velociraptr (version 1.0)

subsampleEvenness: Shareholder Quorum Subsampling

Description

Calculate the richness of a sample after subsampling based on the evenness of the abundance distribution.

Usage

subsampleEvenness(Abundance, Quota = 0.9, Trials = 100,
  IgnoreSingletons = FALSE, ExcludeDominant = FALSE)

Arguments

Abundance

A vector of taxon abundances

Quota

A numeric value greater than zero and less than one

Trials

Number of iterations

IgnoreSingletons

A logical

ExcludeDominant

A logical

Value

A numeric value of estimated taxonomic richness

Details

This is a port of S.M. Holland's port of J. Alroy's shareholder quorum subsampling function.

Alroy, J. (2010) "Fair sampling of taxonomic richness and unbiased estimation of origination and extinction rates" in Quatitative Methods in Paleobiology, Paleontological Society Short Course 2010. The Paleontological Society Papers V. 16, John Alroy and Gene Hunt (eds.)

Examples

# NOT RUN {
# Download a test dataset of Miocene-Pleistocene bivalves.
# DataPBDB<-downloadPBDB(Taxa="Bivalvia",StartInterval="Miocene",StopInterval="Pleistocene")

 # Clean up the taxonomy by removing subgenus designation
 # DataPBDB<-cleanTaxonomy(DataPBDB,"genus")

# Create a community matrix of genera by tectonic plate ids.
# CommunityMatrix<-abundanceMatrix(DataPBDB,Rows="geoplate",Columns="genus")

# Cull out depauperate samples and rare taxa
# CommunityCull<-cullMatrix(CommunityMatrix,5,100)

# Calculate the standardized richness of each plate at a quota of 0.5.
# StandardizedRichness<-apply(CommunityCull,1,subsampleEvenness,0.5)

# }