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

ight. 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

couraged 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/, 2022)

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

h practices 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 Massachusetts Bosto

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

-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-comparat

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

.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-metho

[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

urface-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.edu/liam.revell/

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, Liam Liam

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

explained 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 Professor of Biology, University of M

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

ools/ 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 of Biolo

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

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://faculty.umb.edu

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

make 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 Professor of

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. Revell Professor

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

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/liam.revell/ Book

[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

ne! 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)

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

l 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 version a

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

ciation 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 model karyo

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

://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 ancestral

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

# 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<-c(

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

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 Católica de la S

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

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 problem correctly. All

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

o 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/, http://

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

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=FALSE) class(newtree)<-"multiPhylo" Please

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

n 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/, http://www.phytools.org, http://blog.phyto

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

ranteed! 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 your function call just to get one node ind

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

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 computing an N x N matrix in each i

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.] Univer

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

ks, 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.org,

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

the 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

oint 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 Academic Director U

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

ut 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 Boston Chile Abroad: https:

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

be a 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

in 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 Massachusetts

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

ira-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 Academic Director UM

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

frow=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","reconstructed"

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

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 Boston Chile Abroad

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

ven 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 Professor, Unive

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] 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

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/liam.revell/, http://www.phytools.org Academic Direct

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

is that 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

elps 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 Concepción web: http://faculty.umb.edu/

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

ot;,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$tip.label) beetree<-drop.tip(beetree,beetree$tip.label[ii])

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

ility 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://www.phytools.org

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

="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 outside the ta

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

edges, 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

ompute 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 web:

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] 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()

est, 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 newick string returns

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

ment-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 mailing

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 Massachusetts Boston

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

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 -- Liam J

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

.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 what

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

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 (again!) to ask for

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] Phylogenetic PCA and measurement error

nty 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 AM, Graham

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

ies ID 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

lit(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 'donuts'

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 10:49 AM, Rafael S Ma

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

hich 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 Massachusetts Bost

Re: [R-sig-phylo] Brownian Evolution

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

that 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, Associate

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

: 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 web: http://faculty

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/ email

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

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 3:10 PM, Karla Shikev wrote

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 Massachuse

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] A possible alternate MRCA function to APE\'s getMRCA

On the other hand, phytools does have a function - the somewhat imprecisely named fastMRCA - which can find the MRCA of just a pair of species much faster than getMRCA (however still slower than or only about as fast as Joseph & Klaus's solutions). Liam J. Revell, Associate Profe

Re: [R-sig-phylo] A possible alternate MRCA function to APE\'s getMRCA

Juan. findMRCA was written before getMRCA existed, but the latter was faster so now it just calls getMRCA internally. 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

Re: [R-sig-phylo] Extracting a clade for LTT

<-"multiPhylo" For some "multiPhylo" objects, for instance those read from a NEXUS file, you may also want to first run: trees<-.uncompressTipLabel(trees) All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http:

Re: [R-sig-phylo] Applying standard error in phylogenetic signal measurement using lambda

Hi Ting-Wen. If you could (off-list) send me the simplest possible reproducible example of the error (with your input data files or a saved R workspace) I would be more than happy to look into it. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts

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