search for: aping

Displaying 20 results from an estimated 222 matches for "aping".

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2011 Oct 18
1
How to read data sequentially into R (line by line)?
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 over 14 000 000 records. Now
2006 Dec 22
1
ape-package
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
2004 Feb 08
1
APE: compar.gee( )
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,
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
2013 Jun 05
1
conflicting imports despite using importFrom in NAMESPACE
Dear all, It is my understanding that using 'importFrom' in the NAMESPACE of a package allows to 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'
2007 Apr 25
1
heatmap and phylogram / dendogram ploting problem, ape package
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
2003 Dec 29
1
installing packages on MAC os X
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
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.
2007 Oct 10
2
Rooting trees using ape
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. >
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
2016 Sep 06
2
Re: systemctl libvirt-guests.service fails to start during host boot
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
2007 Nov 12
3
help on drawing a tree with "ape"?
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
2002 Sep 05
0
ape 0.1 is released
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
2006 Oct 17
1
ape -- internal nodes and pie charts
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.
2020 Nov 06
1
Centos 8 and xfs_quota
Folks I'm trying to use xfs_quota to keep track of disk space usage for my users. The documentation states that I should specify "uquota" as an option on the mount data in /etc/fstab. Yet, I cannot find the entry in fstab that corresponds to the Logical Volume that ends up being mounted on /home1. The system in question was installed on a single disk system. Later, after
2010 Feb 23
1
[LLVMdev] LLVM porting Plan9 (probably stupid question)
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
2016 Sep 15
0
Re: systemctl libvirt-guests.service fails to start during host boot
Hi Andrea, > Since you're running an Arch variant, I'm going to assume > all your software is basically at the latest version all > around, isn't it? Yep exactly, all software / kernel are in latest version > Can you try adding > > [Unit] > Requires=libvirtd.service > > to your libvirt-guests.service via 'systemctl edit' and > see if it
2008 Jan 04
1
Howto write a mongrel handler for a CGI app using CGIWrapper
Hello, Just for further reference in case of someone else want to do the same : I wanted to write a mongrel for a CGI app : [[[ require ''cgi'' require ''foo'' cgi = CGI.new if !cgi[''uri''] || (cgi[''uri''] == '''') Foo.error "URI argument is required" end uri = cgi[''uri''] user =
2012 Apr 17
2
Error with Rcmd check library --as-cran
Hello all, I was checking the newest update of my library before submitting it to CRAN, using R 2.15.0 and Rtools for Windows 215 using Rcmd in the Command Prompt, on my x64 Windows7 laptop. I recently heard that for checking packages for CRAN submission one should use the option --as-cran; previously I was submitting packages, so I was trying that for the first time. The check proceeds fine
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