Hi,
I like the poppr package very much. And I like microstallites and don't like
AFLP. ;-) I found a problem with some tree constructing.
When I run bruvo.boot, it crashes at some random point:
ssrs3n.nj.bruvo - bruvo.boot(pop=ssrs3n.missingno, replen=rep(2, 8),
sample=100, tree=upgma,
Hi,
yes, thank You, adegenet uses some functions from pegas. I thought it is
mainly for DNA data. I have problems with AMOVA and HW test.
amova(ssrs3n.dist~ssrs3n.pops, data=NULL, nperm=1000, is.squared=TRUE)
Analysis of Molecular Variance
Call: amova(formula = ssrs3n.dist ~
Hi Renske-
This is a complex question and it would take a manuscript to answer it
properly. The short answer is no, not without doing a lot of work to show that
whatever error model you use leads to acceptable Type I error rates under
various models of trait evolution. It is almost certainly
As a quick follow up, I would add that it is not necessarily the case that your
Type I error rates will be inflated if you use (say) a phylogenetic error
model. It depends on your sampling. If you run BAMM on a phylogenetic tree of X
species, then test a trait-diversification correlation on a
