asim9: Resampling site by site with column species richness fixed

In irhoppe/cooccur: Abundance Matrix Randomizations

Description

Randomizes an abundance matrix by sequentially (column by column) assigning individuals to each column with probabilities proportional to observed row abundance totals until the respective column total species richness is reached.

Usage

asim9(speciesData)

Arguments

speciesData

species-by-site abundance matrix

Details

Resamples species abundances conditional on row sums and constrained to observed site occurrences; equivalent to algorithm ISC in Ulrich and Gotelli (2010), and to the Fortran subroutine isc in Ulrich (2008).

Preserves total occurrences and site richnesses, but allows abundances and species occurrences to vary.

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(), asim2(), asim3_f(), asim3(), asim4_f(), asim4(), asim5_f(), asim5(), asim6_f(), asim6(), asim7_f(), asim7(), asim8_f(), asim8(), asim9_f()

Examples

amat <- rmat(20,12) # creates a random 20 x 12 abundance matrix
asim9(amat)         # performs proportional abundance resampling algorithm

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