pez {pez}

Phylogenetics for the Environmental Sciences

Description

Analysis and manipulation of eco-phylogenetic datasets containing species phylogeny, species traits, community composition, and environmental data. Provide the comparative.comm object to ease data manipulation, and wrappers for common community phylogenetic indices grouped according to Pearse et al. 2014: pez.shape, pez.evenness, pez.dispersion, and pez.dissimilarity. Implementation of Cavender-Bares et al. (2004) correlation of phylogenetic and ecological matrices (fingerprint.regression). Simulation of null assemblages, traits, and phylogenies (scape, sim.meta.comm).

References

Pearse W.D., Purvis A., Cavender-Bares J. & Helmus M.R. (2014). Metrics and Models of Community Phylogenetics. In: Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology. Springer Berlin Heidelberg, pp. 451-464.

Cavender-Bares J., Ackerly D.D., Baum D.A. & Bazzaz F.A. (2004) Phylogenetic overdispersion in Floridian oak communities. The Americant Naturalist 163(6): 823–843.

Examples

require(pez)
data(laja)
data <- comparative.comm(invert.tree, river.sites, invert.traits, river.env)
pez.shape(data)