This package implements some recently developed methods in phyloclimatic modeling.
| Package: | phyloclim |
| Type: | Package |
| Version: | 0.9.5 |
| Date: | 2018-05-25 |
| License: | GPL (>= 2) |
phyloclim is intended to provide methods for the quantification of niche occupancy and niche overlap and combine this data with phylogenetic trees.
Niche overlap can be quantified either from profiles of environmental suitability for a given environmental variable (PNO or predicted niche occupancy profiles, see pno) or from two-dimensional suitability surfaces (environmental niche models (ENMs) or species distribution models (SDMs)) with niche.overlap. Randomization tests for testing the significance of niche overlap in terms of niche identity and niche similarity are available in niche.equivalency.test and bg.similarity.test.
Phylogenetic data can be integrated into comparative methods such as age.range.correlation and the estimation of ancestral environmental tolerances (anc.clim), which is a non-parametric approach based on resampling of PNO profiles.
The functions in phyloclim are in an early stage of development, so they should be used with care! Any feedback is welcome!
Evans, M. E. K., S. A. Smith, R. S. Flynn, and M. J. Donoghue. 2009. Climate, niche evolution, and diversification of the 'bird-cage evening primroses' (Oenothera, sections Anogra and Kleinia). Am. Nat. 173: 225-240. Fitzpatrick, B.M & Turelli, M. 2006. The geography of mammalian speciation: mixed signals from phylogenies and range maps. Evolution 60: 601-615. Phillips, S.J, M. Dudik, & R.E. Schapire. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modeling 190: 231-259.
Warren, D., R.E. Glor, & M. Turelli. 2008. Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution 62: 2868-2883.