Re: [R-sig-phylo] chronos ape substitution rate strict clock

. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ Book: Phylogenetic Comparative Methods in R <https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r> (/Princeton University Press/, 2022) O

[R-sig-phylo] Postdoc at OIST

ons are encouraged to apply. -- Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ Book: Phylogenetic Comparative Methods in R <https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r> (/Princeton University Press/,

[R-sig-phylo] Evolution 2024 Symposium on Replicability & Reproducibility

ractices on the reliability of findings, & 'meta-science' (the science of science) to help ask if ecology & evolutionary biology are on the cusp of their own replication crisis & what can be done about it. -- Liam J. Revell Professor of Biology, University of Massachus

Re: [R-sig-phylo] HPD in threshBayes function (phytools)

al-on-evolutionary.html. I hope this helps you figure out what you need to do! All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ Book: Phylogenetic Comparative Methods in R <https://press.princeton.edu/books/phylogenetic-com

Re: [R-sig-phylo] Highlighting Specific Clades in a Lineage-Through-Time Plot

tools.org/2023/10/visualizing-lineage-accumulation-on.html. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ Book: Phylogenetic Comparative Methods in R <https://press.princeton.edu/books/phylogenetic-comparative-

[R-sig-phylo] Postdoc in phylogenetic comparative methods at UMiami

urie Postdoctoral Fellow. -- Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ Book: Phylogenetic Comparative Methods in R <https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r> (/Princeton University Press/,

Re: [R-sig-phylo] command for access posterior probabilities values of pie charts obtained from make.simmap

Dear Felipe. Assuming your "multiSimmap" object is called /maps/, you can try something like /summary(maps)$ace/. That should be a matrix with the posterior probabilities from stochastic mapping at all the nodes and tips of the tree. All the best, Liam Liam J. Revell Professor

Re: [R-sig-phylo] print circles in the tree nodes coloring by PP

at you might find useful on my blog: http://blog.phytools.org/2023/08/coloring-nodes-by-bootstrap-or-bayesian.html. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ Book: Phylogenetic Comparative Methods in R

Re: [R-sig-phylo] Possible problem with Scaled likelihoods in ancestral state estimation

ce-of-fitted-m.html>) -- but if you'd like help, please send me your tree & data (or, even better, a saved .RData workspace) and I will take a look at your problem. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.ed

Re: [R-sig-phylo] time axis in fan style phylogeny: arcs did not appear in eps file

Dear Felipe. It's possible that .eps doesn't support transparency. Have you tried plotting to a different device, e.g., .pdf or .png? Alternatively, you could undo the transparency by changing /make.transparent("blue",0.1)/ for just /"blue"/. All the best, Lia

Re: [R-sig-phylo] Error in phytools rateshift

probably indicative of unexplained variance in the tip taxa, rather than a genuine temporal rate shift. This could be due, for example, to measurement error / uncertainty in the species means for the trait we're studying. I hope this is helpful. All the best, Liam Liam J. Revell Profess

Re: [R-sig-phylo] Error in phytools rateshift

this /phytools/ function /likeSurface.rateshift/. See more information here: http://blog.phytools.org/2016/08/function-to-plot-likelihood-surface-for.html. Unfortunately, it is also bound to be pretty slow for larger phylogenetic trees. Let us know if this is of help. Sincerely, Liam Liam J. Revell Professor o

Re: [R-sig-phylo] Error in phytools rateshift

e multiple optimization iterations using /foreach/. When I get both of these fixes working I'll push the update to the /phytools/ GitHub and you can install the package from there. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://

Re: [R-sig-phylo] Using results of make.simmap to color edges by most likely state

ke a subsequent follow-up post covering that. Let us know if this works! All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ Book: Phylogenetic Comparative Methods in R <https://press.princeton.edu/books/phylo

Re: [R-sig-phylo] Estimating the posterior prob of the ancestral states of two nodes

Dear Sishuo. Yes, I think this would be a good way to do this. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ Book: Phylogenetic Comparative Methods in R <https://press.princeton.edu/books/phylogene

Re: [R-sig-phylo] NAMESPACE issue

5-1)/ to *Depends:* in your DESCRIPTION file and /importFrom(phytools, rescale)/ to NAMESPACE. (This should work immediately because currently on CRAN /rescale/ is defined & exported by both /phytools/ and /geiger/.) Please let me know if that works. All the best, Liam Liam J. Revell Professo

Re: [R-sig-phylo] Extract and summarise internal branch lengths for different samples

I'm not sure how it scales to a large tree, though! For an example phylogeny of 1,000 tips and a clade of 116 species it ran in the blink of an idea, so I suppose it's probably OK. Obviously, I meant to write "blink of an eye." It's been a long day. Liam J. Re

Re: [R-sig-phylo] Extract and summarise internal branch lengths for different samples

gh! For an example phylogeny of 1,000 tips and a clade of 116 species it ran in the blink of an idea, so I suppose it's probably OK. Let me know if it works for you. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/li

[R-sig-phylo] phytools GitHub version

correctly together. Please let me know if you run into any problems with this while Emmanuel, Klaus, & I try to get both ape & phytools updated on CRAN. That is all. Sincerely, Liam -- Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/l

[R-sig-phylo] R phylogenetics workshop at UMass-Boston

veryone! All the best, Liam -- Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ Book: Phylogenetic Comparative Methods in R <https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r> (/Princeton University Press/, 2

Re: [R-sig-phylo] Error in phytools - locate.fossil?

) All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ On 1/11/2023 7:58 AM, Lindsey Dehaan wrote: > CAUTION: EXTERNAL SENDER > Hey Liam, > > Thanks alot! I really appreciate it! I installed the new vers

Re: [R-sig-phylo] Error in phytools - locate.fossil?

from a fresh R session): remotes::install_github("liamrevell/phytools") Let us know if this fixes everything! All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ On 1/10/2023 4:42 PM, Lindsey Dehaan wr

Re: [R-sig-phylo] Error in phytools - locate.fossil?

best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ On 1/10/2023 4:20 PM, Lindsey Dehaan wrote: > CAUTION: EXTERNAL SENDER > > Hi all, > > I have a question regarding the phytools function locate.fossil(). >

Re: [R-sig-phylo] Counting and getting the age of cherries in a tree

oot of each node with two descendants (cherry). If your tree is ultrametric, to get the /depth/ you would just subtract this value from the total height of the tree. Let me know if it works!! All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://fa

Re: [R-sig-phylo] fitContinuous in Geiger

d with speciation events -- something that a simple Mk model ignores). All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ On 12/14/2022 9:18 AM, William Brown wrote: CAUTION: EXTERNAL SENDER I am using fitContinuous to m

Re: [R-sig-phylo] Phylogenetic bubble plot

easily be modified to just show abundances. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ On 12/9/2022 4:51 PM, Saleh Rahimlou wrote: CAUTION: EXTERNAL SENDER Hello, I require to make a phylogenetic bubble plot

Re: [R-sig-phylo] ancestral state reconstruction with a complex discrete trait

http://blog.phytools.org/2019/07/stochastic-character-mapping-with.html. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ On 11/8/2022 2:35 PM, Krzysztof Kozak wrote: CAUTION: EXTERNAL SENDER Hello, Is there a method for ance

Re: [R-sig-phylo] issue with reading matrix in R package DispRity

arguments dec="," and sep=";".) Hopefully this solves your problem. All the best, Liam Liam J. Revell University of Massachusetts Boston [Assoc. Prof.] Universidad Católica de la Ssma Concepción [Adj. Res.] Web & phytools: http://faculty.umb.edu/liam.r

Re: [R-sig-phylo] Simulate trait evolution with different phylogenetic signal along a tree

on) ## simulate the ancestral states for each subtree in tipward under ## pure Brownian motion aa<-fastBM(rootward) ## create a vector of values xx<-vector() ## simulate on each subtree to populate it. a is the ancestral state ## for each simulation for(i in 1:length(tipward)) xx&l

Re: [R-sig-phylo] Codifying missing data and polymorphic state of characters in the same matrix

ty of 0 at a node. This can be done using phytools::mergeMappedStates and then running the "simmap" summary methods as normal. I hope this is of some help in getting you started Felipe. All the best, Liam Liam J. Revell University of Massachusetts Boston [Assoc. Prof.] Universidad Católi

Re: [R-sig-phylo] Working with BTRTools or BTProcessR

want to show the amount of evolution that's expected to occur on each edge, that would be equivalent to the product of the edge length and it's edge-specific rate. phy.sig2<-phy phy.sig2$edge.length<-phy$edge.length*sig2 phytools::plotTree(phy.sig2) I hope I'm understanding the

Re: [R-sig-phylo] Recovering rate estimates from ape::ace

ity, you need to update phytools from GitHub using devtools -- e.g., devtools::install_github("liamrevell/phytools") All the best, Liam Liam J. Revell University of Massachusetts Boston [Assoc. Prof.] Universidad Católica de la Ssma Concepción [Adj. Res.] Web & phytools: htt

Re: [R-sig-phylo] Recovering rate estimates from ape::ace

lso compare to: as.Qmatrix(fitMk(tree,x,model="ARD")) where the labeling is better. All the best, Liam Liam J. Revell University of Massachusetts Boston [Assoc. Prof.] Universidad Católica de la Ssma Concepción [Adj. Res.] Web & phytools: http://faculty.umb.edu/liam.revell/, ht

Re: [R-sig-phylo] Recovering rate estimates from ape::ace

Dear Rafa. Try this to get the transition matrix, Q: k<-nrow(ace$index.matrix) Q<-matrix(ace$rates[ace$index.matrix],k,k) diag(Q)<--rowSums(Q,na.rm=TRUE) This should match what you get running: as.Qmatrix(fitMk(tree,x,model="ARD")) with phytools. All the best, L

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

fastMRCA instead of getMRCA. newtree<-mapply(bind.tip,tree=tree,where=lapply(tree,fastMRCA, sp1="Cercopithecus_mitis",sp2="Cercopithecus_mitis"), MoreArgs=list(tip.label="Cercopithecus_albogularis", position=0.59,edge.length=0.59),SIMPLIFY=FA

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

you're computing an N x N matrix in each iteration of your function call just to get one node index. Good luck! All the best, Liam -- Liam J. Revell University of Massachusetts Boston Universidad Católica de la Ssma Concepción Web & phytools: http://faculty.umb.edu/liam.revell/, htt

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

uot; (Code is not guaranteed! I don't have the data file, so I didn't actually test it -- but something like this ought to work.) Regardless, I recommend using ape::getMRCA (or phytools::fastMRCA) because otherwise you're computing an N x N matrix in each iteration of you

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

gth=0.59),SIMPLIFY=FALSE) class(newtree)<-"multiPhylo" (Code is not guaranteed! I don't have the data file, so I didn't actually test it -- but something like this ought to work.) Regardless, I recommend using ape::getMRCA (or phytools::fastMRCA) because otherwise you

Re: [R-sig-phylo] question regarding PGLS

phylo(tree)) spp<-names(w) corLambda<-corPagel(1,phy=tree,form=~spp) fit<-gls(...,correlation=corLambda,weights=varFixed(~w)) (I'm not sure the exact code, but it should be something like that.) All the best, Liam Liam J. Revell University of Massachusetts Boston [Assoc. Prof.] U

Re: [R-sig-phylo] Changing the color of text and nodes in arc.cladelabels in phytools

t works, if not I can see about adding the option you need to the function. All the best, Liam Liam J. Revell University of Massachusetts Boston [Assoc. Prof.] Universidad Católica de la Ssma Concepción [Adj. Res.] Web & phytools: http://faculty.umb.edu/liam.revell/, http://www.phytools.o

Re: [R-sig-phylo] host ape source code on GitHub?

Dear Nick. When you encounter a bug or issue in ape have you tried emailing Emmanuel (emmanuel.para...@ird.fr) or this list? Usually he is pretty responsive. All the best, Liam Liam J. Revell University of Massachusetts Boston Universidad Católica de la Ssma Concepción Web & phytools:

Re: [R-sig-phylo] singularity with pgls and ordinal factor

problem as this will tend to give the observations for those tips very high weight in your analysis. Instead, you might consider pruning one or the other species from your analysis. All the best, Liam Liam J. Revell University of Massachusetts Boston Universidad Católica de la Ssma Concepción Web

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

. The point of this article, like Anscombe 1973, was about graphing - but it may also apply to your problem.) All the best, Liam Liam J. Revell University of Massachusetts Boston Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org Acad

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

servations for x - but it may not mean a whole lot about how x & y genuinely co-vary.) All the best, Liam Liam J. Revell University of Massachusetts Boston Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org Academic Director UMass Bo

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

cause for low measured values of phylogenetic signal. Hope this is of some help Karla. All the best, Liam Liam J. Revell University of Massachusetts Boston Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org Academic Director UMass

Re: [R-sig-phylo] prop.clades in Ape package

n the bootstrapping analysis estimates an unrooted tree, you should set prop.clades(rooted=FALSE). *Most* phylogeny inference methods (ML, MP, NJ, ME, LS) estimate *unrooted* trees; only UPGMA and molecular clock methods estimate rooted trees. All the best, Liam Liam J. Revell University of Massachu

Re: [R-sig-phylo] Problem - removing the extinct taxa from trees

g/blog/Elvira-tree.png so it's kind of hard to tell which taxa are extinct Sorry I can't be of more help! All the best, Liam Liam J. Revell University of Massachusetts Boston Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org

Re: [R-sig-phylo] Problem - removing the extinct taxa from trees

ry: par(mfrow=c(1,1),mar=c(5.1,4.1,2.1,2.1),bty="n") ltt(tree,lty="dashed",log.lineages=FALSE,log="y") ltt(pruned,lty="solid",add=TRUE,log.lineages=FALSE, log="y") legend("topleft",c("observed","reconstructe

Re: [R-sig-phylo] Rphylopars changing observed data values

se the phytools version not the posted code). All the best, Liam Liam J. Revell Associate Professor, University of Massachusetts Boston Profesor Asistente, Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org Academic Director UMass Bost

Re: [R-sig-phylo] phyl.RMA error

s has even been discussed on this list); and "The statistical hypothesis testing is based on Clarke (1980; reviewed in McArdle 1988), which differs from some other implementations of non-phylogenetic major axis regression in R." All the best, Liam Liam J. Revell Associate Profes

Re: [R-sig-phylo] Alllowing and considering "missing data" as values for reconstruction of ancestral character states

discrete character with states: 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55" is surprising. Does your discrete character really have 27 states? All the best, Liam Liam J. Revell Associate Professor, University of Massachusetts Bo

Re: [R-sig-phylo] Iterating though multiple FASTA files via rbind.DNAbin

s) <- "DNAbin" for(...) { ## your for loop seqs <- c(seqs, read.dna(file = ..., format="fasta", as.matrix=FALSE)) } (In which you substitute ... for your original code.) In theory, I believe that this (or something like this) should do what you want.

Re: [R-sig-phylo] Alllowing and considering "missing data" as values for reconstruction of ancestral character states

.summary,ftype="off",lwd=1,cex=c(0.7,0.4)) map.summary$ace ## probabilities at nodes All the best, Liam Liam J. Revell Associate Professor, University of Massachusetts Boston Profesor Asistente, Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu/liam.revell/, http:/

Re: [R-sig-phylo] Alllowing and considering "missing data" as values for reconstruction of ancestral character states

you can also set them all to be 1. The likelihood changes, but ancestral states are the same.) I hope this is helpful. All the best, Liam Liam J. Revell Associate Professor, University of Massachusetts Boston Profesor Asistente, Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu

Re: [R-sig-phylo] aov.phylo vs phylANOVA

if you give either method data vectors without taxon names both work, but only phylANOVA gives a warning. Please send along the data that has generated this incongruency if you are unable to figure it out. All the best, Liam Liam J. Revell Associate Professor, University of Massachusetts

Re: [R-sig-phylo] Problem with make.simmap in Phytools

blog. I hope that this helps you find your error. If it does not, please free to send me your saved workspace & I will try to figure it out. All the best, Liam Liam J. Revell Associate Professor, University of Massachusetts Boston Profesor Asistente, Universidad Católica de la Ssma Concepció

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

eetree$tip.label,"_sp.",sep="") for(i in 1:length(species$Genus_species)){ beetree<-add.species.to.genus(beetree,species$Genus_species[i], where="root") } ## prune out these same taxa ii<-grep("sp.",beetree$tip.label) beetree<-drop.tip(b

Re: [R-sig-phylo] change colors in make.simmap

the posterior probability of being in the alphanumerically first state, rather than the second. All the best, Liam Liam J. Revell Associate Professor, University of Massachusetts Boston Profesor Asistente, Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu/liam.revell/, http:

Re: [R-sig-phylo] Issue with SIMMAP on 500 sampled Trees

Hi Kimberly. What version of phytools are you using? Neither make.simmap nor describe.simmap call MatrixExp. All the best, Liam Liam J. Revell Associate Professor, University of Massachusetts Boston Profesor Asistente, Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu

Re: [R-sig-phylo] Aligning tree tip labels together in ape

d",fg="transparent") plotTree(sim_tree,type="fan",lwd=1,add=TRUE) par(fg="black") For a more general solution you might offset your taxon labels by a constant amount, or you can use the function strwidth and some basic trigonometry to find the position outs

Re: [R-sig-phylo] Question regarding log likelihood in OUCH package

es, as this can give very high weight to the associated tips. It might be by pruning one tip or the other from the analysis, or by using some reasonable criterion to modify the terminal edge lengths. All the best, Liam J. Revell Associate Professor, University of Massachusetts Boston Profesor Asi

Re: [R-sig-phylo] p-value in pgls.Ives

Dear Iara. In fact, it is now possible to conduct a null hypothesis test with this method in phytools. I posted about it in my blog in 2017: http://blog.phytools.org/2017/11/bivariate-phylogenetic-regression-with.html. All the best, Liam Liam J. Revell, Associate Professor of Biology

Re: [R-sig-phylo] Simulating tree from a given tree

6. Compute t3=h-(t1+t2). Simulate a birth-death tree for t3 with birth & death rates b & d. Attach the b/d tree to the current tip. Advance to the next tip & go back to step 2. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston

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

is of only whales or only mice it will make relatively little difference whether you use log-scaled data or the original values. I hope this is of some help. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu

Re: [R-sig-phylo] ape-package: unknown states in ace analyses?

ll converge on the marginal ancestral states under the defaults for make.simmap, so long as a flat prior is used on internal nodes. This is also on my blog here: http://blog.phytools.org/2013/03/estimating-ancestral-states-when-tips.html. All the best, Liam Liam J. Revell, Associate Professor

Re: [R-sig-phylo] midpoint.root Error in phy$edge[, 2] : incorrect number of dimensions

No idea. Are they running different R or package versions? phytools::midpoint.root has not been updated recently, but other internally used functions may have been. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston & Profesor Asoc

Re: [R-sig-phylo] midpoint.root Error in phy$edge[, 2] : incorrect number of dimensions

,PfH24:0.00242401):0.002458328,(PfH15:0.003791243,PfH17:0.001056495):0.001058053):0.003886796,PfH23:0.004767665):0.1242874):0.1359654):0.7442934008); Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston & Profesor Asociado, Programa de Biología Universidad del Ros

Re: [R-sig-phylo] midpoint.root Error in phy$edge[, 2] : incorrect number of dimensions

-midpoint.root(tree) t2<-midpoint(tree) all.equal.phylo(t1,t2) I get TRUE. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston & Profesor Asociado, Programa de Biología Universidad del Rosario web: http://faculty.umb.edu/liam.revell/ On 5/1

Re: [R-sig-phylo] is.binary() says "FALSE" after using multi2di()

is helps. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston & Profesor Asociado, Programa de Biología Universidad del Rosario web: http://faculty.umb.edu/liam.revell/ On 5/14/2018 10:41 AM, Graham Slater wrote: Hi Pedro, multi2di on this newi

[R-sig-phylo] Postdoctoral position in R phylogenetics

velopment-in.html. All the best, Liam -- Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston & Profesor Asociado, Programa de Biología Universidad del Rosario web: http://faculty.umb.edu/liam.revell/ ___ R-sig-phylo mai

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

Just to clarify, force.ultrametric is not a formal rate-smoothing method or anything like that. It is intended only for use to resolve numerical precision issues such as the one raised in this thread. Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston & Prof

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

I haven't been closing following this thread, so I'm not sure that this is relevant - but phytools has a function called 'force.ultrametric' (I believe) that does precisely what its name suggests it might. Liam J. Revell, Associate Professor of Biology University of

[R-sig-phylo] Postdoc in PCM development in the Revell lab

ather than the estimation of phylogeny - but please contact me if you'd like clarification. The deadline to apply is May 11. More information along with a link to apply is available on my blog: http://blog.phytools.org/2018/04/postdoc-to-work-on-pcm-development-in.html. All the best, Liam

Re: [R-sig-phylo] grafting chronograms onto backbone phylogeny

$edge.length[which(backbone$edge[,2]==tip)]-h backbone<-bind.tree(backbone,subtrees[[i]],where=tip) } plotTree(backbone) Something like that. (Of course you could also modify this so that you just manually identify the tips to bind to. Given the small size of your problem this is probably

Re: [R-sig-phylo] "Not of class phylo" error when lapply is used

Dear John. You could try running .uncompressTipLabel on the "multiPhylo" object. Let us know if that works. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston & Profesor Asociado, Programa de Biología Universidad del Ros

Re: [R-sig-phylo] Interpretation of standard errors of parameter estimates in OUwie models

data. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston & Profesor Asociado, Programa de Biología Universidad del Rosario web: http://faculty.umb.edu/liam.revell/ On 4/4/2018 2:30 PM, Rafael S Marcondes wrote: Dear all, I'm writing

Re: [R-sig-phylo] plot.cophylo: some edges missing

Try ftype="off". Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston & Profesor Asociado, Programa de Biología Universidad del Rosario web: http://faculty.umb.edu/liam.revell/ On 3/13/2018 11:27 AM, Juan Antonio Balbuena wrote: Hi, Yes!! It worked

Re: [R-sig-phylo] plot.cophylo: some edges missing

ng to the latest version on GitHub using devtools as follows: library(devtools) install_github("liamrevell/phytools") Let us know if the problem persists. Saludos, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston & Profesor Asociado, Programa de B

Re: [R-sig-phylo] Phylogenetic PCA and measurement error

uncertainty in the values of species means has been ignored. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston & Profesor Asociado, Programa de Biología Universidad del Rosario web: http://faculty.umb.edu/liam.revell/ On 3/12/2018 11:29

Re: [R-sig-phylo] Phylogenetic PCA and measurement error

D as a factor, you could compute means and variances for each component by species. I hope this is some help. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston & Profesor Asociado, Programa de Biología Universidad del Rosario web: http://facul

Re: [R-sig-phylo] problem with phylo.toBackbone

run: install_github("liamrevell/phytools") I hope this is of some help. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston & Profesor Asociado, Programa de Biología Universidad del Rosario web: http://faculty.umb.edu/liam.revell/ On

Re: [R-sig-phylo] problem with phylo.toBackbone

Hi Felipe. What version of phytools are you using? A very old phytools version did not default to interactive mode if no translation table (trans) was supplied. Otherwise, I do not know - but it should not be because the tree is not ultrametric. All the best, Liam Liam J. Revell

Re: [R-sig-phylo] plotting geologic time scale on circular tree

-paste(strsplit(obj$colors[i],"")[[1]][1:7],collapse="") draw.circle(0,0,radius=r[i],col=color,border="transparent") } par(fg="transparent") plotTree(tree,type="fan",add=TRUE,fsize=0.6,lwd=1) par(fg="black") I will also post to my bl

Re: [R-sig-phylo] plotting geologic time scale on circular tree

strsplit(obj$colors[i],"")[[1]][1:7],collapse="") draw.circle(0,0,radius=obj$leg[i,1],col=color,border="transparent") } par(fg="transparent") plotTree(tree,type="fan",add=TRUE,lwd=1) par(fg="black") Otherwise you need to plot 

Re: [R-sig-phylo] Error in plotTree.wBars() in phytools

x=dat, lwd=1, type='fan', scale=0.05, width=0.35, col='red') dev.off() Liam J. Revell, Associate 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 11/11/2017 1

Re: [R-sig-phylo] Error in plotTree.wBars() in phytools

Hi Rafael. It seems to just be that some of the values in your data vector are NAs. Try: dat<-dat[!is.na(dat)] tr<-drop.tip(tr,setdiff(tr$tip.label,names(dat))) plotTree.wBars(tr,dat,type="fan",scale=0.1) and you should obtain something that makes sense. All the best, Liam

Re: [R-sig-phylo] Error in plotTree.wBars() in phytools

s) which is in some ways more flexible & robust. Failing any of these options you are welcome to send me your saved workspace so I can investigate (& if there is a bug in phytools - fix it). All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachu

Re: [R-sig-phylo] Brownian Evolution

make it symmetric) is leptokurtic which is why var.test is significant due to idiosyncratic differences in the variance of lambda, even though the values were obtained by the same process. (Invariably lamb_sub and lamb fail a normality test, so this seems like a distinct possibility.) All the best

[R-sig-phylo] Postdoc in R phylogenetics

t the postdoc is for *one year* with only a modest possibility of extension to multiple years contingent on external funding. Please circulate to interested parties. Any questions about the position should be directed to this email address (liam.rev...@umb.edu). Thanks! -- Liam J. Revell, Asso

Re: [R-sig-phylo] Can I get coordinates from plot.phylo and not get blank page

here: http://blog.phytools.org/2017/09/possible-solution-for-functions-that.html I'm not sure if this means I won't run into difficulty with this solution, but I'm eager to hear why. - Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston

Re: [R-sig-phylo] Possible Bug in ape::read.tree

Hi George. Mario is correct that phytools can read a tree with singleton nodes (if that is indeed your problem), but the name of the function is read.newick. Good luck! - Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu

Re: [R-sig-phylo] Simulating traits with different rates of evolution

Hi Alejandro. If the discrete character is mapped on the tree in a "simmap" style, then the student could use the phytools function sim.rates. Let me know if you need more information. Sincerely, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts

Re: [R-sig-phylo] OUwie and simmap trees constructed from prior probabilities of tip states

ttps://goo.gl/Mbx4hn I hope this is of some help. Sincerely, Liam Liam J. Revell, Associate 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 8/11/2017 12:50 PM, Marko Djurakic wrote:

Re: [R-sig-phylo] tip labels-stochastic mapping

Hi Felipe. I can't figure out your code or why tip labels might be being stripped. Can you post a fully reproducible example of this problem? All the best, Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/

Re: [R-sig-phylo] comparing rates of evolution of a phenotypic trait among clades

All the best, Liam J. Revell, Associate 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 7/22/2017 8:51 PM, Karla Shikev wrote: Thanks, Liam! Just a quick follow-up question: in the exa

Re: [R-sig-phylo] comparing rates of evolution of a phenotypic trait among clades

unction you can search for 'ratebytree' on my blog, blog.phytools.org. All the best, Liam Liam J. Revell, Associate 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 7/22/2017 3:

Re: [R-sig-phylo] Nnode not equal to length of node.labels

n you can test as follows: library(phytools) tree<-read.newick(text='((a))A),(((b),(b1)))B)))C;') tree$edge.length<-rep(1,nrow(tree$edge)) plotTree.singletons(tree) nodelabels(tree$node.label) All the best, Liam Liam J. Revell, Associate Professor of Biology University of

Re: [R-sig-phylo] Randomly Resolved Polytomies

Hi Laura. I think multi2di also performs random resolutions, so if you wanted to generate, say, 100 random resolutions could you not do: trees<-replicate(100,multi2di(tree),simplify=FALSE) class(trees)<-"multiPhylo" All the best, Liam Liam J. Revell, Associate Prof

Re: [R-sig-phylo] Randomly Resolved Polytomies

Dear Laura. I also just posted a possible solution to my blog here: http://blog.phytools.org/2017/06/generating-set-of-random-resolutions-of.html. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell

Re: [R-sig-phylo] Randomly Resolved Polytomies

er can be high), you could start with one multifurcating node in the tree, resolve it in all ways using resolveNode, pick one of those resolutions, then move to the next node & so on. I will try to post a formal solution & then share it to the list. All the best, Liam Liam J. Revell, As

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