search for: pgls

Hi there, > > I am using the function pgls in the CAPER package, everything seems to run > fine except for one of my variables. > When using this variable as continuous the anova works without problem, > but if using the same variable as factor (in fact, this is what it is), the > program returns this answer: > > Error in...

...ist 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/toy.R with the tree http://iktp.tu-dresden.de/~prudent/Divers/R/toy3.tree and the data http://iktp.tu-dresden.de/~prudent/Divers/R/toy_cor100.data just copy the .tree and .data files and...

Hello, I'm doing a comparative analysis of mammal brain and body size data. I'm following Charlie Nunn and Natalie Cooper's instructions for "Running PGLS in R using caper". I run into the following error when I create my comparative dataset, combining my phylogenetic tree (mammaltree) and taxon measures (mammaldata): "Error in phy$node.label[which(newNb > 0) - Ntip] : only 0's may be mixed with negative subscripts" My full s...

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 t...

...owing phylogenetic analyses with the caper package: data=read.table(file="data.txt",header=T,sep="\t") tree = read.nexus("Tree.nex") primate = comparative.data(phy=tree, data=data,              names.col=Species, vcv=TRUE, na.omit=FALSE, warn.dropped=TRUE) PGLM_brain=pgls(ln_brain~ln_body,data=primate, lambda="ML")     summary(PGLM_brain) Now I would like the get the phylogenetic residuals of this model, which I should be able to do with the phyres function: resbrain=phyres(PGLM_brain) But then I get the following error message: Error: could not find f...

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

...optimization algorithms based on a simplex. The optimsimplex package may be used in the following optimization methods: the simplex method of Spendley et al., the method of Nelder and Mead, Box's algorithm for constrained optimization, the multi-dimensional search by Torczon, etc... * pGLS (0.0-1) Xianyun Mao http://crantastic.org/packages/pGLS Based on the Generalized Least Square model for comparative Phylogenetics (ref). * plgp (1.0) Robert B. Gramacy http://crantastic.org/packages/plgp Sequential Monte Carlo inference for fully Bayesian Gaussian process (GP) re...