Phylogenetics for the Environmental Sciences
Manipulating and examining comparative.comm objects
Creates a community comparative ecology object, the basis of all funct...
Null models for functional-phylogenetic diversity
Make co-existence matrices based on phylogeny (and/or) traits, and com...
Trim a phylogeny
eco.space scape simulation with a macro-ecological focus
List of eco.xxx.regressions
eco.xxx.regression
fibre.plot (fibrously) plots a phylogeny
Regress trait evolution against trait ecology (following Cavender-Bare...
Calculate any metric(s) (and compare with null distributions)
Internal pez Functions
Calculate (phylogenetic) dispersion: examine assemblages in the contex...
Calculate (phylogenetic) dissimilarity: compare assemblages to one-ano...
Calculate (phylogenetic) endemism
Calculate (phylogenetic) evenness: examine assemblage composition and ...
Phylogenetic and functional trait metrics within pez
Phylogenetics for the Environmental Sciences
Calculate (phylogenetic) shape: examine assemblage composition
Phylogenetic Generalised Linear Mixed Model for Community Data
Build a novel phylogeny from existing data
Calculate phylogenetic `signal'
Dot-plots of community presence/absence or abundance
Simulate phylogenetic community structure across a landscape
Simulate a meta-community (and its phylogeny)
Simulate phylogenies
Produces simulated communities based on species attributes
Traitgram for comparative community object
Eco-phylogenetic and community phylogenetic analyses. Keeps community ecological and phylogenetic data matched up and comparable using 'comparative.comm' objects. Wrappers for common community phylogenetic indices ('pez.shape', 'pez.evenness', 'pez.dispersion', and 'pez.dissimilarity' metrics). Implementation of Cavender-Bares (2004) correlation of phylogenetic and ecological matrices ('fingerprint.regression'). Phylogenetic Generalised Linear Mixed Models (PGLMMs; 'pglmm') following Ives & Helmus (2011) and Rafferty & Ives (2013). Simulation of null assemblages, traits, and phylogenies ('scape', 'sim.meta.comm').