Displaying 20 results from an estimated 1000 matches similar to: "help on drawing a tree with "ape"?"
2004 Feb 08
1
APE: compar.gee( )
Dear all,
I don't understand the following behaviour: Running compar.gee (in
library ape ) with and without the option 'data', it give me different
results
Example:
.... Start R ....
> load("eiber.RData")
> ls()
[1] "gee.na" "mydata" "mytree"
> library(ape)
> # runnig with the option data= mydata
> compar.gee(alt ~ R,
2007 Apr 25
1
heatmap and phylogram / dendogram ploting problem, ape package
I am having trouble displaying a dendrogram of evolutionary
relationships (a phylogram imported from the ape package) as the
vertical component of a heatmap, but keeping the hierarchical
clustering of the horizontal component. The relationships of the
vertical component in the generated heatmap are not that of the
dendrogram, although the ordering is.
In more detail, I am attempting to generate
2009 May 11
1
Using ACE in the ape package
Having a problem running the ace command in ape.
After reading my table into R and then putting the names of the rows in the
table in same order as the tree I can't get ace to run and get the message
Erreur dans as.matrix(x) :
dims [produit 25] ne correspond pas ? la longueur de l'objet [0]
This is the command I am using and each of the vectors used in the
snalysis.
2007 Oct 10
2
Rooting trees using ape
Hi all,
I seem to be having a difficult time using the 'ape' package in R
when it comes to rooting trees. Here's a short screenshot:
> nirK.tree
Phylogenetic tree with 23 tips and 21 internal nodes.
Tip labels:
Burkholder, Burkholde3, Burkholde1, Burkholde4, Burkholde5,
Ralstonia2, ...
Node labels:
, 100, 100, 100, 70, 91,...
Unooted; includes branch lengths.
>
2011 Jan 28
1
Help with ape - read.GenBank()
Hi,
I am trying to work with the ape package, and there is one thing I am
struggling with. When calling the *read.GenBank()* function, I can get it
to work with an object created like this:
*>x <- c("AY395554","AY611035", ...)*
*>read.GenBank(x)*
However, I am trying to use the function to fetch several hundred sequences
at once. So I have been testing with small
2012 Jun 18
0
Obtaining r-squared values from phylogenetic autoregression in ape
Hello,
I am trying to carry out a phylogenetic autoregression to test whether my
data show a phylogenetic signal, but I keep calculating bizzare R-squared
values.
My script is:
> library(ape)
> x <-
2005 Jun 08
2
CRAN task view for genetics
Hello to everyone!
I have built CRAN task view for genetics. For now I have not submit it
to CRAN yet and it can be accessible from:
http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.html
http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.ctv
I have not submitted it to CRAN, since I would like first some opinion
about it. Genetics is really so broad field that I belive one person
2002 Sep 05
0
ape 0.1 is released
Ape is an R package for "analyses of phylogenetics and evolution". The
first version (0.1) has been released on 27 August 2002 and is available on
CRAN.
>From the 'Description' file of version 0.1:
Ape provides functions for reading, and plotting
phylogenetic trees in parenthetic format (standard Newick
format), analyses of comparative data in a
2003 Mar 10
0
ape 1.0 is on CRAN
Dear all,
The version 1.0 of ape (analysis of phylogenetics and evolution) is now on
CRAN. The jump from version 0.2-1 to 1.0 is explained by the fact that the
initial objectives of the project have been completed. The relevant part of
the Changes file is shown below. All comments, suggestions, or bug reports
are welcome.
Emmanuel Paradis
CHANGES IN APE VERSION 1.0
NEW FEATURES
2008 Oct 27
0
dotted lines for branches in ape's plot.phylo?
Hi,
I'm very much enjoying using the ape package to produce phylogenetic
trees with colored branches (using edge.color). Is it also possible to
specify that some branches should be drawn as dotted lines? That would
be really useful.
I've tried messing around with edge.width, but that doesn't seem to
help me get dotted lines.
thanks,
Janet Young
2009 Sep 17
1
How to colour the tip labels in a phylogenetic tree
Hi,
Using Ape, I have constructed an object of class "phylo", using the
method 'nj' (lets call the object 'tree_ja').
I also have a given subset of 'tree_ja' in a vector (lets call the
vector 'subspecies').
What I want to do, is construct a nj tree - plot(tree_ja) - but have the
species in vector 'subspecies' shown as red at the tips of the
2005 Jan 03
1
building phylogenetic trees
Hello,
My name is Sivan and I am a master degree student in statistics,my problem is as follows:
I have a dataset containing gene sequences and I would like to create a phylogenetic tree from it.
The problem that I can't seem to find a function to do this kind of operation. I read the ape package manual and I haven't found a command that takes raw data and turns it into a tree.
does anyone
2006 Dec 22
1
ape-package
Dear Sir or Madam,
I am very new to R, and I am trying to install seqinr-package.
In the manual I read that I need to install ape-package first, and I failed to do it.
I had the following error messges:
/usr/bin/ld: cannot find -lgfortran
collect2: ld returned 1 exit status
make: *** [ape.so] ?????? 1
ERROR: compilation failed for package 'ape'
** Removing
2007 Jan 26
1
Package for phylogenetic tree analyses
Hi
I am looking for a package that
1. reads in a phylogenetic tree in NEXUS format
2. given two members/nodes on the tree, can return the
distance between the two using the tree.
I came across the following packages on CRAN
ouch, ape, apTreeShape, phylgr all of which seem to
provide extensive range of functions for reading in a
Nexus-format tree and performing phylogenetic
analyses, tree
2008 Sep 04
1
Binary Tree Testing in "ape" package (a bug?)
Dear all,
I was testing the wonderful package APE.
However upon testing a particular Newick's format
tree - which I think to be a non-binary tree -
it yields different result as expected.
> library(ape)
> tree.hiv <- read.tree(text="(rat,mouse,(human,chimp));")
> is.binary.tree(tree.hiv)
[1] TRUE
Was that a bug in APE package?
- Gundala Viswanath
Jakarta - Indonesia
2018 Feb 20
1
question regarding the AICcmodavg package
Dear moderator,
If possible I would like to send in the following question for R-help:
I am analyzing a small data set using PGLS with phylogenetic uncertainty
taken into account and thereby including 100 potential phylogenetic tree
scenarios. I've managed to run models on all of the different trees and
performed model averaging to get parameter estimates for the intercept and
most of the
2006 Oct 17
1
ape -- internal nodes and pie charts
Hi,
I've been investigating the ape package for a while, and I was
wondering if it is possible to:
- display the names of the internal nodes (from a newick tree)
- plot a pie-chart on top of each of the internal branches in a phylogram plot
Thanks in advance,
Cheers,
Albert.
2011 Mar 23
1
Corrupt trees
Hi Everyone,
I have been using the "tree" package for a while with no problems until now.
When I run predict(tree, newdata), I get an error with the message "Corrupt tree" for about 50% of the trees that I generate with tree. For other trees, the predict function completes with no errors.
I haven't identified a correlation between the corrupt trees and the working tree.
2013 Jun 03
1
Mixed effects model with a phylogenetic tree/ distance matrix as a random effect
Hi,
I'm trying to build a mixed-effects model in which I'd like to include
either a distance matrix or a phylogenetic tree as a random effect.
The troubles I've had are that:
1. Function lmer() in package lme4 only accepts a data frame column as a
random factor and not a distance matrix.
2. Function MCMCglmm() in package MCMCglmm only accepts a rooted and
ultrametric phylogenetic
2006 Apr 28
1
unrooted tree and margins, ape package
Hello,
I have a question about margins when plotting an unrooted tree
(type="unrooted") with the 'ape' package ver. 1.7. When I plot an unrooted
tree with:
no.margin=TRUE
it seems that the margins are still there. It appears to be only when
type="unrooted".
I'm plotting multiple plots using layout() and would like to be able to get
rid of the margins or if