[adegenet-commits] r983 - in pkg: . inst/doc man src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Dec 22 20:46:24 CET 2011
Author: jombart
Date: 2011-12-22 20:46:24 +0100 (Thu, 22 Dec 2011)
New Revision: 983
Modified:
pkg/DESCRIPTION
pkg/inst/doc/adegenet-spca.Rnw
pkg/man/H3N2.Rd
pkg/man/glAux.Rd
pkg/man/glPca.Rd
pkg/man/glSim.Rd
pkg/man/spca.Rd
pkg/src/sharedAll.c
Log:
Fixes for the new release.
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2011-12-21 19:01:48 UTC (rev 982)
+++ pkg/DESCRIPTION 2011-12-22 19:46:24 UTC (rev 983)
@@ -1,13 +1,13 @@
Package: adegenet
Version: 1.3-3
-Date: 2011/11/11
+Date: 2011/12/22
Title: adegenet: an R package for the exploratory analysis of genetic and genomic data.
Author: Thibaut Jombart <t.jombart at imperial.ac.uk>
with contributions of: Ismail Ahmed <ismail.ahmed at inserm.fr>, Peter Solymos
and contributed datasets from: Katayoun Moazami-Goudarzi, Denis Laloe,
Dominique Pontier, Daniel Maillard, Francois Balloux
Maintainer: Thibaut Jombart <t.jombart at imperial.ac.uk>
-Suggests: genetics, spdep, tripack, ape, pegas, seqinr, adehabitat, multicore, akima, maps
+Suggests: genetics, spdep, tripack, ape, pegas, seqinr, adehabitat, multicore, akima, maps, splancs
Depends: R (>= 2.3.0), methods, MASS, ade4
Description: Classes and functions for genetic data analysis within the multivariate framework.
Collate: classes.R basicMethods.R handling.R auxil.R setAs.R SNPbin.R glHandle.R glFunctions.R glSim.R find.clust.R hybridize.R scale.R fstat.R import.R seqTrack.R chooseCN.R genind2genpop.R loadingplot.R sequences.R gstat.randtest.R makefreq.R colorplot.R monmonier.R spca.R coords.monmonier.R haploGen.R old2new.R spca.rtests.R dapc.R haploPop.R PCtest.R dist.genpop.R Hs.R propShared.R export.R HWE.R propTyped.R inbreeding.R glPlot.R zzz.R
Modified: pkg/inst/doc/adegenet-spca.Rnw
===================================================================
--- pkg/inst/doc/adegenet-spca.Rnw 2011-12-21 19:01:48 UTC (rev 982)
+++ pkg/inst/doc/adegenet-spca.Rnw 2011-12-22 19:46:24 UTC (rev 983)
@@ -154,9 +154,6 @@
In \textit{adegenet}, the matrix of alleles frequencies previously
denoted $\m{X}$ exactly corresponds to the \texttt{@tab} slot of \texttt{genind} or
\texttt{genpop} objects:
-<<echo=FALSE,print=FALSE,results=hide>>=
-if(!require(adehabitat)) install.packages("adehabitat", repos="http://cran.at.r-project.org")
-@
<<print=FALSE,echo=FALSE,results=hide>>=
library(adehabitat)
library(spdep)
Modified: pkg/man/H3N2.Rd
===================================================================
--- pkg/man/H3N2.Rd 2011-12-21 19:01:48 UTC (rev 982)
+++ pkg/man/H3N2.Rd 2011-12-22 19:46:24 UTC (rev 983)
@@ -46,6 +46,7 @@
genetically structured populations. Submitted to \emph{BMC genetics}.
}
\examples{
+\dontrun{
#### H3N2 ####
## LOAD DATA
data(H3N2)
@@ -83,6 +84,6 @@
## see ?fasta2genlight for more details
obj <- fasta2genlight(myPath, chunk=10) # process 10 sequences at a time
obj
-
}
+}
\keyword{datasets}
Modified: pkg/man/glAux.Rd
===================================================================
--- pkg/man/glAux.Rd 2011-12-21 19:01:48 UTC (rev 982)
+++ pkg/man/glAux.Rd 2011-12-22 19:46:24 UTC (rev 983)
@@ -82,7 +82,7 @@
}
\seealso{
- - \code{\link{genlight}}: class of object for storing massive binary
+ - \code{\linkS4class{genlight}}: class of object for storing massive binary
SNP data.
- \code{\link{dapc}}: Discriminant Analysis of Principal Components.
Modified: pkg/man/glPca.Rd
===================================================================
--- pkg/man/glPca.Rd 2011-12-21 19:01:48 UTC (rev 982)
+++ pkg/man/glPca.Rd 2011-12-22 19:46:24 UTC (rev 983)
@@ -155,7 +155,7 @@
}
\seealso{
- - \code{\link{genlight}}: class of object for storing massive binary
+ - \code{\linkS4class{genlight}}: class of object for storing massive binary
SNP data.
- \code{\link{glSim}}: a simple simulator for \linkS4class{genlight} objects.
Modified: pkg/man/glSim.Rd
===================================================================
--- pkg/man/glSim.Rd 2011-12-21 19:01:48 UTC (rev 982)
+++ pkg/man/glSim.Rd 2011-12-22 19:46:24 UTC (rev 983)
@@ -80,7 +80,7 @@
}
\seealso{
- - \code{\link{genlight}}: class of object for storing massive binary
+ - \code{\linkS4class{genlight}}: class of object for storing massive binary
SNP data.
- \code{\link{glPlot}}: plotting \linkS4class{genlight} objects.
@@ -97,6 +97,7 @@
x <- glSim(100, 1e3, n.snp.struc=100, ploid=2)
plot(x)
+\dontrun{
## 1,000 non structured SNPs, 100 structured SNPs, ploidy=4
x <- glSim(100, 1e3, n.snp.struc=100, ploid=4)
plot(x)
@@ -108,6 +109,6 @@
## same thing, loci with LD structures
x <- glSim(100, 1e3, n.snp.struc=100, ploid=2, alpha=0.4, LD=TRUE, block.size=100)
plot(x)
-
}
+}
\keyword{multivariate}
\ No newline at end of file
Modified: pkg/man/spca.Rd
===================================================================
--- pkg/man/spca.Rd 2011-12-21 19:01:48 UTC (rev 982)
+++ pkg/man/spca.Rd 2011-12-22 19:46:24 UTC (rev 983)
@@ -177,7 +177,7 @@
\code{\link{global.rtest}} and \code{\link{local.rtest}} \cr
\code{\link{chooseCN}}, \code{\link[ade4]{multispati}},
\code{\link[ade4]{multispati.randtest}}\cr
- \code{\link[PBSmapping]{convUL}}, from the package 'PBSmapping' to convert longitude/latitude to
+ \code{convUL}, from the package 'PBSmapping' to convert longitude/latitude to
UTM coordinates.
}
\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
Modified: pkg/src/sharedAll.c
===================================================================
--- pkg/src/sharedAll.c 2011-12-21 19:01:48 UTC (rev 982)
+++ pkg/src/sharedAll.c 2011-12-22 19:46:24 UTC (rev 983)
@@ -19,7 +19,7 @@
#include "adesub.h"
-
+/* THIS FUNCTION IS DEPRECATED */
void sharedAll(int *matAll, int *nRow, int *nCol, double *resVec)
{
/* Declare local C variables */
@@ -113,9 +113,16 @@
+/* SMALL FUNCTION TO RETURN THE SMALLEST OF 2 INTEGERS */
+int min_int(int a, int b){
+ if(a<b) return a;
+ return b;
+}
+
+/* THIS IS THE FUNCTION TO USE */
void nb_shared_all(int *in, int *out, int *nind, int *ncol){
int i, j, k, counter=0, **mat, n = *nind, p = *ncol;
@@ -132,11 +139,6 @@
/* perform computations */
- int min_int(int a, int b){
- if(a<b) return a;
- return b;
- }
-
counter = 0;
for(i=1;i<=(n-1);i++){
for(j=i+1;j<=n;j++){
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