taxonAlpha {velociraptr}R Documentation

Additive Diversity Partitioning functions

Description

Functions for calculating alpha, beta, and gamma richness of a community matrix under the Additive Diversity partitioning paradigm of R. Lande.

Usage

taxonAlpha(CommunityMatrix)

meanAlpha(CommunityMatrix)

taxonBeta(CommunityMatrix)

sampleBeta(CommunityMatrix)

totalBeta(CommunityMatrix)

totalGamma(CommunityMatrix)

Arguments

CommunityMatrix

a matrix

Details

Takes a community matrix (see presenceMatrix or abundanceMatrix) and returns the either the alpha, beta, or gamma richness of a community matrix.

These functions were originally presented in Holland, SM (2010) "Additive diversity partitioning in palaeobiology: revisiting Sepkoskiā€™s question" Paleontology 53:1237-1254.

Value

A vector of the alpha, beta, or gamma richness of a taxon, sample, or entire community matrix.

Author(s)

Andrew A. Zaffos

Examples

# Download a test dataset of pleistocene bivalves.
# DataPBDB<-downloadPBDB(Taxa="Bivalvia",StartInterval="Pleistocene",StopInterval="Pleistocene")

# Create a community matrix with tectonic plates as "samples"
# CommunityMatrix<-abundanceMatrix(DataPBDB,"geoplate")

# Calculate the average richness of all samples in a community.
# meanAlpha(CommunityMatrix)

# The beta diversity of all samples in a community.
# totalBeta(CommunityMatrix)

# This is, by definition, equivalent to the gamma diversity - mean alpha diversity.
# totalBeta(CommunityMatrix)==(totalGamma(CommunityMatrix)-meanAlpha(CommunityMatrix))


[Package velociraptr version 1.1.0 Index]