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 an der Donau
08431-53 96
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,
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 -
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 phyloch.
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
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 (but
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
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
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, 2009, at 7:43 AM, Gustavo
(?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
D-80638 München
GERMANY
phone
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