Hi, I am trying to get a matrix of shared proportion distances from a
phylogeny, as can be exported in the PDAP module of Mesquite. However, for some
odd reason the newick files written from R don't quite seem to be read
correctly in Mesquite. Having had a look at exporting vcv matrices of vario
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 (cdpos
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
eers,
Kev
From: Nicholas Crouch [ncro...@uic.edu]
Sent: 14 March 2014 16:46
To: Arbuckle, Kevin
Subject: Re: [R-sig-phylo] profiles.plot legends
This thread might be useful as well
http://www.talkstats.com/showthread.php/16691-greek-letter-and-equal-sign-in-legend-of-a-plot
Nick
On Fri, Ma
Hi,
I am trying to run a set of MuSSE models in diversitree but getting error
messages that I can't seem to figure out (fortunately the models are only an
adjunct to my main premise, not particularly vital). The trait has 4 levels and
the full model works fine, with the following code:-
lik<-m
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 diversitre
Subject: Re: [R-sig-phylo] Error in diversitree with MuSSE models
(Arbuckle, Kevin)
Message-ID: <533d9431.6010...@gmail.com>
Content-Type: text/plain
Hi Kev,
Your constrain looks fine but I think you should double check your index
for the 'find.mle' function in this line:
&q
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
variatio
Hi everyone,
I am attempting to run sister group analyses as one way to look at the effect
of a binary trait on diversification. Two of the functions from ape that I'm
looking at are diversity.contrast.test and richness.yule.test, but both have
the same limitation. They require the data to be
ran)
trait<-data.frame(sp=tree$tip.label,bt=getStates(phy,type="tips"))
rownames(trait)<-tree$tip.label
Cheers,
Kev
____
From: Fran�ois Michonneau [francois.michonn...@gmail.com]
Sent: 23 October 2014 14:54
To: Arbuckle, Kevin
Subject: Re: [R-sig-p
ober 2014 16:05
To: Arbuckle, Kevin
Cc: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] Extracting sister groups
HI Kevin,
If I understand correctly what you're trying to do, you'll first need to
collapse some of your tips to create clades, a proportion of which will have
the t
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 c
cross 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.o
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 i
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 cas
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 standa
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 essential
David intended to send his response below to the list, and that combined with
my reply (also below) might help clarify things a bit.
Cheers,
Kev
From: Arbuckle, Kevin
Sent: 27 February 2017 18:30
To: David Bapst
Subject: RE: [R-sig-phylo] Plotting
: 27 February 2017 21:57
To: Arbuckle, Kevin; R phylo list
Subject: Re: [R-sig-phylo] Plotting uncertainty in continuous ASR
Hi Kevin.
I now show one way to do this here:
http://blog.phytools.org/2017/02/more-on-adding-error-bars-to-contmap.html.
All the best, Liam
Liam J. Revell, Associate
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 isn't
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 MCMCgl
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