asim8_f: Resampling species by species with row site occurrences fixed

In irhoppe/cooccur: Abundance Matrix Randomizations

Description

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

Usage

asim8_f(speciesData)

Arguments

speciesData

species-by-site abundance matrix

Details

Resamples species abundances conditional on column sums and constrained to observed species richness; equivalent to algorithm ISR in Ulrich and Gotelli (2010), and to the Fortran subroutine isr in Ulrich (2008).

Preserves total occurrences and species occurrences, but allows abundances and site richnesses 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(), asim9_f(), asim9()

Examples

amat <- rmat(20,12) # creates a random 20 x 12 abundance matrix
asim8_f(amat)       # performs proportional abundance resampling algorithm

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