at 5:58 AM Emmanuel Paradis
wrote:
> What about this (after reading 'tree' using your code):
>
> n <- Ntip(tree)
> dates <- estimate.dates(tree, rep(0, n), .0221)
> plot(compute.brtime(tree, -dates[-(1:n)]))
> axisPhylo()
>
> ?
>
> E.
>
> - Le 6 Mar
ock model.
> Kind regards,
> Klaus
>
>
>
>
> Von meinem iPhone gesendet
>
> > Am 04.03.2024 um 21:06 schrieb Vincenzo Ellis :
> >
> > Dear Liam,
> >
> > Thank you for your answer. Yes, I have a hypothesized average clock rate
> > and no explicit ca
etts Boston
> Web: http://faculty.umb.edu/liam.revell/
> Book: Phylogenetic Comparative Methods in R
> <https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r>
> (*Princeton University Press*, 2022)
>
>
> On 3/4/2024 11:09 AM, Vincenzo Ellis wrote:
>
rtainly right to look for an approach where you don't need to
> estimate the rates.
>
> Best,
>
> Emmanuel
>
> - Le 27 Fév 24, à 22:40, Vincenzo Ellis vael...@udel.edu a écrit :
>
> > Dear R-sig-phylo members,
> >
> > I've made a maximum likelihood tree in R
Dear R-sig-phylo members,
I've made a maximum likelihood tree in Raxml for several thousand taxa
using a single gene that has an estimated substitution rate of 0.006
substitutions/nucleotide/My. Is there a way to use chronos in ape to apply
that substitution rate as a fixed clock rate and
Dear list users,
I'm interested in testing for phylogenetic signal in a trait of parasites:
the number of host species a parasite infects. I have a phylogeny for the
parasites and I have tabulated the number of host species each parasite
infects from the literature. However, some parasites are
