Displaying 20 results from an estimated 1000 matches similar to: "ape 1.0 is on CRAN"
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
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 <-
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
2019 Apr 05
0
new R packages for phylogenetic compartive methods
Dear all,
I wanted to let you know about four phylogenetic comparative methods (PCM) packages that have become available on (3 on CRAN and 1 on GitHub) recently that hopefully will be interesting to somebody. Three of them go significantly beyond the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes.
1) There is a new version of mvSLOUCH available. The most important change is that
the
2019 Apr 05
0
new R packages for phylogenetic compartive methods
Dear all,
I wanted to let you know about four phylogenetic comparative methods (PCM) packages that have become available on (3 on CRAN and 1 on GitHub) recently that hopefully will be interesting to somebody. Three of them go significantly beyond the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes.
1) There is a new version of mvSLOUCH available. The most important change is that
the
2010 Dec 09
0
convert non-ultrametric phylo to dendrogram
I am beginning to work with the 'ape' package in R, and have run into some
trouble. I generated a UPGMA tree based on DNA sequence distance in Paup*
and read it into R, where it became an object of class "phylo". However, I
need it to be classified as a "dendrogram" for my purposes (to use it to
order the layout of a heatmap). I get an error using as.hclust.phylo
2006 May 09
1
problem accessing trees after read.nexus from ape package
Hello,
I've been trying to figure out how to access the individual elements
from an object of class phylo.
I am reading in 201 trees created by paup as below.
> read.nexus("A_30knj_200t.txt", tree.names= NULL) -> anj30
> anj30[1]
$tree1
$edge
[,1] [,2]
[1,] "-1" "-2"
[2,] "-2" "-3"
[3,] "-3" "1"
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.
2013 Jan 18
1
Hclust tree to Figtree w/ branch lengths
Hi,
I'm doing hierarchical clustering, and want to export my dendrogram to a
tree-viewing/editing software. I can do this by converting the data to
Newick format (hc2Newick in ctc package), but I can't get branch lengths to
show in the resulting phylogram. I figured it might help to convert my
hclust object into a phylo object (as.phylo in ape package), but the
following lines give me
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
2010 Jul 19
1
possible bug in ape::extract.clade()
Hi,
I was recently splitting some massive phylo class objects with extract.clade()
and noticed what appears to be a bug in how tip labels are copied from the
full tree to the pruned tree. This possible bug was also mentioned here:
http://www.mail-archive.com/r-sig-phylo at r-project.org/msg00537.html
An example:
library(ape)
set.seed(5)
x <- matrix(rnorm(100), ncol=10)
p <-
2007 Mar 02
0
Dice dissimilarity output and 'phylo' function in R
Dear All,
I get some problems using the 'phylo' and
dissimilarity functions in R. I converted an output
from 'hclust' into an order of phylo so as to be able
to use the 'consensus' function on it. Each time I
submit the consensus codes, my computer hangs. When I
tried to see what the contents of the object converted
into order phylo is, I get the message
2012 May 14
0
phyloclim could not be installed in linux - problems on tkrplot dependence
Dear R-helpers, Christoph (author of phyloclim) and Luke (author of
tkrplot),
I would like to get your helps on installing of phyloclim in Ubuntu linux.
It seems a package named 'tkrplot' could not be installed at firstly, then
packages depends on it could not be installed latter.
As I have tested, installation of phyloclim works smoothly in Mac. I
attempted to install these packages in
2013 Jun 04
0
Mixed effects model with a phylogenetic tree/ distance, matrix as a random effect
Take a look at lmekin() in the coxme package. The motivating data set for my development
of coxme was the Minnesota Family Breast Cancer project: 24050 subjects in 462 families.
The random effect is an intercept per subject with sigma^2 K as its variance where K is
the kinship matrix (1 for self-self, .5 for parent-child or sib-sib, .25 for uncle-neice,
etc). lmekin is a linear models front
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
2011 Jun 20
0
Average skyline plot from newick trees stored
Dear all,
Does anyone know how can one loop through the newick phylogenetic trees
stored in a nexus file and generate an "average" skyline plot with
coalescent intervals?
I have managed to generate the plot with one tree, but is it possible to
create that "consensus/average" plot in R?
tr<-"((((8.1:0, 20.1:0):0, 6.1:3):123, (((((35.1:0, (22.1:0, (43.1:1,
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.
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,
2010 Nov 25
0
question about importing phylogenetic tree
Hello,
I am trying to import a phylogenetic tree from Mesquite into R. When I use
the read.nexus command I get the following message:
Warning message:
In matrix(x, ncol = 2, byrow = TRUE) :
data length [589] is not a sub-multiple or multiple of the number of rows
[295]
A phylo object is created but I am unable to plot it (when I try R freezes)
and I can tell by looking at the tip labels that
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