[adegenet-commits] r996 - pkg/R www

[noreply at r-forge.r-project.org]

Author: jombart
Date: 2012-04-11 11:16:10 +0200 (Wed, 11 Apr 2012)
New Revision: 996

Modified:
   pkg/R/haploGen.R
   www/literature.html
Log:
+2 ref; uncommited old change to haploGen


Modified: pkg/R/haploGen.R
===================================================================
--- pkg/R/haploGen.R	2012-03-19 17:33:23 UTC (rev 995)
+++ pkg/R/haploGen.R	2012-04-11 09:16:10 UTC (rev 996)
@@ -19,28 +19,28 @@
     if(!require(ape)) stop("The ape package is required.")
 
 
-    ## HACK TO FIX APE'S BUG ##
-    env <- environment(as.list.DNAbin)
-    as.list.DNAbin.new <- function (x, ...){
-        if (is.list(x))
-            return(x)
-        if (is.null(dim(x)))
-            obj <- list(x)
-        else {
-            n <- nrow(x)
-            obj <- vector("list", n)
-            for (i in 1:n) obj[[i]] <- x[i, ]
-            names(obj) <- rownames(x)
-        }
-        class(obj) <- "DNAbin"
-        obj
-    }
+    ## ## HACK TO FIX APE'S BUG ##
+    ## env <- environment(as.list.DNAbin)
+    ## as.list.DNAbin.new <- function (x, ...){
+    ##     if (is.list(x))
+    ##         return(x)
+    ##     if (is.null(dim(x)))
+    ##         obj <- list(x)
+    ##     else {
+    ##         n <- nrow(x)
+    ##         obj <- vector("list", n)
+    ##         for (i in 1:n) obj[[i]] <- x[i, ]
+    ##         names(obj) <- rownames(x)
+    ##     }
+    ##     class(obj) <- "DNAbin"
+    ##     obj
+    ## }
 
-    as.list.DNAbin <- as.list.DNAbin.new
-    unlockBinding("as.list.DNAbin", env)
-    assignInNamespace("as.list.DNAbin", as.list.DNAbin.new, ns="ape", envir=env)
-    assign("as.list.DNAbin", as.list.DNAbin.new, envir=env)
-    lockBinding("as.list.DNAbin", env)
+    ## as.list.DNAbin <- as.list.DNAbin.new
+    ## unlockBinding("as.list.DNAbin", env)
+    ## assignInNamespace("as.list.DNAbin", as.list.DNAbin.new, ns="ape", envir=env)
+    ## assign("as.list.DNAbin", as.list.DNAbin.new, envir=env)
+    ## lockBinding("as.list.DNAbin", env)
 
     ## END HACK ##
 

Modified: www/literature.html
===================================================================
--- www/literature.html	2012-03-19 17:33:23 UTC (rev 995)
+++ www/literature.html	2012-04-11 09:16:10 UTC (rev 996)
@@ -345,7 +345,8 @@
 Dense
 SNP
 Data
-on 47
+on
+47
 Worldwide Breeds. </span> <span style="font-style: italic;"
  class="citation_journal_title">PLoS ONE</span><span
  class="citation_issue"> <span style="font-weight: bold;">5(9)</span>:</span>
@@ -398,7 +399,8 @@
 Recently
 Colonized
 Habitat
-in a Butterfly. </span> <span style="font-style: italic;"
+in
+a Butterfly. </span> <span style="font-style: italic;"
  class="citation_journal_title">PLoS ONE</span><span
  class="citation_issue"> 5(11):</span> <span
  class="citation_start_page">e13810.</span> <span class="citation_doi">doi:10.1371/journal.pone.0013810<br>
@@ -724,10 +726,20 @@
  style="font-style: italic;">Online first. </span>DOI:
 10.1007/s10709-012-9640-2<br>
 <br>
+[76] Samantha Baldwin, Meeghan Pither-Joyce, Kathryn Wright, Leshi Chen
+and John McCallum (2012) Development of robust genomic simple sequence
+repeat markers for estimation of genetic diversity within and among
+bulb onion (Allium cepa L.) populations. MOLECULAR BREEDING. DOI:
+10.1007/s11032-012-9727-6<br>
 <br>
+[77] Nishiyama T, Kishino H, Suzuki S, Ando R, Niimura H, et al. (2012)
+Detailed Analysis of Japanese Population Substructure with a Focus on
+the Southwest Islands of Japan. PLoS ONE 7(4): e35000.
+doi:10.1371/journal.pone.0035000<br>
 <br>
 <br>
 <br>
+<br>
 <p class="intro">* adegenet not or wrongly cited, but actually used in
 the paper. <br>
 </p>