additiveBeta: Additive Diversity Partitioning functions
In velociraptr: Fossil Analysis

Description Usage Arguments Details Value Author(s) Examples

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

taxonAlpha(CommunityMatrix)

meanAlpha(CommunityMatrix)

taxonBeta(CommunityMatrix)

sampleBeta(CommunityMatrix)

totalBeta(CommunityMatrix)

totalGamma(CommunityMatrix)

CommunityMatrix

a matrix

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 Sepkoski’s question" Paleontology 53:1237-1254.

taxonAlpha(CommunityMatrix) Calculates the contribution to alpha diversity of each taxon.
meanAlpha(CommunityMatrix) Calculates the average alpha diversity of all samples.
taxonBeta(CommunityMatrix) Calculates the contribution to beta diversity of each taxon.
sampleBeta(CommunityMatrix) Calculates the contribution to beta diversity of each sample.
totalBeta(CommunityMatrix) Calculates the total beta diversity.
totalGamma(CommunityMatrix) Calculates the richness of all samples in the community matrix.

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

Andrew A. Zaffos

# 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))