[adegenet-commits] r209 - in pkg: . misc/bug-report.1.2-2.03

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

Author: jombart
Date: 2008-11-20 11:52:23 +0100 (Thu, 20 Nov 2008)
New Revision: 209

Modified:
   pkg/TODO
   pkg/misc/bug-report.1.2-2.03/.Rhistory
Log:
entering in monmonier's wonderful world.


Modified: pkg/TODO
===================================================================
--- pkg/TODO	2008-11-20 10:38:57 UTC (rev 208)
+++ pkg/TODO	2008-11-20 10:52:23 UTC (rev 209)
@@ -30,6 +30,8 @@
 * fix bug 1.2-2.02 (read.genetix issue) -- fixed: was due to an error in the data file (wrong nloc); now read.genetix corrects that automatically and issues a warning. (TJ)
 * fix bug 1.2-2.03 (monmonier issue) -- fixed: was a non-detected code 2 due to intersection check with previously drawn segment (was not always removed). (TJ)
 * fix request 1.2-2.04 (implement adjusted heretozygosity in summary)
+* fix bug 1.2-2.05 (monmonier is such a pain is the ass)
+* !! comment the if(DEBUG) in monmonier when it is fixed
 
 # DOCUMENTATION ISSUES:
 =======================

Modified: pkg/misc/bug-report.1.2-2.03/.Rhistory
===================================================================
--- pkg/misc/bug-report.1.2-2.03/.Rhistory	2008-11-20 10:38:57 UTC (rev 208)
+++ pkg/misc/bug-report.1.2-2.03/.Rhistory	2008-11-20 10:52:23 UTC (rev 209)
@@ -1,53 +1,4 @@
-        prevSeg <- prevSeg[length(prevSeg]
-
-        prevSeg <- prevSeg[length(prevSeg)]
-prevSeg
-paste("dir",curDur,sep="")
-paste("dir",curDir,sep="")
-curDir
-curDir=as.integer(1)
-paste("dir",curDir,sep="")
-       prevSeg <- grep(paste("dir",curDir,sep=""),rownames(subsetSeg))
-        prevSeg <- prevSeg[length(prevSeg)]
-
-prevSeg
-subsetSeg
-        subsetSeg <- segMat[-prevSeg,,drop=FALSE]
-
-subsetSeg
-Q
-undebug(monmonier)
 mon <- monmonier(coords, Da, cn, threshold=0.1, nrun=1, skip.local.diff = rep(1, 1)) 
-source("/home/master/dev/adegenet/pkg/R/monmonier.R")
-mon <- monmonier(coords, Da, cn, threshold=0.1, nrun=1, skip.local.diff = rep(1, 1)) 
-debug(monmonier)
-debug(checkNext)
-mon <- monmonier(coords, Da, cn, threshold=0.1, nrun=1, skip.local.diff = rep(1, 1)) 
-debug(checkNext)
-mon <- monmonier(coords, Da, cn, threshold=0.1, nrun=1, skip.local.diff = rep(1, 1)) 
-debug(checkNext)
-checkNext(result[[run]]$dir1[[length(result[[run]]$dir1)]]$M, 
-        currentDir1$M, result[[run]]$dir1[[length(result[[run]]$dir1)]]$A[1], 
-        result[[run]]$dir1[[length(result[[run]]$dir1)]]$B[1], 
-        currentDir1$A[1], currentDir1$B[1], curDir = as.integer(1)))
-checkNext(result[[run]]$dir1[[length(result[[run]]$dir1)]]$M, 
-        currentDir1$M, result[[run]]$dir1[[length(result[[run]]$dir1)]]$A[1], 
-        result[[run]]$dir1[[length(result[[run]]$dir1)]]$B[1], 
-        currentDir1$A[1], currentDir1$B[1], curDir = as.integer(1))
-prevSeg
-subsetSeg
-setMat
-segMet
-segMat
-segMat[integer(0),]
-segMat[-integer(0),]
-Q
-source("/home/master/dev/adegenet/pkg/R/monmonier.R")
-mon <- monmonier(coords, Da, cn, threshold=0.1, nrun=1, skip.local.diff = rep(1, 1)) 
-example(monmonier)
-q()
-y
-mon <- monmonier(coords, Da, cn, threshold=0.1, nrun=1, skip.local.diff = rep(1, 1)) 
 warnings()
 example(monmonier)
 q()
@@ -185,3 +136,21 @@
 
 q()
 y
+plot(mon1,x1)
+orig_coords <- read.table("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.03/boot_coord.7.input")
+numpops <- length(orig_coords[,1])
+
+coords <- orig_coords
+numpops <- length(coords[,1])
+Da <- read.table("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.03/boot_dist.7.input")
+Da <- as.dist(Da)
+
+	# Calc monmonier barrier
+	cn <- chooseCN(coords, ask=FALSE, type=1)
+	mon <- monmonier(coords, Da, cn, threshold=0, nrun=1, skip.local.diff = rep(1, 1)) #threshold is arbitrarily set at 0
+plot(mon)
+plot(mon,add.arr=FALSE)
+	mon <- optimize.monmonier(coords, Da, cn, threshold=0)
+
+q()
+n