[adegenet-commits] r441 - pkg pkg/R www www/files

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Sep 8 01:53:25 CEST 2009


Author: jombart
Date: 2009-09-08 01:53:24 +0200 (Tue, 08 Sep 2009)
New Revision: 441

Added:
   www/files/globaldiv-PC.1.3.pdf
   www/files/globaldiv-PC.1.3.rnw
   www/files/globaldiv-TJ.1.3.odp
   www/files/globaldiv-TJ.1.3.pdf
Modified:
   pkg/R/haploSim.R
   pkg/TODO
   www/documentation.html
Log:
added files for the globaldiv summer school


Modified: pkg/R/haploSim.R
===================================================================
--- pkg/R/haploSim.R	2009-09-07 10:20:47 UTC (rev 440)
+++ pkg/R/haploSim.R	2009-09-07 23:53:24 UTC (rev 441)
@@ -248,28 +248,29 @@
         res$xy <- matrix(rep(locStart, ini.n), byrow=TRUE, nrow=ini.n)
         colnames(res$xy) <- c("x","y")
 
-        cat("nb.strains","iteration.time",file="haploSimTime.out") # for debugging
+        ##cat("nb.strains","iteration.time",file="haploSimTime.out") # for debugging
 
 
         ## simulations: isn't simplicity beautiful?
         while(any(toExpand)){
-            time.previous <- Sys.time() # FOR DEBUGGING
+            ##time.previous <- Sys.time() # FOR DEBUGGING
             idx <- min(which(toExpand))
             expand.one.strain.xy(res$seq[idx,], res$dates[idx], idx, res$xy[idx,])
             resize.result.xy()
             ## VERBOSE OUTPUT FOR DEBUGGING ##
-            cat("\nNb strains:",length(res$ances),"/",max.nb.haplo)
-            cat("\nLatest date:", max(res$dates),"/",Tmax)
-            cat("\nRemaining strains to duplicate", sum(toExpand))
-            cat("\n",append=TRUE,file="haploSimTime.out")
-            iter.time <- as.numeric(difftime(Sys.time(),time.previous,unit="sec"))
-            time.previous <- Sys.time()
-            cat(c(length(res$ances), iter.time),append=TRUE,file="haploSimTime.out")
-            ## END DEBUGGING VERBOSE ##
+            ## cat("\nNb strains:",length(res$ances),"/",max.nb.haplo)
+            ##             cat("\nLatest date:", max(res$dates),"/",Tmax)
+            ##             cat("\nRemaining strains to duplicate", sum(toExpand))
+            ##             cat("\n",append=TRUE,file="haploSimTime.out")
+            ##             iter.time <- as.numeric(difftime(Sys.time(),time.previous,unit="sec"))
+            ##             time.previous <- Sys.time()
+            ##             cat(c(length(res$ances), iter.time),append=
+            ##TRUE,file="haploSimTime.out")
+        ## END DEBUGGING VERBOSE ##
         }
 
         ## VERBOSE OUTPUT FOR DEBUGGING ##
-        cat("\nSimulation time stored in haploSimTime.out\n")
+        ##cat("\nSimulation time stored in haploSimTime.out\n")
 
         ## SHAPE AND RETURN OUTPUT ##
         res$ances <- as.character(res$ances)

Modified: pkg/TODO
===================================================================
--- pkg/TODO	2009-09-07 10:20:47 UTC (rev 440)
+++ pkg/TODO	2009-09-07 23:53:24 UTC (rev 441)
@@ -31,6 +31,7 @@
 ==============
 * fix request 1.2-2.04 (implement adjusted heretozygosity in summary)
 * use packageStartupMessage() instead of cat in .First.lib
+* bug: makefreq does not work after a seploc
 
 # DOCUMENTATION ISSUES:
 =======================

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2009-09-07 10:20:47 UTC (rev 440)
+++ www/documentation.html	2009-09-07 23:53:24 UTC (rev 441)
@@ -44,6 +44,8 @@
 - a <span style="font-weight: bold;">sPCA tutorial</span> (<a
  href="files/tutorial-spca.pdf">pdf</a>), showing how to use the
 spatial Principal Component Analysis (Jombart et al. 2008)<br>
+- globaldiv summer school 2009 - <a href="files/globaldiv-TJ.1.3.pdf">talk</a>
+- <a href="files/globaldiv-PC.1.3.pdf">practical course</a><br>
 <span style="text-decoration: underline;"></span><br>
 <span style="color: rgb(255, 0, 0);"></span></div>
 </body>

Added: www/files/globaldiv-PC.1.3.pdf
===================================================================
--- www/files/globaldiv-PC.1.3.pdf	                        (rev 0)
+++ www/files/globaldiv-PC.1.3.pdf	2009-09-07 23:53:24 UTC (rev 441)
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 441


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