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
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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
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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
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,
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
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
;)
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
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
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
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
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.
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
edges to a phylo class.
y-read.tree(text=(A,(B,(C,D)E)F)G;)
y$edge
Thanks again,
Chris
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Hi Jürgen,
Jürgen Kluge klugejuer...@gmx.de a écrit :
Dear all.
I search for a possibility to transform phylogenetic data from class
'phylog' (which is processed by ade4) to calss 'phylo' which I want to
use within commands of 'picante'
Here is a short dataframe with 5 species, transformed
'pegas' on CRAN. It's still under development
though.
or (b) it is possible to pipe to Arlequin.
I don't know.
Cheers,
EP
Any suggestions are highly appreciated.
Best regards,
Roland
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has
been implemented. For those interested to try the new version, it can be
downloaded here:
http://ape.mpl.ird.fr/misc/plot.phylo.R
I welcome any test because a number of changes has been done, so I'm
still waiting to put it on SVN.
Cheers,
Emmanuel
Emmanuel Paradis wrote on 05/08/2009 12
Hi Christoph Gustavo,
Quoting Christoph Heibl christoph.he...@gmx.net:
Hi Gustavo,
Hava a look at:
?`%in%`
Given a matrix 's' of class DNAbin and a tree 'tr' of class phylo, you
simply do:
s - s[-(rownames(s) %in% tr$tip.label), ]
Yes but replace '-' with '!':
s - s[!(rownames(s) %in%
Felsenstein, j...@gs.washington.edu
Dept. of Genome Sciences, Univ. of Washington
Box 355065, Seattle, WA 98195-5065 USA
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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.
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
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
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
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, 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
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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
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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
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
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
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
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
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
. 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
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
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
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
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
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University
(406) 370-7157
jfmea...@gmail.com
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University, EEB Dept.
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for your help.
Cheers,
Alastair
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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
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
, intern = TRUE, input = c(W, A, Y))
Cheers,
Emmanuel
cheers, popko
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(around next week).
Best,
Emmanuel
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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
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know if it is reproducible in that version.
-Dave
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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.
NC 27708
CP (605) 553-1057
charlie.wil...@duke.edu
http://www.duke.edu/~cgw6/
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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
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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
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
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to this problem?
Regards,
Brian.
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: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
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Thanks!
Frank
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Emmanuel Paradis
IRD, Jakarta, Indonesia
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-phylo
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Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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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
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:
And howmanytrees() in ape tells you how many trees there are for a given number
of tips (if it returns Inf, it's because this number is beyond the largest
representable number on your computer).
Best,
Emmanuel
-Original Message-
From: David Bapst dwba...@uchicago.edu
Sender:
deleted]]
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http://ape.mpl.ird.fr/
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https
RF.dist(reorder(clado1),reorder(clado2))# 4
RF.dist(reorder(midpoint(clado1)),reorder(midpoint(clado2)))# 6
RF.dist(midpoint(clado1),midpoint(clado2))# 6
Thanks!
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Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr
because if drop.extinct is set to TRUE, then the crown age
of the pruned tree can be smaller than in the full tree if some lineages
arising at the root of the tree do not leave any extant descendants.
- Liam
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Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr
www.robertlanfear.com http://www.robertlanfear.com
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Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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Hi all,
It can be done with phyloch but I forgot the name of the function.
HTH
Emmanuel
-Original Message-
From: Leandro Jones lrj...@gmail.com
Sender: r-sig-phylo-boun...@r-project.org
Date: Mon, 19 Sep 2011 07:35:32
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] Show
Hello Daniel,
Try this small manipulation ('tr' is your tree and 'node' stores the label of
the node):
i - which(tr$node.label == node)
j - which(tr$edge[, 2] == i + Ntip(tr))
tr$edge.length[j] - 0
Then di2multi(tr) will do the job. (Hopefully, there's originally no
zero-length branch in
My suggestion below should work with trees initially with zero-length branch if
using a negative value instead of 0, e.g.:
tr$edge.length[j] - -1
Then di2multi(tr, tol = -0.5)
Emmanuel
-Original Message-
From: Emmanuel Paradis emmanuel.para...@ird.fr
Sender: r-sig-phylo-boun...@r
to solve this?
In the above example, you can delete the 3rd tree and replace it by these 2:
(A,(D,(B,(C,((E,F),G);
(A,(D,(B,(C,(E,(F,G));
since the consensus will collapse (E,F,G) but with real data this might
not be practical.
Best,
Emmanuel
All the best,
Daniel
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Emmanuel
in prop.clades
prop.clades(ml.tree, bs.trees)
If anyone knows of a better way to re-arrange tip labels, constrained by
topology, then I would love to hear it.
Thanks,
Josh
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Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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. That does not occur,
if the rotation succeeds the first few times.
The GUIs are not closed. They just hang and it is impossible neither
to stop the interaction via right click nor to close the GUI. It has
to be killed.
Any idea what's going wrong?
--
Kind regards,
Mathias
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Emmanuel Paradis
IRD
rotate hangs (Emmanuel Paradis)
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Message: 1
Date: Sun, 13 Nov 2011 07:37:30 -0600
From: Anthony R Ivesari...@wisc.edu
To: R-phylo Mailing-listr-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] R squared in PGLS
Message
Hi Mathias and Antigoni,
It seems worth writing a method function as.phylo.pvclust since other users are
also interested in such functionality. If anybody has some code, that'd be a
good start.
Cheers,
Emmanuel
-Original Message-
From: Antigoni Kaliontzopoulou antig...@mail.icav.up.pt
version deleted]]
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