[adegenet-commits] r988 - / pkg/inst pkg/man pkg/vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 18 17:41:31 CET 2012
Author: jombart
Date: 2012-01-18 17:41:30 +0100 (Wed, 18 Jan 2012)
New Revision: 988
Added:
adegenetSrcR.zip
pkg/vignettes/base-mon6.pdf
pkg/vignettes/base-njAA.pdf
pkg/vignettes/base-pcaaflp.pdf
pkg/vignettes/devilsign.png
pkg/vignettes/glsim1.png
pkg/vignettes/spca-globalrtest.pdf
pkg/vignettes/spca-screeplot.pdf
sourceAdegenet.R
Modified:
pkg/inst/CITATION
pkg/man/HWE.Rd
pkg/man/Hs.Rd
pkg/man/as-methods.Rd
pkg/man/chooseCN.Rd
pkg/man/colorplot.Rd
pkg/man/dapcIllus.Rd
pkg/man/dist.genpop.Rd
pkg/man/find.clusters.Rd
pkg/man/genind.Rd
pkg/man/genind2genpop.Rd
pkg/man/genpop.Rd
pkg/man/glPlot.Rd
pkg/man/inbreeding.Rd
pkg/man/isPoly.Rd
pkg/man/makefreq.Rd
pkg/man/na.replace.Rd
pkg/man/propTyped.Rd
pkg/man/read.PLINK.Rd
pkg/man/repool.Rd
pkg/man/scale.Rd
pkg/man/selpopsize.Rd
pkg/man/seqTrack.Rd
pkg/man/sequences.Rd
pkg/man/spca.Rd
Log:
preparing for new release (1.3-4)
Added: adegenetSrcR.zip
===================================================================
(Binary files differ)
Property changes on: adegenetSrcR.zip
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: pkg/inst/CITATION
===================================================================
--- pkg/inst/CITATION 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/inst/CITATION 2012-01-18 16:41:30 UTC (rev 988)
@@ -11,3 +11,16 @@
doi = "10.1093/bioinformatics/btn129",
textVersion = "Jombart, T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403-1405. doi: 10.1093/bioinformatics/btn129"
)
+
+
+citEntry(
+entry="Article",
+title = "adegenet 1.3-1: new tools for the analysis of genome-wide SNP data",
+journal= "Bioinformatics",
+year = "2011",
+author = "T. Jombart and I. Ahmed",
+volume = "",
+pages = "",
+doi = "10.1093/bioinformatics/btr521",
+textVersion = "Jombart T. and Ahmed I. (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. doi: 10.1093/bioinformatics/btr521"
+)
Modified: pkg/man/HWE.Rd
===================================================================
--- pkg/man/HWE.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/HWE.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -52,6 +52,7 @@
}
\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
+\dontrun{
data(nancycats)
obj <- nancycats
if(require(genetics)){
@@ -64,5 +65,6 @@
obj.test$fca90$P10
}
}
+}
\keyword{manip}
\keyword{multivariate}
\ No newline at end of file
Modified: pkg/man/Hs.Rd
===================================================================
--- pkg/man/Hs.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/Hs.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -28,7 +28,9 @@
\value{A vector of Hs values (one value per population).}
\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
+\dontrun{
data(nancycats)
Hs(genind2genpop(nancycats))
}
+}
\keyword{multivariate}
\ No newline at end of file
Modified: pkg/man/as-methods.Rd
===================================================================
--- pkg/man/as-methods.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/as-methods.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -51,6 +51,7 @@
}
\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
\examples{
+\dontrun{
data(microbov)
x <- na.replace(microbov,method="0")
as(x[1:3],"data.frame")
@@ -71,4 +72,5 @@
plot(statis1)
}
}
+}
\keyword{methods}
\ No newline at end of file
Modified: pkg/man/chooseCN.Rd
===================================================================
--- pkg/man/chooseCN.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/chooseCN.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -68,6 +68,7 @@
}
\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
+\dontrun{
data(nancycats)
if(require(spdep) & require(ade4)){
@@ -79,5 +80,6 @@
par(mfrow=c(1,1))
}
}
+}
\keyword{spatial}
\keyword{utilities}
\ No newline at end of file
Modified: pkg/man/colorplot.Rd
===================================================================
--- pkg/man/colorplot.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/colorplot.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -49,6 +49,7 @@
df <- data.frame(x=1:100, y=100:1, z=runif(100,0,100))
colorplot(xy,df,cex=10,main="colorplot: toy example")
+\dontrun{
# a genetic example using a sPCA
if(require(spdep) & require(ade4)){
data(spcaIllus)
@@ -59,5 +60,6 @@
mtext("P1-P2 in cline\tP3 random \tP4 local repulsion")
}
}
+}
\keyword{multivariate}
\keyword{hplot}
Modified: pkg/man/dapcIllus.Rd
===================================================================
--- pkg/man/dapcIllus.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/dapcIllus.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -46,6 +46,7 @@
structured populations. Submitted to \emph{Genetics}.
}
\examples{
+\dontrun{
if(require(MASS) & require(ade4)){
data(dapcIllus)
@@ -88,4 +89,5 @@
detach(dapcIllus)
}
}
+}
\keyword{datasets}
Modified: pkg/man/dist.genpop.Rd
===================================================================
--- pkg/man/dist.genpop.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/dist.genpop.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -105,6 +105,7 @@
\seealso{ \code{\link[ade4]{cailliez}},\code{\link[ade4]{dudi.pco}}
}
\examples{
+\dontrun{
if(require(ade4)){
data(microsatt)
obj <- as.genpop(microsatt$tab)
@@ -117,4 +118,5 @@
for(i in 1:5) {scatter(listPco[[i]],sub=paste("Dist:", i))}
}
}
+}
\keyword{multivariate}
Modified: pkg/man/find.clusters.Rd
===================================================================
--- pkg/man/find.clusters.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/find.clusters.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -242,9 +242,9 @@
## and then, to plot BIC values:
plot(grp$Kstat, type="b", col="blue")
-}
+
## ANOTHER SIMPLE EXAMPLE ##
data(sim2pop) # this actually contains 2 pop
@@ -277,6 +277,6 @@
plot(x)
grp <- find.clusters(x, n.pca=100, choose=FALSE, stat="BIC")
plot(grp$Kstat, type="o", xlab="number of clusters (K)",ylab="BIC",main="find.clusters on a genlight object\n(two groups)")
-
}
+}
\keyword{multivariate}
Modified: pkg/man/genind.Rd
===================================================================
--- pkg/man/genind.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/genind.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -86,7 +86,6 @@
gtest
plot(gtest)
}
-}
# perform a between-class PCA
if(require(ade4)){
@@ -98,6 +97,7 @@
add.scatter.eig(pcabet1$eig,2,xax=1,yax=2)
}
}
+}
\keyword{classes}
\keyword{manip}
\keyword{multivariate}
Modified: pkg/man/genind2genpop.Rd
===================================================================
--- pkg/man/genind2genpop.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/genind2genpop.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -56,11 +56,11 @@
}
\examples{
## simple conversion
- data(nancycats)
- nancycats
- catpop <- genind2genpop(nancycats)
- catpop
- summary(catpop)
+data(nancycats)
+nancycats
+catpop <- genind2genpop(nancycats)
+catpop
+summary(catpop)
## processing the @other slot
data(sim2pop)
Modified: pkg/man/genpop.Rd
===================================================================
--- pkg/man/genpop.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/genpop.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -61,6 +61,7 @@
obj2 <- genind2genpop(obj1)
obj2
+\dontrun{
if(require(ade4)){
data(microsatt)
# use as.genpop to convert convenient count tab to genpop
@@ -78,6 +79,7 @@
add.scatter.eig(ca1$eig,2,xax=1,yax=2,posi="top")
}
}
+}
\keyword{classes}
\keyword{manip}
\keyword{multivariate}
Modified: pkg/man/glPlot.Rd
===================================================================
--- pkg/man/glPlot.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/glPlot.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -46,6 +46,7 @@
}
\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
+\dontrun{
## simulate data
x <- glSim(100, 1e3, n.snp.struc=100, ploid=2)
@@ -58,6 +59,6 @@
## use other colors
plot(x, col=heat.colors(3), bg="white")
-
}
+}
\keyword{multivariate}
\ No newline at end of file
Modified: pkg/man/inbreeding.Rd
===================================================================
--- pkg/man/inbreeding.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/inbreeding.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -61,6 +61,7 @@
Thibaut Jombart \email{t.jombart at imperial.ac.uk}\cr
}
\examples{
+\dontrun{
## cattle breed microsatellite data
data(microbov)
@@ -85,5 +86,5 @@
## plot the first 10 functions
invisible(sapply(Fdens[1:10], plot, ylab="Density", main="Density of probability of F values"))
-
+}
}
\ No newline at end of file
Modified: pkg/man/isPoly.Rd
===================================================================
--- pkg/man/isPoly.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/isPoly.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -26,10 +26,12 @@
}
\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
+\dontrun{
data(nancycats)
isPoly(nancycats,by="loc", thres=0.1)
isPoly(nancycats[1:3],by="loc", thres=0.1)
genind2df(nancycats[1:3])
}
+}
\keyword{methods}
\keyword{manip}
Modified: pkg/man/makefreq.Rd
===================================================================
--- pkg/man/makefreq.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/makefreq.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -33,6 +33,7 @@
}
\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
+\dontrun{
data(microbov)
obj1 <- microbov
@@ -55,5 +56,6 @@
add.scatter.eig(pca1$eig,nf=2,xax=1,yax=2,posi="top")
}
}
+}
\keyword{manip}
\keyword{multivariate}
Modified: pkg/man/na.replace.Rd
===================================================================
--- pkg/man/na.replace.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/na.replace.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -43,6 +43,7 @@
}
\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
+\dontrun{
data(nancycats)
obj1 <- genind2genpop(nancycats)
@@ -60,5 +61,6 @@
# missing values where replaced
truenames(obj2)[,obj2$loc.fac=="L4"]
}
+}
\keyword{methods}
\keyword{manip}
Modified: pkg/man/propTyped.Rd
===================================================================
--- pkg/man/propTyped.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/propTyped.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -38,9 +38,11 @@
}
\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
+\dontrun{
data(nancycats)
propTyped(nancycats,by="loc")
propTyped(genind2genpop(nancycats),by="both")
}
+}
\keyword{methods}
\keyword{manip}
Modified: pkg/man/read.PLINK.Rd
===================================================================
--- pkg/man/read.PLINK.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/read.PLINK.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -106,7 +106,4 @@
\code{snpMatrix}.
}
\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
-% \examples{
-
-% }
\keyword{manip}
Modified: pkg/man/repool.Rd
===================================================================
--- pkg/man/repool.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/repool.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -27,6 +27,7 @@
\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\seealso{\code{\link{seploc}}, \code{\link{seppop}}}
\examples{
+\dontrun{
## use the cattle breeds dataset
data(microbov)
temp <- seppop(microbov)
@@ -40,4 +41,5 @@
nastyCattle <- repool(microbov, zebler)
nastyCattle
}
+}
\keyword{manip}
Modified: pkg/man/scale.Rd
===================================================================
--- pkg/man/scale.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/scale.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -49,6 +49,7 @@
}
\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
+\dontrun{
## load data
data(microbov)
obj <- genind2genpop(microbov)
@@ -82,5 +83,6 @@
s.match(pro1$scor1,pro1$scor2,clab=0,sub="usual -> binom (procustean rotation)")
}
}
+}
\keyword{methods}
\keyword{manip}
Modified: pkg/man/selpopsize.Rd
===================================================================
--- pkg/man/selpopsize.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/selpopsize.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -28,6 +28,7 @@
\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\seealso{\code{\link{seploc}}, \code{\link{repool}}}
\examples{
+\dontrun{
data(microbov)
table(pop(microbov))
@@ -35,6 +36,6 @@
obj
table(pop(obj))
-
}
+}
\keyword{manip}
\ No newline at end of file
Modified: pkg/man/seqTrack.Rd
===================================================================
--- pkg/man/seqTrack.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/seqTrack.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -150,6 +150,7 @@
\code{\link[ape]{dist.dna}} in the ape package to compute pairwise genetic distances in aligned sequences.
}
\examples{
+\dontrun{
if(require(ape)){
## ANALYSIS OF SIMULATED DATA ##
## SIMULATE A GENEALOGY
@@ -165,7 +166,6 @@
## PLOT RESULTS
-\dontrun{
if(require(graph) && require(Rgraphviz)){
## quick convertion method to graphNEL ##
setOldClass("seqTrack")
Modified: pkg/man/sequences.Rd
===================================================================
--- pkg/man/sequences.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/sequences.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -38,6 +38,7 @@
}
\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
+\dontrun{
if(require(ape)){
data(woodmouse)
x <- DNAbin2genind(woodmouse)
@@ -65,4 +66,5 @@
}
}
}
+}
\keyword{manip}
Modified: pkg/man/spca.Rd
===================================================================
--- pkg/man/spca.Rd 2012-01-18 16:14:16 UTC (rev 987)
+++ pkg/man/spca.Rd 2012-01-18 16:41:30 UTC (rev 988)
@@ -172,8 +172,7 @@
of Moran's I and Geary's c. \emph{Geographical Analysis}, \bold{16}, 17--24.
}
-\seealso{\code{\link{spcaIllus}}, a set of simulated data illustrating
- the sPCA \cr
+\seealso{\code{\link{spcaIllus}} and \code{\link{rupica}} for datasets illustrating the sPCA \cr
\code{\link{global.rtest}} and \code{\link{local.rtest}} \cr
\code{\link{chooseCN}}, \code{\link[ade4]{multispati}},
\code{\link[ade4]{multispati.randtest}}\cr
@@ -185,9 +184,10 @@
## data(spcaIllus) illustrates the sPCA
## see ?spcaIllus
##
-
+\dontrun{
example(spcaIllus)
-
+example(rupica)
}
+}
\keyword{spatial}
\keyword{multivariate}
\ No newline at end of file
Added: pkg/vignettes/base-mon6.pdf
===================================================================
--- pkg/vignettes/base-mon6.pdf (rev 0)
+++ pkg/vignettes/base-mon6.pdf 2012-01-18 16:41:30 UTC (rev 988)
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+00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
+00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
+00 00 00 11 63 70 72 74 00 00 01 50 00 00 00 33
+64 65 73 63 00 00 01 84 00 00 00 6c 77 74 70 74
+00 00 01 f0 00 00 00 14 62 6b 70 74 00 00 02 04
+00 00 00 14 72 58 59 5a 00 00 02 18 00 00 00 14
+67 58 59 5a 00 00 02 2c 00 00 00 14 62 58 59 5a
+00 00 02 40 00 00 00 14 64 6d 6e 64 00 00 02 54
+00 00 00 70 64 6d 64 64 00 00 02 c4 00 00 00 88
+76 75 65 64 00 00 03 4c 00 00 00 86 76 69 65 77
+00 00 03 d4 00 00 00 24 6c 75 6d 69 00 00 03 f8
+00 00 00 14 6d 65 61 73 00 00 04 0c 00 00 00 24
+74 65 63 68 00 00 04 30 00 00 00 0c 72 54 52 43
+00 00 04 3c 00 00 08 0c 67 54 52 43 00 00 04 3c
+00 00 08 0c 62 54 52 43 00 00 04 3c 00 00 08 0c
+74 65 78 74 00 00 00 00 43 6f 70 79 72 69 67 68
+74 20 28 63 29 20 31 39 39 38 20 48 65 77 6c 65
+74 74 2d 50 61 63 6b 61 72 64 20 43 6f 6d 70 61
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/adegenet -r 988
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