asim13: Resampling with total abundance fixed

In irhoppe/cooccur: Abundance Matrix Randomizations

Description

Randomizes an abundance matrix by assigning all individuals to matrix cells with probabilities proportional to observed row and column abundance totals until the matrix-wide total abundance is reached.

Usage

asim13(speciesData)

Arguments

speciesData

species-by-site abundance matrix

Details

Resamples species abundances conditional on row and column sums and constrained to observed total abundance; equivalent to algorithm IA in Ulrich and Gotelli (2010), and to the Fortran subroutine ia in Ulrich (2008).

Value

shuffled abundance matrix

Caution

May generate matrices with empty rows(species) or columns (sites).

References

Ulrich, W. 2008. Program Co-Occurrence. Version 1.

Ulrich, W. and Gotelli, N.J. 2010. Null model analysis of species associations using abundance data. Ecology 91:3384-3397.

See Also

Other abundance matrix null models: asim10_f(), asim10(), asim11_f(), asim11(), asim12_f(), asim12(), asim13_f(), asim14_f(), asim14(), asim1_f(), asim1(), asim2_f(), asim2(), asim3_f(), asim3(), asim4_f(), asim4(), asim5_f(), asim5(), asim6_f(), asim6(), asim7_f(), asim7(), asim8_f(), asim8(), asim9_f(), asim9()

Examples

amat <- rmat(20,12) # creates a random 20 x 12 abundance matrix
asim13(amat)        # performs proportional abundance resampling algorithm

irhoppe/cooccur documentation built on Jan. 1, 2021, 4:23 a.m.