similar to: help with ancestral.pars in phangorn package

Hi, I'm trying to calculate a ratematrix for a RNA aligment (U instead of T) in order to use it as a ratematrix in Profidst (a phylogenetic program which takes into account both the primary sequence and the secondary structure of the RNA, in my case rRNA). The sequence-structure aligment has been made in 4SALE (a java app) and saved as one-letter encoded (using a 12 letters alphabet,

Hello, I am trying to get Personal Ancestral File (which is free Genealogy software from The Church of Latter Day Saints) to run with wine. I have tried configuring wine in different ways following different suggestions in the HOWTOs and Wine user guides with varying results. I have also tried installing the software using Wine rather than just running the windows-installed program.

Dear R-helpers and Klaus, I would like to know how to write out a tree file with bootstrap from phangorn package. That tree file could be in newick format or others. I am new for phylogenetic operation in R. Could you please give me any directions on that? Thanks in advance. Best wishes, Jian-Feng, ######## # as a example # I accomplished 1000 bootstrap simulation on a fit object (a maximum

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

Hi All, is there any chance of vectorising the two ifelse() statements in the following code: for(i in gp){ new[i,1] = ifelse(srow[i]>0, new[srow[i],zippo[i]], sample(1:100, 1, prob =Y1, rep = T)) new[i,2] = ifelse(drow[i]>0, new[drow[i]>0,zappo[i]], sample(1:100, 1, prob =Y1, rep = T)) } Where I am forced to check if the value of drow and srow are >0 for each line... in

I'm running Personal Ancestral File (PAF) 5.2 under Wine 0.9.26, and it defaults to the bizarre "Captain Podd" font as its default screen and print font. It appears there are no knobs or registry entries to override this default font for some things when printing. My Wine is compiled from source to include the patch fix for bug #5669 (unrelated to fonts and printing). I'm

Hello, I managed to install playwith package and all its prerequisites. My R version is R 2.14: R version 2.14.1 (2011-12-22) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i486-pc-linux-gnu (32-bit) All my packages were updated, and recently installed. When I attempt to use the command playwith I get the following error message: >

Dear all, I have data.frame object in R. I want to export it in tab-delimited file with several lines of header initiated with comment sign (#). I do not know how to do that in R. Could you please give helps on this problem? Thanks in advance. Best, Jian-Feng, ################################################################## The lines I want to write in the header lines look like, with words

Hi, I've written a function which I load with a source command. The function requires a certain library, phangorn, to work. I would like the function to check if phangorn is loaded as a library before running. For some reason, just putting require(phangorn) into the sourced function doesn't do anything. This must be simple, but I can't figure it out! Any help appreciated...

I''m about to embark on a project and am seeking advice on my approach. I have an automotive site that needs to have shared categories. I''ve checked out different nested set, ancestral, acts_as_tree, acyclic plugins but feel they don''t exactly fit. So I am about to roll my own simple solution. Any feedback as to whether this looks good is appreciated. Essentially I

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

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 <-

Hi all, I am a phylogenetic student, I'm running SH test to examine free (tree1) and constrained (tree2) trees using R phangorn package. The outputs are like the following and i'm confused how should i interpret them!!!   Trees      ln L           Diff ln L    p-value [1,]     1 -1422.921   0.00000  0.4952 [2,]     2 -1457.282  34.36085  0.0201 Why it gives us two p values? Would you

On Wed, Jul 20, 2005 at 12:00:36PM +0000, freebsd-security-request@freebsd.org wrote: > From: Joachim Str?mbergson <watchman@ludd.ltu.se> > Subject: Adding OpenBSD sudo to the FreeBSD base system? > To: freebsd-security@freebsd.org > Message-ID: <42DCC503.5000408@ludd.ltu.se> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Aloha! > >

Hi everyone I am trying to reconstruct ancestral character states with R. I used the ace function of the package ape. I have discrete characters and tried to use the ER and ARD model. The problem is, that I get negative lik$anc values. Does anybody by chance have an idea what might be wrong? Thanks in advance [[alternative HTML version deleted]]

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

When something is assigned to an element of a vector that was previously of length 0, the vector is coerced to the mode of the something, regardless of whether the coercion is necessary under normal R rules. In particular, if NA is assigned to an element of a vector that was previously length 0, the mode of the vector is coerced to 'logical'. For example, here's the normal behaviour:

Wayne, I see you committed my man page improvements for --filter (from a long time ago) and --hard-links, except you omitted the mention of --link-dest as a second potential source of unwanted hard links among destination files (the original focus of bug 3693). You don't think this is worthy of mention? Matt

Dear colleagues, dear members of the R Core Team, This was an issue raised by Prof. Brian Ripley and sent privately to all developers of CRAN packages that suggest Bioconductor packages (see original message below). As mentioned in my message enclosed below, it was easy for me to fix the error in examples (new version not submitted to CRAN yet), but it might turn into a major effort for the

Windows 2000 R 1.4 I have a split-split plot design that I am analyzing with model <- aov(). I tried using model.tables(model) and it replied "Error: subscript out of bounds." I have monkeyed with it a little, but am wondering if this is indicative of something in particular. Thanks, Hank Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami