velociraptr (version 1.1.0)

taxonAlpha: 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

Value

A vector of the alpha, beta, or gamma richness of a taxon, sample, or entire community 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 Sepkoski<U+2019>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.

Examples

# NOT RUN {
# 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))

# }