search for: ape

I have a data set like this in one .txt file (cols separated by !): APE!KKU!684! APE!VAL!! APE!UASU!! APE!PLA!1! APE!E!10! APE!TPVA!17122009! APE!STAP!1! GG!KK!KK! APE!KKU!684! APE!VAL!! APE!UASU!! APE!PLA!1! APE!E!10! APE!TPVA!17122009! APE!STAP!1! GG!KK!KK! APE!KKU!684! APE!VAL!! APE!UASU!! APE!PLA!1! APE!E!10! APE!TPVA!17122009! APE!STAP!1! GG!KK!KK! it contains ov...

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 '/usr/lib/R/library/ape' What to do with this and ho...

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, fa...

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...

...o avoid conflicts between different packages defining objects with identical names. However, I can still see conflicts while loading the package using 'library'. Here is a toy example, with a package 'foo' importing 'as.igraph' from the igraph package, and 'nj' from ape. 'foo' uses the following DESCRIPTION file: ---------------------- Package: foo Version: 0.0-0 Date: 2013/06/04 Title: foo Author: John Doe Maintainer: John Doe <jdoe at nowhere.org> Imports: igraph, ape Description: just a test. License: GPL (>=2) LazyLoad: yes -----------------...

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 a heatma...

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 'lib' is missing: using ~/Library/R...

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...

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...

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 (val...

On Thu, 2016-08-11 at 20:41 +0200, Benoit wrote: > Thanks Andrea, >  > Yes I confirm to you that I have enabled libvirt as well. >  > I don't see any error right now but I have to investigate a little bit more. >  > My guests are in autostart in virsh so everything is fine on this, the  > only issue I got is in case of shutdown. >  > The strange thing is that

Dear all, I'm using the "ape" package in R and want to draw a phylogenetic tree with not only the tip labels but also some labels for the edges. e.g. Mark the edge AB as "m" in the tree ABC. Couldn't find a way to do that. Can someone help? Thanks, Hua

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...

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.

...gle disk system. Later, after install, I added a second disk, created a Logical Volume on it, and mounted it as /home1, where all the user data gets stored. It holds an xfs file system. Upon examining /etc/fstab, there's no evidence of the second disk, yet it does get mounted: [root at ape ~]# cat /etc/fstab # # /etc/fstab # Created by anaconda on Fri May 1 21:05:38 2020 # # Accessible filesystems, by reference, are maintained under '/dev/disk/'. # See man pages fstab(5), findfs(8), mount(8) and/or blkid(8) for more info. # # After editing this file, run 'systemctl daem...

I am not sure whether this would work or if there are other limitations that would block this very simplistic porting strategy to work. Since it looks so easy on paper, I expect it to be more complicated otherwise it would probably already have been done. According to the LLVM FAQ the important dependencies for LLVM are a unix-type shell and sed [1], but those dependencies are provided by APE [4]. (according the the Plan9 mailing list there are issues with C+...

...I start again, and try to do a systemctl status libvirt-guests.service, I got the same FAILED status as before.... I made a research on my logs : Sep 15 17:39:29 libvirt-guests.sh[1164]: Shutting down guests on default URI... Sep 15 17:39:29 libvirt-guests.sh[1164]: Starting shutdown on guest: ape Sep 15 17:39:30 libvirt-guests.sh[1164]: Waiting for guest ape to shut down, 30 seconds left Sep 15 17:39:35 libvirt-guests.sh[1164]: Waiting for guest ape to shut down, 25 seconds left Sep 15 17:39:36 libvirtd[326]: internal error: End of file from monitor Sep 15 17:39:36 libvirtd[326]: Cannot w...

...;') response.start(200, true) do |header, body| Foo.error("URI argument is required", output=body) end end format = request.params[''HTTP_ACCEPT''] == ''text/plain'' ? ''text'' : ''html'' ape = Ape.new({ :crumbs => true, :output => format }) if cgi[''user''] && cgi[''pass''] ape.check(cgi[''uri''], cgi[''user''], cgi[''pass'']) else ape.check(cgi[''uri''])...

...roduces the following error message: > pkgname <- "paleotree" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > options(pager = "console") > library('paleotree') Loading required package: ape Error in loadNamespace(i, c(lib.loc, .libPaths())) : there is no package called 'Matrix' Error: package/namespace load failed for 'paleotree' Execution halted My package depends on ape, but not Matrix. Matrix is installed, though, on my workstation, as are the other ape dependenc...

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. Emm...