[R-sig-phylo] profiles.plot legends

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

Re: [R-sig-phylo] profiles.plot legends

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

Re: [R-sig-phylo] Error in diversitree with MuSSE models

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

[R-sig-phylo] Random sampling of branch lengths

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

Re: [R-sig-phylo] Extracting sister groups

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

Re: [R-sig-phylo] Plotting ancestral states from estimation on multiphylo object

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

[R-sig-phylo] Plotting ancestral states from estimation on multiphylo object

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

[R-sig-phylo] BiSSE models on multiphylo objects

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

Re: [R-sig-phylo] corHMM reconstruction not estimating internal node states

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

Re: [R-sig-phylo] R package for testing correlation between two multistate discrete traits on a phylogeny?

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

[R-sig-phylo] Plotting uncertainty in continuous ASR

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

[R-sig-phylo] rayDISC model not running in corHMM

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

Re: [R-sig-phylo] correlation of binary and multistate

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