Using R for phylogenetics and phylogeography
R offers a great and steadily growing capacity for analysing phylogenetic data (see Taskview on r-phylo.org).
Here, I present some additional collections of functions, which provide some functionalities that I could not find elsewhere.
LAGOPUS: Bayesian relaxed clock dating with the multidivtime method
R package developed together with my collegue Natalie Cusimano. See the LAGOPUS website for more information.
PHYLOCLIM: phyloclimatic modelling in R
- Predicted niche occupancy (PNO) profiles sensu Evans et al. 2009. Am. Nat. 137: 225-240.
- Quantification of niche overlap from PNOs and ENMs
- Niche equivalency and background similarity test with MAXENT after Warren et al. 2008. Evolution. 62: 2868-2883.
- Age-range/niche overlap correlation
- Estimation of ancestral climatic tolerances sensu Evans et al. 2009. Am. Nat. 137: 225-240.
This version contains a bug fix in age.range.correlation and adopts changes in the raster package (see ChangeLog of the package source).
PHYLOCH: interfaces and graphic tools for phylogenetic data in R
- Reading and writing of DNA sequences in FASTA, PHYLIP, and NEXUS files
- Concatenation of DNA sequence alignments
- Calling MAFFT or PRANK for sequence alignment
- Calling GBLOCKS or ALISCORE for elimination of poorly aligned sites from sequence alignments
- Chi-square test for homogeneity of base frequencies
- Calling RAxML for ML tree search
- Parsing NEXUS tree files from Bayesian analyses (TreeAnnotator/BEAST and MrBayes)
- Plotting error bars on phylogenetic trees
- Plotting support values on phylogenetic trees
- Drawing shaded and non-shaded colored boxes around clades in phylogenetic trees
- Plotting clade summary bars with text, piecharts, etc ... on phylogenetic trees
- Plotting geolocial and user-defined timescales on time-calibrated phylogenetic trees
- Plotting trendlines for some environmental variables on time-calibrated phylogenetic trees
- Wrappers for Multistate (BayesTraits package by M. Pagel and A. Meade)
