pam2bioindex {bamm}

pam2bioindex: PAM to biodiversity index

Description

pam2bioindex estimates various biodiversity indices for a certain PAM.

Usage

pam2bioindex(pam, biodiv_index = "dispersion_field", as_sparse = FALSE)

Arguments

pam

A Presence-Absence-Matrix of matrix class or sparse matrix.

biodiv_index

Possible values are alpha, omega, wbeta (Whittaker’s multiplicative beta index), laBeta (Lande’s additive beta index) dispersion_field, all.

as_sparse

Return indices as sparse objects

Details

The biodiversity indices can be found in Soberón and Cavner (2015).

Value

An object of class bioindex with three slots each represents a matrix of diversity indices: alpha, omega, and dispersion field, richness_field.

Author(s)

Luis Osorio-Olvera & Jorge Soberón

References

Soberon J, Cavner J (2015). “Indices of Biodiversity Pattern Based on Presence-Absence Matrices: A GIS Implementation.” Biodiversity Informatics, 10, 22–34.

Examples

set.seed(111)
pam <- matrix(rbinom(100,1,0.3),nrow = 10,ncol = 10)
bioindices <- bamm::pam2bioindex(pam=pam,biodiv_index="all")
# Return results as sparse models
bioindices <- bamm::pam2bioindex(pam=pam,biodiv_index="all",as_sparse=TRUE)
bioindices@alpha
bioindices@omega
bioindices@dispersion_field