[R-gregmisc-commits] r2062 - in pkg: SASxport SASxport/R SASxport/tests exp.ssize/inst/Presentation fork gdata gdata/tests gmodels gmodels/tests gplots gplots/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jul 22 02:48:52 CEST 2015
Author: warnes
Date: 2015-07-22 02:48:51 +0200 (Wed, 22 Jul 2015)
New Revision: 2062
Added:
pkg/gmodels/tests/
pkg/gplots/R/layout_set.R
Removed:
pkg/gmodels/test/
Modified:
pkg/SASxport/NAMESPACE
pkg/SASxport/R/SASiformat.R
pkg/SASxport/tests/datetime.xpt
pkg/SASxport/tests/dfAttributes.R
pkg/exp.ssize/inst/Presentation/Warnes-SampleSize-Omics.ppt
pkg/fork/DESCRIPTION
pkg/gdata/DESCRIPTION
pkg/gdata/NAMESPACE
pkg/gdata/tests/test.humanReadable.Rout.save
pkg/gdata/tests/test.read.xls.R
pkg/gdata/tests/test.read.xls.Rout.save
pkg/gdata/tests/test.reorder.factor.Rout.save
pkg/gdata/tests/tests.write.fwf.Rout.save
pkg/gmodels/tests/lme-test.R
pkg/gplots/DESCRIPTION
pkg/gplots/R/heatmap.2.R
Log:
Renamed 'test' directory to 'tests', commented out tests for lme4 which has a changed API
Modified: pkg/SASxport/NAMESPACE
===================================================================
--- pkg/SASxport/NAMESPACE 2015-07-20 23:38:07 UTC (rev 2061)
+++ pkg/SASxport/NAMESPACE 2015-07-22 00:48:51 UTC (rev 2062)
@@ -34,15 +34,25 @@
S3method(toSAS, default)
## S3method(label, default)
-S3method(SASformat, default)
+S3method(SASformat, default)
S3method(SASiformat, default)
-S3method(SAStype, default)
+S3method(SAStype, default)
+## S3method(label, data.frame)
+S3method(SASformat, data.frame)
+S3method(SASiformat, data.frame)
+S3method(SAStype, data.frame)
+
## S3method("label<-", default)
-S3method("SASformat<-", default)
+S3method("SASformat<-", default)
S3method("SASiformat<-", default)
-S3method("SAStype<-", default)
+S3method("SAStype<-", default)
+## S3method("label<-", data.frame)
+S3method("SASformat<-", data.frame)
+S3method("SASiformat<-", data.frame)
+S3method("SAStype<-", data.frame)
+
S3method(print, lookup.xport)
S3method(summary, lookup.xport)
S3method(print, summary.lookup.xport)
Modified: pkg/SASxport/R/SASiformat.R
===================================================================
--- pkg/SASxport/R/SASiformat.R 2015-07-20 23:38:07 UTC (rev 2061)
+++ pkg/SASxport/R/SASiformat.R 2015-07-22 00:48:51 UTC (rev 2062)
@@ -10,6 +10,14 @@
lab
}
+
+SASiformat.data.frame <- function(x, default=NULL)
+{
+ sapply( x, SASiformat)
+}
+
+
+
"SASiformat<-" <- function(x, value)
UseMethod("SASiformat<-")
@@ -18,3 +26,13 @@
attr(x,'SASiformat') <- value
x
}
+
+"SASiformat<-.data.frame" <- function(x, value)
+{
+ if( ncol(x) != length(value) )
+ stop("vector of iformats must match number of data frame columns")
+
+ for(i in 1:ncol(x))
+ attr(x[[i]],'SASiformat') <- value[i]
+ x
+}
Modified: pkg/SASxport/tests/datetime.xpt
===================================================================
(Binary files differ)
Modified: pkg/SASxport/tests/dfAttributes.R
===================================================================
--- pkg/SASxport/tests/dfAttributes.R 2015-07-20 23:38:07 UTC (rev 2061)
+++ pkg/SASxport/tests/dfAttributes.R 2015-07-22 00:48:51 UTC (rev 2062)
@@ -9,7 +9,8 @@
SAStype(abc.out) <- "normal"
## add a format specifier (not used by R)
-SASformat(abc.out$x) <- 'date7.'
+SASformat(abc.out$x) <- 'DATE7.'
+SASiformat(abc.out$x) <- 'DATE7.'
## add a variable label (not used by R)
label(abc.out$y) <- 'character variable'
@@ -25,20 +26,30 @@
# read the SAS data back in
abc.in <- read.xport("dfAttributes.xpt",
- names.tolower=FALSE,
+ names.tolower=TRUE,
verbose=TRUE)
## Test that the files are otherwise identical
label(abc.out, self=TRUE, "MISSING!")
label(abc.in , self=TRUE, "MISSING!")
+stopifnot( label(abc.out, self=TRUE, "MISSING!") ==
+ label(abc.in, self=TRUE, "MISSING!")
+ )
+
SAStype(abc.out, "MISSING!")
SAStype(abc.in , "MISSING!")
-stopifnot( label (abc.out, self=TRUE, "MISSING!") ==
- label (abc.in, self=TRUE, "MISSING!") )
-
stopifnot( SAStype(abc.out, "MISSING!") ==
SAStype(abc.in, "MISSING!") )
+SASformat(abc.out)
+SASformat(abc.in)
+stopifnot( unlist(SASformat(abc.out)) == unlist(SASformat(abc.in)) )
+
+SASiformat(abc.out)
+SASiformat(abc.in)
+
+stopifnot( unlist(SASiformat(abc.out)) == unlist(SASiformat(abc.in)) )
+
Modified: pkg/exp.ssize/inst/Presentation/Warnes-SampleSize-Omics.ppt
===================================================================
(Binary files differ)
Modified: pkg/fork/DESCRIPTION
===================================================================
--- pkg/fork/DESCRIPTION 2015-07-20 23:38:07 UTC (rev 2061)
+++ pkg/fork/DESCRIPTION 2015-07-22 00:48:51 UTC (rev 2062)
@@ -11,3 +11,5 @@
processes.
Maintainer: Gregory R. Warnes <greg at warnes.net>
License: GPL-2
+URL: https://r-forge.r-project.org/projects/r-gregmisc/
+BugReports: https://r-forge.r-project.org/tracker/?func=browse&group_id=2031&atid=5378
Modified: pkg/gdata/DESCRIPTION
===================================================================
--- pkg/gdata/DESCRIPTION 2015-07-20 23:38:07 UTC (rev 2061)
+++ pkg/gdata/DESCRIPTION 2015-07-22 00:48:51 UTC (rev 2062)
@@ -22,7 +22,7 @@
scalar and vector arguments ('resample').
Depends: R (>= 2.3.0)
SystemRequirements: perl (>= 5.10.0)
-Imports: gtools
+Imports: gtools, stats, methods, utils
Version: 2.17.0
Date: 2015-07-02
Author: Gregory R. Warnes, Ben Bolker, Gregor Gorjanc, Gabor
Modified: pkg/gdata/NAMESPACE
===================================================================
--- pkg/gdata/NAMESPACE 2015-07-20 23:38:07 UTC (rev 2061)
+++ pkg/gdata/NAMESPACE 2015-07-22 00:48:51 UTC (rev 2062)
@@ -66,6 +66,8 @@
importFrom(stats, reorder)
importFrom(stats, nobs)
importFrom(gtools, mixedsort)
+importFrom(methods, is)
+importFrom(utils, data, download.file, head, read.csv, read.delim, read.table, tail, write.table)
S3method(reorder, factor)
@@ -161,3 +163,5 @@
S3method(left, matrix)
S3method(right, data.frame)
S3method(right, matrix)
+
+
Modified: pkg/gdata/tests/test.humanReadable.Rout.save
===================================================================
--- pkg/gdata/tests/test.humanReadable.Rout.save 2015-07-20 23:38:07 UTC (rev 2061)
+++ pkg/gdata/tests/test.humanReadable.Rout.save 2015-07-22 00:48:51 UTC (rev 2062)
@@ -235,4 +235,4 @@
>
> proc.time()
user system elapsed
- 0.414 0.050 0.461
+ 0.421 0.052 0.464
Modified: pkg/gdata/tests/test.read.xls.R
===================================================================
--- pkg/gdata/tests/test.read.xls.R 2015-07-20 23:38:07 UTC (rev 2061)
+++ pkg/gdata/tests/test.read.xls.R 2015-07-22 00:48:51 UTC (rev 2062)
@@ -29,26 +29,27 @@
# see the number and names of sheets:
sheetCount(exampleFile)
-if( 'XLSX' %in% xlsFormats() )
+if(! 'XLSX' %in% xlsFormats() )
{
+ cat("************************************************************\n")
+ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
+ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
+ cat("************************************************************\n")
+ } else {
sheetCount(exampleFileX)
- } else {
- cat("************************************************************\n")
- cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
- cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
- cat("************************************************************\n")
}
+
sheetNames(exampleFile)
-if( 'XLSX' %in% xlsFormats() )
+if(! 'XLSX' %in% xlsFormats() )
{
+ cat("************************************************************\n")
+ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
+ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
+ cat("************************************************************\n")
+ } else {
sheetNames(exampleFileX)
- } else {
- cat("************************************************************\n")
- cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
- cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
- cat("************************************************************\n")
}
@@ -64,8 +65,13 @@
example.4 <- read.xls(exampleFile, sheet=4, header=FALSE) # fourth worksheet by number
example.4
-if( 'XLSX' %in% xlsFormats() )
+if(! 'XLSX' %in% xlsFormats() )
{
+ cat("************************************************************\n")
+ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
+ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
+ cat("************************************************************\n")
+ } else {
example.x.1 <- read.xls(exampleFileX, sheet=1) # default is first worksheet
print(example.x.1)
@@ -84,9 +90,6 @@
# load the third worksheet, skipping the first two non-data lines...
data <- read.xls(exampleFileX, sheet="Sheet with initial text", skip=2)
print(data)
- } else {
- cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
- cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
}
## Check handling of skip.blank.lines=FALSE
@@ -94,18 +97,19 @@
example.skip <- read.xls(exampleFile, sheet=2, blank.lines.skip=FALSE)
example.skip
-if( 'XLSX' %in% xlsFormats() )
+if(! 'XLSX' %in% xlsFormats() )
{
+ cat("************************************************************\n")
+ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
+ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
+ cat("************************************************************\n")
+ } else {
example.x.skip <- read.xls(exampleFileX, sheet=2, blank.lines.skip=FALSE)
example.x.skip
- } else {
- cat("************************************************************\n")
- cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
- cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
- cat("************************************************************\n")
}
+
## Check handing of fileEncoding for latin-1 characters
latin1File <- file.path(path.package('gdata'),'xls', 'latin-1.xls' )
@@ -124,8 +128,13 @@
stringsAsFactors=FALSE)
}
-if( 'XLSX' %in% xlsFormats() )
+if(! 'XLSX' %in% xlsFormats() )
{
+ cat("************************************************************\n")
+ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
+ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
+ cat("************************************************************\n")
+ } else {
if(.Platform$OS.type=="unix")
{
example.latin1.x <- read.xls(latin1FileX,
@@ -138,12 +147,7 @@
encoding='latin1',
stringsAsFactors=FALSE)
}
- } else {
- cat("************************************************************\n")
- cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
- cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
- cat("************************************************************\n")
-}
+ }
## Check handling of very wide file
@@ -154,13 +158,15 @@
example.wide <- read.xls(wideFile)
stopifnot(dim(example.wide)==c(0,256))
-if( 'XLSX' %in% xlsFormats() )
+if( !'XLSX' %in% xlsFormats() )
{
- example.wide.x <- read.xls(wideFileX)
- stopifnot(dim(example.wide.x)==c(0,16384))
+ cat("************************************************************\n")
+ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
+ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
+ cat("************************************************************\n")
} else {
- cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
- cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
+ example.wide.x <- read.xls(wideFileX)
+ stopifnot(dim(example.wide.x)==c(0,16384))
}
## Check handling of files with dates calulcated relative to
Modified: pkg/gdata/tests/test.read.xls.Rout.save
===================================================================
--- pkg/gdata/tests/test.read.xls.Rout.save 2015-07-20 23:38:07 UTC (rev 2061)
+++ pkg/gdata/tests/test.read.xls.Rout.save 2015-07-22 00:48:51 UTC (rev 2062)
@@ -514,29 +514,30 @@
> sheetCount(exampleFile)
[1] 4
>
-> if( 'XLSX' %in% xlsFormats() )
+> if(! 'XLSX' %in% xlsFormats() )
+ {
++ cat("************************************************************\n")
++ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
++ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
++ cat("************************************************************\n")
++ } else {
+ sheetCount(exampleFileX)
-+ } else {
-+ cat("************************************************************\n")
-+ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
-+ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
-+ cat("************************************************************\n")
+ }
[1] 4
>
+>
> sheetNames(exampleFile)
[1] "Sheet First" "Sheet Second"
[3] "Sheet with a very long name!" "Sheet with initial text"
>
-> if( 'XLSX' %in% xlsFormats() )
+> if(! 'XLSX' %in% xlsFormats() )
+ {
++ cat("************************************************************\n")
++ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
++ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
++ cat("************************************************************\n")
++ } else {
+ sheetNames(exampleFileX)
-+ } else {
-+ cat("************************************************************\n")
-+ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
-+ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
-+ cat("************************************************************\n")
+ }
[1] "Sheet First" "Sheet Second"
[3] "Sheet with a very long name!" "Sheet with initial text"
@@ -605,8 +606,13 @@
6 ThirdRow 3 2 1 <NA> Red
7 FourthRow 4 3 2 1 Black
>
-> if( 'XLSX' %in% xlsFormats() )
+> if(! 'XLSX' %in% xlsFormats() )
+ {
++ cat("************************************************************\n")
++ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
++ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
++ cat("************************************************************\n")
++ } else {
+ example.x.1 <- read.xls(exampleFileX, sheet=1) # default is first worksheet
+ print(example.x.1)
+
@@ -625,9 +631,6 @@
+ # load the third worksheet, skipping the first two non-data lines...
+ data <- read.xls(exampleFileX, sheet="Sheet with initial text", skip=2)
+ print(data)
-+ } else {
-+ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
-+ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
+ }
A B C
1 1 1 1
@@ -702,15 +705,15 @@
4 ThirdRow 3 2 1 NA Red
5 FourthRow 4 3 2 1 Black
>
-> if( 'XLSX' %in% xlsFormats() )
+> if(! 'XLSX' %in% xlsFormats() )
+ {
++ cat("************************************************************\n")
++ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
++ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
++ cat("************************************************************\n")
++ } else {
+ example.x.skip <- read.xls(exampleFileX, sheet=2, blank.lines.skip=FALSE)
+ example.x.skip
-+ } else {
-+ cat("************************************************************\n")
-+ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
-+ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
-+ cat("************************************************************\n")
+ }
X D E. F G Factor
1 FirstRow 1 NA NA NA Red
@@ -720,6 +723,7 @@
5 FourthRow 4 3 2 1 Black
>
>
+>
> ## Check handing of fileEncoding for latin-1 characters
>
> latin1File <- file.path(path.package('gdata'),'xls', 'latin-1.xls' )
@@ -738,8 +742,13 @@
+ stringsAsFactors=FALSE)
+ }
>
-> if( 'XLSX' %in% xlsFormats() )
+> if(! 'XLSX' %in% xlsFormats() )
+ {
++ cat("************************************************************\n")
++ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
++ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
++ cat("************************************************************\n")
++ } else {
+ if(.Platform$OS.type=="unix")
+ {
+ example.latin1.x <- read.xls(latin1FileX,
@@ -752,12 +761,7 @@
+ encoding='latin1',
+ stringsAsFactors=FALSE)
+ }
-+ } else {
-+ cat("************************************************************\n")
-+ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
-+ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
-+ cat("************************************************************\n")
-+ }
++ }
>
>
> ## Check handling of very wide file
@@ -768,13 +772,15 @@
> example.wide <- read.xls(wideFile)
> stopifnot(dim(example.wide)==c(0,256))
>
-> if( 'XLSX' %in% xlsFormats() )
+> if( !'XLSX' %in% xlsFormats() )
+ {
-+ example.wide.x <- read.xls(wideFileX)
-+ stopifnot(dim(example.wide.x)==c(0,16384))
++ cat("************************************************************\n")
++ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
++ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
++ cat("************************************************************\n")
+ } else {
-+ cat("** DIFF IN THIS SECTION IS EXPECTED BECAUSE PERL PACKAGES **\n")
-+ cat("** FOR SUPPORTING XLSX ARE NOT INSTALLED **\n")
++ example.wide.x <- read.xls(wideFileX)
++ stopifnot(dim(example.wide.x)==c(0,16384))
+ }
>
> ## Check handling of files with dates calulcated relative to
@@ -898,4 +904,4 @@
>
> proc.time()
user system elapsed
- 14.560 0.980 15.861
+ 13.495 0.834 14.549
Modified: pkg/gdata/tests/test.reorder.factor.Rout.save
===================================================================
--- pkg/gdata/tests/test.reorder.factor.Rout.save 2015-07-20 23:38:07 UTC (rev 2061)
+++ pkg/gdata/tests/test.reorder.factor.Rout.save 2015-07-22 00:48:51 UTC (rev 2062)
@@ -53,4 +53,4 @@
>
> proc.time()
user system elapsed
- 0.411 0.059 0.489
+ 0.341 0.046 0.381
Modified: pkg/gdata/tests/tests.write.fwf.Rout.save
===================================================================
--- pkg/gdata/tests/tests.write.fwf.Rout.save 2015-07-20 23:38:07 UTC (rev 2061)
+++ pkg/gdata/tests/tests.write.fwf.Rout.save 2015-07-22 00:48:51 UTC (rev 2062)
@@ -231,4 +231,4 @@
>
> proc.time()
user system elapsed
- 0.517 0.054 0.583
+ 0.426 0.048 0.462
Modified: pkg/gmodels/tests/lme-test.R
===================================================================
--- pkg/gmodels/test/lme-test.R 2015-06-29 22:40:22 UTC (rev 2055)
+++ pkg/gmodels/tests/lme-test.R 2015-07-22 00:48:51 UTC (rev 2062)
@@ -1,76 +1,76 @@
-library(gmodels)
-library(lme4)
-set.seed(314159)
+## library(gmodels)
+## library(lme4)
+## set.seed(314159)
-sleepstudy$dayGroup <- cut(sleepstudy$Days, seq(-1,9,by=2), include=T)
+## 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)
+## # 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...
+## # 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 )
+## # 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 )
-# Example from Ariel.Muldoon at oregonstate.edu
-homerange=c(
- "male","1","fall","0.1",
- "male","1","winter","0.3",
- "male","1","spring","5.2",
- "male","1","summer","3.1",
- "male","2","fall","3.4",
- "male","2","winter","1.3",
- "male","2","spring","4.8",
- "male","2","summer","4.3",
- "male","3","fall","3.9",
- "male","3","winter","3.8",
- "male","3","spring","5.7",
- "male","3","summer","2.0",
- "male","4","fall","3.7",
- "male","4","winter","4.3",
- "male","4","spring","6.0",
- "male","4","summer","1.8",
- "female","5","fall","4.3",
- "female","5","winter","1.9",
- "female","5","spring","7.2",
- "female","5","summer","6.9",
- "female","6","fall","5.3",
- "female","6","winter","4.3",
- "female","6","spring","6.2",
- "female","6","summer","4.8",
- "female","7","fall","7.1",
- "female","7","winter","4.9",
- "female","7","spring","8.3",
- "female","7","summer","7.7"
- )
-
-homerange <- data.frame(matrix(homerange,ncol=4, byrow=T))
-names(homerange) <- c("sex", "animal", "season", "area")
-homerange$area = as.numeric(as.character(homerange$area))
+## # Example from Ariel.Muldoon at oregonstate.edu
+## homerange=c(
+## "male","1","fall","0.1",
+## "male","1","winter","0.3",
+## "male","1","spring","5.2",
+## "male","1","summer","3.1",
+## "male","2","fall","3.4",
+## "male","2","winter","1.3",
+## "male","2","spring","4.8",
+## "male","2","summer","4.3",
+## "male","3","fall","3.9",
+## "male","3","winter","3.8",
+## "male","3","spring","5.7",
+## "male","3","summer","2.0",
+## "male","4","fall","3.7",
+## "male","4","winter","4.3",
+## "male","4","spring","6.0",
+## "male","4","summer","1.8",
+## "female","5","fall","4.3",
+## "female","5","winter","1.9",
+## "female","5","spring","7.2",
+## "female","5","summer","6.9",
+## "female","6","fall","5.3",
+## "female","6","winter","4.3",
+## "female","6","spring","6.2",
+## "female","6","summer","4.8",
+## "female","7","fall","7.1",
+## "female","7","winter","4.9",
+## "female","7","spring","8.3",
+## "female","7","summer","7.7"
+## )
-fit1 <- lmer(area ~ sex*season + (1|animal), data=homerange)
-summary(fit1)
-anova(fit1)
-
+## homerange <- data.frame(matrix(homerange,ncol=4, byrow=T))
+## names(homerange) <- c("sex", "animal", "season", "area")
+## homerange$area = as.numeric(as.character(homerange$area))
-#matrix to give estimable for making estimates
+## fit1 <- lmer(area ~ sex*season + (1|animal), data=homerange)
+## summary(fit1)
+## anova(fit1)
-spr <- rbind(c(1,0,1,0,0,0,0,0),
- c(1,1,0,0,0,1,0,0),
- c(1,0,0,1,0,0,0,0),
- c(1,1,0,0,0,0,1,0),
- c(1,0,0,0,1,0,0,0),
- c(1,1,0,0,0,0,0,1))
-
-estimable(fit1, spr)
+## #matrix to give estimable for making estimates
+
+## spr <- rbind(c(1,0,1,0,0,0,0,0),
+## c(1,1,0,0,0,1,0,0),
+## c(1,0,0,1,0,0,0,0),
+## c(1,1,0,0,0,0,1,0),
+## c(1,0,0,0,1,0,0,0),
+## c(1,1,0,0,0,0,0,1))
+
+
+## estimable(fit1, spr)
Modified: pkg/gplots/DESCRIPTION
===================================================================
--- pkg/gplots/DESCRIPTION 2015-07-20 23:38:07 UTC (rev 2061)
+++ pkg/gplots/DESCRIPTION 2015-07-22 00:48:51 UTC (rev 2062)
@@ -1,7 +1,7 @@
Package: gplots
Title: Various R Programming Tools for Plotting Data
Description: Various R programming tools for plotting data, including:
- - calculating and plotting locally smoothed summary functionas
+ - calculating and plotting locally smoothed summary functionals
('bandplot', 'wapply'),
- enhanced versions of standard plots ('barplot2', 'boxplot2',
'heatmap.2', 'smartlegend'),
@@ -14,11 +14,11 @@
- displaying textual data in plots ('textplot', 'sinkplot'),
- plotting a matrix where each cell contains a dot whose size
reflects the relative magnitude of the elements ('balloonplot'),
- - plotting venn diagrams ('venn'),
- - displaying Open-Office syle plots ('ooplot'),
- - plotting multiple datasets on same region, with separate axes
+ - plotting Venn diagrams ('venn'),
+ - displaying Open-Office style plots ('ooplot'),
+ - plotting multiple data sets on same region, with separate axes
('overplot'),
- - plotting means and cofidence intervals ('plotCI', 'plotmeans'),
+ - plotting means and confidence intervals ('plotCI', 'plotmeans'),
- spacing points in an x-y plot so they don't overlap ('space').
Depends: R (>= 3.0)
Imports: gtools, gdata, stats, caTools, KernSmooth
Modified: pkg/gplots/R/heatmap.2.R
===================================================================
--- pkg/gplots/R/heatmap.2.R 2015-07-20 23:38:07 UTC (rev 2061)
+++ pkg/gplots/R/heatmap.2.R 2015-07-22 00:48:51 UTC (rev 2062)
@@ -107,6 +107,9 @@
if(length(col)==1 && is.character(col) )
col <- get(col, mode="function")
+ if(!missing(breaks) && any(duplicated(breaks)) )
+ stop("breaks may not contian duplicate values")
+
if(!missing(breaks) && (scale!="none"))
warning("Using scale=\"row\" or scale=\"column\" when breaks are",
"specified can produce unpredictable results.",
@@ -384,14 +387,18 @@
on.exit(par(op))
layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
+ plot.index <- 1
+
## draw the side bars
if(!missing(RowSideColors)) {
par(mar = c(margins[1],0, 0,0.5))
image(rbind(1:nr), col = RowSideColors[rowInd], axes = FALSE)
+ plot.index <- plot.index + 1
}
if(!missing(ColSideColors)) {
par(mar = c(0.5,0, 0,margins[2]))
image(cbind(1:nc), col = ColSideColors[colInd], axes = FALSE)
+ plot.index <- plot.index + 1
}
## draw the main carpet
par(mar = c(margins[1], 0, 0, margins[2]))
@@ -576,6 +583,13 @@
col=notecol,
cex=notecex)
+ plot.index <- plot.index + 1
+
+ ## increment plot.index and then do
+ ## latout_set( lmat, plot.index )
+ ## to set to the correct plot region, instead of
+ ## relying on plot.new().
+
## the two dendrograms :
par(mar = c(margins[1], 0, 0, 0))
if( dendrogram %in% c("both","row") )
@@ -614,6 +628,7 @@
if(!is.null(main)) title(main, cex.main = 1.5*op[["cex.main"]])
## Add the color-key
+ browser()
if(key)
{
mar <- c(5, 4, 2, 1)
@@ -721,7 +736,6 @@
if (is.null(key.title))
title("Color Key")
-
if(trace %in% c("both","column") )
{
vline.vals <- scale01(vline, min.raw, max.raw)
Added: pkg/gplots/R/layout_set.R
===================================================================
--- pkg/gplots/R/layout_set.R (rev 0)
+++ pkg/gplots/R/layout_set.R 2015-07-22 00:48:51 UTC (rev 2062)
@@ -0,0 +1,13 @@
+layout_set <- function(mat, index)
+ {
+ mfg <- par("mfg")
+ mfg[1:2] = which(mat==index, arr.ind=TRUE)[1,]
+ par(mfg=mfg)
+ invisible(mfg)
+ }
+
+layout_show <- function(mat)
+ {
+ graphics::layout.show( max(mat) )
+ mat
+ }
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