search for: phylogenetic

Hi, I'm trying to build a mixed-effects model in which I'd like to include either a distance matrix or a phylogenetic tree as a random effect. The troubles I've had are that: 1. Function lmer() in package lme4 only accepts a data frame column as a random factor and not a distance matrix. 2. Function MCMCglmm() in package MCMCglmm only accepts a rooted and ultrametric phylogenetic tree as a pedigree argument...

Can you recommend an R library that will help me create a diagram of a phylogenetic tree on which specific images are placed at appropriate nodes of the tree? For example, I have specific image files associated with each member of the phylogenetic tree, and I would like to automate the display of the image next to the correct node of the tree. I can provide an image file with...

Hello, Is it possible to include information about phylogenetic relatedness among species (when species are replicates for each study within a meta-analysis) in a meta-anlaysis in the metafor package? Alternatively, I wonder if the method f Lajeunesse 2009 American Naturalist has been adopted in R in any fashion? Thanks, Scott Chamberlain [[alternative HTML...

Hi I am looking for a package that 1. reads in a phylogenetic tree in NEXUS format 2. given two members/nodes on the tree, can return the distance between the two using the tree. I came across the following packages on CRAN ouch, ape, apTreeShape, phylgr all of which seem to provide extensive range of functions for reading in a Nexus-format tree and performi...

Dear all, I wanted to let you know about four phylogenetic comparative methods (PCM) packages that have become available on (3 on CRAN and 1 on GitHub) recently that hopefully will be interesting to somebody. Three of them go significantly beyond the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes. 1) There is a new version of mvSLOUCH availabl...

Dear all, I wanted to let you know about four phylogenetic comparative methods (PCM) packages that have become available on (3 on CRAN and 1 on GitHub) recently that hopefully will be interesting to somebody. Three of them go significantly beyond the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes. 1) There is a new version of mvSLOUCH availabl...

Hello, I am trying to carry out a phylogenetic autoregression to test whether my data show a phylogenetic signal, but I keep calculating bizzare R-squared values. My script is: > library(ape) > x <- "((((((((R:1,GK:1)d:1,(MW:1,G:1)n:1)a:1,SPW:1)a:1,WB:1)b:1,(((SPBF:1,PBF:1)n:1,(HBF:1,SWF:1)c:1)i:1,(PE:1,((P:1,C:1)w:1,(MF:1,HF:1...

Dear all, I would like to ask you the following: I have data about different manuscripts, together with data about the presence/absence of copying errors, in the days when manuscript were really manuscripts. I would ideally like to use the data to draw a phylogenetic tree, so that I can infer which ms was copied from which. The error presence/absence is coded in binary format. The plan is to use a maximun parsimony tree approach. The data looks like this toy example: "ms1" "ms2" "ms3" "ms4" "err1"...

Hello, My name is Sivan and I am a master degree student in statistics,my problem is as follows: I have a dataset containing gene sequences and I would like to create a phylogenetic tree from it. The problem that I can't seem to find a function to do this kind of operation. I read the ape package manual and I haven't found a command that takes raw data and turns it into a tree. does anyone know if such a command exist? thank you in advance, sivan [[alternative HTML ve...

Hello R users, Can any one please help me to find a way to build phylogenetic tree by R program from any distance matrix. Suppose I have a data like : MATRIX [1] '1' 0.0 [2] '2' 0.071 0.0 [3] '3' 0.036 0.286 0.0 [4] '4' 0.429 0.75 0.714 0.0 [5] '5' 0.679 0.179 0.214 0.536 0.0 [6] '6' 0.893 0.929 0.964 0.464 0.35...

...herneau (In general I agree with Bert & Ben to try the other list, but I don't happen to read it.) On 06/04/2013 05:00 AM, r-help-request at r-project.org wrote: > Hi, > I'm trying to build a mixed-effects model in which I'd like to include > either a distance matrix or a phylogenetic tree as a random effect. > The troubles I've had are that: > 1. Function lmer() in package lme4 only accepts a data frame column as a > random factor and not a distance matrix. > 2. Function MCMCglmm() in package MCMCglmm only accepts a rooted and > ultrametric phylogenetic tree...

Hello, I would like to place shaded boxes on different areas of a phylogenetic tree plot. Since I can not determine how to find axes on the phylogenetic tree plot I am not able to place the box over certain areas. Below is example code for the shaded box that I have tried to use, and the first four values specify the position. rect(110, 400, 135, 450, col="grey", b...

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 am trying to import a phylogenetic tree from Mesquite into R. When I use the read.nexus command I get the following message: Warning message: In matrix(x, ncol = 2, byrow = TRUE) : data length [589] is not a sub-multiple or multiple of the number of rows [295] A phylo object is created but I am unable to plot it (when I try R f...

...fail.default(list(Phenology = c(NA_integer_, NA_integer_, : missing values in object" I'm having trouble navigating around this error message, and any suggestions would be appreciated. Thanks! Rose -- View this message in context: http://r.789695.n4.nabble.com/Model-Selection-with-Phylogenetic-Independent-Contrasts-tp3814652p3814652.html Sent from the R help mailing list archive at Nabble.com.

Hi all, I want to calculate distances between phylogenetic trees. I found functions for symmetric difference (e.g. in ape and in some other packages). In addition to this I also want to calculate quartets and nearest neighbor interchange distances; are there any functions for this? My apologies if they exist and I overlooked. best regards

...other hosts. PRIMARY RESPONSIBILITIES The position is funded by a National Institutes of Health NIAID award to discover, characterize, and model the risk of new potential zoonoses from bats. The primary focus of the Research Fellow will be to model the risk of spillover, patterns of infection, co-phylogenetic and phylogenetic relationships, and phylodynamics of emerging zoonotic diseases from bats. Research will be focused on viruses and applying phylogenetic and comparative analyses to existing models and data, including a large number of newly discovered viruses. The position may involve some fieldwor...

Dear all I have undertaken some phylogenetic and non-phylogenetic regressions with gls() in nlme with single preictor variables. A p value is associated with the intercept (upper p value) and another with the predictor variable (lower). Which p value is important? What does it mean if the intercept p value is insignificant but the predictor i...

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

Dear moderator, If possible I would like to send in the following question for R-help: I am analyzing a small data set using PGLS with phylogenetic uncertainty taken into account and thereby including 100 potential phylogenetic tree scenarios. I've managed to run models on all of the different trees and performed model averaging to get parameter estimates for the intercept and most of the predictor variable slopes using the *AICcmodavg* pa...