
+++ trunk/gmodels/R/ci.R 2013-07-15 18:13:11 UTC (rev 1706)
@@ -71,7 +71,6 @@
ci.mer <- function (x,
confidence = 0.95,
alpha = 1 - confidence,
- sim.mer = TRUE,
n.sim = 1e4,
...)
{
Modified: trunk/gmodels/man/ci.Rd
===================================================================
--- trunk/gmodels/man/ci.Rd 2013-07-07 00:11:06 UTC (rev 1705)
+++ trunk/gmodels/man/ci.Rd 2013-07-15 18:13:11 UTC (rev 1706)
@@ -19,8 +19,7 @@
\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}{mer}(x, confidence = 0.95, alpha = 1 - confidence,
- sim.mer=TRUE, n.sim=10000, ...)
+ \method{ci}{mer}(x, confidence = 0.95, alpha = 1 - confidence, n.sim=10000, ...)
}
\arguments{
\item{x}{ object from which to compute confidence intervals. }
@@ -29,9 +28,6 @@
\item{na.rm}{boolean indicating whether missing values should be
removed. Defaults to \code{FALSE}.}
\item{\dots}{Arguments for methods}
- \item{sim.mer}{Logical value. If TRUE confidence
- intervals will be estimated using \code{mcmcsamp}. This option only takes effect for mer
- objects.}
\item{n.sim}{Number of samples to take in \code{mcmcsamp}.}
}
%\details{
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From: <wa...@us...> - 2013-07-07 00:11:09
|
Revision: 1705
http://sourceforge.net/p/r-gregmisc/code/1705
Author: warnes
Date: 2013-07-07 00:11:06 +0000 (Sun, 07 Jul 2013)
Log Message:
-----------
Fix typo.
Modified Paths:
--------------
trunk/gtools/man/lastAdd.Rd
Modified: trunk/gtools/man/lastAdd.Rd
===================================================================
--- trunk/gtools/man/lastAdd.Rd 2013-07-06 23:55:54 UTC (rev 1704)
+++ trunk/gtools/man/lastAdd.Rd 2013-07-07 00:11:06 UTC (rev 1705)
@@ -5,7 +5,7 @@
Non-destructively construct a \code{.Last} function to be executed when R exits.
}
\usage{
-addLast(fun)
+lastAdd(fun)
}
\arguments{
\item{fun}{Function to be called.}
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From: <wa...@us...> - 2013-07-06 23:55:57
|
Revision: 1704
http://sourceforge.net/p/r-gregmisc/code/1704
Author: warnes
Date: 2013-07-06 23:55:54 +0000 (Sat, 06 Jul 2013)
Log Message:
-----------
Fix Rd warning.
Modified Paths:
--------------
trunk/gtools/man/lastAdd.Rd
Modified: trunk/gtools/man/lastAdd.Rd
===================================================================
--- trunk/gtools/man/lastAdd.Rd 2013-07-06 23:49:26 UTC (rev 1703)
+++ trunk/gtools/man/lastAdd.Rd 2013-07-06 23:55:54 UTC (rev 1704)
@@ -5,14 +5,14 @@
Non-destructively construct a \code{.Last} function to be executed when R exits.
}
\usage{
-.Last <- addLast(fun)
+addLast(fun)
}
\arguments{
\item{fun}{Function to be called.}
}
\details{
- \code{lastAdd} constructs a new function to be used to replace the
- exising definition of \code{.Last}, which will be executed when R
+ \code{lastAdd} constructs a new function which can be used to replace
+ the exising definition of \code{.Last}, which will be executed when R
terminates normally.
If a \code{.Last} function already exists in the global environment,
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From: <wa...@us...> - 2013-07-06 23:49:28
|
Revision: 1703
http://sourceforge.net/p/r-gregmisc/code/1703
Author: warnes
Date: 2013-07-06 23:49:26 +0000 (Sat, 06 Jul 2013)
Log Message:
-----------
Include lastAdd in NAMESPACE
Modified Paths:
--------------
trunk/gtools/NAMESPACE
Modified: trunk/gtools/NAMESPACE
===================================================================
--- trunk/gtools/NAMESPACE 2013-07-06 23:46:26 UTC (rev 1702)
+++ trunk/gtools/NAMESPACE 2013-07-06 23:49:26 UTC (rev 1703)
@@ -16,6 +16,7 @@
inv.logit,
invalid,
keywords,
+ lastAdd,
logit,
logratio2foldchange,
mixedorder,
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