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 pvalues, which are essential for null model comparisons. Among other functions, the package provides efficient computation of richnessstandardized versions for indices such as the net relatedness index (NRI), nearest taxon index (NTI), phylogenetic diversity index (PDI), and the corresponding indices of twosample measures. The package also introduces a new singlesample 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 abundanceweighted models.
Package details 


Author  Constantinos Tsirogiannis [aut, cre], Brody Sandel [aut] 
Maintainer  Constantinos Tsirogiannis <tsirogiannis.c@gmail.com> 
License  GPL3 
Version  2.1 
Package repository  View on CRAN 
Installation 
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