[adegenet-commits] r320 - pkg/R

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

Author: jombart
Date: 2009-05-22 13:34:06 +0200 (Fri, 22 May 2009)
New Revision: 320

Modified:
   pkg/R/seqTrack.R
Log:
cleaning the code


Modified: pkg/R/seqTrack.R
===================================================================
--- pkg/R/seqTrack.R	2009-05-21 18:21:35 UTC (rev 319)
+++ pkg/R/seqTrack.R	2009-05-22 11:34:06 UTC (rev 320)
@@ -221,7 +221,6 @@
 
 
 
-
 ##############
 ## .pAbeforeB # no longer used, never totally finished
 ##############
@@ -260,6 +259,9 @@
 
 
 
+
+
+
 #############
 ## .dTimeSeq
 #############
@@ -387,25 +389,6 @@
     }
 
 
-    ##  ## LOOK FOR AMBIGUOUS DATES ##
-    ##     isAmbig <- .ambigDates(res.ini, mu0, seq.length, p=0.99)
-    ##     if(!any(isAmbig)){
-    ##         cat("\nNo ambiguity in dates was found; unique solution returned.\n")
-    ##         return(res)
-    ##     }
-
-
-    ## ## DEFINE NEW TEMPORAL ORDER ##
-    ##     permutDate <- function(res, id, newDates){ # id: segment whose vertices are permuted
-    ##         idAnc <- unlist(res[2,id])
-    ##         idDes <- unlist(res[1,id])
-    ##         temp <- newDates[idAnc]
-    ##         newDates[idAnc] <- newDates[idDes]
-    ##         newDates[idDes] <- temp
-    ##         return(newDates)
-    ##     }
-
-
     ## DO THE OPTIMISATION ##
     RANGE.DATES <- diff(range(seq.dates)) # time window of the sample, in days
     NB.DATES.TO.SIM <- length(seq.dates)