Displaying 20 results from an estimated 140 matches similar to: "Rooting trees using ape"
2009 Aug 26
0
Grid lines in cloud plot for lattice
Hi all,
I was wondering if there was a way to draw out grid lines in the cloud
plots for lattice. I hunted all throughout the panel.cloud and panel.
3dscatter help pages and couldn't find anything to help me move
forward with this. Do I have to get deeper into the drawing commands,
or is there something more obvious I'm just not seeing? My goal would
be to place grid lines on the
2011 May 10
1
Rooting FreeBSD , Privilege Escalation using Jails (P??????tur)
On 10 May 2011 16:10, "Jamie Landeg Jones" <jamie@bishopston.net> wrote:
>
> > It used to confuzzle sysadmins on SUNos when the mount point was
> > 0700. The underlying mode disapeared when the mount was made, but it
> > was still being enforced. Suddenly no one but root could use say /usr
> > even though it was apparently 0755
>
> I remember that
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 <-
2009 Jan 06
0
problems with ace (ape-package)
Hi everyone
I am trying to reconstruct ancestral character states with R. I used the ace
function of the package ape. I have discrete characters and tried to use the
ER and ARD model.
The problem is, that I get negative lik$anc values. Does anybody by chance
have an idea what might be wrong?
Thanks in advance
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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
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
2018 Jan 22
1
what does the within component of varcomp (ape library) output indicate?
I am trying to use varcomp to obtain the variance partitioning across
different nested levels of random effects (say x,y and z). I get the
three variance components (for each of my along with an additional one
called 'within' from varcomp output. I am using the 'scale total
variance to 1' option and though the within component is small, it
does form a part of what explains the
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
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
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.
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
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
2009 Feb 19
0
change the label size when drawing trees with ape
Hi All,
I want to be able to change the labe size on a tree
when using ape package so that the graph can look
nicer, but don't know how. Playing with the "font"
doesn't seem to help. (Right now the labels barely
show.)
Thanks for your help!
Code I'm using now
#-------------------------
t1 = "(((1:77.37,2:77.37):9.4,4:86.77):7.56,3:94.33);"
t2 =
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.
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 <-
Is there some command or alternative using dist.dna in ape package for models not included like GTR?
2011 Apr 12
1
Is there some command or alternative using dist.dna in ape package for models not included like GTR?
Hi,
I am making some DNA distances and I would like to use dist.dna as matrix in
R, but this command does not include models like GTR...
Is there some command or alternative using dist.dna in ape package for
models not included like GTR?
I would appreciate any help given
Thank you very much,
Ignacio Quintero
Laboratorio de biologĂa evolutiva de vertebrados (Evolvert)
Departamento de Ciencias
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"
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
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,
2006 May 10
1
ape comparative analysis query
I've been comparing variables among objects (taxa) related by known
trees, using phylogentically independent contrasts in the ape package,
and want to move on to more complex models e.g. by using gls with
appropriate correlation terms. My trees contain lots of (hard)
polytomies and information about ancestors, which I've been including-
creating fully dichotomous trees by using zero branch