similar to: Binary Tree Testing in "ape" package (a bug?)

Dear list, I am trying to replace Unicode notation of German and Spanish special characters (as read in by read.csv from excel spreadsheets) by character strings that can be interpreted by LaTeX. E.g.: uni2latex <- function(x){ x <- gsub("&", "et", x, fixed = TRUE) # Deutsch x <- gsub("\u0080", "\\\"A", x, fixed = TRUE) x

Hello, anybody know the procedure to plot the geneland result in a map? thank you ********************************************************** Vincenzo Landi Post Doctorate student Animal genomic and breeding cell:0039/3395388713 Fax. 075-5857122 [[alternative HTML version deleted]]

Hi Wondering if anyone knows of a package that does Nested Clade Analysis? Thanks -- View this message in context: http://www.nabble.com/Nested-Clade-Analysis-tp20637180p20637180.html Sent from the R help mailing list archive at Nabble.com.

Dear list, After searching many old posts, I can't find the solution to a simple problem. can someone tell me how to create a character string with multiple backslashes, as in: file_dir <- c("C:\files\data\") I need to create this string and then paste it to many files names for batch processing in another software program. R won't accept the backslash and removes

Dear list, I want to run latex from an R script: system("latex mysource.tex") or: texi2dvi("mysource.tex", pdf = TRUE, clean = FALSE, quiet = TRUE, texi2dvi = latex) but latex does not seem to be on the search path: /bin/sh: line 1: latex: command not found. Although 'printenv PATH' tells me that the usr/texbin is looked for executables:

I do the these passages: library(Geneland) set.seed(1) data <- simdata(nindiv=200, coord.lim=c(0,1,0,1) , number.nuclei=5 , allele.numbers=rep(10,20), IBD=FALSE, npop=2, give.tess.grid=FALSE) geno <- data$genotypes coord <- t(data$coord.indiv) path.mcmc <-

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'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'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

Hi, It's unfortunate that with recent revisions of R 2.13 (this appeared in revision 54640, March 2), 'R CMD build' now removes empty dirs in the package. People might have good reasons for having empty dirs in their packages. For example, in Bioconductor, we have some tools to automatically generate annotation packages and those tools are implemented in software packages that use

Hi list, The function is.integer tests if an object is of type integer: see e.g.: is.integer(12) # FALSE is.real(12) # TRUE mode(12) # "numeric" But how can I test if a number is actually an integer? R seek is difficult to search in this case because it mainly yields entries about the integer()-function family. Thanks for any hint! Christoph Heibl

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

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

Hello, This must be simple... Thanks a lot - Christoph # Imagine you have a list, e.g: K <- list(1:10, 2:11, 9:18) K # Transforming to dataframe... KK <- as.data.frame(K) # ... one obtaines the list elements as column. KK # But I need the list elements as rows # How can I achieve this? Is there a simple way to transpose data.frames?

i've just lost $2000 dollars or so on my first commercial asterisk installation .. i'm running a PIV class server, three Digium Wildcard FXO cards, and 10 Grandstream Budgettone SIP phones. The system was to be a PBX for a small company. After over 2 months of pissing about, the client has had his fill of asterisk problems, and asked me to take my equipment out of the building. Obviously,

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

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.

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,

Hi all, I seem to be having a difficult time using the 'ape' package in R when it comes to rooting trees. Here's a short screenshot: > nirK.tree Phylogenetic tree with 23 tips and 21 internal nodes. Tip labels: Burkholder, Burkholde3, Burkholde1, Burkholde4, Burkholde5, Ralstonia2, ... Node labels: , 100, 100, 100, 70, 91,... Unooted; includes branch lengths. >

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 <-