[adegenet-commits] r205 - in pkg/misc: bug-report.1.2-2.01 bug-report.1.2-2.02

Wed Nov 19 12:24:43 CET 2008

Author: jombart
Date: 2008-11-19 12:24:43 +0100 (Wed, 19 Nov 2008)
New Revision: 205

Added:
   pkg/misc/bug-report.1.2-2.01/FIXED
   pkg/misc/bug-report.1.2-2.02/.Rhistory
   pkg/misc/bug-report.1.2-2.02/FIXED
Log:
pp


Added: pkg/misc/bug-report.1.2-2.01/FIXED
===================================================================

--- pkg/misc/bug-report.1.2-2.01/FIXED	                        (rev 0)
+++ pkg/misc/bug-report.1.2-2.01/FIXED	2008-11-19 11:24:43 UTC (rev 205)
@@ -0,0 +1 @@
+This bug has been fixed.
\ No newline at end of file

Added: pkg/misc/bug-report.1.2-2.02/.Rhistory
===================================================================
--- pkg/misc/bug-report.1.2-2.02/.Rhistory	                        (rev 0)
+++ pkg/misc/bug-report.1.2-2.02/.Rhistory	2008-11-19 11:24:43 UTC (rev 205)
@@ -0,0 +1,139 @@
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+debug(read.genetix)
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+nloc
+Q
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu-NoSpace.gtx.gtx")
+Q
+undebug(read.genetix)
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu-NoSpace.gtx.gtx")
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu-NoSpace.gtx")
+debug(read.genetix)
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+nloc
+nloc
+npop
+txt
+loc.names
+nloc
+Q
+read.genetix("/home/master/dev/adegenet/pkg/inst/files/nancycats.gtx")
+nloc
+Q
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+nloc
+Q
+undebug(read.genetix)
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+x
+x$loc.names
+x$loc.all
+x$all.names
+x$loc.nall
+x$pop.names
+q()
+n
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+debug(read.genetix)
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+text
+txt
+txt[length(txt)]
+Q
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+tail(txt)
+Q
+txt[length(txt)]
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+txt[length(txt)]
+.rmspaces(txt[length(txt)])
+temp <- .rmspaces(txt[length(txt)])
+temp
+strsplit(temp, "\t")
+unlist(strsplit(temp, "\t"))
+unlist(strsplit(temp, "\t"))
+?strsplit
+unlist(strsplit(temp, "[[:space:]]"))
+unlist(strsplit(temp, "[[:space:]]+"))
+length(unlist(strsplit(temp, "[[:space:]]+")))
+length(unlist(strsplit(temp, "[[:space:]]+")))-1
+length(unlist(strsplit(temp, "[[:space:]]+")))-1Q
+Q
+  warning(paste("== Genetix file error == \n",
+                      "provided number of locus (", nloc, ")\n",
+                      "does not match actual number (", nlocbis, ")\n",
+                      "Using ", nlocbis, " as number of locus.\n",
+                      "Please check your file."))
+source("/home/master/dev/adegenet/pkg/R/import.R")
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+source("/home/master/dev/adegenet/pkg/R/import.R")
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+source("/home/master/dev/adegenet/pkg/R/import.R")
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+debug(read.genetix)
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+nloc
+is.integer(nloc)
+as.integer(scan(file, nlines = 1, what = "character", quiet = TRUE)[1])
+1+as.integer(scan(file, nlines = 1, what = "character", quiet = TRUE)[1])
+Q
+undebug(read.genetix)
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+source("/home/master/dev/adegenet/pkg/R/import.R")
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+source("/home/master/dev/adegenet/pkg/R/import.R")
+x <- read.genetix("/home/master/dev/adegenet/pkg/misc/bug-report.1.2-2.02/PhylogenieclariasAllozymestotalmanu.gtx")
+example(read.genetix)
+x
+x$pop.names
+class(x$pop.names)
+is.vector(x$pop.names)
+:=matrix(1:4,ncol=2)
+M=matrix(1:4,ncol=2)
+N
+M
+storage.mode(M)
+mode(M)
+is.numeric(M)
+is.numeric(as.integer(M))
+2 != 1+1 != 3-1
+(2 != 1+1) != 3-1
+(2 != 1+1)
+(2 != 1+1)
+?mat2listw
+library(spdep)
+?mat2listw
+?mat2listw
+M
+matrix(1:9,ncol=3)
+M=matrix(1:9,ncol=3)
+diag(M) <- 0
+M
+prop.table(M,1)
+mat2nprop.table(M,1)
+ mat2listw(prop.table(M,1))
+temp <- mat2listw(prop.table(M,1))
+temp[1]
+temp[2]
+temp$weights
+listw2mat(temp)
+?listw2mat
+adegenetTutorial{which="spca"}
+adegenetTutorial(which="spca")
+if(FALSE) cat("titi") else if (FALSE) cat("toto") else cat("tutu")
+if(TRUE) cat("titi") else if (FALSE) cat("toto") else cat("tutu")
+if(FALSE) cat("titi") else if (TRUE) cat("toto") else cat("tutu")
+if(FALSE) cat("titi") else if (FALSE) cat("toto") else cat("tutu")
+if(FALSE) cat("titi") else if (TRUE) cat("toto") else cat("tutu")
+if(TRUE) cat("titi") else if (TRUE) cat("toto") else cat("tutu")
+if(TRUE) cat("titi") else if (FALSE) cat("toto") else cat("tutu")
+Q
+data(sim2pop)
+chooseCN(sim2pop$other$xy, ask=FALSE, plot=FALSE)
+chooseCN(sim2pop$other$xy, ask=FALSE, plot=FALSE, type=3)
+chooseCN(sim2pop$other$xy, ask=FALSE, plot=FALSE, type=3, res.type="listw")
+chooseCN(sim2pop$other$xy, ask=FALSE, plot=FALSE, type=3, res="listw")
+class(chooseCN(sim2pop$other$xy, ask=FALSE, plot=FALSE, type=3, res="listw"))
+class(chooseCN(sim2pop$other$xy, ask=FALSE, plot=FALSE, type=3, res="nb"))
+q()
+n

Added: pkg/misc/bug-report.1.2-2.02/FIXED
===================================================================
--- pkg/misc/bug-report.1.2-2.02/FIXED	                        (rev 0)
+++ pkg/misc/bug-report.1.2-2.02/FIXED	2008-11-19 11:24:43 UTC (rev 205)
@@ -0,0 +1 @@
+This bug has been fixed.
\ No newline at end of file

