R package 'pdiv'

Purpose

This R package contains functions related broadly to "biodiversity" topics, as opposed to general functions (which are in the package pascal) and "geography"- related function (which are in the package pgeo)

Groups of functions

Additive and tripartite partitioning

• addpart partitions biodiversity effects following Loreau and Hectors scheme.
• tripart partitions biodiversity effects following Fox' scheme.

Both functions support parallelization.

Biodiversity indices

These functions calculate indices which are part of Hill's series of biodiversity numbers, plus a few related indiced.

• hill.Na(x,a=1)
• hill.Ha(x,a=1)
• shannon.H(x)
• simpson.D(x)
• evennes.1overD(x)

Interconversion between data formats representing community composition

• communityFromMatrix(...)
• communityToMatrix(...)

Niche breadth and overlap

• levinsB calculates niche breadth as defined by Levins
• prop.sim calculates Colwell and Futuyma's proportional similarity index

Functional and phylogenetic diversity

These functions calculate functional and phylogenetic diversity as total branch length of a functional trait dendrogram or a phylogenetic tree, following Petchey & Gastons 2002 scheme (including their 2006 update). Also, a function to calculate mean phylogenetic distances, with and without abundance weighing, is provided (Warwick and Clark 1995).

• calcFD(...)
• calcPD(...)
• calcMPD(...)

Installation

• download the ready-built package from the pkgs directory
• use install_github:
  library(devtools)
install_github("pascal-niklaus/pdiv/pdiv")