Re: [R-sig-phylo] Simulation function from Discrete

Hi Ekaphan, See the function rTraitMult. You have to program your model though. Cheers, Emmanuel -Original Message- From: Ekaphan Kraichak ekraic...@gmail.com Sender: r-sig-phylo-boun...@r-project.org Date: Tue, 6 Dec 2011 09:58:34 To: r-sig-phylo@r-project.org Subject: [R-sig-phylo]

Re: [R-sig-phylo] taxonomic tables and trees

Hi David, It's in ape: ?as.phylo.formula Cheers, Emmanuel -Original Message- From: David Buckley dbuck...@mncn.csic.es Sender: r-sig-phylo-boun...@r-project.org Date: Tue, 13 Dec 2011 12:56:18 To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] taxonomic tables and trees Hi all, I

Re: [R-sig-phylo] Meaning of Transformed Phylogenetically Dependent Variables in GLS?

]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https

Re: [R-sig-phylo] 2 root edges in phylocom tree, but suggested fix in ape FAQ doesn't help

that phylocom is using. Someone else will probably respond more helpfully ... Ben Bolker -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r

Re: [R-sig-phylo] Add new leaves to a tree

-1),replace=T)#Branch lengths for tree tr-rtree(nleaf,br=br) #Tree crown Thanks for your help. Sincerely, Brian ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel

Re: [R-sig-phylo] randomizing clades within a node

. ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr

Re: [R-sig-phylo] plotting character states on a circular cladogram

of mapping of trait states at the tips when using plot(phy, type=fan) Thanks in advance, Rafa -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo

Re: [R-sig-phylo] Estimating MRCA dates

-- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] plotting character states on a circular cladogram

to plot your tree with: plot(phy, c, FALSE) You might want to try 'thermo' instead of 'pie'. Best, Emmanuel Cheers, Rafa On 2/2/2012 7:03 AM, Emmanuel Paradis wrote: Hi Rafael, Rafael Rubio de Casas wrote on 02/02/2012 06:24: Hi Nicolai, Thanks for your message. I guess I wasn't completely

[R-sig-phylo] query about the option 'original.data' in write.nexus()

will make write.tree() slightly more efficient. Any advice/comment welcome. Cheers, Emmanuel -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig

Re: [R-sig-phylo] collapse nodes based on node labels

-- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] adding a new taxa to an existing clade in a tree set

Hi Annemarie, Annemarie Verkerk wrote on 16/02/2012 09:57: Hi all, I have a question regarding the manual addition of a leaf to an existing clade in a set of trees. The reason I ask is because I want to test the influence of adding ancestral data to an ancestral state estimation. I have some

Re: [R-sig-phylo] How to replace a clade with a single node?

Hello Ania, See the functions drop.tip and bind.tree. They both have an 'interactive' option. If you want to use node labels, if available, you can find a node number from its label, say xyz, with: grep(xyz, phy$node.label) + Ntip(phy) Best, Emmanuel -Original Message- From: Ania

Re: [R-sig-phylo] 3. partial correlation with gls residuals? (Tom Schoenemann)

-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] plot.phylo x.lim/y.lim problem

Hi Alex, To fix this, do fix(plot.phylo) and look for this bit (around line #259): if (phyloORclado direction == downwards) yy - y.lim[2] - yy Change the second line for: yy - max(yy) - yy This will be in the next release. Thank you for the report. Cheers, Emmanuel -Original

Re: [R-sig-phylo] behavior of is.monophyletic()

Hi Bret, This is fixed and will be in the next release. In the meantime, you can edit the function and change the last line to: all.equal(tips, desc) Thanks for the report. Cheers, Emmanuel -Original Message- From: Bret Larget lar...@stat.wisc.edu Sender:

Re: [R-sig-phylo] Error with PGLS under OU model using corMartins

Hi Nick, You can fix the value of alpha in corMartins: corMartins(1, tree, fixed=TRUE) You can try with different values to see which one gives the best fit. Best, Emmanuel -Original Message- From: Nicholas Mason nicholas.albert.ma...@gmail.com Sender:

Re: [R-sig-phylo] trouble with subtreeplot returning a tree object on exit

-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] birthdeath {ape} fails every time.

for this? Kind regards, Simon ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig

Re: [R-sig-phylo] problems with assign(), paste(), and data.frame() for folders containing trees

Hi John, You seem to transform a (relatively) simple problem into a complicated one. First, you can get all the tree file names in one command, such as (I moved to a directory with one subdir with trees estimated by ML and another one by NJ; this is slightly arranged): f - grep(\\.tre,

Re: [R-sig-phylo] read.dna warnings and pitfalls

Hi Dan, The reason for this implementation (searching the first 10 IUPAC-coded bases) is because the exact formatting is not inconsistent among different programs. Some files have: 0123456789acgt. that is a 10-character name and the sequence starting on the 11th position. I think this is

[R-sig-phylo] ape's web site

the figures plotted with rgl. Best, Emmanuel -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] read.dna warnings and pitfalls

textwrangler) to quickly find potential problems. Just search for [ACGTUMRWSYKVHDBN]{10}.+\t with grep matching enabled. Cheers, ~Dan On Apr 26, 2012, at 2:16 AM, Emmanuel Paradis wrote: Hi Dan, The reason for this implementation (searching the first 10 IUPAC-coded bases) is because the exact

Re: [R-sig-phylo] compar.gee: how to extract SE, t, and P from output?

an error message I can't seem to figure out: Error in coef[, 2] - sqrt(diag(x$W)) : replacement has length zero. What does R mean or want here? Thanks again, Nina On 2012-05-09, at 3:19 PM, Emmanuel Paradis wrote: Hi Nina, You cannot do it directly: you have to get the code from

Re: [R-sig-phylo] compar.gee: how to extract SE, t, and P from output?

? Thank you very much, Nina On 2012-05-09, at 5:24 PM, Emmanuel Paradis wrote: Maybe check that the code of foo has not been altered with a line break from the email (eg, by editing it with fix(foo)). If this is ok, try it with the examples from the help page ?compar.gee. You may also check

Re: [R-sig-phylo] Problems useing query() function of package seqinr

://augustoribas.heliohost.org Lattes: http://lattes.cnpq.br/7355685961127056 -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] nonparametric PGLS

least squares, is there any method that is nonparametric? Thanks! -Pascal Title -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] exporting nexus tree in APE

-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r

Re: [R-sig-phylo] unrooted tree, spread tips

Hi, Walter, Mathias wrote on 18/05/2012 16:42: Hi, I use ape to plot my phylogenetic trees. Often I have to plot unrooted trees with few clades, but a lot of tips per clade. The tip labels are hard to read, even if I use lab4ut=axial. Is there any way to spread the tips? No. The only

Re: [R-sig-phylo] unrooted tree, spread tips

https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] length of attribute (names) when calculating independent contrasts

. Agus ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list

Re: [R-sig-phylo] as.phylo.hclust

Bapst Sender: dwba...@gmail.com To: R Sig Phylo Listserv Cc: Emmanuel Paradis Subject: as.phylo.hclust Sent: 21 Jun 2012 05:08 Hello all, I was having some problems with getting the information I wanted from an hclust object so decided I would make it a tree and use all the tools I already know

Re: [R-sig-phylo] using ace() with fixed internal node - singularity error

, as always, Annemarie -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] R package for detecting positive selection?

-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman

Re: [R-sig-phylo] Ape: dist.dna, P-distance calculation

Hi, Try the option pairwise.deletion = TRUE. If you still find abnormal values please give some example data. Emmanuel -Original Message- From: Jessica Sabo sabo.j...@gmail.com Sender: r-sig-phylo-boun...@r-project.org Date: Sun, 29 Jul 2012 14:42:17 To: r-sig-phylo@r-project.org

Re: [R-sig-phylo] sort / select trees by backbone constraint?

Dear Annemarie, Annemarie Verkerk wrote on 30/07/2012 16:48: Dear all, I have a follow-up question about how to sort or select trees from a tree sample as originally asked here: https://stat.ethz.ch/pipermail/r-sig-phylo/2011-March/001194.html I would like to select a set of trees from a

Re: [R-sig-phylo] plotting a coloured tree

/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] ladderize + drop.tip = shuffled node labels

,show.node.label=TRUE) plot(drop.mytree.lad,show.node.label=TRUE) ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr

Re: [R-sig-phylo] Scale parameter in compar.gee()

/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] breaking up phylogeny figure

Hi Ben, You should be able to play with extract.clade() and drop.tip(): they both have an option 'interactive' so you may click on the plotted backbon tree to build your subtrees. Best, Emmanuel Ben Weinstein wrote on 03/10/2012 23:45: Hi all, I'm wondering if there is a way to plot a

Re: [R-sig-phylo] Reverting or setting axis label in plottet phylo tree

-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] drop.tip weird handling of node labels

-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] Why no branch lengths on consensus trees?

-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman

Re: [R-sig-phylo] Modification of figures produced using cophyloplot

: glo.tree$edge.length - 100 * glo.tree$edge.length epi.tree$edge.length - 100 * epi.tree$edge.length where you have to find the value that best suits your data. Cheers, Emmanuel I would be grateful for any suggestions. Thank you very much in advance. David Hembry -- Emmanuel Paradis IRD

Re: [R-sig-phylo] read.nexus error message

://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Emmanuel Paradis IRD, Jakarta Visiting Professor, Agricultural University of Bogor http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list

Re: [R-sig-phylo] plotting a time axis on a circular phylogram

could be squeezed (my tree has 170 tips). Any advice gratefully accepted. cheers Marcel Cardillo -- Emmanuel Paradis - IRD Visiting Professor, Agricultural University of Bogor http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list - R-sig-phylo@r

Re: [R-sig-phylo] plotting a time axis on a circular phylogram

Cardillo wrote on 19/12/2012 07:52: Thanks Emmanuel. It works nicely with 'open.angle' as an argument in the function call. Marcel On 18/12/2012 11:06 PM, Emmanuel Paradis wrote: Hi Marcel, Here's what you can do: fix(plot.phylo) Find the line 104 which should be: xx - seq(0, 2 * pi * (1 - 1/Ntip

Re: [R-sig-phylo] using gamma parameter with dist.dna

___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Emmanuel Paradis - IRD Visiting Professor Agricultural University of Bogor http://ape.mpl.ird.fr

[R-sig-phylo] Pre-release of ape 3.0-7

on Windows than on other OSs. The release date on CRAN is planned around mid-January. Best, Emmanuel -- Emmanuel Paradis - IRD Visiting Professor Agricultural University of Bogor http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list - R-sig-phylo@r

Re: [R-sig-phylo] read.dna line endings in ape 3.0-7

/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Emmanuel Paradis - IRD Visiting Professor Agricultural University of Bogor http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list - R-sig-phylo@r

Re: [R-sig-phylo] Ancestral state estimates of continuous traits

Alejandro and Liam, You can also try method=REML which gives much better estimates of sigma^2 than ML. I think I'll make it the default for continuous characters. Best, Emmanuel -Original Message- From: Liam J. Revell liam.rev...@umb.edu Sender: r-sig-phylo-boun...@r-project.org Date:

Re: [R-sig-phylo] Input Format for nuc.div

Hi Mark, On Fri, 22 Mar 2013 10:24:36 -0400 (EDT) markharriso...@aol.com wrote: Hello, I'd like to measure nuc.div for a list of about 20,000 loci across 170 individuals. What is the best way to format the input data? Is it possible to integrate the whole data within one file or would I

Re: [R-sig-phylo] read.dna

Hi again, It's a bug already identified: https://stat.ethz.ch/pipermail/r-sig-phylo/2013-February/002514.html The release of ape 3.0-8 will be done next week. Best, Emmanuel -Original Message- From: markharriso...@aol.com Sender: r-sig-phylo-boun...@r-project.org Date: Fri, 22 Mar

Re: [R-sig-phylo] ML ancestral state reconstruction using different softwares

Hi, You cannot really say that in both ace and Mesquite, it slightly favors the asymmetrical model: the increase in log-likelihood is less than 1 which is far from being significant with one additional parameter. So it seems that all three pieces of software agree well on the estimate of rate

Re: [R-sig-phylo] ML ancestral state reconstruction using different softwares

). However I do have biological evidence that transition from 0 to 1 might be extremely hard. So maybe I can also try set q01 to 0 (which is actually what ace gave me under the asymmetrical model)? Cheers, Jingchun On Thu, Apr 4, 2013 at 9:21 PM, Emmanuel Paradis emmanuel.para...@ird.frwrote

Re: [R-sig-phylo] Seeking list of nucleotide substitution models

Hi Daniel, Have you looked at the help page of dist.dna? The list of references there is focused on calculating distances but some are general. There are a few more references in my book too. I suggest you also look at Inferring Phylogenies. Best, Emmanuel -Original Message- From:

Re: [R-sig-phylo] ML ancestral state reconstruction using different softwares

the two models? Should I simply avoid using the equal rates model? Cheers, Jingchun On Fri, Apr 5, 2013 at 9:12 AM, Emmanuel Paradis emmanuel.para...@ird.frwrote: ** Jingchun, Thanks to Daniel for giving a detailed answer to your first question. You can use ace() to fit a model

Re: [R-sig-phylo] NaN rates and error running ace()

Hi Zhenjiang, This is because some branch lengths are zero. You can change them for a small value, eg: tree$edge.length[tree$edge.length == 0] - 1e-7 I have added a check of this in ace(). Cheers, Emmanuel Fri, 12 Apr 2013 12:22:53 -0600 zhenjiang xu zhenjiang...@gmail.com: Hi all, I am

Re: [R-sig-phylo] Find common ancestor of multiple taxa

Hi Klaus and others, I have now documented getMRCA() and modified it so that it accepts a vector of labels and does some checks. This will be in the next release of ape. The SVN repository is not yet updated: there's a technical problem there. I'll fix that next week. Cheers, Emmanuel

Re: [R-sig-phylo] nlm error when using ace for discrete characters

Hi Graeme, The reason of the error is because this custom model does fit your data, so the calculation of the SEs fails. I have modified ace() so that the error is caught and a better message is printed. For these data, you should try to fit the models that are pre-programmed in ace (ER, SYM,

Re: [R-sig-phylo] Extracting Independent Subclades

anyone dealt with this issue before? Is there some simple solution I'm missing? Cheers, Glenn On Tue, May 21, 2013 at 12:11 AM, Emmanuel Paradis emmanuel.para...@ird.frwrote: Hi Glenn, An alternative is to use prop.part(tree) which returns the composition of all clades in tree. You can

Re: [R-sig-phylo] extracting order of tips as in plotted ladderized tree

Hi, Your question is not very specific but I guess you want something like: i - which(tr$edge[, 2] = Ntip(tr)) tr$edge[i, 2] Best, Emmanuel -Original Message- From: Ivalu ivalu.ca...@gmail.com Sender: r-sig-phylo-boun...@r-project.org Date: Thu, 23 May 2013 09:42:32 To:

Re: [R-sig-phylo] Calling Clustal in R the DNAbin format for storing nucleotides

Hi Ben, Clustal accepts labels up to 30-character long. You can solve your problem by changing the labels using the function makeLabel (see its help page for some details). I'll change clustal() to avoid this problem in the future. You can find details on DNAbin here:

Re: [R-sig-phylo] dist.dna returning NaN's for 3 alignments

Hi Ben, See the option pairwise.deletion of dist.dna. You can use image() also to have a view on the distribution of the -. Cheers, Emmanuel -Original Message- From: Ben Ward (TSL) ben.w...@sainsbury-laboratory.ac.uk Sender: r-sig-phylo-boun...@r-project.org Date: Tue, 28 May 2013

[R-sig-phylo] new ape's web site (and singleton nodes)

Hi all, ape's web site has been moved to this URI: http://ape-package.ird.fr/ (Currently, the redirection from the old URI does not work correctly. I hope it will be fixed soon.) Regarding the issue of singleton nodes and phylomatic, this is mentioned in ape's FAQ (FAQ #15) but in a

Re: [R-sig-phylo] compare.gee issues with multiple predictor models

Hi Sandra, Le 01/07/2013 22:03, sandra goutte a écrit : Hello all, I am sorry if the question has already been answered, i have not found it int the archive. I am using compar.gee to look at possible correlations between behavioral traits and ecological variables. I have two problems: 1) if i

Re: [R-sig-phylo] Problems with write.nexus of the package ape

Hi Agus, The problem is that spaces are ignored in Newick and NEXUS files. Maybe you do not need to replace _ for ? Best, Emmanuel Le 29/06/2013 15:15, Agus Camacho a écrit : Dear all, After correcting the names of a otherwise perfectly functional tree using gsub,

[R-sig-phylo] workshop on phylogeography

Hi all, I'm looking for information on workshops, trainings or courses that include phylogeography. That could be with R of course, but not absolutely necessarily. If you organize, or know about, such a course or workshop, at the PhD-candidate level and/or above, and in English preferably,

Re: [R-sig-phylo] PGLS vs lm

Hi Tom, In an OLS regression, the residuals from both regressions (varA ~ varB and varB ~ varA) are different but their distributions are (more or less) symmetric. So, because the residuals are independent (ie, their covariance is null), the residual standard error will be the same (or very

Re: [R-sig-phylo] PGLS vs lm

Hi all, I would like to react a bit on this issue. Probably one problem is that the distinction correlation vs. regression is not the same for independent data and for phylogenetic data. Consider the case of independent observations first. Suppose we are interested in the relationship y = b

Re: [R-sig-phylo] number of fitted parameters in lm and pgls in R

Hi Sereina, You will get the same AIC with lm and gls, for a given regression model, if: 1. the GLS model is fitted assuming independence of observations (this is the default in nlme::gls), 2. the GLS model is fitted by ML (this is not the default). Some correlation structures require to

Re: [R-sig-phylo] problem with corMartins (ape)

Hi, Xavier: if I understand correctly what you describe, this can be done with: V - vcv(phy, corr = TRUE) diag(V) - 0 vcv() returns the expected variance-covariance matrix under Brownian motion for a given tree. If this tree is not ultrametric (I guess this is what you mean with where the

Re: [R-sig-phylo] rooting multiple trees

Hi Silvia, Check the help page of root(): it says the tree is unrooted before before being rooted. So your 2nd output is as expected. See the options of this function to resolve the root. For the 1st method, I think you should not do unclass(). best, Emmanuel -Original Message- From:

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

Hi Mariana, You may try the function bd.time in ape. The companion paper gives examples similar to what laser does. Best, Emmanuel -Original Message- From: Mariana Vasconcellos marian...@utexas.edu Sender: r-sig-phylo-boun...@r-project.org Date: Tue, 3 Sep 2013 23:20:17 To: Liam J.

Re: [R-sig-phylo] selecting sequences from an alignment

Hi, What about this: match(selected, rownames(woodmouse)) ? If this is not what you want yet, please give an example of the output you wish to get. Best, Emmanuel -Original Message- From: john d dobzhan...@gmail.com Sender: r-sig-phylo-boun...@r-project.org Date: Sat, 5 Oct 2013

Re: [R-sig-phylo] most efficient way to read trees from huge text file

Hi, Le 10/10/2013 21:07, Juan Antonio Balbuena a écrit : Hello, I need to handle in R 10M trees produced with the program evolver of PAML. With a smaller number of trees one could create a multi-phylo object with ape as tree.m - read.tree(filename.tre) but this is impractical in this case

Re: [R-sig-phylo] Problems with bootstraps of NJ tree from SSRs data

Le 16/10/2013 00:20, Vojtěch Zeisek a écrit : Hi, Emmanuel, thank You very much! Dne Út 15. října 2013 21:45:12, Emmanuel Paradis napsal(a): Hi Vojtěch, Le 14/10/2013 23:14, Vojtěch Zeisek a écrit : Hello, I know this is FAQ, but I still haven't found solution, which would work for me

Re: [R-sig-phylo] match two tree edges

Hi, Have a look at the function makeNodeLabel with the option method = md5sum: it will create a label to each node depending on the tips descending from it. You can then use them to match nodes and edges of different trees. Best, Emmanuel -Original Message- From: Jingchun Li

Re: [R-sig-phylo] About function .getSEs

Hi, From R: ape:::.getSEs You can also get the code from the sources on CRAN. Best, Emmanuel --Original Message-- From: Tane Kim Sender: r-sig-phylo-boun...@r-project.org To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] About function .getSEs Sent: 16 Nov 2013 02:54 Hi,I have

Re: [R-sig-phylo] Mismatch distribution (pegas): expected versus empirical and other questions

Hi David, Thanks for this. I have included it into pegas with an option to select the types of lines, and the legend is moved to the top of the plot. I'll release this new version by the end of the year. I'm taking this opportunity to advertise the last version of coalescentMCMC (0.4) which

Re: [R-sig-phylo] plotting support value

Hi Thomas, Have you tried prop.clades? Best, Emmanuel -Original Message- From: Thomas Manke ma...@ie-freiburg.mpg.de Sender: r-sig-phylo-boun...@r-project.org Date: Mon, 16 Dec 2013 11:52:33 To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] plotting support value Dear Forum, I have

Re: [R-sig-phylo] Using the function mst in APE to produce coloured graphs

Hi, Try mst() in pegas. It returns an object of class haploNet with a more flexible plot method. Best, Emmanuel -Original Message- From: Stefani stef...@irsa1.irsa.cnr.it Sender: r-sig-phylo-boun...@r-project.org Date: Wed, 18 Dec 2013 17:35:26 To: r-sig-phylo@r-project.org Subject:

Re: [R-sig-phylo] Warning messages if using family=poisson in compar.gee, and changing link function

Hi Nina, Don't confound warning with error. If you have the former, then R certainly didn't crash. These warnings seem to come from the fact that the model fitting did not converge after the default number of iterations. Unfortunately, this cannot be controlled from compar.gee, so you can

Re: [R-sig-phylo] ape package gives 'Error in FI[i]:LA[i] : NA/NaN argument'

Hi Matt, This is because this accession number does not point to the sequence. For this particular one, you could use: seq1 - read.GenBank(U00096.3) Best, Emmanuel Le 27/02/2014 01:35, Matt Curcio a écrit : Greetings all,, I received this error while using R version 2.15.1 and ape 3.0.11.

Re: [R-sig-phylo] Phylogenetic regression available in R (Grafen, 1989)

Hi Gustavo, Grafen's method is partially implemented in ape. The function corGrafen defines a correlation structure according to Grafen's method (see ?corClasses for all corStruct defined in ape). When used with nlme::gls this makes possible to estimate the parameter of the branch length

Re: [R-sig-phylo] Difference running Rscript vs source with ape library

Hi Carlos, I tested your script in both ways and it may work or fail depending on the tree which is generated. However, it seems that failure is more frequent with source (about 70%) than with Rscript (about 40%). One possible explanation for this may be that the random number generator

Re: [R-sig-phylo] What order are the tips of a tree plotted in?

Hi Henry, I suppose the two trees do not have the same topology (otherwise there would be no difficulty). Have you considered using rotateConstr() on the second tree? That'd be something like: tree2 - rotateConstr(tree2, tree1$tip.label) The node numbering won't be changed, so you can still

Re: [R-sig-phylo] adjacency matrix / edgelist from igraph into a phylo class

Hi Wesley, You are right: this definition is out-dated. Have a look at: http://ape-package.ird.fr/ in the 'Development' section, there is a document explaining the structure of the class phylo. Also the second edition of APER has been updated on this point. Best, Emmanuel Le 12/05/2014

Re: [R-sig-phylo] plot bars across tips of a circular phylogeny

Hi Matt, See ?phydataplot in ape. This has a couple of examples. Best, Emmanuel Le 14/05/2014 16:44, Matthew Helmus a écrit : Hi all, Does anyone know of R code (or perhaps another program) to plot bars across the tips of a radial/fan phylogeny? Specifically, I have a large phylogeny and a

Re: [R-sig-phylo] Distances from nods to the root.

Alexey, See ?dist.nodes in ape. If your tree is named tr, you'll get exactly what you want with: dist.nodes(tr)[, Ntip(tr) + 1] which extracts one column of the matrix returned by dist.nodes. best, Emmanuel Le 21/05/2014 06:56, Alexey Fomin a écrit : Which package allow calculate all

Re: [R-sig-phylo] cophyloplot: how to marks links differently

Hi Juan, cophyloplot() has the options col, lwd, and lty which specify the aspects of the association lines. Le 27/05/2014 16:09, Juan Antonio Balbuena a écrit : Hello This is a simple question and hope that there is a simple answer. Plotting a tanglegram, I would like to write a function

Re: [R-sig-phylo] Pegas Tajimas Test

Hi Peters, This test cannot be used with 3 sequences. I've added a warning message about this. Best, Emmanuel Le 25/06/2014 12:17, Peters, Stuart a écrit : Hi, I am trying to run the Tajimas.test function from the r package 'Pegas' on a small sample of 3 DNA sequences and I get this

Re: [R-sig-phylo] convergence in compar.gee (ape)

Dear Sereina, The number of iterations is not output by default. You can modify the function with fix(compar.gee), find this line: geemod - do.call(gee, list(formula, and insert this command after it: cat(number of iterations:, geemod$iterations, \n) save and close. HTH

Re: [R-sig-phylo] Trying to read a tree with numerical node labels, but without edge length

Hi Liam and others, read.nexus() can read NEXUS files that have no TRANSLATE block. There are two problems with this file: the extra spaces between begin.../end and the semicolon, and the linebreak between the tree declaration and the Newick string. So the following file can be read by

Re: [R-sig-phylo] problem with write.nexus.data

Hi Liam and Nicholas. write.nexus.data() accepts only lists as specified in the help page, but it's a bit of an anomaly since the same help page says the sequences must be aligned. I have modified this function so that it now accepts both lists and matrices. Best, Emmanuel Le 18/09/2014

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

Hi, compute.brtime() can use a set of pre-calculated branching times (the default is indeed a set of coalescent times), for instance: tr - read.tree(text = (A,(((B,C),D),E));) compute.brtime(tr, method = 4:1/4) will produce a tree with root time = 1 and regular inter-node times. Best,

[R-sig-phylo] new version system for ape

Dear all, There is a new system of package version for ape. A package repository has been set up at ape-package.ird.fr hosting testing versions as sources and Windows binaries (also for pegas and coalescentMCMC). The version numbers of the testing packages are always higher than the current

Re: [R-sig-phylo] Potential glitch in phymltest

Hi Luiz, Thanks for the fix. It will be in the next release. Cheers, Emmanuel Le 07/11/2014 20:42, Luiz Max Carvalho a écrit : Hello Phylofolks, I've been using ape::phymltest() for a while now on a project and I just realised there is a potential glitch in the function. The reason is that

Re: [R-sig-phylo] overall p-value from multiple PGLS regression

Hi Pascal, See ?anova.gls. HTH Emmanuel Le 08/11/2014 17:49, Pascal Title a écrit : Hi all, I am running a number of PGLS regressions, some of which are multiple regressions. I am using the nlme package with the corBrownian error structure. If I build a model M via multiple regression, then

Re: [R-sig-phylo] advice about diversification analyses

Hi Karla, You may consider using the methods we developed in this paper: Paradis E., Tedesco P. A. Hugueny B. 2013. Quantifying variation in speciation and extinction rates with clade data. Evolution 67: 3617–3627. The associated R code is available on-line as SI of the paper. Best,

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