[adegenet-commits] r987 - in pkg: . R man vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed Jan 18 17:14:17 CET 2012 

Author: jombart
Date: 2012-01-18 17:14:16 +0100 (Wed, 18 Jan 2012)
New Revision: 987

Added:
   pkg/vignettes/
   pkg/vignettes/Rplots.pdf
   pkg/vignettes/adegenet-basics.Rnw
   pkg/vignettes/adegenet-basics.pdf
   pkg/vignettes/adegenet-dapc.Rnw
   pkg/vignettes/adegenet-dapc.pdf
   pkg/vignettes/adegenet-dapc.tex
   pkg/vignettes/adegenet-genomics.Rnw
   pkg/vignettes/adegenet-genomics.pdf
   pkg/vignettes/adegenet-spca.Rnw
   pkg/vignettes/adegenet-spca.pdf
   pkg/vignettes/ascore.pdf
   pkg/vignettes/base-caexpl.pdf
   pkg/vignettes/base-mon1.pdf
   pkg/vignettes/base-mon4.pdf
   pkg/vignettes/base-sumry.pdf
   pkg/vignettes/densIbd.png
   pkg/vignettes/eigen-dapc.pdf
   pkg/vignettes/findclust-bic.pdf
   pkg/vignettes/findclust-noclearcut.pdf
   pkg/vignettes/findclust-pca.pdf
   pkg/vignettes/glsim2.png
   pkg/vignettes/loadingplotGL.png
   pkg/vignettes/monthres1.png
   pkg/vignettes/monthres2.png
   pkg/vignettes/pca1.pdf
   pkg/vignettes/rupicacolors.png
   pkg/vignettes/spca-boxplot.pdf
   pkg/vignettes/spca-colorplot.pdf
   pkg/vignettes/spca-localrtest.pdf
   pkg/vignettes/spca-plotspca.pdf
   pkg/vignettes/spca-plotspca.png
   pkg/vignettes/spca-svaluedem.pdf
Modified:
   pkg/DESCRIPTION
   pkg/R/zzz.R
   pkg/man/adegenet.package.Rd
Log:
moving vignettes from inst/doc/ to vignettes/


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2012-01-09 10:47:07 UTC (rev 986)
+++ pkg/DESCRIPTION	2012-01-18 16:14:16 UTC (rev 987)
@@ -8,7 +8,7 @@
   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, splancs
-Depends: R (>= 2.3.0), methods, MASS, ade4
+Depends: R (>= 2.10), 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
 License: GPL (>=2)

Modified: pkg/R/zzz.R
===================================================================
--- pkg/R/zzz.R	2012-01-09 10:47:07 UTC (rev 986)
+++ pkg/R/zzz.R	2012-01-18 16:14:16 UTC (rev 987)
@@ -2,7 +2,9 @@
 #.initAdegenetClasses()
 #.initAdegenetUtils()
     library.dynam("adegenet", pkg, lib)
-    startup.txt <- "   ==========================\n    adegenet 1.3-4 is loaded\n   ==========================\n\n - to start, type '?adegenet'\n - to browse adegenet website, type 'adegenetWeb()'\n - to post questions/comments: adegenet-forum at lists.r-forge.r-project.org\n\n"
+    pkg.version <- packageDescription("adegenet", fields = "Version")
 
+    startup.txt <- paste("   ==========================\n    adegenet", pkg.version, "is loaded\n   ==========================\n\n - to start, type '?adegenet'\n - to browse adegenet website, type 'adegenetWeb()'\n - to post questions/comments: adegenet-forum at lists.r-forge.r-project.org\n\n")
+
     packageStartupMessage(startup.txt)
 }

Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd	2012-01-09 10:47:07 UTC (rev 986)
+++ pkg/man/adegenet.package.Rd	2012-01-18 16:14:16 UTC (rev 987)
@@ -190,7 +190,7 @@
   \tabular{ll}{
     Package: \tab adegenet\cr
     Type: \tab Package\cr
-    Version: \tab 1.3-3\cr
+    Version: \tab 1.3-4\cr
     Date: \tab 2011-12-21 \cr
     License: \tab GPL (>=2)
   } 

Added: pkg/vignettes/Rplots.pdf
===================================================================
--- pkg/vignettes/Rplots.pdf	                        (rev 0)
+++ pkg/vignettes/Rplots.pdf	2012-01-18 16:14:16 UTC (rev 987)
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 987

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