1. 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.
2. 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).
3. 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.
5. OMearaLab- This project hosts scripts being developed by the O'Meara lab ( http://www.brianomeara.info ), typically for use in comparative methods. This is primarily an incubator for things in a raw state (before becoming projects of their own) or one-off scripts.
6. Models of trait macroevolution on trees- The motmot (models of trait macroevolution on trees) package provides methods for testing hypotheses about the tempo of trait evolution on phylogenetic trees.
7. 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.
8. OUwie- Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck (OU) models that allow the strength of selection and drift to vary across selective regimes.
13. Phylobase Extension- This package provides classes and methods which help read/write/manipulate branch-annotated phylogenetic trees (SIMMAP-format) and supports for a few other extra phylogenetic tree features (like tree weight).
14. 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.
15. 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.