[adegenet-commits] r207 - in pkg: . misc/bug-report.1.2-2.03
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Nov 19 17:54:27 CET 2008
Author: jombart
Date: 2008-11-19 17:54:26 +0100 (Wed, 19 Nov 2008)
New Revision: 207
Added:
pkg/misc/bug-report.1.2-2.03/FIXED
Modified:
pkg/TODO
pkg/misc/bug-report.1.2-2.03/.RData
pkg/misc/bug-report.1.2-2.03/.Rhistory
Log:
Modified: pkg/TODO
===================================================================
--- pkg/TODO 2008-11-19 16:40:16 UTC (rev 206)
+++ pkg/TODO 2008-11-19 16:54:26 UTC (rev 207)
@@ -28,7 +28,7 @@
==============
* fix bug 1.2-2.01 (read.structure issue) -- fixed: was due to the default of "onerowperind" argument.
* 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)
+* 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)
# DOCUMENTATION ISSUES:
Modified: pkg/misc/bug-report.1.2-2.03/.RData
===================================================================
(Binary files differ)
Modified: pkg/misc/bug-report.1.2-2.03/.Rhistory
===================================================================
--- pkg/misc/bug-report.1.2-2.03/.Rhistory 2008-11-19 16:40:16 UTC (rev 206)
+++ pkg/misc/bug-report.1.2-2.03/.Rhistory 2008-11-19 16:54:26 UTC (rev 207)
@@ -1,46 +1,3 @@
-AB.idx
-AB.idx
-subsetSeg
-PRECISION
-subsetSeg
-M
-N
-.C("CheckAllSeg", as.integer(nrow(subsetSeg)), as.integer(ncol(subsetSeg)),
- as.double(as.matrix(subsetSeg)), as.double(M), as.double(N),
- temp, PACKAGE = "adegenet")[[6]]
-subsetSeg.old <- subsetSeg
-subsetSeg.new <- subsetSeg
-subsetSeg.new[2,] <- NULL
-subsetSeg.new
-subsetSeg.new <- subsetSeg.new[1,,drop=FALSE]
-subsetSeg.new
-subsetSeg.new
-.C("CheckAllSeg", as.integer(nrow(subsetSeg.new)), as.integer(ncol(subsetSeg.new)),
- as.double(as.matrix(subsetSeg.new)), as.double(M), as.double(N),
- temp, PACKAGE = "adegenet")[[6]]
-datBug <- list(subsetSeg=subsetSeg, M=as.double(M), N=as.double(N), call=".C("CheckAllSeg", as.integer(nrow(subsetSeg.new)), as.integer(ncol(subsetSeg.new)), as.double(as.matrix(subsetSeg.new)), as.double(M), as.double(N), temp, PACKAGE = "adegenet")[[6]]" )
-datBug
-datBug <- list(subsetSeg=subsetSeg, M=as.double(M), N=as.double(N), call=".C("CheckAllSeg", as.integer(nrow(subsetSeg.new)), as.integer(ncol(subsetSeg.new)), as.double(as.matrix(subsetSeg.new)), as.double(M), as.double(N), temp, PACKAGE = 'adegenet')[[6]]" )
-datBug <- list(subsetSeg=subsetSeg, M=as.double(M), N=as.double(N), call='.C("CheckAllSeg", as.integer(nrow(subsetSeg.new)), as.integer(ncol(subsetSeg.new)), as.double(as.matrix(subsetSeg.new)), as.double(M), as.double(N), temp, PACKAGE = "adegenet")[[6]]' )
-datBug
-save(datBug, file="datBug.RData")
-points(subsetSeg[2,c(1,3)],subsetSeg[2,c(2,4)], col="red")
-Q
-mon <- monmonier(coords, Da, cn, threshold=0.1, nrun=1, skip.local.diff = rep(1, 1))
-mon <- monmonier(coords, Da, cn, threshold=0.1, nrun=1, skip.local.diff = rep(1, 1))
-mon <- monmonier(coords, Da, cn, threshold=0.1, nrun=1, skip.local.diff = rep(1, 1))
-debug(checkNext)
-subsetSeg
-segMat
-currentDir1
-result[[1]]
-result[[1]]$dir1
-subsetSeg
-rownames(subsetSeg)
-grep(rownames(subsetSeg),"dir1")
-?grep
-grep("dir1",rownames(subsetSeg))
- prevSeg <- grep("dir1",rownames(subsetSeg))
prevSeg <- prevSeg[length(prevSeg]
prevSeg <- prevSeg[length(prevSeg)]
@@ -160,3 +117,71 @@
source("")
q()
n
+plot(mon1)
+example(monmonier)
+rm(monmonier)
+rm(plot.monmonier)
+save.image()
+example(monmonier)
+?monmonier
+ plot(mon1,x1,met="greylevel",csize=.6)
+
+ data(sim2pop)
+
+ gab <- chooseCN(sim2pop at other$xy,ask=FALSE,type=2)
+
+ pca1 <- dudi.pca(sim2pop at tab,scale=FALSE, scannf=FALSE, nf=1)
+
+ gab <- chooseCN(sim2pop at other$xy,ask=FALSE,type=2)
+
+ mon1 <- monmonier(sim2pop at other$xy,dist(pca1$l1[,1]),gab,scanthres=FALSE)
+
+plot(mon1,var=pca1$l1[,1])
+
+plot(mon1,var=pca1$l1[,1])
+ temp <- sim2pop at pop
+ levels(temp) <- c(17,19)
+ temp <- as.numeric(as.character(temp))
+ plot(mon1)
+ points(sim2pop at other$xy,pch=temp,cex=2)
+ legend("topright",leg=c("Pop A", "Pop B"),pch=c(17,19))
+
+ xy <- matrix(runif(120,0,10), ncol=2)
+ x1 <- rnorm(60)
+ x1[xy[,2] > 5] <- x1[xy[,2] > 5]+3
+ cn1 <- chooseCN(xy,type=1,ask=FALSE)
+ mon1 <- optimize.monmonier(xy,dist(x1)^2,cn1,ntry=10)
+
+ # graphics
+ plot(mon1,x1,met="greylevel",csize=.6)
+
+10
+plot(mon1)
+ mon1 <- optimize.monmonier(xy,dist(x1)^2,cn1,ntry=10)
+
+d
+plot(mon1)
+plot(mon1,x1)
+ x2 <- rnorm(60)
+ sel <- (xy[,1]>3.5 & xy[,2]>3.5 & xy[,1]<6.5 & xy[,2]<6.5)
+ x2[sel] <- x2[sel]+4
+ cn2 <- chooseCN(xy,type=1,ask=FALSE)
+ mon2 <- optimize.monmonier(xy,dist(x2)^2,cn2,ntry=10)
+
+ # graphics
+ plot(mon2,x2,method="greylevel",add.arr=FALSE,bwd=6,col="red",csize=.5)
+ ## End(Not run)
+d
+ plot(mon2,x2,method="greylevel",add.arr=FALSE,bwd=6,col="red",csize=.5)
+
+ x2 <- rnorm(60)
+ sel <- (xy[,1]>3.5 & xy[,2]>3.5 & xy[,1]<6.5 & xy[,2]<6.5)
+ x2[sel] <- x2[sel]+4
+
+ mon2 <- optimize.monmonier(xy,dist(x2)^2,cn2,ntry=10)
+
+d
+ plot(mon2,x2,method="greylevel",add.arr=FALSE,bwd=6,col="red",csize=.5)
+
+q()
+y
Added: pkg/misc/bug-report.1.2-2.03/FIXED
===================================================================
--- pkg/misc/bug-report.1.2-2.03/FIXED (rev 0)
+++ pkg/misc/bug-report.1.2-2.03/FIXED 2008-11-19 16:54:26 UTC (rev 207)
@@ -0,0 +1 @@
+This bug has been fixed.
\ No newline at end of file
More information about the adegenet-commits
mailing list