similar to: problems with ace (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.

Hello RUser! I try to use ace for an ancestral state reconstruction but got back an error message. ace(FacVar,Tree, type="discrete") Warning messages: 1: In nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE) : NA/Inf durch gr??te positive Zahl ersetzt (NA/Inf replaced by positive number) 2: In nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian

Hi, I have reconstructed ancestral character states on a phylogeny using MuSSE in the diversitree package and plotted the character state probabilities as pie charts on the nodes. I would, however, like to colour the character states of my extant species, i.e. the tip labels, the same colours as my pie charts, such that all species in state 1 are e.g. blue, species in state 2 red and species in

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

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

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"

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

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,

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

Hello, I've just downloaded and installed the RAqua onto my Mac and I have R up and running fine. Now I'm trying to get 'ape' downloaded and installed and having quite the difficulty. I am following the directions specified under 'Installing packages' where packages can be downloaded and installed from within R. I get the following error messages: 1: argument

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

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 <-

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

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 =

Dear all, I am still trying to find out what goes wrong when I use ace (I get an 'NAs in foreign fuction call (arg3)' but when I go through it with debug there seem no data to be missing). I had some errors (see at end of message) while installing 'acepack'. Do you think it is possible that these lead to the fact, that simple problems run ok but larger problems result in an

Dear all, I am trying to use ace on a 446 x 14 Matrix, with two categorical variables in the first two columns. If I try to run it I get: > aceiH <- ace (data.mat, resp, cat= 1:length(x.cat)) Error: NAs in foreign function call (arg 3) There is only one .Fortran call in ace () with the third argument being x = t(x). Thus I tried to debug ace, i.e. I went through ace until just before

Good morning, I have succesfully buil ovirt on fedora 11 but running ace -d l /tmp/ace.log install ovirt I got en error (I think it is krb5 issue). My server was not a kerberos server before installing ovirt, so I think ace procedure has installed it. Attacchede here there is the ace.log file. Could anyone help me ? Thanks & Regards Ignazio -------------- next part -------------- A non-text

Call us on +91-9666 4000 48 - Mobiles <http://www.fosila.com/mobiles> - Cameras <http://www.fosila.com/cameras> - Laptops <http://www.fosila.com/laptops> - Bags <http://www.fosila.com/bags> - Watches <http://www.fosila.com/watches> - Toys <http://www.fosila.com/TeddyBears> Dear *User*, Unbelievable offer Limited stock. Grab it!! Samsung

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.

I found the old ace function (from acepack) valuable a couple of years ago in helping to find a transformation of the response to approximate additivity in smooth functions of the predictors. ace used alternating conditional expectations, but I'm not overly fixated on algorithms as long as it works pretty well. Is there another package that has that sort of functionality? I haven't been