[adegenet-commits] r258 - pkg/R

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

Author: jombart
Date: 2009-01-27 20:05:05 +0100 (Tue, 27 Jan 2009)
New Revision: 258

Modified:
   pkg/R/propShared.R
Log:


Modified: pkg/R/propShared.R
===================================================================
--- pkg/R/propShared.R	2009-01-27 17:22:34 UTC (rev 257)
+++ pkg/R/propShared.R	2009-01-27 19:05:05 UTC (rev 258)
@@ -20,19 +20,16 @@
     ## if ploidy = 1
     if(x$ploidy == as.integer(1)){
         stop("not implemented for ploidy = 1")
-        #### have to think how AFLP should be handled here.
-        #### maybe dist would do the job..
         ## compute numbers of common alleles
-        ##   X <- x at tab
-        ##         X[is.na(X)] <- 0
-        ##         M <- X %*% t(X)
+        ## X <- x at tab
+        ## X[is.na(X)] <- 0
+        ## M <- X %*% t(X)
 
-        ##         ## compute numbers of alleles used in each comparison
-        ##         nAllByInd <- propTyped(x,by="ind")*x at ploidy
+        ## compute numbers of alleles used in each comparison
+        ## nAllByInd <- propTyped(x,by="ind") * nLoc(x)
         ##         idx <- expand.grid(1:nrow(x$tab), 1:nrow(x$tab))
         ##         temp <- cbind(nAllByInd[idx[,1]] , nAllByInd[idx[,2]])
         ##         N <- matrix(apply(temp, 1, min), ncol=nrow(x$tab))
-
     }
 
     ## if ploidy = 2