Datasets and R code
This page currently provides access to R code used in publications as well as functions that I've written that are of potentially general use. Code is commented, but no documentation is provided beyond that. Most functions are not very intuitive, as I wrote them primarily for my own use. Please feel free to contact me if you have questions about using them.
- Phylogenetic comparative analysis
- Molecular dating using the ITS clock calibrations provided in Kay et al. 2006 (BMC Evolutionary Biology 6:36), drawing node depths from a posterior distribution estimated using MCMC in BEAST conditioned on the distribution of calibrations reported by Kay et al. 2006 [R]
- Permutations and partial regression analyses used in Pearse and Hipp (in press) [Bayes trees analyses] [Mantel]
- MATICCE: mapping transitions in continuous character evoltuion [R] [PDF - vignette]
- Population genetics
- Merging AFLP datasets (already in 1/0 format) and exporting to STRUCTURE and PC-ORD [R]
- Importing microsatellite data from GeneMapper (ABI) and exporting to STRUCTURE and GenePop [R]
- Distance matrices: Nei's unbiased genetic distance [R] and the Haversine distance [R]
- Partial Mantel tests with an indefinite number of predictor matrices [R]
- Import raw ABI binary genotype output and change to 1/0 file [R]
- Miscellaneous
- Information criterion weights for a user-supplied vector of deviances (u = -2 * lnL) and sample sizes [R]
- Remove all-zero columns from a Phylip file [R]; probably only necessary if you are analyzing AFLP, RFLP, or morphological data for a subset of larger dataset.
- Parsing herbarium names data with approximate matching to names lists [R]
- Parsing author names from a scientific name string and matching to a list, with recommendations [R]
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Research areas
- Phylogenetics and comparative analysis
- Plant taxonomy and floristics
- Molecular ecology
- Chromosome evolution
- Datasets and code
Current Projects
- Systematics and genome evolution in Carex subg. Vignea
- Interaction between gene flow and chromosome rearrangement in Carex scoparia
- Molecular genetic evidence of serpentine adaptation in Quercus ilex
- Patterns of hybridization in the Hill's oak group (Quercus ellipsoidalis and relatives)
- Systematics of elms (Ulmus)
- Reconstructing continuous character transitions on phylogenetic trees