Re: [R-sig-phylo] writing list of trees to file

2008-09-03 Thread Emmanuel Paradis
intensive jobs, it's good to know that the for-loop will not have the effect of discarding the object's attributes. Stacey Quoting Emmanuel Paradis [EMAIL PROTECTED]: Since lists of trees have various attributes, it is better to use a 'for' loop for this kind of operation: for (i in 1:length

Re: [R-sig-phylo] Detecting non-Brownian trait evolution

2008-09-09 Thread Emmanuel Paradis
-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax: +33 (0)4 67 16

Re: [R-sig-phylo] circle plot

2008-11-13 Thread Emmanuel Paradis
Shota Nakamura [EMAIL PROTECTED] a écrit : Thank you very much for your prompt response. Actually, I've already tried a radial plot. The tree I want to make is like radial plot as tournament format. I hope this reply makes sense. Not to me. Can you send a picture with this format? EP

Re: [R-sig-phylo] question about drop.tip

2008-12-10 Thread Emmanuel Paradis
-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax: +33 (0)4 67 16 64 40 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] negative likelihoods in ancestral character reconstruction

2009-01-08 Thread Emmanuel Paradis
Betty Schirrmeister betty.schirrmeis...@googlemail.com a écrit : Hi I am trying to reconstruct anestral character states with the *ace* function of the *ape* package. I have a discrete character which among the taxa of my phylogeny is present or not (1or 0). When I use the ER model assuming

Re: [R-sig-phylo] binding phylogenetic trees

2009-01-08 Thread Emmanuel Paradis
Dan Rabosky dl...@cornell.edu a écrit : Howdy - Does anyone have functional code that allows grafting of phylogenetic trees? Ideally, I'd like to take two trees X (the recipient)and Y, and: (1) specify a target terminal or internal node for grafting Y (call it node Z...) (2) Drop all

Re: [R-sig-phylo] compar.gee- Generalized estimating equations and inflated type 1 errors

2009-02-18 Thread Emmanuel Paradis
Hi Tom, We had a discussion related to this topic last year. Here's my main comment: https://stat.ethz.ch/pipermail/r-sig-phylo/2008-April/70.html You may have a look also at other messages in the same thread, of course. HTH EP Tom Oliver toli...@ceh.ac.uk a écrit : Hello Helplist,

Re: [R-sig-phylo] still problems using ace

2009-02-19 Thread Emmanuel Paradis
Birgit Lemcke birgit.lem...@systbot.uzh.ch a écrit : Hello Helplist! This is a question of somebody who has not a lot of experience using R (me).So please excuse me if it is an obvious problem for somebody who is good in R. I try to use ace with a treefile containing 2500 Bayesian trees and

Re: [R-sig-phylo] compar.gee- Generalized estimating equations and inflated type 1 errors

2009-02-19 Thread Emmanuel Paradis
-Wilk normality test data: temp.slope W = 0.6392, p-value = 6.403e-09 Many thanks, Tom Emmanuel Paradis emmanuel.para...@mpl.ird.fr 02/18/09 9:52 am Hi Tom, We had a discussion related to this topic last year. Here's my main comment: https://stat.ethz.ch/pipermail/r-sig-phylo/2008-April

Re: [R-sig-phylo] compar.gee- Generalized estimating equations and inflated type 1 errors

2009-02-20 Thread Emmanuel Paradis
Oliver Biological Records Centre Centre for Ecology and Hydrology (CEH) Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB Tel: 01491 692517 Emmanuel Paradis emmanuel.para...@mpl.ird.fr 02/19/09 6:06 PM Tom Oliver toli...@ceh.ac.uk a écrit : Hi Emmanuel

Re: [R-sig-phylo] compar.gee- (re-sent as last digest exceeded max length and missed out msg!)

2009-03-17 Thread Emmanuel Paradis
;) Since you seem to have a continuous response, I suggest you switch to GLS and compare different correlation structures with AIC. EP Thanks for all your help, Tom Emmanuel Paradis emmanuel.para...@mpl.ird.fr 03/03/09 3:25 pm Actually, I have already observed the same thing

Re: [R-sig-phylo] Negative state probabilities with ace

2009-03-23 Thread Emmanuel Paradis
of the month). Emmanuel Paradis Le 17.03.2009 20:20, Dan Rabosky a écrit : Hi folks- This is following up on a post from last year. When estimating state probabilities with ace() for discrete characters, you can get negative probabilities. They still sum to 1 for each internal node

Re: [R-sig-phylo] Consensus frequencies

2009-05-18 Thread Emmanuel Paradis
Hi Sam, Have a look at the function prop.part: it is the working function of consensus and other similar functions. EP Sam Brown s_d_j_br...@hotmail.com a écrit : Hello one and all I'm wondering if there is any way of obtaining the consensus frequencies of nodes in majority-rule

Re: [R-sig-phylo] Trait simulations

2009-05-20 Thread Emmanuel Paradis
Liam, The package MASS has the function mvrnorm that simulates from a multivariate normal distribution. Its help page says: The matrix decomposition is done via 'eigen'; although a Choleski decomposition might be faster, the eigen decomposition is stabler. The package mvtnorm (on

Re: [R-sig-phylo] question about ape library

2009-06-03 Thread Emmanuel Paradis
Dear Yasumasa, You may try the png() function. Alternatively, you may try to write an EPS file with postscript(), then convert it with appropriate tools such qs ImageMagick. HTH EP Yasumasa Shigemoto yshig...@genes.nig.ac.jp a écrit : Dear all, I have a question about ape library.

Re: [R-sig-phylo] ace question: Error in eigen(Q * phy$edge.length[i], symmetric = FALSE)

2009-06-09 Thread Emmanuel Paradis
possibilities. EP Le 06.06.2009 01:14, Andy Raduski a écrit : Hi Everyone, I have a problem with the ace function in the ape package. The same problem appears whether or not I use Emmanuel Paradis' patch posted on this discussion group recently. Specifically, the problem seems to be related

Re: [R-sig-phylo] convert edge list to phylo object

2009-07-16 Thread Emmanuel Paradis
edges to a phylo class. y-read.tree(text=(A,(B,(C,D)E)F)G;) y$edge Thanks again, Chris ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4

Re: [R-sig-phylo] conversion class phylog into class phylo

2009-08-06 Thread Emmanuel Paradis
Hi Jürgen, Jürgen Kluge klugejuer...@gmx.de a écrit : Dear all. I search for a possibility to transform phylogenetic data from class 'phylog' (which is processed by ade4) to calss 'phylo' which I want to use within commands of 'picante' Here is a short dataframe with 5 species, transformed

Re: [R-sig-phylo] Mismatch distribution and demographic models in R?

2009-09-02 Thread Emmanuel Paradis
'pegas' on CRAN. It's still under development though. or (b) it is possible to pipe to Arlequin. I don't know. Cheers, EP Any suggestions are highly appreciated. Best regards, Roland -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax: +33 (0)4 67 16 64 40 http

Re: [R-sig-phylo] plot.phylo downwards/leftwards

2009-09-07 Thread Emmanuel Paradis
has been implemented. For those interested to try the new version, it can be downloaded here: http://ape.mpl.ird.fr/misc/plot.phylo.R I welcome any test because a number of changes has been done, so I'm still waiting to put it on SVN. Cheers, Emmanuel Emmanuel Paradis wrote on 05/08/2009 12

Re: [R-sig-phylo] ape matrix manipulation

2009-09-28 Thread Emmanuel Paradis
Hi Christoph Gustavo, Quoting Christoph Heibl christoph.he...@gmx.net: Hi Gustavo, Hava a look at: ?`%in%` Given a matrix 's' of class DNAbin and a tree 'tr' of class phylo, you simply do: s - s[-(rownames(s) %in% tr$tip.label), ] Yes but replace '-' with '!': s - s[!(rownames(s) %in%

Re: [R-sig-phylo] is maximum likeyhood a phylogenetic approach?

2009-09-29 Thread Emmanuel Paradis
Felsenstein, j...@gs.washington.edu Dept. of Genome Sciences, Univ. of Washington Box 355065, Seattle, WA 98195-5065 USA ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD

Re: [R-sig-phylo] Tree manipulations (pruning and grafting)

2009-10-08 Thread Emmanuel Paradis
]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax: +33 (0)4 67 16 64 40 http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list

Re: [R-sig-phylo] Repeated measures on Phylogenies

2009-10-29 Thread Emmanuel Paradis
]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier

Re: [R-sig-phylo] axial tip label

2009-11-05 Thread Emmanuel Paradis
Hi Claire, Have you tried with a random tree to check? eg: tr - rcoal(235) plot(tr, f) If the results are different with your tree, this might a bug that occurs with your particular tree. EP Quoting claire.ho...@inserm.fr: Hi everybody ! I have a tree with 235 tips with branchs length.

Re: [R-sig-phylo] Simulate continuous character evolution on phylogenetic trees using different models of evolution

2009-11-05 Thread Emmanuel Paradis
We discussed on the list a few months ago about using any correlation matrix to simulate characters. At the moment, it's tedious to get the correlation matrix from a corStruct object in ape, but I'll improve that soon (following several requests) so that it'll be straightforward to

Re: [R-sig-phylo] Simulate continuous character evolution on phylogenetic trees using different models of evolution

2009-11-05 Thread Emmanuel Paradis
Quoting Joe Felsenstein j...@gs.washington.edu: Emmanuel said -- We discussed on the list a few months ago about using any correlation matrix to simulate characters. At the moment, it's tedious to get the correlation matrix from a corStruct object in ape, but I'll improve that soon

Re: [R-sig-phylo] axial tip label

2009-11-09 Thread Emmanuel Paradis
are : my tree has got bootstraps as nodes label and some tip labels are number. In this case I have written the tip label between two ' : example : '24'. Maybe it's the origin of the trouble ? What do you think about that ? Claire Hoede Emmanuel Paradis emmanuel.para...@mpl.ird.fr a écrit

Re: [R-sig-phylo] Significance in PGLS

2009-11-24 Thread Emmanuel Paradis
://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax: +33 (0)4 67 16 64 40 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] Estimate correlation coefficient of a linear GLS model

2010-01-04 Thread Emmanuel Paradis
-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47

Re: [R-sig-phylo] diagnostic character

2010-01-13 Thread Emmanuel Paradis
/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax: +33 (0)4 67 16 64 40 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] maximum parsimony ancestral reconstruction

2010-01-25 Thread Emmanuel Paradis
-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax

[R-sig-phylo] Bayesian dating in R vs. Multidivtime

2010-01-26 Thread Emmanuel Paradis
, and calculate posteriors. I have two questions: 1. Has someone attempted a similar implementation? 2. Has someone written an interface between R and Multidivtime? Many thanks in advance for any reply. Best, Emmanuel -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax: +33 (0

Re: [R-sig-phylo] selecting terminal branch lengths?

2010-02-10 Thread Emmanuel Paradis
-- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax: +33 (0)4 67 16 64 40 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] Editing names of DNAbin object

2010-02-10 Thread Emmanuel Paradis
with object tmp.names that is the same length as names(dat), where dat is the DNAbin object. However, try as I might, I cannot accomplish this. I can extract the names, but can't edit. Any help would be appreciated. Wade -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax: +33 (0

Re: [R-sig-phylo] Merging multiPhylo objects

2010-02-12 Thread Emmanuel Paradis
://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax: +33 (0)4 67 16 64 40 http

Re: [R-sig-phylo] a bug in boot.phylo?

2010-03-18 Thread Emmanuel Paradis
]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax: +33 (0)4 67 16 64 40 http://ape.mpl.ird.fr

Re: [R-sig-phylo] Errors with ace and Confidence Intervals for Ancestral Traits

2010-08-16 Thread Emmanuel Paradis
___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France

Re: [R-sig-phylo] Multistate characters

2010-09-22 Thread Emmanuel Paradis
Murcia ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax: +33 (0)4 67 16 64 40 http://ape.mpl.ird.fr

Re: [R-sig-phylo] PIC vs. PGLS

2010-09-27 Thread Emmanuel Paradis
-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax: +33 (0)4 67 16 64 40 http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R

Re: [R-sig-phylo] PIC vs. PGLS

2010-09-27 Thread Emmanuel Paradis
___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Montpellier, France ph: +33 (0)4 67 16 64 47 fax

Re: [R-sig-phylo] PIC vs. PGLS

2010-09-27 Thread Emmanuel Paradis
This one left my outbox too fast: Emmanuel Paradis wrote on 27/09/2010 19:08: tr - rtree(10) Cannot be closer to the PIC model. And both models have the same number of df (4 - 2 for the PICs; 5 - 3 for the GLS). This should be... 9 - 2 for the PICs; 10 - 3 for the GLS (number of points

Re: [R-sig-phylo] barplot next to phylo plot

2010-09-29 Thread Emmanuel Paradis
Hi Darren, On Tue, 28 Sep 2010 15:07:54 +0100 Darren Obbard darren.obb...@ed.ac.uk wrote: Hi, I wish to achieve a plot that looks like the one linked from the APE homepage http://ape.mpl.ird.fr/image/Figure2_TEJEDO.png Does anyone have code that will do this, or could provide me with

Re: [R-sig-phylo] bug on as.hclust.phylo()

2010-09-30 Thread Emmanuel Paradis
Hi Filipe, On Thu, 30 Sep 2010 17:22:43 +0200 Filipe G. Vieira fgar...@ub.edu wrote: Hi all, I'm using R v2.10.1 and I've recently found a bug in APE's as.hclust.phylo() function. It occurred when I read a tree with names on the internal nodes and tried to convert it. In the end I've

Re: [R-sig-phylo] base composition

2010-10-29 Thread Emmanuel Paradis
Hi Jason, See base.freq() that you can combine with apply() to lapply() depending on how your data are structured. Emmanuel On Fri, 29 Oct 2010 14:12:35 -0700 (PDT) Jason S jas2...@yahoo.com wrote: Dear all, Is there a function to take an alignment (say, using read.nexus.data()) and

Re: [R-sig-phylo] Incorrect dimensions of dist.nodes() matrix

2010-11-15 Thread Emmanuel Paradis
Hi Miguel, You found a bug in this function. It resolves all unrooted trees as well as multichotomies prior to calculating the distances. This has no indicence for rooted, fully dichotomous trees, or if you are interested in among-tip distances, but it returns duplicated columns with

Re: [R-sig-phylo] fitContinuous running for days

2010-11-15 Thread Emmanuel Paradis
Hi all, gls() with 'corPagel' correlation structure and an intercept-only model also estimates lambda. The results will not be identical with fitContinuous but usually close. To compare the timings, with n = 100: tr - rcoal(100) co - corPagel(1, tr) x - rTraitCont(tr)

Re: [R-sig-phylo] Detailed definition of number generated by axisPhylo function

2010-11-15 Thread Emmanuel Paradis
Hi Yasumasa, It uses the same scale than the branch lengths of the plotted tree. HTH Emmanuel On Tue, 16 Nov 2010 13:52:27 +0900 Yasumasa Shigemoto yshig...@genes.nig.ac.jp wrote: Hi everyone, I am using axisPhylo function in ape library. This function adds a scale bar in a phylogenetic

Re: [R-sig-phylo] Newbie PGLS question about graphical display of results

2010-11-17 Thread Emmanuel Paradis
___ 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] Newbie PGLS question about graphical display of results

2010-11-18 Thread Emmanuel Paradis
other helpful list participants. Cheers, Andrew Barr On Wed, Nov 17, 2010 at 10:54 PM, Emmanuel Paradis emmanuel.para...@ird.fr wrote: Hi Andrew, Andrew Barr wrote on 17/11/2010 22:29: Hello all, First a very condensed version of my question.  I am running a PGLS (using gls() from package nlme

Re: [R-sig-phylo] Possible bug in drop.tip{ape}

2010-11-24 Thread Emmanuel Paradis
Hi Liam, It is fixed and on the SVN: https://svn.mpl.ird.fr/ape/dev/ape/R/drop.tip.R Do not hesitate to test it because this function has been written some years ago and has been patched quite a few times. Thanks for the accurate report. Emmanuel On Sat, 20 Nov 2010 15:57:05 -0500 Liam

Re: [R-sig-phylo] trees to matrix and gamma-statistic

2010-12-02 Thread Emmanuel Paradis
Hi Bryan, On Thu, 02 Dec 2010 03:06:39 -0300 Bryan Morales Pallero feano...@gmail.com wrote: Hello all, I'm working in the evolution of lizards in Chile, and I will very grateful if you can help me with the next questions: 1. I need to transform the sample of trees generated

Re: [R-sig-phylo] trees to matrix and gamma-statistic

2010-12-02 Thread Emmanuel Paradis
. Revell NESCent, Duke University web: http://anolis.oeb.harvard.edu/~liam/ NEW email: lrev...@nescent.org On 12/2/2010 10:01 PM, Emmanuel Paradis wrote: Hi Bryan, On Thu, 02 Dec 2010 03:06:39 -0300 Bryan Morales Pallero feano...@gmail.com wrote: Hello all, I'm working

Re: [R-sig-phylo] problems with as.hclust.phylo() in ape Rpackage (2.6-2)

2010-12-14 Thread Emmanuel Paradis
Laboratory for Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences Nanxincun 20,Xiangshan, Beijing 100093 E-mails: zhan...@ibcas.ac.cn jinlongzhan...@gmail.com 发件人: Emmanuel Paradis 发送时间: 2010-12-14 19:15:21 收件人: T.G. Homan; r-sig-phylo@r-project.org 抄送: 主题

Re: [R-sig-phylo] How to write.nexus or write.tree with spaces in the tip labels?

2011-01-07 Thread Emmanuel Paradis
Hi John, On Tue, 4 Jan 2011 16:21:58 -0800 John Cumbers johncumb...@gmail.com wrote: Hi all, I'm stuck on how to write.nexus or write.tree with spaces in the tip labels? It's in ape's FAQ. I'm trying to rearrange branches on a tree and the most satisfying way seems to be to load the

Re: [R-sig-phylo] similarity of trees

2011-01-18 Thread Emmanuel Paradis
Hi Damien Scott, I don't know the formula of Icong or MAST, but I'd like to remind you the function prop.part() that finds all the clades in a set of trees and returns the compositions and frequencies, eg: a - rtree(4) b - rtree(4) prop.part(c(a, b)) 1: t2 2: t1 3: t3 4: t4 == 2

Re: [R-sig-phylo] Allele frequency estimation using pegas

2011-01-22 Thread Emmanuel Paradis
Dear Thibaut Ayman, The solution is to do it with standard R code. Here're two possibilities with lapply and rapply, respectively: lapply(s, lapply, function(x) x/sum(x)) $fca8 $fca8$genotype 117/133 119/133 121/135 121/137 121/145 0.004608295 0.004608295

Re: [R-sig-phylo] Simulate discrete characters on tree constrained to phylogenetic signal K

2011-01-28 Thread Emmanuel Paradis
On Fri, 28 Jan 2011 17:20:57 -0600 Scott Chamberlain myrmecocys...@gmail.com wrote: Dear R community, I would like to simulate discrete characters on a randomly generated tree. However, I would like to create different sets of trees and associated characters at certain levels of phylogenetic

Re: [R-sig-phylo] iterative pruning from alignment and tree

2011-01-30 Thread Emmanuel Paradis
-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] NEVERMIND -read.tree and read.nexus error

2011-02-21 Thread Emmanuel Paradis
University (406) 370-7157 jfmea...@gmail.com ___ 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] Multiple sequence alignment in R?

2011-02-23 Thread Emmanuel Paradis
University, EEB Dept. -- 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] Mixup with plotted bootstrap values

2011-02-23 Thread Emmanuel Paradis
for your help. Cheers, Alastair ___ 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

Re: [R-sig-phylo] Mixup with plotted bootstrap values

2011-02-24 Thread Emmanuel Paradis
...@gmail.com University Private Bag, Rondebosch 7700, South Africa or PO Box 115, Loxton 6985, South Africa Cell: 082 491-7275 - Emmanuel Paradis wrote: Hi Alastair, I copied the Newick string below into R, read it with read.tree

Re: [R-sig-phylo] Mixup with plotted bootstrap values

2011-03-01 Thread Emmanuel Paradis
and it may be generalized further to decode Newick strings in an efficient and fast way. Emmanuel Emmanuel Paradis wrote on 24/02/2011 16:14: Alastair, That's indeed the correct work-around. The is because a different code is used whether the NEXUS file has a TRANSLATE block or not. I'll fix

Re: [R-sig-phylo] Cannot get varCompPhilip to work

2011-03-01 Thread Emmanuel Paradis
, intern = TRUE, input = c(W, A, Y)) Cheers, Emmanuel cheers, popko ___ 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] haplotype networks

2011-03-02 Thread Emmanuel Paradis
/people/bernardi ___ 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

Re: [R-sig-phylo] Comparing the topology of two trees

2011-03-03 Thread Emmanuel Paradis
-- 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] The Speed of Different Methods For Obtaining the Descendant Tip Taxa per Node

2011-03-06 Thread Emmanuel Paradis
/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr

Re: [R-sig-phylo] consensus function hanging

2011-03-09 Thread Emmanuel Paradis
___ 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] bug in read.nexus -- ape 2.7

2011-03-17 Thread Emmanuel Paradis
(around next week). 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] How can I collapse clades when viewing trees?

2011-03-22 Thread Emmanuel Paradis
___ 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] weirdness in confidence intervals returned by ace, pic option

2011-03-23 Thread Emmanuel Paradis
Hi Nick, With method = pic, the CIs are computed using the expected variances under the model, so they depend only on the tree. I've added a paragraph in the man page to explain this. Cheers, Emmanuel Nick Matzke wrote on 22/03/2011 12:30: Hi all, This isn't crucial to my work at the

Re: [R-sig-phylo] reading nexus file from treebase?

2011-03-24 Thread Emmanuel Paradis
[[alternative HTML version deleted]] ___ 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

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

2011-03-26 Thread Emmanuel Paradis
know if it is reproducible in that version. -Dave -- 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] reading nexus file from treebase?

2011-03-26 Thread Emmanuel Paradis
Hi Mark, Brian and others, Mark Holder wrote on 25/03/2011 23:12: Hi all, Adding a command skipping feature to ape, might make it a good bit more robust to some of the weird files that are out there. I'm afraid that I'm not familiar enough with the code to suggest where those changes should go.

Re: [R-sig-phylo] Adding a taxon to a pre-exisiting tree

2011-04-02 Thread Emmanuel Paradis
Hi Liam, Yes bind.tree() is the function to use here. Two notes below: On Sat, 02 Apr 2011 00:03:51 -0400 Liam J. Revell liam.rev...@umb.edu wrote: Of course, we could generalize my preceding suggestion with the following function: add.everywhere-function(tree,tip.name){

Re: [R-sig-phylo] Erro in rTraitCont()

2011-04-02 Thread Emmanuel Paradis
) arvore-rtree(20) alfa-sample(0:2,1) rTraitCont(arvore,model=OU,alpha=alfa) Sometimes, it yields very strange results, including Inf's and NaN's. I then realized that the function sample(0:2,1) returns a number of the class integer. I wrote to Emmanuel Paradis and he told me to try using as.double

Re: [R-sig-phylo] Multistate Trait Polymorphism

2011-04-06 Thread Emmanuel Paradis
NC 27708 CP (605) 553-1057 charlie.wil...@duke.edu http://www.duke.edu/~cgw6/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis

Re: [R-sig-phylo] Simulate node ages given known topology

2011-04-10 Thread Emmanuel Paradis
-- 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] chronopl

2011-04-10 Thread Emmanuel Paradis
-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] Trouble with a phylogenetic independent contrast

2011-04-11 Thread Emmanuel Paradis
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Re: [R-sig-phylo] Multistate Trait Polymorphism

2011-04-11 Thread Emmanuel Paradis
Box 355065, Seattle, WA 98195-5065 USA -- 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] chronopl

2011-04-11 Thread Emmanuel Paradis
Hi Hilmar, Hilmar Lapp wrote on 11/04/2011 21:54: Hi Emmanuel: On Apr 11, 2011, at 12:55 AM, Emmanuel Paradis wrote: You should not used the transformation suggested on this wiki (it is a bit outdated, NPRS has been removed from ape). In most situations, you should just leave S=1

Re: [R-sig-phylo] Simulate node ages given known topology

2011-04-11 Thread Emmanuel Paradis
mailing list R-sig-phylo@r-project.org mailto: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/ -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr

Re: [R-sig-phylo] Ives et al. 2007 Matlab code converted to R code?

2011-04-22 Thread Emmanuel Paradis
problem), then GLS can't be used. Of course, this doesn't mean the gls can't solve it. Cheers, Tony On Apr 21, 2011, at 10:34 AM, Emmanuel Paradis wrote: Tony, It's possible to specify a fixed variance function in gls(), eg: vf - varFixed(~ v) gls(y ~ x, correlation = cor, weights = vf

Re: [R-sig-phylo] Bootstrap values and NJ when there is no genetic distance between samples

2011-05-06 Thread Emmanuel Paradis
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Re: [R-sig-phylo] Bootstrap values and NJ when there is no genetic distance between samples

2011-05-10 Thread Emmanuel Paradis
) associated with a zero-length branch is an indication that something's wrong there. Again, it can be a problem even when the branch lengths are nonzero. Joe Joe Felsenstein, j...@gs.washington.edu Dept. of Genome Sciences, Univ. of Washington Box 355065, Seattle, WA 98195-5065 USA -- Emmanuel

Re: [R-sig-phylo] Unexpected behavior in birth death simulations

2011-05-18 Thread Emmanuel Paradis
Hi Carl Matt, ape has drop.fossil() with a tol option set to 1e-8 by default. I wonder whether it gives different outputs than geiger's function. Best, Emmanuel -Original Message- From: Carl Boettiger cboet...@gmail.com Sender: r-sig-phylo-boun...@r-project.org Date: Wed, 18 May 2011

Re: [R-sig-phylo] Unexpected behavior in birth death simulations

2011-05-19 Thread Emmanuel Paradis
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Re: [R-sig-phylo] Displaying branch support after rooting

2011-05-21 Thread Emmanuel Paradis
Hi Brian, You are plotting a tree and adding the node labels from another tree. You'd better do something like: a - root(tree, plot(a, nodelabels(a$node.label, best, Emmanuel -Original Message- From: Brian Bourke brianbou...@hotmail.com Sender:

Re: [R-sig-phylo] specifying line type (lty) for a polytomy using plot.phylo()

2011-05-25 Thread Emmanuel Paradis
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Re: [R-sig-phylo] Displaying branch support after rooting

2011-05-25 Thread Emmanuel Paradis
to this problem? Regards, Brian. [[alternative HTML version deleted]] ___ 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] mixedFontLabel and rotation

2011-05-27 Thread Emmanuel Paradis
. [[alternative HTML version deleted]] ___ 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

Re: [R-sig-phylo] ape Crashes latest version does not install

2011-06-07 Thread Emmanuel Paradis
:07 PM, Emmanuel Paradis emmanuel.para...@ird.frwrote: Hi Alfredo, I recently fixed a bug in bionj() which makes R crash if some distances are too large( 100). Is that your case? (I guess not since you analyse DNA with K80.) Cheers, Emmanuel -Original Message- From: alfredo tello

Re: [R-sig-phylo] Statistical congruence tests for phylogenetic trees, e.g. CADM.global {ape}

2011-06-26 Thread Emmanuel Paradis
-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://stat.ethz.ch/mailman

Re: [R-sig-phylo] Cross Validation for PL in R

2011-07-06 Thread Emmanuel Paradis
Thanks! Frank -- 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] query: how to use an existing covariance matrix directly in a gls procedure in R?

2011-07-08 Thread Emmanuel Paradis
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Re: [R-sig-phylo] Assigning node ages to a tree, revisited

2011-07-14 Thread Emmanuel Paradis
-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] Converting a List of Trees into a multiPhylo Object

2011-07-18 Thread Emmanuel Paradis
Hello David, Simply: class(y) - multiPhylo Best, Emmanuel -Original Message- From: David Bapst dwba...@uchicago.edu Sender: r-sig-phylo-boun...@r-project.org Date: Mon, 18 Jul 2011 19:02:17 To: R Sig Phylo Listservr-sig-phylo@r-project.org Subject: [R-sig-phylo] Converting a List of

Re: [R-sig-phylo] Dating trees using date.phylo - ape problem?

2011-07-21 Thread Emmanuel Paradis
Hi Roland, Just after the error, type: traceback() This will show you, hopefully, where the error happened. Best, Emmanuel -Original Message- From: Roland Sookias r.sook...@gmail.com Sender: r-sig-phylo-boun...@r-project.org Date: Thu, 21 Jul 2011 12:44:30 To:

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