[adegenet-commits] r374 - pkg/R

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

Author: jombart
Date: 2009-06-05 16:20:24 +0200 (Fri, 05 Jun 2009)
New Revision: 374

Modified:
   pkg/R/haploSim.R
   pkg/R/seqTrack.R
Log:
commented debugging lines; fixed the retrieving of mu0 from call in optimize.haplo


Modified: pkg/R/haploSim.R
===================================================================
--- pkg/R/haploSim.R	2009-06-05 13:02:25 UTC (rev 373)
+++ pkg/R/haploSim.R	2009-06-05 14:20:24 UTC (rev 374)
@@ -343,7 +343,7 @@
 ## labels.haploSim
 ##################
 labels.haploSim <- function(object, ...){
-    return(rownames(x$seq))
+    return(rownames(object$seq))
 }
 
 
@@ -388,7 +388,7 @@
     if(is.null(prevCall$mu)){
         mu0 <- 0.0001
     } else {
-        mu0 <- prevCall$mu
+        mu0 <- eval(prevCall$mu)
     }
 
     res <- optimize.seqTrack.default(x=myX, seq.names=seq.names, seq.dates=seq.dates,

Modified: pkg/R/seqTrack.R
===================================================================
--- pkg/R/seqTrack.R	2009-06-05 13:02:25 UTC (rev 373)
+++ pkg/R/seqTrack.R	2009-06-05 14:20:24 UTC (rev 374)
@@ -517,10 +517,10 @@
             date <- date[,toKeep,drop=FALSE] # retained posterior
 
             ## DEBUGING ##
-            cat("\ntoKeep:\n")
-            print(toKeep)
-            cat("\nhead date (posterior):\n")
-            print(head(date))
+            ## cat("\ntoKeep:\n")
+            ##             print(toKeep)
+            ##             cat("\nhead date (posterior):\n")
+            ##             print(head(date))
             ## END DEBUGING ##
 
             newDates <- apply(date, 1, function(vec)