[R-sig-phylo] Estimating ancestral states of a trait under selection

Hello all, I've read some past posts and tried to figure this one out myself. It appears that the short answer is if there are not some extinct lineages in the tree with known trait values, it's difficult to do. I have a data set of the current climatic niches of a continental radiation of taxa.

Re: [R-sig-phylo] Estimating ancestral states of a trait under selection

Postdoc collaborators wanted: Check NIMBioS' website Calendar: http://www.brianomeara.info/calendars/omeara On Fri, Apr 19, 2013 at 4:00 PM, Eliot Miller eliotmil...@umsl.edu wrote: Hello all, I've read some past posts and tried to figure this one out myself. It appears

[R-sig-phylo] Fwd: Listing all tips with 0 length terminal branches

message -- From: Roey Angel an...@mpi-marburg.mpg.de Date: Wed, Jun 12, 2013 at 3:11 PM Subject: Re: [R-sig-phylo] Listing all tips with 0 length terminal branches To: Eliot Miller em...@mail.umsl.edu Works great, thanks. I just wonder if it's really necessary to convert to an S4 object

[R-sig-phylo] question about measurement error in phylogenetic signal

Hello all, I have been trying to get something to work in a number of different packages and with a number of different approaches today that I couldn't get to run in a believable way. Before I spend another day on this, I was wondering what people think about the idea in general. I have a

Re: [R-sig-phylo] Getting started making R packages

Tristan, Check out the package devtools, and before submitting to CRAN make sure you read: cran.us.r-project.org/doc/manuals/R-exts.pdf There are obviously people on here who know a million times more than me, and not that I've gotten very far, but I'm trying to figure this out myself at the

Re: [R-sig-phylo] Problem with R package checking

Tristan, I ran into that problem when I wasn't exporting the function (i.e. it was an internal function). If you use the package devtools to make your package than you add a roxygen comment to the effect of #' @export and it will pass the example checks. Not sure what the equivalent is with

Re: [R-sig-phylo] Substitute for functions on the laser package

Hi Mariana, To install from tar.gz: rtm.wustl.edu/writings/htrtargz.pdf See also Liam's functions ltt() in phytools. Cheers, Eliot On Tue, Sep 3, 2013 at 11:20 PM, Mariana Vasconcellos marian...@utexas.eduwrote: Thanks, Liam! But, unfortunately I don't know how to build from source. I

Re: [R-sig-phylo] APE error message

Are you trying to load a single tree or multiple trees in a single Nexus file? What function are you trying to use to load the tree(s)? On Mon, Sep 16, 2013 at 5:46 PM, BIGANZOLI FERNANDO bigan...@agro.uba.arwrote: Hello all I'm new with APE. I'm trying to open a NEXUS tree with 109 sp and

Re: [R-sig-phylo] Displaying posterior probability in BEAST tree output

Mariana, see: https://stat.ethz.ch/pipermail/r-sig-phylo/2013-June/002829.html On Fri, Jan 17, 2014 at 4:31 PM, Mariana Vasconcellos marian...@utexas.eduwrote: Dear all: I am trying to label the posterior probabilities in the nodes of the tree I generated in BEAST. Using nodelabels() doesn't

Re: [R-sig-phylo] algorithm for maximum and minimum phylogenetic diversity

Hello Leonardo, I'm I understand your question correctly, I believe that when using mean pairwise phylogenetic distance (e.g., MPD from the picante package) the maximum MPD will occur between the two most distantly related species in the phylogeny, and the minimum will occur between the two most

Re: [R-sig-phylo] Adding random branches to tree recursively

What I'm about to describe is essentially an elaborate wrapper for Liam's bind.tip, so he deserves the credit for figuring this all out. But if you are interested, I have a small package on GitHub that will automate this for you. It probably doesn't make much difference with so few taxa you need

Re: [R-sig-phylo] Add terminal branches to tree

Just to add to the slew of other good options, I have a small package up on GitHub (https://github.com/eliotmiller/addTaxa/tree/master/R) that is basically a big loop around Liam's bind.tip. There are examples included with the package. The main function you'd be interested in is

Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

Your Newick string is badly formatted. See: plot(t1) Error in plot.phylo(t1) : there are single (non-splitting) nodes in your tree; you may need to use collapse.singles() On Thu, Jun 1, 2017 at 1:31 AM, Mario José Marques-Azevedo < mariojm...@gmail.com> wrote: > Dears, > > I'm using

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

/Ornithology) > > > > Museum of Natural Science > > Louisiana State University > > 119 Foster Hall > > Baton Rouge, LA 70803, USA > > > > Twitter: @brown_birds > > > > > > > > On Fri, May 4, 2018 at 8:22 AM Eliot Miller <eliot.is...@

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

I suggest calling min(tree$edge.length) on any tree you plan to use for comparative methods, including the one you're having trouble with Rafael. If you get a negative value, then something is really funny and you need to solve it. If you get a zero then various comparative methods will throw

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

What does: min(tree$edge.length) say? Eliot On Wed, May 2, 2018 at 2:22 PM, Rafael S Marcondes wrote: > Here's a little more info that may be relevant: the tree is not supposed to > have negative dates. Although when I do is.ultrametric(tr) I get FALSE, I > have always

Re: [R-sig-phylo] Adding species to genera tree as polytomies

Hi there, If I read this right, you're also wanting to loop this over multiple genera. If so, it might save some time to try this with the addTaxa package (https://github.com/eliotmiller/addTaxa/blob/master/DESCRIPTION). I haven't worked on this project in a while, and I left the documentation in

Re: [R-sig-phylo] patristic distance doubts and meanings

The amount of time two taxa have been evolving independently from one another is, barring some complex introgression, independent of other species in the tree. Pruning the tree from however many species to 700 won't affect the distances between those 700. After pruning, use cophenetic() to nearly

Re: [R-sig-phylo] issue with add.species.to.genus

Hi Karla, Check out the addTaxa package I wrote a while back ( https://github.com/eliotmiller/addTaxa). I suspect it can do what you want. We hope to publish some formal tests of how this approach performs, but I've been sidetracked. In the meantime if you use it there's the original reference in

Re: [R-sig-phylo] Using bind.tip and lapply on a multiPhylo object

Hi Russell, A package I wrote a while back should be able to do that fairly easily. https://github.com/eliotmiller/addTaxa The only paper it's described in remains https://bsapubs.onlinelibrary.wiley.com/doi/full/10.3732/ajb.1500195 It's a wrapper for bind.tip, with some additional stuff. You

Re: [R-sig-phylo] Using bind.tip and lapply on a multiPhylo object

History (Negaunee >> Integrative Research Center) >> >> Chair, Biodiversity Committee, American Society of Mammalogists >> >> Taxonomy Advisor, IUCN/SSC Small Mammal Specialist Group >> >> personal web: n8u.org | Google Scholar < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.google.com%2Fc

Re: [R-sig-phylo] identifying phylogenetically equivalent nodes

Assuming trees are rooted and fully bifurcating, I think the following will work. I tried a few tests and it seemed to work. I traded a few emails back and forth with Jake to make sure I understood what he wanted. Guess what I was supposed to be working on wasn't holding my attention... Best,

Re: [R-sig-phylo] Extracting interspecific distances as a matrix

I haven't used the dist.dna function before, so apologies if I'm off base, but I see it returns a distance object. You can simply do dMat <- as.matrix(d) And now it's a matrix of the more familiar form. I haven't used the split function before either, but rows (or columns) can just be extracted

[R-sig-phylo] Fwd: Extracting interspecific distances as a matrix

Sent on Jan 17th but perhaps using the wrong email address. -- Forwarded message - From: Eliot Miller Date: Tue, Jan 17, 2023 at 8:41 AM Subject: Re: [R-sig-phylo] Extracting interspecific distances as a matrix To: Jarrett Phillips Cc: I haven't used the dist.dna function