Hi,
A much more efficient way for doing this process is to use the poppr function
"aboot()" with the genind object.
Best,
Zhian
Sent from my iPhone
>
>
> Hello,
> I have probably very simple problem, but I can't find the solution... :-( I
> wish to make bootstraped tree of attached microsatellite diploid data. It
> works fine with DNA sequences and I was using same code last year and it was
> working. :-)
>
> library(pegas)
> library(ape)
> LOCI <- read.loci("ssrs.txt", header=TRUE, loci.sep="\t", allele.sep="/",
> col.pop=2, col.loci=3:14, row.names=1)
> # Looks OK
> GENIND <- loci2genind(LOCI)
> DIST <- dist(x=GENIND, method="euclidean", diag=TRUE, upper=TRUE)
> NJ <- nj(DIST)
> BOOT <- boot.phylo(phy=NJ, x=LOCI, FUN=function(X) nj(dist(loci2genind(X))),
> B=1000)
> |=
>
> | 1%Error in df2genind(as.matrix(x[, attr(x, "locicol")]), sep = "[/\\|]",
> :
> length of factor pop differs from nrow(X)
>
> Any idea what could went wrong?
> Thank You,
> Vojt?ch
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