similar to: Help

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

Hi, I try to run the Iramuteq software with R, on Windows 7 professional (latest version of Iramuteq, and I tried with the three latest versions of R). I properly installed the packages and coded the texts, but anytime I want to run the analysis, I receive this error message : Erreur R None1 None None. Could someone help me to deal with that problem ? Thank you !!! Arthur Borriello PhD student -

Hello, I'm doing a comparative analysis of mammal brain and body size data. I'm following Charlie Nunn and Natalie Cooper's instructions for "Running PGLS in R using caper". I run into the following error when I create my comparative dataset, combining my phylogenetic tree (mammaltree) and taxon measures (mammaldata): "Error in phy$node.label[which(newNb > 0) -

Hi, all. Ubuntu host, attempting to get virsh working with VirtualBox... and failing. Here's what happens: root@foobox:~# virsh -c vbox:///session list error: failed to connect to the hypervisor error: internal error: unable to initialize VirtualBox driver API ------------------------------------------------------ Now, most of the docs I read about "failed to connect to the

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

On Mon, Oct 19, 2015 at 03:57:39PM -0400, Ken D'Ambrosio wrote: >Hi, all. Ubuntu host, attempting to get virsh working with >VirtualBox... and failing. Here's what happens: > >root@foobox:~# virsh -c vbox:///session list >error: failed to connect to the hypervisor >error: internal error: unable to initialize VirtualBox driver API > What version of VirtualBox do you

On Tue, Oct 20, 2015 at 11:59:03AM -0400, Ken D'Ambrosio wrote: >On 2015-10-20 05:33, Martin Kletzander wrote: >>On Mon, Oct 19, 2015 at 03:57:39PM -0400, Ken D'Ambrosio wrote: >>>Hi, all. Ubuntu host, attempting to get virsh working with >>>VirtualBox... and failing. Here's what happens: >>> >>>root@foobox:~# virsh -c vbox:///session list

On 2015-10-20 05:33, Martin Kletzander wrote: > On Mon, Oct 19, 2015 at 03:57:39PM -0400, Ken D'Ambrosio wrote: >> Hi, all. Ubuntu host, attempting to get virsh working with >> VirtualBox... and failing. Here's what happens: >> >> root@foobox:~# virsh -c vbox:///session list >> error: failed to connect to the hypervisor >> error: internal error:

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

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"

Hello, The following code does'nt work for me. The last command reports an error. I have created a consensus tree using the consensus comand from phylo but cannot manipulate the phylo object afterwards to create a dendogram , by transforming the phylo object into a hclust object and then into a dendogram ?? Thanks for any help library(ade4) library(cluster) library(stats) library(ape)

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<-

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

Group It's unlikely I'm trying this the best way, but I'm trying to create a data structure from elements like nNode = 2 nn = vector("list",nNode) nn[[1]] = list(Node = "1", Connect.up = c(NULL), Connect.down = c(2,3)) nn[[2]] = list(Node = "2", Connect.up = c(1), Connect.down = c(4,5)) .... #( and eventually many more nodes) NodeList =

Hi, I would be very grateful if anyone could give me a bit of help with this. I am trying to run Samba 3.0.5, as distributed with Mac OS X server 10.3.8, on an Apple Xserve. Things were working beautifully until I had problems with an IP address change and had to reinstall everything. At present, the situation seems to be that the smb protocol is operating, since I can make an smb

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

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 <-

Hi there, I am trying to interface c++ code in R and make a package. With R CMD SHLIB the dll was created, but when I try R CMD check, I am getting 'undefined reference to..' linkage error messages. The relevant c++ source from conf-infomap.cpp: #include "conf-infomap.h" #include "R.h" // R functions #include "Rinternals.h" #include "Rmath.h" //

Hi there, I'm sorry if I a send it for second time, I've just subscribed for the list. I am trying to interface c++ code in R and make a package. With R CMD SHLIB the dll was created, but when I try R CMD check, I am getting 'undefined reference to..' linkage error messages. The relevant c++ source from conf-infomap.cpp: #include "conf-infomap.h" #include

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