search for: phylogenies

Hi all, I'm hoping I might be able to get some help with some issues specifying priors for MCMCglmm. I'm trying to fit a gaussian glmm using MCMCglmm to a data set with two (correlated) response variables. The response variables are both logit-transformed proportions (there are a few reasons why I've chosen these with gaussian error over binomal glmm, which I won't go into).

Buenos dias para todos, Estoy trabajando en una aplicación que involucra análisis de clusters. Básicamente el objetivo es determinar a qué cluster pertenece cada observación de una matriz de datos "mydata" y luego generar muestras aleatorias de los mismos datos para determinar la proporción de veces que cada observación es clasificada en el cluster k. Este tipo de análisis es muy común

Hello Everyone, I would like to know if I can call one of the columns of a list, to use it as a variable in a function. Thanks in advance for any advice! Jana -- Jana Makedonska, B.Sc. Biology, Universite Paul Sabatier Toulouse III M.Sc. Paleontology, Paleobiology and Phylogeny, Universite de Montpellier II Ph.D. candidate in Physical Anthropology and Part-time lecturer Department of

Dear all, I'm testing the effect of species and sex in my sample by using the principal component scores of a PCA analysis. I have 30 PCs and I tried to see if there is any significant difference from males to females, given that there is a significant effect of phylogeny (factor with several species). I didi it like this: Y<-PCA$pc.scores[,1:30] fit <- manova(Y ~ sp*sex)

Hi, I'm attempting a comparative analysis using the function compare.gee, package (ape), which uses phylogeny as a correlation matrix in gee (package gee), in R version 2.2.0 on a Windows XP PC. I'm looking to model the relationship between a continuous explanatory variable and a binary response variable for 600 species, taking into account the phylogeny of those species. Here's

Hi, I'm interested in using pbtree (package phytools) to simulate a phylogeny, but would first like to understand how the simulation works (i.e. when does a split occur and how is the split chosen?). Can anyone point me to the model that is used? Thank you! [[alternative HTML version deleted]]

Hi Everyone, I am working with the R function "dataEllipse". I plot the 95% confidence ellipses for several different samples in the same plot and I color-code the ellipse of each sample, but I do not know how to specify a different line pattern for each ellipse. I can only modify the pattern for all ellipses with the "lty" argument. Any help will be highly appreciated.

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 Sergio Doing those tests 30 times is going to give you a huge Type I error rate, even if there was a function that did that. There is a reason why TukeyHSD doesn't make it easy. In general, if there are useful comparisons among the species, you are better off setting up and testing contrasts than doing all-pairwise Tukey tests. Also, the PCA scores are ordered in terms of variance

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 available. The most important change is that the

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 available. The most important change is that the

Full_Name: Emily Green Version: 2.8.0 GUI 1.26 OS: MacBrook Pro with 2.5 GHz processor, using Mac OS X 10.5.5 Submission from: (NULL) (144.32.69.137) I am wanting to correct for phylogeny using a phylogenetic tree of 296 birds species, which I have constructed myself. The file format is correct and I have checked its display in Mesquite, which exported the nexus file (I've pasted the text of

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

Dear R experts, I hope this is the right list for my question. As a newcomer in R, I am testing the R CAPER package, applying a simple regression on a phylogeny tree with three binary traits: (t1, t2, t3). My goal is to test the sensitivity to a correlation between t1 and t3. But if a correlation of 100% is considered (i.e. t3 = t1). The pgls method of CAPER seems to crash: You can find there

Hello, I've been trying to figure out how to access the individual elements from an object of class phylo. I am reading in 201 trees created by paup as below. > read.nexus("A_30knj_200t.txt", tree.names= NULL) -> anj30 > anj30[1] $tree1 $edge [,1] [,2] [1,] "-1" "-2" [2,] "-2" "-3" [3,] "-3" "1"

Hi, I'm a newbie to R package submission. I've written a program using basic functions inside R to manipulate phylogeny tree data. I've relied on the APE package. After almost year of working on it, it's time for me to submit the package and I have very little time to rewrite it as S3/4 style unless it is required. It's just very basic at the moment with 30+ functions and

Hi R helpers, I was wondering if anybody knows if is possible to generate bootstrap values for a cluster analysis in R. What I am trying to do is obtain some confidence on the clusters formed by resampling the data set. A similar type of analysis is used in molecular taxonomy and the confidence values of each cluster are placed in the nodes of the dendogram. Any ideas on how to do this

Dear List, I'm trying to interpret the results of the Kruskal's Non-metric Multidimensional Scaling algorithm (isoMDS, MASS package). The 'goodness of fit' is reported as "The final stress achieved (in percent)". What does this mean exactly? I've tried to google for an answer but I've not come up with a definitive answer. Regards, Dieter -- Dieter Vanderelst

I have a host-parasite association matrix in which parasite species are rows and host species columns and cells contain the frequency of interactions. Some parasites are associated with many hosts, and some hosts harbor several parasites, and I want to repeatedly select only one single representative host per "generalized" (multi-host) parasite to create a new matrix in which no hosts

CRAN (and crantastic) updates this week New packages ------------ * allan (1.0) Alan Lee http://crantastic.org/packages/allan Automates Large Linear Analysis Model Fitting * andrews (1.0) Jaroslav Myslivec http://crantastic.org/packages/andrews Andrews curves for visualization of multidimensional data * anesrake (0.3) Josh Pasek http://crantastic.org/packages/anesrake This