[adegenet-commits] r927 - in pkg: . inst/doc inst/doc/Robjects inst/doc/figs man src

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Fri Jun 24 09:54:10 CEST 2011 

Author: jombart
Date: 2011-06-24 09:54:07 +0200 (Fri, 24 Jun 2011)
New Revision: 927

Removed:
   pkg/inst/doc/Robjects/dapcGL.RData
   pkg/inst/doc/Robjects/x.RData
Modified:
   pkg/DESCRIPTION
   pkg/inst/doc/adegenet-genomics.Rnw
   pkg/inst/doc/adegenet-genomics.pdf
   pkg/inst/doc/adegenet-genomics.tex
   pkg/inst/doc/adegenet-spca.Rnw
   pkg/inst/doc/adegenet-spca.pdf
   pkg/inst/doc/adegenet-spca.tex
   pkg/inst/doc/figs/genomics-027.pdf
   pkg/inst/doc/figs/genomics-030.pdf
   pkg/inst/doc/figs/genomics-037.pdf
   pkg/inst/doc/figs/genomics-038.pdf
   pkg/inst/doc/figs/genomics-044.pdf
   pkg/inst/doc/figs/genomics-053.pdf
   pkg/inst/doc/figs/genomics-055.pdf
   pkg/inst/doc/figs/genomics-056.pdf
   pkg/inst/doc/figs/spca-009.pdf
   pkg/inst/doc/figs/spca-022.png
   pkg/inst/doc/figs/spca-023.png
   pkg/inst/doc/figs/spca-024.png
   pkg/inst/doc/figs/spca-025.pdf
   pkg/inst/doc/figs/spca-029.png
   pkg/inst/doc/figs/spca-035.pdf
   pkg/inst/doc/figs/spca-040.png
   pkg/inst/doc/figs/spca-044.pdf
   pkg/inst/doc/figs/spca-045.pdf
   pkg/inst/doc/figs/spca-046.pdf
   pkg/inst/doc/figs/spca-047.pdf
   pkg/inst/doc/figs/spca-051.png
   pkg/inst/doc/figs/spca-052.png
   pkg/inst/doc/figs/spca-boxplot.pdf
   pkg/inst/doc/figs/spca-colorplot.pdf
   pkg/inst/doc/figs/spca-globalrtest.pdf
   pkg/inst/doc/figs/spca-localrtest.pdf
   pkg/inst/doc/figs/spca-screeplot.pdf
   pkg/inst/doc/figs/spca-svaluedem.pdf
   pkg/man/dapc.Rd
   pkg/man/dapcGraphics.Rd
   pkg/man/hybridize.Rd
   pkg/man/inbreeding.Rd
   pkg/man/microbov.Rd
   pkg/man/propShared.Rd
   pkg/src/snpbin.c
Log:
Modifications of the new release.


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2011-06-22 16:48:34 UTC (rev 926)
+++ pkg/DESCRIPTION	2011-06-24 07:54:07 UTC (rev 927)
@@ -7,7 +7,7 @@
   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, multicore
+Suggests: genetics, spdep, tripack, ape, pegas, seqinr, multicore, adehabitat
 Depends: 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

Deleted: pkg/inst/doc/Robjects/dapcGL.RData
===================================================================
(Binary files differ)

Deleted: pkg/inst/doc/Robjects/x.RData
===================================================================
(Binary files differ)

Modified: pkg/inst/doc/adegenet-genomics.Rnw
===================================================================
--- pkg/inst/doc/adegenet-genomics.Rnw	2011-06-22 16:48:34 UTC (rev 926)
+++ pkg/inst/doc/adegenet-genomics.Rnw	2011-06-24 07:54:07 UTC (rev 927)
@@ -966,24 +966,13 @@
 allele frequencies at a time, thereby minimizing RAM requirements.
 \\
 
-Below, we illustrate DAPC on a \texttt{genlight} including only 50 structured SNPs out of 100,000
+Below, we illustrate DAPC on a \texttt{genlight} including only 50 structured SNPs out of 50,000
 non-structured SNPs:
-<<eval=FALSE>>=
-x <- glSim(100, 1e5, 50)
-@
-<<echo=FALSE>>=
-load("Robjects/x.RData")
-load("Robjects/dapcGL.RData")
-@
 <<>>=
+x <- glSim(100, 5e4, 50)
 x
-@
-<<eval=FALSE>>=
 dapc1 <- dapc(x, n.pca=20, n.da=1)
 @
-<<>>=
-dapc1
-@
 
 For the last 50 structured SNPs (located at the end of the alignment), the two groups of individuals have different (random) distribution of
 allele frequencies, while they share the same distributions in other loci.

Modified: pkg/inst/doc/adegenet-genomics.pdf
===================================================================
--- pkg/inst/doc/adegenet-genomics.pdf	2011-06-22 16:48:34 UTC (rev 926)
+++ pkg/inst/doc/adegenet-genomics.pdf	2011-06-24 07:54:07 UTC (rev 927)
@@ -122,16 +122,9 @@
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 S
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 927

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