On Jan 20, 2012, at 12:33 PM, Emmanuel Paradis wrote:
> Todd,
>
> If you just want to color edges, what about using the option 'edge.color' in
> plot? You may use which.edge() to identify the edge indices you want to
> color. edgelabels() without options also displays the edge indices on a
>
Hi Pascal,
I cannot give you any specific help on the code you have presented below, but
if you are only interested in performing a background similarity test, you
could have a look at the phyloclim package, which implements a basic wrapper
for MAXENT.
library(phyloclim)
?bg.similarity.test
?n
> I'm trying to import a MrBayes consensus tree into R using the read.nexus
> function. Only problem is the function does not read the posterior
> probabilities of the file.
> I did check summary(mytree) and there are indeed no node labels.
> Any ideas?
Hi Rens,
there'a function in phyloch, but
Dear Ricardo,
There was a line missing in the code; it is fixed now in version 1.4-80 of
phyloch.
Cheers,
Christoph
On Nov 8, 2012, at 12:58 PM, Ricardo Kriebel wrote:
> Dear List,
>
> I have been annotating a target tree with support values from different
> analyses using the package phyloc
Hi Tom,
you can try ?append2tips from the phyloch package
(http://www.christophheibl.de/Rpackages.html). See also ?match to get the order
of your habitat labels right.
One general example:
library(phyloch)
data(viperidae)
plot.phylo(viperidae, cex = 0.8, label.offset = 0.02)
NTips <- length(vip
Hi Mariana,
extract.clades2 hasn't been well tested. I wrote it for a specific dataset two
years ago and I don't know if someone else has used it successfully. You can
send me your tree off list and I'll see if I can fix it. Alternatively, you can
identify the nodes concerned (?nodelabels, ?noi
to unaligned sequences
to speed up data assembly prior to alignment.
Best wishes,
Christoph
PS: Parts of phyloch are poorly documented. Anyone interested, please
do not hesitate to ask.
On Mar 17, 2009, at 5:46 PM, Brian O'Meara wrote:
Christoph Heibl has some R code that calls mafft
The node numbers would change again and I
could not find out which values belong to which node.
It might be possible to use the node.labels in the Trees as
identifier. But how can I assign same node labels to same nodes
over all trees.
Many thanks in advance for comments hints and any kind
are objects of class DNAbin (?DNAbin in the ape package), so
partitions must be aligned before concatenation.
Maybe this helps ...
Christoph
____
Christoph Heibl
Systematic Botany
Ludwig-Maximilians-Universität München
Menzinger Str. 67
nd tr...
HTH
Christoph
________
Christoph Heibl
Systematic Botany
Ludwig-Maximilians-Universität München
Menzinger Str. 67
D-80638 München
GERMANY
phone: +49-(0)89-17861-251
e-mail:he...@lmu.de
http://www.christophheibl.de/ch-home.html
SAVE PAPER - THINK BEFORE YOU PRINT
On Sep 28, 20
A question to the comparative method gurus:
I have a phylogeny for a group of plants that repeatedly evolved
annuality from perennial ancestors. For each tip in the tree I have
characterized the climatic tolerances (e.g. temperature,
precipitation, ...)
.
I would like to assess if there is
.
Stacey
Quoting Christoph Heibl :
A question to the comparative method gurus:
I have a phylogeny for a group of plants that repeatedly evolved
annuality from perennial ancestors. For each tip in the tree I
have characterized the climatic tolerances (e.g. temperature,
precipitation, ...)
gt; ___
> R-sig-phylo mailing list
> R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Christoph Heibl
Systematic Botany
Ludwig-Maximilians-Universität
Hi Alastair (and Emmanuel),
DNAbin objects can either be lists or matrices. The idea behind lists is to be
able to store sequences of different length, like those supported by the FASTA
format.
What happens here is that 'read.dna' reads your FASTA file into a list because
a priori it does not
than both of them put together."
>
> Isaac Asimov (1989). "The Relativity of Wrong." The Skeptical Inquirer,
> 14(1), 35-44. Fall 1989.
> http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm
>
> _______
> R-sig-phylo mai
Hi Joris,
Have you tried RAxML [1]or GARLI [2]? Both programs are well suited for large
alignments.
Christoph
--
[1] http://icwww.epfl.ch/%7Estamatak/index-Dateien/Page443.htm
[2] http://www.nescent.org/informatics/download.php?software_id=4
On May 28, 2010, at 1:47 PM, J
On Jun 3, 2010, at 8:52 AM, José Eduard Soto Guzmán wrote:
> HI everyone:
>
> Is it possible to draw a figure (a triangle, a square, an arrow, whatever)
> only in some specific branches of a tree with APE package?
José:
Yes it is, using the 'edge' argument of 'edgelabels'.
Try the example belo
Hi Dave,
the coordinates of the tips are invisibly returned by 'plot.phylo':
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
lastPP$xx # x-coordinates of tips
lastPP$yy # y-coordinates of tips
Then you can use 'lines' to plot your lines. (Use 'lty = 3' for dotted lines).
In the phyloch
Hi,
On Oct 27, 2010, at 1:03 AM, Andy Rominger wrote:
> Hi John,
>
> This is the default plotting style in package ade4 (using an object of class
> phylog to store your tree, and plot.phylog(...) for plotting).
>
> You can convert between an object of class `phylo' from ape to `phylog' in
> ad
)
>> taxo.fonts(woodmouse.nj, align = TRUE, offset = 0.1)
>> #produces the above error
>>
>> But this works fine:
>> data(vipera)
>> plot.phylo(vipera, tip.color = 0, x.lim = c(0, 1.3))
>> taxo.fonts(vipera, align = TRUE, offset = 0.1)
>>
>> Any h
Hi Alastair,
On Nov 16, 2010, at 12:18 PM, Alastair Potts wrote:
> Good day all,
> Two questions:
> 1) I was wondering if there was anyway to plot node timing uncertainty
> associated with beast trees in R (i.e. have similar 'uncertainty' bars as
> produced by figtree)?
> I have imported the
Hi Alastair,
On Feb 24, 2011, at 12:40 PM, Alastair Potts wrote:
> Hi all,
> Me again. I was wondering if anyone had a way to plot the bootstrap values
> from one tree onto another tree. I have a majority rule consensus tree and a
> bootstrap tree, both generated by PAUP, but not identical (
om numeric support values, node.support() let's you depict support as colored
node symbols or thickened edges depending on a chosen threshold (see Examples
section).
Cheers,
Christoph
>
> Best,
>
> Emmanuel
>
> Christoph Heibl wrote on 24/02/2011 22:06:
>> Hi Al
want to add
## will work only if your tip labels are of the form
"Genus_epithet-or-any-other-string"
library(megaptera)
tax <- data.frame(genus = strip.spec(species),
species = species,
stringsAsFactors = FALSE)
Christoph Heibl
An der Weiherleite 3
86633 Neuburg a
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