velociraptr (version 1.1.0)

cullMatrix: Cull rare taxa and depauperate samples

Description

Functions for recursively culling community matrices of rare taxa and depauperate samples.

Usage

cullMatrix(CommunityMatrix, Rarity = 2, Richness = 2, Silent = FALSE)

Arguments

CommunityMatrix

a matrix

Rarity

a whole number

Richness

a whole number

Silent

logical

Value

A community matrix with depauperate samples and rare taxa removed.

Details

Takes a community matrix (see presenceMatrix or abundanceMatrix) and removes all samples with fewer than a certain number of taxa and all taxa that occur below a certain threshold of samples. The function operates recursively, and will check to see if removing a rare taxon drops a sampe below the input minimum richness and vice-versa. This means that it is possible to eliminate all taxa and samples if the rarity and richness minimums are too high. If the Silent argument is set to FALSE the function will throw an error and print a warning if no taxa or samples are left after culling. If Silent is set to TRUE the function will simply return NULL. The latter case is useful if many matrices are being culled as a part of a loop, and you do not want to break the loop with an error.

These functions originally appeared in the R script appendix of Holland, S.M. and A. Zaffos (2011) "Niche conservatism along an onshore-offshore gradient". Paleobiology 37:270-286.

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")

# Remove taxa that occur in less than 5 samples and samples with fewer than 25 taxa.
# cullMatrix(CommunityMatrix,Rarity=5,Richness=25,Silent=FALSE)

# }