PhyloMeasures (version 2.1)
Fast and Exact Algorithms for Computing Phylogenetic
Biodiversity Measures
Description
Given a phylogenetic tree T and an assemblage S of species represented as
a subset of tips in T, we want to compute a measure of the diversity
of the species in S with respect to T. The current package offers
efficient algorithms that can process large phylogenetic data for several such measures.
Most importantly, the package includes algorithms for computing
efficiently the standardized versions of phylogenetic measures and their p-values, which are
essential for null model comparisons. Among other functions,
the package provides efficient computation of richness-standardized versions
for indices such as the net relatedness index (NRI),
nearest taxon index (NTI), phylogenetic
diversity index (PDI), and the corresponding indices of two-sample measures.
The package also introduces a new
single-sample measure, the Core Ancestor Cost (CAC); the package provides
functions for computing the value and the standardised index of the CAC and,
more than that, there is an extra function available that can compute exactly
any statistical moment of the measure. The package supports computations
under different null models, including abundance-weighted models.