PhyloMeasures: Fast and Exact Algorithms for Computing Phylogenetic Biodiversity Measures

Given a phylogenetic tree T and a sample 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 the implementations of efficient algorithms for several such measures. Most importantly, the package includes algorithms for computing exactly and efficiently the expectation and the variance of these measures, which are essential for null model comparisons. Efficient computation of richness-standardized versions of these metrics, such as the net relatedness index (NRI), nearest taxon index (NTI), phylogenetic diversity index (PDI), and the corresponding indices of two-sample measures are also available in this package. 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.

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