[adegenet-commits] r675 - pkg/R

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

Author: jombart
Date: 2010-09-23 13:45:14 +0200 (Thu, 23 Sep 2010)
New Revision: 675

Modified:
   pkg/R/fstat.R
   pkg/R/handling.R
   pkg/R/zzz.R
Log:
added treatOther arg passed to seppop


Modified: pkg/R/fstat.R
===================================================================
--- pkg/R/fstat.R	2010-09-23 09:52:36 UTC (rev 674)
+++ pkg/R/fstat.R	2010-09-23 11:45:14 UTC (rev 675)
@@ -65,7 +65,7 @@
 
 
     ## compute pairwise Fst for all pairs
-    lx <- seppop(x)
+    lx <- seppop(x,treatOther=FALSE)
     temp <- pop(x)
     levPop <- levels(temp)
     allPairs <- combn(1:length(levPop), 2)

Modified: pkg/R/handling.R
===================================================================
--- pkg/R/handling.R	2010-09-23 09:52:36 UTC (rev 674)
+++ pkg/R/handling.R	2010-09-23 11:45:14 UTC (rev 675)
@@ -186,7 +186,7 @@
 setGeneric("seppop", function(x, ...) standardGeneric("seppop"))
 
 ## genind
-setMethod("seppop", signature(x="genind"), function(x,pop=NULL,truenames=TRUE,res.type=c("genind","matrix"), drop=FALSE){
+setMethod("seppop", signature(x="genind"), function(x,pop=NULL,truenames=TRUE,res.type=c("genind","matrix"), drop=FALSE, treatOther=TRUE){
     ## checkType(x)
 
     ## misc checks
@@ -206,7 +206,7 @@
     ## pop <- x at pop # comment to take pop arg into account
 
     ## make a list of genind objects
-    kObj <- lapply(levels(pop), function(lev) x[pop==lev, , drop=drop])
+    kObj <- lapply(levels(pop), function(lev) x[pop==lev, , drop=drop, treatOther=treatOther])
     names(kObj) <- levels(pop)
 
     ## res is a list of genind

Modified: pkg/R/zzz.R
===================================================================
--- pkg/R/zzz.R	2010-09-23 09:52:36 UTC (rev 674)
+++ pkg/R/zzz.R	2010-09-23 11:45:14 UTC (rev 675)
@@ -2,7 +2,7 @@
 #.initAdegenetClasses()
 #.initAdegenetUtils()
     library.dynam("adegenet", pkg, lib)
-    startup.txt <- "   ==========================\n    adegenet 1.2-6 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"
+    startup.txt <- "   ==========================\n    adegenet 1.2-7 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)