0. caper - Comparative Analysis package- The Comparative Analyses of Phylogenetics and Evolution in R (caper) package implements a range of methods for the comparative analysis of taxa including methods based on phylogenetic independent contrasts and phylogenetically corrected linear models.
1. RMesquite- RMesquite establishes interoperability between Mesquite (http://mesquiteproject.org) and R. It exposes Mesquite methods transparently as R functions that consume and provide native R data types, and converts seamlessly between Java and R data types.
4. Continuous Character Transitions- maticce: Mapping Transitions In Continuous Character Evolution
This project provides tools for an information-theoretic approach to estimating the probability of continuous character transitions on phylogenetic trees.
6. BayesSDEmacroevolution- The purpose of this project is to provide a focus for developing methods for analysing biological macroevolution of traits, using nonGaussian diffusion stochastic differential equation models. We plan to take a Bayesian approach to the problem.
9. Analysis of Independent Contrasts- The CAIC package provides methods for the comparative analysis of taxa using independent contrasts methods. It reimplements the methods of the CAIC and MacroCAIC programs will implement alternative methods such as those provided in LDAP.
10. SPecies' LImits by Threshold Statistics- splits contains tools for delimiting species and automated taxonomy at many levels of biological organization (eg. DNA barcoding, morphometrics), top-down (merging phylogenetic and phylogeographic methods) and bottom-up (single samples into >1 groups).
11. paleoPhylo- 'paleoPhylo' will contain tools to assess how speciation, extinction & character change contribute to biodiversity. Currently it features graphical tools to draw phylogenies with time axes and ancestors that persist after speciation.