asim2: Abundance swap within columns

In irhoppe/cooccur: Abundance Matrix Randomizations

Description

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

Usage

asim2(speciesData)

Arguments

speciesData

species-by-site abundance matrix

Details

Performs a series of abundance swaps within columns (sites); equivalent to algorithm PC in Ulrich and Gotelli (2010), and to the Fortran subroutine pc in Ulrich (2008).

Preserves total matrix abundance and occurrences as well as site abundances (column totals), but allows species abundances (row totals) 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_f(), asim1(), asim2_f(), 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
asim2(amat)         # performs equiprobable column abundance swap algorithm

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