[adegenet-commits] r940 - in pkg: R inst/doc man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon Jul 4 22:58:08 CEST 2011 

Author: jombart
Date: 2011-07-04 22:58:07 +0200 (Mon, 04 Jul 2011)
New Revision: 940

Added:
   pkg/inst/doc/Rplots.pdf
   pkg/inst/doc/ascore.pdf
   pkg/inst/doc/base-caexpl.pdf
   pkg/inst/doc/base-mon1.pdf
   pkg/inst/doc/base-mon4.pdf
   pkg/inst/doc/base-mon6.pdf
   pkg/inst/doc/base-njAA.pdf
   pkg/inst/doc/base-pcaaflp.pdf
   pkg/inst/doc/base-sumry.pdf
   pkg/inst/doc/densIbd.png
   pkg/inst/doc/devilsign.png
   pkg/inst/doc/eigen-dapc.pdf
   pkg/inst/doc/findclust-bic.pdf
   pkg/inst/doc/findclust-noclearcut.pdf
   pkg/inst/doc/findclust-pca.pdf
   pkg/inst/doc/glsim1.png
   pkg/inst/doc/glsim2.png
   pkg/inst/doc/loadingplotGL.png
   pkg/inst/doc/monthres1.png
   pkg/inst/doc/monthres2.png
   pkg/inst/doc/pca1.pdf
   pkg/inst/doc/rupicacolors.png
   pkg/inst/doc/spca-boxplot.pdf
   pkg/inst/doc/spca-colorplot.pdf
   pkg/inst/doc/spca-globalrtest.pdf
   pkg/inst/doc/spca-localrtest.pdf
   pkg/inst/doc/spca-plotspca.pdf
   pkg/inst/doc/spca-plotspca.png
   pkg/inst/doc/spca-screeplot.pdf
   pkg/inst/doc/spca-svaluedem.pdf
Removed:
   pkg/inst/doc/figs/
Modified:
   pkg/R/dapc.R
   pkg/inst/doc/adegenet-basics.Rnw
   pkg/inst/doc/adegenet-dapc.Rnw
   pkg/inst/doc/adegenet-genomics.Rnw
   pkg/inst/doc/adegenet-spca.Rnw
   pkg/man/read.structure.Rd
Log:
Removed the /figs directory; moved all required figures (not produced by the vignette) to /doc.
New package size 8.5MB. Passes the check with no warning.


Modified: pkg/R/dapc.R
===================================================================
--- pkg/R/dapc.R	2011-07-04 17:42:08 UTC (rev 939)
+++ pkg/R/dapc.R	2011-07-04 20:58:07 UTC (rev 940)
@@ -570,7 +570,13 @@
     ## group legend
     if(legend){
         ## add a legend
-        legend(posi.leg, fill=col, legend=txt.leg, cex=cleg, bg=bg.inset)
+        temp <- list(...)$cex
+        if(is.null(temp)) temp <- 1
+        if(ONEDIM | temp<0.5 | all(pch=="")) {
+            legend(posi.leg, fill=col, legend=txt.leg, cex=cleg, bg=bg.inset)
+        } else {
+            legend(posi.leg, col=col, legend=txt.leg, cex=cleg, bg=bg.inset, pch=pch, pt.cex=temp)
+        }
     }
 
     ## eigenvalues discriminant analysis

Added: pkg/inst/doc/Rplots.pdf
===================================================================
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 940

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