Displaying 20 results from an estimated 400 matches similar to: "problem accessing trees after read.nexus from ape package"
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 <-
2006 Aug 05
0
cor of two matrices whose columns got shuffled
Hello,
I'm trying to take the correlation of two distance matrices and get
the r2 value
ex)
Ndisc PS1 Ntet Nsito NcB NcA PS3 NcC
NiB NiA
PS1
0.08945
Ntet 0.08601
0.02020
Nsito 0.09361 0.02780
0.02260
2016 Apr 21
2
"cophenetic" function for objects of class "dendrogram"
Hello,
I have been using the "cophenetic" function for objects of class "dendrogram" and I have realised that it gives different results when it is used with objects of class "hclust". For instance, running the first example in the help file of the "cophenetic" function,
d1 <- dist(USArrests)
hc <- hclust(d1, "ave")
d2 <-
2016 Apr 21
1
"cophenetic" function for objects of class "dendrogram"
Note that cophenetic.default (which works on the output of hclust(dist(X)))
uses the
row names of X as labels. as.dendrogram.hclust does not retain those row
names
so cophenetic.dendrogram cannot use them (so it orders them based on the
topology of the dendrogram).
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Thu, Apr 21, 2016 at 7:59 AM, William Dunlap <wdunlap at tibco.com> wrote:
2010 Jun 02
1
compute the associate vector of distances between leaves in a binary non-rooted tree
Hello.
I'd like to compute the associate vector of distances between leaves in a binary non-rooted tree. The definition of a distance between two leaves in a binary non-rooted tree is the number of edges in the path joining the two leaves.
I've tried the ape package but I'm unable to find this vector.
For example, using rtree(5,rooted=F) I've obtained the following tree:
$edge
2001 Jun 12
1
cophenetic matrix
Hello,
I analyse some free-sorting data so I use hierarchical
clustering.
I want to compare my proximity matrix with the tree
representation to evalute the fitting. (stress, cophenetic correlation
(pearson's correlation)...)
"The cophenetic similarity of two objects a and b is defined as the
similarity level at wich objects a and b become members of the same
cluster during the course of
2013 Oct 07
1
Why read.table replacing space with "." in the header
Hi,
Use `check.names=FALSE`
head(dd,2)
#? Phylo.Tree Genesis.Tree
#1????????? 1??????????? 2
#2????????? 2??????????? 3
?dd <- data.frame("Phylo Tree"= c(1:10), "Genesis Tree"= c(2:11),check.names=FALSE)
head(dd,2)
#? Phylo Tree Genesis Tree
#1????????? 1??????????? 2
#2????????? 2??????????? 3
write.csv(dd,"Crish.csv",row.names=FALSE)
?yy<-
2009 Nov 10
2
All possible combinations of functions within a function
Dear All,
I wrote a function for cluster analysis to compute cophenetic correlations
between dissimilarity matrices (using the VEGAN library) and cluster
analyses of every possible clustering algorithm (SEE ATTACHED)
http://old.nabble.com/file/p26288610/cor.coef.R cor.coef.R . As it is now,
it is extremely long, and for the future I was hoping to find a more
efficient way of doing this sort of
2013 May 17
2
peering inside functions in a package?
Let's say I would like to look inside the function corBrownian in library
(ape). When I type in the function name I get the following, which is not
nearly the detail that goes into this function. I am wondering how to
begin cracking this function open (and others) so I can learn more about it
and perhaps code my own corClass one day. Thanks.
> corBrownian
function (value = 1, phy, form
2010 Jun 17
1
plotting radial dendrograms
Dear list,
I am trying to plot a radial dendrogram using the ape package, which
requires my data to be of class 'phylo'. Currently I have my
dendrogram stored as an object of class 'dendrogram' which was
produced from an outside bit of C code, but was made into an object of
class 'igraph.eigenc' and converted to a dendrogram using
'as.dendrogram()' from the igraph
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
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
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
2007 Feb 17
1
help with cluster stopping rules
Is there a function available in R that implements Mojena's Upper Tail Rule or that draws a Mojena plot?
I would also like to find a function that implements Duda and Hart's stopping rule.
Finally with function cophenet how can I achieve a straightforward Cophenet correlation coefficient (i.e. one number for example 0.876) that gives the agreement between the structure of the
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
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
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 <-
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 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.
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