Hi Emmanuel
Thank you for that insightful reply. Indeed, my input was not in NEWICK
format, which when I fixed solved this problem of not being able to read it
in and manipulate it using "ape" in R.
So now I can modify my species tree in NEWICK, using read.newick, and ape
package in R, to a dendr
Hi Liam,
Thank you for your reply. I indeed checked my *.tre file again, found and
removed some additional pairs of parentheses, removed spaces ( there were
no carriage returns)
The bigger problem was that it was not in NEWICK format, which when I fixed
solved the remaining problem. Thank you agai
Alberto Gallano asked:
>
> Would this also be the case in the situation where n is small enough (~ <15)
> to enumerate all possible unique permutations? I was under the impression
> that such an 'exact' test provided the true p-value without error.
In a case that small, one might be able to evalu
Would this also be the case in the situation where n is small enough (~
<15) to enumerate all possible unique permutations? I was under the
impression that such an 'exact' test provided the true p-value without
error.
Alberto
On Mon, Jun 8, 2015 at 2:29 AM, Joe Felsenstein
wrote:
> A number of
Fwd'ing to the list because I neglected to do so ...and in case others
have something to add
Original Message
Subject: Re: [R-sig-phylo] Phylogenetic regression with a trait
homologous within lower taxonomic groups, but analogous between higher
taxonomic levels
Date: Sun
Hi James,
One key issue is that you’ve got multiple components in the GLS model - the
data and the covariance matrix. If you change the covariance matrix, then
changes in residuals in the model aren’t comparable.
What caper does internally is to fit the intercept-only model for the data
using
Hi,
I have a question regarding the adjusted r-squared supplied in the summary
of pgls analyses in caper.
I have read in other discussion on his list that r-squared from GLS does
not have the same meaning as r-squared in LS, and presumably this is why it
is not provided in the summary of a gls mo
