search for: phylogeny

...es. 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). Each probability represents a response for a single plant species (c.150 species), and I want to incorporate the phylogeny (almost fully resolved with only 2 polytomies, including branch lengths) in the error structure. There is only 1 explanatory variable, a 5-level factor. I'm using uninformative priors for fixed parameters (i.e. not specifying any priors). Here's my code: #prior model1 prior1<-list(R...

...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 en aplicaciones de Phylogeny < http://en.wikipedia.org/wiki/Phylogeny> Suponiendo que el método de cluster a utilizar es fijo y que de alguna manera se determinó que el número de clusters óptimo, conocen alguna libreria en R que permita hacer lo que describo? Este es un ejemplo en R en el que utilizo ksmeans y 7 cluste...

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 Anthropology College of Arts & Sciences State University of New York at Albany 1400 Washington Avenue 12222 Albany, NY Office phone: 518-442-4699 http://electricsongs.academia.edu/JanaMak...

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) summary(fit, test="Wilks") I get a barely significant p-value for the effect of sex and I'd like to know for which of the species there is a difference between males and...

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 an example of...

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]]

...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. Thanks in advance! 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 Anthropology College of Arts & Sciences State University of New York at Albany 1400 Washington Avenue 12222 Albany, NY Office phone: 518-442-4699 http://electricsongs.academia.edu/JanaMak...

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, speci...

...doso wrote: > 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) > summary(fit, test="Wilks") > > I get a barely significant p-value for the effect of sex and I'd like to know for which of the species there is a...

...tip species) instead of quadratic time. Furthermore, as there is no need to store the between-species-between-traits variance covariance matrix much larger clades, then previously can be handled. From the user's perspective the main changes are the interface and increased functionality: a) the phylogeny has to be now in the phylo (instead of ouch) format, b) the trait data has to be a matrix (and not a data frame), c) the package can automatically compare multiple models (BM, OUOU, OUBM and different assumed structures on the drift and diffusion matrices of the multivariate OU procees), function...

...tip species) instead of quadratic time. Furthermore, as there is no need to store the between-species-between-traits variance covariance matrix much larger clades, then previously can be handled. From the user's perspective the main changes are the interface and increased functionality: a) the phylogeny has to be now in the phylo (instead of ouch) format, b) the trait data has to be a matrix (and not a data frame), c) the package can automatically compare multiple models (BM, OUOU, OUBM and different assumed structures on the drift and diffusion matrices of the multivariate OU procees), function...

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 the file at the end of this message, the matrices are purposefully blank). As a text fil...

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 the code I used http://iktp.tu-dresden.de/~prudent/Divers/R/to...

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 there's a driver class. Ther...

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

...ign and a case-control design. Functions in this packages provides Monte Carlo based evaluation of operating characteristics such as powers for estimators of the components of a logistic regression model. * TreePar (1.0) Tanja Stadler http://crantastic.org/packages/TreePar For a given phylogeny on present day data (e.g. species or viruses), a likelihood method is provided where the maximum likelihood speciation and extinction rates are estimated. The method accounts for rate changes and mass extinction events: Time is split into intervals, and in each interval, the rates can be di...