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
