Dear Jeremie.
I agree with Julien. If your tree is non-ultrametric or if you use
different fitting methods ("REML" vs. "ML") then you could obtain
different results. The other circumstance in which you might have a
different result is if your estimated value of lambda is outside the
default
Dear colleagues.
I am currently advertising a postdoc in my lab at the University of
Massachusetts Boston & the deadline to apply has been extended until
this Friday, Dec. 20th. The idea of this appointment is to work on
applying phylogenetic analysis methods (phylogenetic inference or
Dear list members.
I'm currently advertising a postdoctoral position in my lab at the
University of Massachusetts Boston. The postdoc has a maximum duration
of 2 years & is to work on the NSF project entitled 'ABI Development:
Computational infrastructure for phylogenetic analysis in the R
Hi Elizabeth.
This does not do exactly what you want, but it is possible to use
capture.output() to grab the printout of checkValidPhylo() and then
grep() to see if it contains instances of "MODERATE" or "FATAL" errors.
The following simple function does that. It returns 0 if neither
MODERATE
Dear Saleh.
You can do this using my package phytools or using ape::axisPhylo. I
have an example using both options on my blog:
http://blog.phytools.org/2018/02/another-technique-for-including-time.html.
All the best, Liam
Liam J. Revell
Associate Professor, University of Massachusetts Boston
Dear Ivan.
phytools::fitMk does not do ancestral state reconstruction. What
function did you use to obtain the estimates at internal nodes?
If you want to constrain the states at particular nodes during ancestral
state reconstruction this can be done in a fairly straightforward way.
Here is a
transforming AIC into AICc? the
> number of tips on the tree?
>
> Karla
>
> On Thu, Sep 5, 2019 at 10:27 AM Liam Revell wrote:
>
>> Dear Karla.
>>
>> You could try & create your own logLik method for the object class
>> "brownie.lite"
Dear Karla.
You could try & create your own logLik method for the object class
"brownie.lite" as follows:
## method
logLik.brownie.lite<-function(object,...){
lik<-setNames(
c(object$logL1,object$logL.multiple),
c("single-rate","multi-rate"))
.
On the first 2.5 days of the workshop, course leaders Drs. April Wright,
Josef Uyeda, Klaus Schliep, Claudia Solís-Lemus, & Liam Revell will
provide an introduction to the primary data structures and methods of
common phylogenetic R packages, the basics of computational algori
Hi Jake.
[Edit: I see just now that Brian has also responded to this inquiry. I
have no doubt that his message is more insightful than mine - but I'll
nonetheless send what I was writing anyway just in case it contributes
anything useful to the discussion.]
If you're simply interested in the
Dear Mario.
From your drawing it looks like each node & tip has a value, and then
you update these values by reassigning each node a value equal to the
sum of its value and that of all its descendants. Is this correct?
If so, then assuming you have ordered your quantities in x such that
they
I also just pushed an update to phytools that now permits exact
duplicate tip labels in a cophylo plot. You can get this update by running:
library(devtools)
install_github("liamrevell/phytools")
with devtools installed.
More details about the update can be seen on my blog:
Yes. Just to echo Juan, there should be no problem in your case if you
specify the desired matching in your association table, provided to
cophylo via the argument assoc.
In your case, for instance, you may have M._loti_1 and M._loti_2 in one
tree, but just M._loti in the other, in which case
l=1:36)
> Cécile
>
>> On Mar 8, 2019, at 8:42 PM, Liam Revell > <mailto:liam.rev...@umb.edu>> wrote:
>>
>> Dear Amanda.
>>
>> I'm a little confused by your code. If you want to use
>> control=list(col.edge) you need to set col.edge to a ve
Dear Amanda.
I'm a little confused by your code. If you want to use
control=list(col.edge) you need to set col.edge to a vector of colors,
but in your example col.edge is a numeric vector from 1 to 36.
For your particular case, there is actually a much simpler way to set
all the edges in a
Dear Bruno.
> To estimate species divergence time between pair of species, I'm using
> the phylogeny in Smith & Brown 2018 which is rooted and contain
> 353 185 seed plant species along with 85 679 nodes, branch lengths
> are dated. I'm applying the R function phytools::fastDist for a list
>
ld the same as SCP would (in Mesquite at
> least) for this kind of data?
>
> Best wishes
>
> Roland
>
> On Thu, Jan 31, 2019 at 8:03 PM Liam Revell wrote:
>
>> Dear Roland.
>>
>> I didn't really solve your problem of reading a Mesquite result into R;
Dear Roland.
I didn't really solve your problem of reading a Mesquite result into R;
however I just posted about the relationship between unweighted &
weighted square-change-parsimony & ML ancestral character estimation on
my blog:
Hi Alina.
Since you mentioned some functions of phytools, I thought it might be
helpful to describe what each function is actually doing:
1) The function ls.consensus computes a least-squares (LS) consensus
tree. This is the LS tree on the average patristic distance matrix of
the input trees,
Dear Jesse.
The most logical explanation is that in the fitted ARD model the rate of
transition away from the rare state is >> than the fitted transition
rates to it (or even that the ML value of these rates is zero).
Conditioning on this fitted model make it highly probably that the root
is
I didn't see the email that this addresses, but I will add a couple of
comments to Juan's suggestion:
(1) phytools::cophylo does not require the input trees to have branch
lengths. If they do not, arbitrary branch lengths for plotting are
computed using ape::compute.brlen.
(2) The code
The function add.species.to.genus may do what you want. It adds a single
species to the group defined by the MRCA of members of a genus, according to
multiple criteria (randomly and so on). It can add only one species at a time,
so you will need to write a for loop or something to iterate over
This is a bug that is related to how the function optimizes xlim to permit
space for the tip labels. By not showing tip labels, there is no optimization,
and thus no error.
This doesn�t seem to create an issue for plotTree in phytools, which has many
of the same options (and some additional
Hi Marian.
You should be able to do it with the phytools function plotTree.barplot using
the argument args.barplot, supplied as a list containing the arguments you want
to pass to barplot. Not sure if this is on CRAN yet so you might have to
install from GitHub.
Let me know if you need
Hi Zach.
What is your objective here? reorder.phylo reorders the edges in the �phylo�
object, but does not usually change the order in which the tips are plotted.
For that, you should look at ape::rotate or phytools::rotateNodes (I believe),
ape::ladderize, or the argument tips in
Hi Jonas.
One option is to use the function splitPlotTree in phytools. By default it
plots the split tree in two columns, but there is an option to split it into
two windows. Then each plotted tree could be saved as a PDF.
I will also investigate this to see if there is a better possibility.
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