model Ted evoked in his post.
I hope it helps...
Florian Boucher
PhD student, Laboratoire d'Ecologie Alpine,
Grenoble, France
2011/1/28 David Bapst dwba...@uchicago.edu
Hello all,
Apologies for leaving the replies to get cold for a week, but now I
finally have some time to respond.
On Thu
Elaine,
you can read the tree using the 'ape' package in R:
library(ape)
tree-read.nexus('path_to_your_tree.nex')
then, you will find the tip labels in the following vector:
tree$tip.label
you can change the names by selecting one element in the vector and
modifying it, for example:
Hi Simon,
one solution is to extract a vector of branching times and sort this vector
for each tree (using branching.times in ape).
From that you can create a matrix with the branching events (ordered in
time) as columns and the corresponding time in each tree as rows.
Using the quantile function
Hi Eugen,
to compute a distance matrix from a phylogeny, you can use the
cophenetic.phylo function in {ape}.
You then have to rescale all distances in you matrix (which are expressed
in million years) by the total depth of the tree:
dist=cophenetic.phylo(tree)
dist2=dist/max(dist)
Best,
Dear Sereina,
the transform.phylo function in the {geiger} package will help you do what
you want:
for (2) you may transform your original tree using the 'white' model or the
'lamba' model with a parameter of 0
for (3) a 'delta' model with a high value of delta (1) will do what you
want
for (4)
-project.org/
--
Florian Boucher
Postdoctoral researcher, Institute of Systematic Botany, Zürich
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Hi Branchlizard and list,
in order to do this you would first need to rename one of the foo's in each
clade (I would always rename the first one) as '6 foo's', '4 foo's', etc.
Then you can apply drop.tip on all the foos, as you did before.
I hope this helps.
Cheers,
Florian
2016-09-14 21:32
. <branch.liz...@gmail.com>:
> Florian and list,
>
> What is your preferred method to go about this? phy$tip.label? If so, how
> would one label a tip label from each clade of foo's without having to hard
> code the clade number? I am trying to prevent any hard coding.
>
>
Hi Franz,
I don't know about anything like what you propose but maybe you could
sine-transform your trait and then use phylogenetic linear or logistic
regression?
Florian
2017-07-27 13:06 GMT+02:00 f.k...@mailbox.org :
> Hi all,
>
> it there something like a phylogenetic
Hi Roi,
you can fit the BBM model using the 'BBMV' package.
You will first need to create a likelihood function as follows:
BBM <- lnL_BBMV(tree,trait,Npts=100,bounds=c(min(trait),max(trait)),a=0,b=0,c=0)
And then you need to find the maximum of the likelihood function:
fit_BBM <-
Hi Karla,
you're almost right, but since sigsq is the variance of the random walk per
unit time its unit is actually [unit of the trait]^2/[unit of time]
Cheers,
Florian
Le ven. 19 mars 2021 à 19:12, Karla Shikev a écrit :
> Dear all,
>
> Please indulge me in a simple (newbie) question.
>
>
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