I think there's a question there that need to be addressed: why were the
>> trees non ultrametric at the first place?
>>
>>
>> Giulio Valentino Dalla Riva
>>
>> Beaty Biodiversity Research Centre
>> University of British Columbia
>> Vancouver, Canad
va
>
> Beaty Biodiversity Research Centre
> University of British Columbia
> Vancouver, Canada
>
> From: R-sig-phylo on behalf of
> Alejandro Gonzalez Voyer
> Sent: October 31, 2016 12:56:02 PM
> To: Emmanuel Paradis
> Cc: R-phylo Mail
16 12:56:02 PM
To: Emmanuel Paradis
Cc: R-phylo Mailing-list; Shinichi Nakagawa
Subject: Re: [R-sig-phylo] Making ultrametric trees
Hi,
>> Note that vcv(nonultrametric_tree, cor=TRUE) is different from
>> vcv(chronoMPL(nonultrametric_tree), cor = TRUE), which is relates to my
>&g
Hi,
>> Note that vcv(nonultrametric_tree, cor=TRUE) is different from
>> vcv(chronoMPL(nonultrametric_tree), cor = TRUE), which is relates to my
>> previous question (which one is preferred?)
>
> It (mainly) depends whether you want to assume a "clock-like" evolution for
> the traits you are stu
Le 30/10/2016 à 03:09, Shinichi Nakagawa a écrit :
Dear Emmanuel and Alejandro
Many thanks for your replies.
Emmanuel, I understand what you said if I use vcv(nonultrametric_tree,
cor=FALSE) in a phylogenetic comparative method (PCM). But if I use
vcv(nonultrametric_tree, cor=TRUE), isn't this
Dear Brian
This is extremely useful. Many thanks for taking your time to write this
for me.
Best wishes,
Shinichi
_
Dr Shinichi Nakagawa (Associate Professor / ARC Future Fellow)
Deputy Director of Research, Evolution & Ecology Researc
Emmanuel's way is the most general and quickest (well, other than just
making up branch lengths entirely, using ape::compute.brlen() -- that's
even faster!). However, the original question was "best and most general"
for making ultrametric trees for phylogenetic comparative analysis. For an
analysi
Dear Emmanuel and Alejandro
Many thanks for your replies.
Emmanuel, I understand what you said if I use vcv(nonultrametric_tree,
cor=FALSE) in a phylogenetic comparative method (PCM). But if I use
vcv(nonultrametric_tree, cor=TRUE), isn't this the same as assuming a
ultrametric tree? I may be mis
Hi,
I would venture in adding that with an additive tree the differences in evol
rates among species are determined by the genes used to estimate the tree,
given differences in substitution rates among genes. I do think its important
to bear in mind.
Cheers
Alejandro
Alejandro Gonzalez Voye
Sure they are different. I forgot to mention that.
In comparative analyses, the expected quantity of trait change (= the
variance in the VCV matrix) is given by the product of the rate of
evolution of the trait with branch length. So using a non-ultrametric
tree is a way to assume different ra
Dear Emmanuel
Many thanks for your swift reply.
If we get a correlation matrix, via chronoMPL [i.e.
vcv(chronoMPL(nonultrametric_tree,cor=T))], this correlation matrix is
different from a correlation matrix obtained directly from vcv [i.e.
vcv(nonultrametric_tree, cor=T)].
Could you enlighten m
Dear Shinichi,
A fast solution is provided by the function chronoMPL in ape; it does
not require calibration points (see the references in the help page of
this function for the assumptions). The function chronos (also in ape)
is another possibility but it needs at least one calibration point
Dear List
We would like make several non-ultrametic trees (based on molecular data;
downloaded from treeBASE) into ultrametric trees using R. Could you advice
us what is the best and the most general way of doing this please?
We would like to use resultant ultrametric trees in phyologenetic
compa
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