Hi all,
I have a very simple question (I'm sure) that I can't quite seem to figure out.
I have been trying to plot posterior distributions of parameter estimates from
a BiSSE analysis using MCMC in diversitree. I have used the following code to
compare the speciation rates between states
Thanks Nick, I am beginning to suspect that adding the legend separately is the
way to go.
Kev
From: Nicholas Crouch [ncro...@uic.edu]
Sent: 14 March 2014 14:59
To: Arbuckle, Kevin
Subject: Re: [R-sig-phylo] profiles.plot legends
Kev,
I'm pretty sure
Hi Nick, it's running (or trying to) on diversitree v0.9-7
Kev
From: Nicholas Crouch [ncro...@uic.edu]
Sent: 01 April 2014 17:01
To: Arbuckle, Kevin
Subject: Re: [R-sig-phylo] Error in diversitree with MuSSE models
Kev,
What version of diversitree
Hi,
I have a problem that I am not entirely sure how to code appropriately, and any
help here would be gratefully appreciated.
Imagine we have a tree consisting only of a topology, for example this newick
format tree: '(A,(((B,C),D),E));'. Now, consider that we wish to explore how
Cheers,
Kev
From: Fran�ois Michonneau [francois.michonn...@gmail.com]
Sent: 23 October 2014 14:54
To: Arbuckle, Kevin
Subject: Re: [R-sig-phylo] Extracting sister groups
Hi Kevin,
We should be able to help you but it would be much easier if you provided
multiple and
different trees, it's a huge advantage to be able to sensibly plot the results
of such analyses.
Thanks again,
Kev
From: Liam J. Revell [liam.rev...@umb.edu]
Sent: 04 November 2015 19:21
To: Arbuckle, Kevin; r-sig-phylo@r-project.org
Subject
Hi folks,
I am currently trying to estimate ancestral states for a binary trait on a set
of 500 ultrametric trees (obtained from birdtree.org) of 105 bird species (and
in some cases there are multiple records per species). I have completed this
part using make.simmap in phytools for which I
Hi, I've trying to fit some BiSSE models in diversitree onto a set of fairly
large trees (>9k species) stored as a multiphylo object. However, due to the
size of the trees it quickly becomes a very time-consuming task to fit such
models to each individual tree.
Given that the implementation
Hi Michael,
When I run your code I get states for the nodes, so I'm not sure what the
problem is. However, I notice in your message you tried to get the node states
from $States, so I wonder if this is a typo or if this is the problem: the node
reconstructions are in $states (note the lower
Hi,
I think the biggest problem you'll have is interpreting the results, which I
suspect will get very complicated very quickly.
Nevertheless, if you have specific hypotheses you could feasibly build and
compare models representing them using the rayDISC function in corHMM, a bit
like a
Hi all,
I was wondering about plotting the output of an ancestral state
'reconstruction' of a continuous trait while incorporating at least some of the
uncertainty around the estimates.
One approach I thought of was to map the ASR onto a tree in a standard way,
then at each node have
Hi all,
I hope someone can help me out here as I've been wracking my brain trying to
figure out what the problem is. In short, I'm trying to fit a bunch of pathway
models with the rayDISC function in corHMM, which I've done before with no
issues. However, on this occasion the model just
Hi John,
In addition to Brian's suggestion, depending on what you are interested in
testing you could also set this up in GLM-style format either with the binary
trait as the response in a package like phylolm or as a phylogenetic mixed
model in ape (with the binary trait as response) or
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