[R-sig-phylo] Fwd: Postdoc Position: Phylogenetic Climate Modeling & 3D Morphometrics

Please see the job ad below -- this postdoc at A looks like it might be of interest for those here on R-Sig-Phylo. -Dave -- Forwarded message - From: Michelle Lawing Date: Thu, Jul 14, 2022 at 9:06 AM Subject: Postdoc Position: Phylogenetic Climate Modeling & 3D Morphometrics To:

Re: [R-sig-phylo] Model Selection and PGLS

Hi all, Russell, Nate, I took an interest with some of the commentary here, so here's my two cents. > I was surprised that AIC would vary this much in a dataset where the trait > data, number of tips, and branching > topology used to compute the model are more or less constant between trees. I

Re: [R-sig-phylo] evolutionary rate for species with low phylogenetic signal

Karla et al., There isn't, necessarily, a good alternative. If phylogenetic signal is very poor, our ability to estimate rates is extremely hindered. There's no rate of evolution in a white noise model -- values are simply assigned independently of phylogeny. One thought I had is that you might

Re: [R-sig-phylo] A test for valid phylo object (ape package) for package developers

Hi Elizabeth, There's a lot of ways for trees to be wrong, and surely no tree-checking or tree-fixing function can handle all possibilities. Dating trees and simulating trees can be a messy business, so I used to often hard-crash R with C++ errors all the time until I wrote functions to try to

[R-sig-phylo] Phylogenetic Paleobiology Short Course at GSA 2019 - This Saturday in Phoenix, AZ - Sponsored by PaleoSoc

son, Peter Wagner, April Wright, David Wright, Laura Soul, Rachel Warnock, & David Bapst -- David W. Bapst, PhD Assistant Instructional Professor Geology & Geophysics Texas A & M University https://github.com/dwbapst/paleotree [[alternative HTML

[R-sig-phylo] 2019 Paleo Society Short Course: Quant Methods in Phylogenetic Paleo - Sept 21st, 2019 - Phoenix, AZ

-serv. Cheers, -Dave Bapst ## We are pleased to announce the 2019 Paleontological Society Short Course, “Quantitative Methods in Phylogenetic Paleobiology,” organized by David Bapst, Sandy Carlson, Laura Soul, Peter Wagner, Rachel Warnock, April Wright & Davey Wr

[R-sig-phylo] Logarithmic Scales for Plotting Dated Phyogenies (e.g. Log of Time Axis?)

Hi all, I've been dealing with a tree with one very deep divergence and many very shallow divergences recently, and I was curious if there was an R plotting capability that allows for the depth axis of the tree to be non-linear or logarithmic - helpful if there can be a time axis bar as well, as

Re: [R-sig-phylo] mixing trait values from distinct models of evolution to reconstruct null morphospace

My biggest issue with this setup, as you give it, is that it isn't clear how you'll make this into a test - is there some summary statistic of the null morphospace you'll be generating many times, and then comparing that distribution to the observed value of the observed, real data? I would

Re: [R-sig-phylo] OU for non-ultrametric trees

Danielle, Apologies for the late comment on this, but what do you mean by non-rooted? Do you mean the tree is rooted, but has a three-way split with the outgroup at the root node? You shouldn't do OU on a tree you can't assign a root to. I'm also just a bit curious what gave you the sense that

[R-sig-phylo] Extended Majority Consensus Topology (Allcompat Summary) in R? And some observations on ape's consensus() function

Hi all, I was interested if anyone was familiar with R code that can estimate an extended majority consensus tree (referred to as an 'allcompat' tree by the sumt command in MrBayes)? This is a fully bifurcating summary of a tree posterior, where each clade is maximally resolved by the split that

Re: [R-sig-phylo] No PCOA Correction Applied but Corrected Eigenvalues Returned? (ape::pcoa)

_eig" "Cumul_br_stick" > R> names(res.lingoes$values) > [1] "Eigenvalues" "Corr_eig" "Rel_corr_eig" "Broken_stick" > [5] "Cum_corr_eig" "Cum_br_stick" > R> any(res.lingoes$values$Corr_eig < 0) &g

[R-sig-phylo] No PCOA Correction Applied but Corrected Eigenvalues Returned? (ape::pcoa)

Hi all, Not exactly phylogenetic, but I've recently uncovered some odd behavior with `pcoa` in `ape` and I was curious if anyone understood what was going on. Usually, if you don't have negative eigenvalues and aren't using a correction, `pcoa` will return the raw eigenvalues. However, I've

Re: [R-sig-phylo] Measuring Phylogenetic Signal

Alyson- Following off of what Liam said, one thing to consider is as most measures of phylogenetic signal aren't relative to the units of the traits considered, any transformation of the data should be about equally interpretable. To take a spin with Liam's example, if , if the log-scale trait

Re: [R-sig-phylo] estimate ancestral state with OUwie models

odel ranking > may change depending on the underlying models too, I guess). > > Jake > > > > On Jun 14, 2018, at 9:32 AM, David Bapst wrote: > > > > Simone, Marguerite, others, > > > > I'll also add that I think there's a great deal to be skeptica

Re: [R-sig-phylo] estimate ancestral state with OUwie models

ni8p58-9Xpxcc2aQgYVVI=a0SwA8yTo1qWJZLpuWR9cVHuO_cxYqknynO9BdyATbs=> > > > On Jun 11, 2018, at 7:33 PM, Simone Blomberg > wrote: > > This sounded wrong to me, as the OU process should be agnostic to the > dataset: There are no restrictions inherent in the OU process that apply >

Re: [R-sig-phylo] estimate ancestral state with OUwie models

it is clear that you can use branch length > transformations with OU, so long as you use the (correct) Hansen formula, > not the Butler-king formula, which does indeed require an ultrametric tree. > > Cheers, > > Simone. > > Sent from my iPhone > > > On 12 Jun 2018,

Re: [R-sig-phylo] estimate ancestral state with OUwie models

Just to follow off what Lucas said, but please note you cannot rescale branches of a phylogeny using an OU model when the tree is non-ultrametric (such as when it contains extinct, fossil taxa as tips). Slater (2014, MEE) discusses this more in a brief correction to Slater (2013). I don't know if

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

ttp://idea.ucr.edu/>Educational Applications <http://idea.ucr.edu/> >>>> >>>> >>>> Editor in Chief, /Physiological and Biochemical Zoology >>>> <http://www.press.uchicago.edu/ucp/journals/journal/pbz.html>/ >>>> >>>> >>

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

have elsewhere in the R-phylo universe. -Dave On Wed, May 2, 2018 at 2:30 PM, Brian O'Meara <bome...@utk.edu> wrote: > On Wed, May 2, 2018 at 2:53 PM, David Bapst <dwba...@tamu.edu> wrote: >> >> Given that your tree appears to be non-ultrametric enough to cause >&

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

out why the tips seem to not quite be at the same distance from the root. Cheers, -Dave. On Wed, May 2, 2018 at 1:35 PM, David Bapst <dwba...@tamu.edu> wrote: > Rafael, > > That error message is from paleotree's dateNodes function, which is > called as part of OUwie's approa

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

Rafael, That error message is from paleotree's dateNodes function, which is called as part of OUwie's approach to getting node dates. I think I see what Elliot is trying to get at, but this might be quicker: node.depth.edgelength(tree) That should tell us how far each node, including the tips,

Re: [R-sig-phylo] threshDIC value error: Inf for DIC Values

Do you have any zero-length branches in your tree, Aja? Cheers, -Dave Bapst On Mon, Dec 18, 2017 at 3:22 PM, Aja Carter wrote: > I am using the ancThresh model in the phytools package for 172 taxa. For > model we have the liabilities, parameters, MCMC and alpha values

[R-sig-phylo] Unable to install ape on R-devel?

Hi all, I know R-devel is meant to be unstable, but I was curious if anyone else has had issues with getting ape v4.1, installed as a binary from CRAN, to work with R-devel recently on Windows (3.5.0 pre-release, timestamp: 2017-10-19 r73560, specifically Windows 10, although I don't think its

Re: [R-sig-phylo] Why does ace set a random number generator seed?

For a reason I ignore, it seems that a random seed is initialized > when calling a function linked to Rcpp. Here is an example: > > R> rm(".Random.seed") > R> library(RcppEigen) > R> exists(".Random.seed") > [1] FALSE > R> o <- fastLm(1, 1) > R

[R-sig-phylo] Why does ace set a random number generator seed?

Emmanuel, all- I noticed today that a workspace I was working with had a random number seed set in it, but didn't remember setting one. Finally, I discovered the culprit was ace. Here's a reproducible example, demonstrating that a seed exists after running ace: library(ape) tree<-rtree(10)

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

ll for your advice. > > Cheers, > Sérgio. > > - Mensagem original - >> De: "David Bapst" <dwba...@gmail.com> >> Para: "Sergio Ferreira Cardoso" <sergio.ferreira-card...@umontpellier.fr> >> Cc: "Eliot Miller" <et...@corn

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

Hi Sergio, Sorry for being late to the party, but maybe expandTaxonTree in paleotree does what you're looking for? I wrote it for turning trees of genera into trees of species, with the resulting generic polytomies collapsed or not (in case we know that the genera is paraphyletic). Cheers, -Dave

Re: [R-sig-phylo] How to test stratification of sampling across tree?

Ross, An interesting question. I understand it as that you want to test if the trait is overdispersed relative to phylogeny, which still makes me think that measures of 'phylogenetic signal' might be still be useful, even though the typical interpretation is 'signal' as 'heritability'. I would

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

That's really cool, Liam. Would it also be possible for one to do multiple such error bars per node, for plotting ASRs for multiple traits? -Dave On Mon, Feb 27, 2017 at 12:13 PM, Liam J. Revell wrote: > Hi Kevin. > > This is not automatic - but it is indeed fairly easy to

Re: [R-sig-phylo] A question about phylogenetic signal significance with 1000 trees

A deep thought on this topic, from a mind run aground amidst grading papers. While I am a big fan of using multiple trees, we should keep in mind that phylogenetic uncertainty makes signal into a rather snaky concept. By this, I mean that there could have only been one true history (which may or

Re: [R-sig-phylo] fatal error plotting trees

Manabu- Can you give us a reproducible example? Is it as simple as plotting any tree does it or is it only particular trees? Cheers, -Dave On Fri, Oct 28, 2016 at 7:53 AM, Manabu Sakamoto wrote: > Dear List, > > I'm getting fatal errors when plotting phylo objects,

Re: [R-sig-phylo] ape functions to become generic

Thanks, Emmanuel. That answers my questions. Cheers, -Dave On Tue, Oct 4, 2016 at 4:03 AM, Emmanuel Paradis <emmanuel.para...@ird.fr> wrote: > Hi David, > > Le 03/10/2016 à 17:25, David Bapst a écrit : >> >> Hi Emmanuel (and list!), >> >> These changes

Re: [R-sig-phylo] ape functions to become generic

Hi Emmanuel (and list!), These changes are appreciated, and will make dealing with multiPhylo objects much easier. I know I certainly have blocks of code where I need to 'carry' the multiPhylo class tag through every other line; it always been a bit of a chore. However, two questions from the

Re: [R-sig-phylo] extracting from mrbayes

John, I had to double-check this with someone who knew better first, but they confirmed for me that the answer is that MrBayes doesn't infer a Q matrix. By default, the Q matrix for Mk in MrBayes is always held fixed so the rates of transition are always equal and fully reversible, i.e. a simple

Re: [R-sig-phylo] 'T151: New Approaches to Phylogenetic Paleobiology' at GSA Annual Meeting 2016. Sept 25-28 in Denver

Hi all, Just a short reminder, that abstract submission for GSA (and thus for our session) closes on July 12th, which is less than a week away. Cheers! -Dave On Mon, Apr 4, 2016 at 10:25 AM, David Bapst <dwba...@gmail.com> wrote: > Hello all, > > We are pleased to announce a

Re: [R-sig-phylo] BiSSE/MacroCAIC on Non-Ultrametric Tree with Polytomies?

Brian- Is your tree non-ultrametric because it contains extinct taxa from the fossil record, or is it simply an undated tree of extant taxa? To my knowledge, there isn't yet a satisfactory solution to the first (no BISSE for paleo-phylogenies) but if the second then, it seems the best route

[R-sig-phylo] 'T151: New Approaches to Phylogenetic Paleobiology' at GSA Annual Meeting 2016. Sept 25-28 in Denver

Hello all, We are pleased to announce a topical session that we believe is of special interest to the R-Sig-Phylo list, scheduled for the 2016 annual Geological Society of America meeting held from September 25th-28th in Denver, Colorado, USA. Our oral topical session, “New Approaches to

Re: [R-sig-phylo] summary stats for comparative methods p-values

Darrin, list- I'm sure there's people on this list with better answers, so I'll throw in first with what might be the wrong answer (but feels right to me), and say you more or less need to report all of them: like, show a full histogram of the p-values. At least, as a reviewer, that is what would

Re: [R-sig-phylo] new testing version of ape

FYI, in case one wants to install the testing version of ape to R-devel (in my case, also a Windows machine), I found I needed: install.packages("ape",contriburl="http://ape-package.ird.fr/bin/windows/contrib/3.2;) Emmanuel, I've tested the testing version with paleotree and a few other projects

Re: [R-sig-phylo] getBtimes vs. branching.times

Lev, This is easy, if the newick strings are structured the same so that the resulting edge matrix and tip labels are identical. Here's a worked example: ``` library(ape) # with edge lengths

Re: [R-sig-phylo] Plotting sampled-ancestor trees in R

Hi Roger, I'm not aware of any existing solution. Could you send around a small example of the data format of an output sampled ancestor tree from BEAST or MrBayes? Are they just typical Newick/NEXUS format with ancestors indicated tipis with zero-length branches or something more complicated?

Re: [R-sig-phylo] branching time to branch length (eg. mcmctree)

Tristan, It's alright. To be honest, I am (and should be) quite embarrassed that I overlooked an ape function... I was a nice warm-up exercise, nonetheless, and I can see how to extend it to handle dates for non-ultrametric fossil trees, which is a case not covered by compute.brtimes, and would

Re: [R-sig-phylo] branching time to branch length (eg. mcmctree)

Hello Tristan, Does the code below work for your purpose? I don't know of a function off the top of my head that does this in a current package on CRAN (and although I might have missed such, I try to keep myself aware of time-scaling functions in R, given my interests). However, its not too

Re: [R-sig-phylo] dist.nodes crashing with big trees

Hi Gustavo, I'm paleotree's author and maintainer. Just to be clear that I understand your problem, I believe you are saying that when you use timeSliceTree, you are getting an error that the internal call to dist.nodes is failing? Is that right? The first thought I have is that maybe the

Re: [R-sig-phylo] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels

is the part of the code that renumbers the nodes which is thus used in all cases (even if there are no node labels). I'll conduct some tests later, but in the mean time if you see something strange, just tell me. I attach the new source file. Best, Emmanuel Le 25/07/2015 18:54, David Bapst

[R-sig-phylo] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels

Hello all, Recently I noticed a complex function of mine that does some tree transformations was randomly scrambling node.label elements. In the course of doing so, I found this old email (below) from Rebecca Best in 2012, which outlined an issue that occurred when a ladderized tree had tips

Re: [R-sig-phylo] PGLS with non-ultrametric tree

Hi Solomon, Comparatives methods are routinely applied to non-ultrametric trees, contrary to the text you quoted. See the last chapter of that book. The phylogeny-based analyses that do generally require ultrametric trees are those that fit some form of a lineage diversification model, because

Re: [R-sig-phylo] doubt

Just to clarify for future users who stumble on Liam's solution for Lilian, the second block of code attaches the new tips to non-ultrametric trees at the same distance as the current tips at maximum distance from the root. If this is a time-scaled phylogeny and the tree's root depth is equal to

[R-sig-phylo] Margin Artifact in plot.phylo with Very Long Tip Labels, despite show.tip.label=FALSE

Hi all, I was plotting some trees with obscenely long taxon names (long story) and found an odd plotting artifact that leaves white-space when show.tip.labels=FALSE, as if the plot was trying make room for the extraordinarily long tip labels, even though they wouldn't be plotted. I'm using R

[R-sig-phylo] Missing States in ML Reconstruction of Discrete Ancestral States (phytools, ape)

Hello all, (I'm a troublemaker today.) Sometimes, in ordered discrete data, there are states we know might exist as intermediary between observed states but aren't observed themselves. I suppose this is probably common for meristic data. At least to me, it seems like it should be possible to

Re: [R-sig-phylo] Missing States in ML Reconstruction of Discrete Ancestral States (phytools, ape)

: liam.rev...@umb.edu blog: http://blog.phytools.org On 6/17/2015 1:46 PM, David Bapst wrote: Hello all, (I'm a troublemaker today.) Sometimes, in ordered discrete data, there are states we know might exist as intermediary between observed states but aren't observed themselves. I suppose

Re: [R-sig-phylo] Missing States in ML Reconstruction of Discrete Ancestral States (phytools, ape)

://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 6/17/2015 3:06 PM, David Bapst wrote: Liam, Ah, I see, rerootingMethod(), unlike ace, will accept a matrix representation of discrete trait values. However, it doesn't appear that one can define a model matrix

[R-sig-phylo] collapse.singles() can be confused by node numbering (Was: Bug in reorder.phylo() (related to cleaning phylo objects))

, Emmanuel Le 12/06/2015 22:41, David Bapst a écrit : Hi Klaus (and others), Ah, I see! The real bug then appears to be in collapse.singles, as it does not reorder the ID numbers in $edge. Here's a quick function to return the root ID: getRootID-function(tree){ uniqueNode-unique(tree$edge

Re: [R-sig-phylo] Bug in reorder.phylo() (related to cleaning phylo objects)

that would be tough to find otherwise. Cheers, Emmanuel Le 12/06/2015 22:41, David Bapst a écrit : Hi Klaus (and others), Ah, I see! The real bug then appears to be in collapse.singles, as it does not reorder the ID numbers in $edge. Here's a quick function to return the root ID: getRootID

Re: [R-sig-phylo] Bug in reorder.phylo() (related to cleaning phylo objects)

Whoops, I meant a 'function in ape?' -Dave On Mon, Jun 15, 2015 at 10:26 AM, David Bapst dwba...@gmail.com wrote: Hi Brian, I was already aware of the read.tree(write.tree()) fix, however I've run into (corner?) cases where a particular sorting of edges or whatever can lead to a loss of tip

Re: [R-sig-phylo] Bug in reorder.phylo() (related to cleaning phylo objects)

(tree1, 131, 151) plot(tree2) # now works for me Cheers and have a nice weekend, Klaus On Fri, Jun 12, 2015 at 2:53 PM, David Bapst dwba...@gmail.com wrote: Hello all, As those of you who directly manipulate the guts of phylo objects in your code (or construct new phylo objects

[R-sig-phylo] Bug in reorder.phylo() (related to cleaning phylo objects)

Hello all, As those of you who directly manipulate the guts of phylo objects in your code (or construct new phylo objects whole cloth from un-phylo-like data structures) have probably experienced, it is sometimes easy to create $edge matrices that aren't accepted by ape functions (I often use

Re: [R-sig-phylo] Constraining node values in an OUCH analysis

Aaron, While contemplating Nate's question, I wondered, doesn't hansen currently support NA codings for missing variables for tip taxa? Unfortunately the donotrun{} example for hansen() using geiger data isn't currently functioning, so I couldn't test this. -Dave Bapst On Thu, Jun 4, 2015 at

Re: [R-sig-phylo] ancestor vs. change plots

Milton, Brian, etc, Just wanted to add some background on Alroy's anc-desc change analyses, and the recognition of these relationships in the fossil record. This may be tangential; it isn't clear to me what sort of dataset that Milton has. So, Brian said... In Paleo, you can (well, arguably)

Re: [R-sig-phylo] (P)GLS (nlme) vs. PGLS (caper)

William, Yes, the different PCM models make very different statements about what is happening biologically in your data. Additionally, the three Pagel parameters are not always easy to interpret biologically. Carl Boettiger has some particularly lucid thoughts on Pagel's lambda:

Re: [R-sig-phylo] hierarchical model with phylogenetic dependence term

Cecile, Peter, Joe and all- As far as I understand, Peter's analysis involves paleontological data with non-ultrametric trees, and based on my understanding of Slater (2014), the Freckleton approach using PIC is invalid for that type of dataset, although Fitzjohn's pruning algorithm might still

Re: [R-sig-phylo] Plotting Posterior Probabilities from MrBayes Trees (An Update)

to plot posterior probabilites from MrBayes in R! Cheers, -Dave On Fri, Oct 3, 2014 at 10:29 AM, David Bapst dwba...@gmail.com wrote: Just to clarify, off-list discussion with Graham reveals (after some confusion on my part) that if the simple format option is used in sumt in MrBayes

[R-sig-phylo] MrBayes Trees are Misread by read.annotated.nexus() in OutbreakTools

Hello all, Recently, I wanted to display posterior probabilities on a 50% compatibility tree from a MrBayes run, created with the 'sumt' command. I looked around for ways to do this and found this email thread from last year: https://stat.ethz.ch/pipermail/r-sig-phylo/2013-June/002825.html

Re: [R-sig-phylo] MrBayes Trees are Misread by read.annotated.nexus() in OutbreakTools

Department of Paleobiology National Museum of Natural History The Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 (202) 633-1316 slat...@si.edu www.fourdimensionalbiology.com On Oct 3, 2014, at 10:42 AM, David Bapst dwba...@gmail.com wrote: Hello all, Recently, I wanted to display

Re: [R-sig-phylo] Early burst branch rescale

Julien- Does mvSHIFT account for the OU rescaling issue on non-ultrametric trees that Graham mentions? If so, how? Cheers, -Dave On Mon, Jun 2, 2014 at 5:26 PM, Julien Clavel julien.cla...@hotmail.fr wrote: Hi Jon, Take a look at the mvSHIFT function in mvMORPH. This is typically what you

Re: [R-sig-phylo] drop trees from multiphylo list

Hi John, A fully reproducible example of the error you have encountered would be this: trees.pool-rmtree(N=10,n=100) trees.pool[[1]]-NULL Which returns the same error; the reason for this is that 'multiphylo' is an S3 class so ape has a specific function that replaces the generic replacement

Re: [R-sig-phylo] utilise more data by making polytomies

At the risk of inundating you with options, Henry, there is also expandTaxonTree in the package paleotree (on CRAN) which is similar to the above, but also lets you collapse higher taxa you list as paraphyletic, which can be useful if the taxonomic work of your group has never been concerned with

Re: [R-sig-phylo] The Curious Behavior of is.binary.tree

this ambiguity, so: (A,B,C):0; is a (non-binary) rooted tree (note that both trees are graphically identical). Ape considers the first tree as unrooted because it is the kind of trees produced by many functions such as nj, bionj, etc. Best, Emmanuel Le 16/01/2014 17:32, David Bapst

Re: [R-sig-phylo] The Curious Behavior of is.binary.tree

J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 1/15/2014 3:34 PM, David Bapst wrote: Hi Emmanuel and the rest of the list, In some code, I use the ape

[R-sig-phylo] The Curious Behavior of is.binary.tree

Hi Emmanuel and the rest of the list, In some code, I use the ape function is.binary.tree to test if a phylogeny is fully dichotomous. However, some recent analyses have made me wonder if this wasn't the right choice. I'm not sure if the following is a bug report me or me not understand the

Re: [R-sig-phylo] Simulation of extinct taxa onto a phylogeny of extant taxa?

Hi Jurriaan- I've been thinking about this after your email and my sense is that such a simulation would be very difficult. Just dropping onto the tree branching events on the extant tree that only produced one living daughter might not be too difficult under a homogenous birth-death model.

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

Tristan- I found this to be the most important how-to reference, but I am a windows user. http://robjhyndman.com/hyndsight/building-r-packages-for-windows/ For distributing on CRAN, making help files and examples is the most critical step. package.skeleton() is helpful in setting up the

Re: [R-sig-phylo] collapse descendants of a node to a polytomy

Hi John, I'm not familiar with any such function either. However, a handy trick for doing this sort of thing is changing the branch lengths of descendant nodes to zero and using the ape function di2multi to collapse those edges, creating a polytomy. Now, it isn't clear to me from your email

Re: [R-sig-phylo] Lineages Through Time Plot with Confidence / HPD Interval

/ -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ http://cran.r-project.org/web/packages/paleotree/index.html ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https

[R-sig-phylo] Fwd: Deadline extended: Unifying paleobiological and comparative perspectives on character evolution, Lisbon 2013 (ESEB)

studies, using character evolution as a focal point. Sincerely, Lee Hsiang Liow Thomas F. Hansen -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ http://cran.r-project.org/web/packages/paleotree/index.html

[R-sig-phylo] Fwd: Symposium announcement: Unifying paleobiological and comparative perspectives on character evolution, Lisbon 2013 (ESEB)

will be assigned time slots of 15 minutes and selected based on relevance for the symposium. Sincerely, Lee Hsiang Liow Thomas F. Hansen -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ http://cran.r-project.org/web/packages

Re: [R-sig-phylo] prop.clades() errors

On Thu, Nov 8, 2012 at 2:04 PM, Jeremy Yoder jbyo...@gmail.com wrote: All, I'm working on some analyses that require comparison of tree structures, and I've bumped into the problem David Bapst posted about back in March: http://www.mail-archive.com/r-sig-phylo@r-project.org/msg01840.html

Re: [R-sig-phylo] fitContinuous-Early Burst Model

[[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL

Re: [R-sig-phylo] fitContinuous-Early Burst Model

] 0.001813503 $Trait1$aic [1] 534.8593 $Trait1$aicc [1] 535.1042 $Trait1$k [1] 3 On Sun, Nov 4, 2012 at 2:01 PM, David Bapst dwba...@uchicago.edu wrote: Nicolas, Not certain how you are time-scaling your tree, but I often get warnings of singularity from various comparative analysis functions

Re: [R-sig-phylo] fitContinuous-Early Burst Model

the College of Staten Island as one of “America’s Best-Bang-for-the-Buck Colleges” ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical Sciences University

Re: [R-sig-phylo] Add species branches to genus level tree

Tom ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst

Re: [R-sig-phylo] mccr test for non ultrametric trees

size as the orginal (e.g. with TreeSim functions) to get the null distribution of gamma values. Is that feasible? thanks, Pas ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst

Re: [R-sig-phylo] Continuous character simulation

/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ http://cran.r-project.org/web/packages/paleotree/index.html ___ R-sig-phylo mailing list R

[R-sig-phylo] Problems with prop.clades and compar.ou

: Error in chol.default(V) : the leading minor of order 10 is not positive definite Any tree I generate with rtree or rcoal seems to generate this or a similar error with compar.ou, so it doesn't seem to be an issue with me using a non-ultrametric tree. Any ideas? Thanks, all! -Dave -- David

Re: [R-sig-phylo] diversitree with multicore

]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ http://cran.r-project.org/web/packages

[R-sig-phylo] Comparative Methods and Pseudo-Traits

degradation example. So, what do people think? How should we test for correlation when non-evolving quasi-traits are involved? I'm very interested to hear people's thoughts on this matter. -Dave Bapst, UChicago -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL

Re: [R-sig-phylo] Simulating binomial trait shifts on a phylogeny

deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst

Re: [R-sig-phylo] Getting ACE information out of R

://morganlangille.com ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu

Re: [R-sig-phylo] R: Re: R: ancestral state reconstruction for tips

       [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL

[R-sig-phylo] Session on Phylogenetic Paleobiology at GSA 2011 (Abstracts Due TODAY!)

Hello all, Just wanted to send a final reminder that abstracts for our session at GSA 2011 is due today, June 26th. See my previous email below for more details. Thanks, -Dave Bapst and Emily King, UChicago On Mon, Jul 18, 2011 at 11:39 AM, David Bapst dwba...@uchicago.edu wrote: Hello all

Re: [R-sig-phylo] Generating all possible phylogenies...

, Liutauras ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst

[R-sig-phylo] Session on Phylogenetic Paleobiology at GSA 2011 (Abstracts Due in a Week!)

questions. -Dave Bapst, UChicago -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo

Re: [R-sig-phylo] cut a tree in a given time interval

-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ [[alternative HTML version deleted

Re: [R-sig-phylo] Branch and Bound Maximum Parsimony

___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ [[alternative

[R-sig-phylo] Possible Error in prop.part() ?

haven't updated to 2.7 since I use read.nexus() quite a bit; let me know if it is reproducible in that version. -Dave -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ [[alternative HTML version deleted

[R-sig-phylo] Conditioning on Total Tips in Birth-Death Trees

looking for. Thanks, -Dave -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r

Re: [R-sig-phylo] Q: Likelihood ratio test and rate shift test on complete dated phylogeny

one draw if the pure birth model fits better than the birth-death model? That the extinction rate is negligible? -Dave -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst

Re: [R-sig-phylo] Q: Likelihood ratio test and rate shift test on complete dated phylogeny

https://stat.ethz.ch/mailman/listinfo/r-sig-phylo        [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical

Re: [R-sig-phylo] multi2di: any way to return all possible combinations of polytomy to dichotomous trees?

for your time, Cheers, Alastair David Bapst wrote: Alistair- How many multifurcations are there, with how many branches each? If the number of potentially resulting trees is too high, it may not be possible to store all the possible trees in memory. If your tree is small, you might try

Re: [R-sig-phylo] multi2di: any way to return all possible combinations of polytomy to dichotomous trees?

Private Bag, Rondebosch 7700, South Africa or PO Box 115, Loxton 6985, South Africa Cell: 082 491-7275 ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical

  1   2   >