This repository contains tutorials structured in 7 different lectures that gives examples of application of phylogenetic comparative methods in the statistical software R.
I would like to thank people that share their own tutorials on the web. I have consulted many of them over the years and they have been important my understanding of comparative methods and for the developpement of these tutorials. I thank Liam Revell, Samantha Price, Brian O'Meara, and many others...
There are several ways you could use the material. You could for example download the whole folder by choosing the download zip option. But it is perhaps more interesting to fork the repository (you will need to create an account on github) and then clone your new forked repository on your desktop (you will have to browse the help pages of githup to get started). This will take longer to set-up, but it will give you the opportunity to automatically recieve updates when the tutorials get modified (which might well happen) and even propose modifications to the tutorials if you find mistakes or to propose new analyses.
Introduction to phylogenies in R
The Brownian Motion (BM) model, Phylogenetic Independent Contrasts (PIC), Phylogenetic General Least Squares (PGLS), Phylogenetic Principal Component Analysis (pPCA).
Phylogenetic Comparative Methods
Reading and making phylogenetic trees in R
Reconstruction of ancestral states on phylogenies for quantitative and qualitative (discrete) characters, marginal vs joint estimation, model selection, stochastic character mapping.
Ancestral states reconstruction
Bayesian reconstruction of ancestral states using BayesTraits, Testing the correlated evolution of discrete traits, Markov chain Monte Carlo (MCMC) analyses, MCMC chain convergence.
Ornstein-Uhlenbeck (OU) model, Early-Burst model, Speciational model, Simulating data under different evolutionary models, OU models with multiple selection regimes, Accounting for phylogenetic uncertainty.
Phylogenetic signal (Moran's I, Abouheif's c, Pagel's lambda, Blomberg's K, Moran's I correlograms); Phylogenetic diversity; Evolutionary distinctiveness; phylogenetic beta-diversity; Parametric bootstrapping; Phylogenies in community ecology.
Lineage through-time (ltt) plots; diversification rate estimation; Yule and Birth-and-death models; Diversification through time (dtt) plots; Trait dependent speciaton and extinction (BISSE model).
Paradis, E. 2012. Analysis of Phylogenetics and Evolution with R. Springer: New York. (available in pdf)
Bodega's applied phylogenetic workshop website: Tree thinkers
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