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

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] 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] 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] 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] 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] 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] 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] 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