Re: [R-sig-phylo] test correlated evolution using two phylogenies?(consumerresource)

Hi Mick, I am not entirely sure of the best approach to analyze your data, but here are a few comments (IN CAPS): Dear r sig phylo users, I am doing a phylogenetic comparative analysis of (quantitative) foraging behaviour and body size ratio between consumers resources, and am not sure how

Re: [R-sig-phylo] Simulate continuous character evolution on phylogenetictrees using different models of evolution

Hi Christian, try the function shown below (an example follows). Everybody else is welcome to give it a try and diagnose if everything works fine (which seems to be the case as far as I am aware). Cheers, Enrico 'cor.brown' -

Re: [R-sig-phylo] PIC vs. PGLS

Hi everybody, I am able replicate the results of independent contrasts and PGLS employing R (mapping the intercept to the phylogenetic means). I also recall comparing results of PDAP employing a star phylogeny against a regular regression in SPSS for Windows. And as far as I can tell, this

Re: [R-sig-phylo] fitContinuous running for days

Manuela and David, perhaps you want to try the OU-transformation syntax I wrote to translate the MATLAB code developed by Blomberg, Ives Garland. It works well with small phylogenies, I never tried it in large ones and am actually curious to see what would be the outcome. You will find the

Re: [R-sig-phylo] PICs in non-ultrametric trees

Hi Peter, the non-standardized contrasts tells you how much sister lineages differ phenotypically (i.e., phenotype lineage A - phenotype lineage B) during the computation of contrasts (assumptions of brownian motion, etc). When you standardize them, you are dividing this difference by the

Re: [R-sig-phylo] K for discrete unordered traits

Hi Stacey, you can try this function, which is analogous to Blomberg's K for discrete traits and follows Maddison Slatkin 1991. An example is available at the bottom of the syntax. Cheers, Enrico ## Function phylo.signal.disc

Re: [R-sig-phylo] Dealing with Bounded Trait Measures

David, on the top of my head, if no species measurement strictly corresponds to zero, you may log-transform the data. You may then simulate Brownian motion in log-transformed values, which will correspond to a boundary of zero in a linear scale (i.e., the more negative the log number, the

Re: [R-sig-phylo] Comparing means under a phylogenetic perspective?

Rafael, a phylogenetic paired t-test should do the job. Please check this reference: Lindenfors P, Revell LJ, and Nunn CL. Sexual dimorphism in primate aerobic capacity: a phylogenetic test. J Evolution Biol 23: 1183-1194, 2010. Liam, any comments on this? Enrico Rafael Maia escribió:

Re: [R-sig-phylo] Normality requirement for assessment of lambda withphylosig (phytools) and fitContinuous (geiger)

Complementing Ted's comment, the randomization test in Blomberg et al. (2003) and the K statistics is available the package picante. Now, caution is warranted because having many species with the same phenotypic value in the dataset (i.e., many zeros) can dramatically decrease the statistical