asim1_f: Abundance swap

In irhoppe/cooccur: Abundance Matrix Randomizations

Description

Randomizes an abundance matrix by reshuffling populations equiprobably among the nonempty cells of the entire matrix.

Usage

asim1_f(speciesData, swaps = NULL)

Arguments

speciesData

species-by-site abundance matrix

Details

Performs an abundance swap equivalent to algorithm PM in Ulrich and Gotelli (2010), and to the Fortran subroutine pm in Ulrich (2008).

Preserves total matrix abundance and occurrences, but allows marginal sums (i.e. species and site abundances) to vary equiprobably.

Value

shuffled abundance matrix

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(), asim13(), asim14_f(), asim14(), 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
asim1_f(amat)       # performs equiprobable abundance swap algorithm

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