asim7: Resampling with row/column species richness fixed

In irhoppe/cooccur: Abundance Matrix Randomizations

Description

Randomizes an abundance matrix by assigning individuals to matrix cells with probabilities proportional to observed row and column abundance totals until the total number of occurrences is reached for each row and column.

Usage

asim7(speciesData)

Arguments

speciesData

species-by-site abundance matrix

Details

Resamples total abundance conditional on marginal sums and constrained to observed species occurrences and site richnesses; equivalent to algorithm IS in Ulrich and Gotelli (2010), and to the Fortran subroutine is in Ulrich (2008).

Value

shuffled abundance matrix

Caution

May generate matrices with empty 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(), asim13(), asim14_f(), asim14(), asim1_f(), asim1(), asim2_f(), asim2(), asim3_f(), asim3(), asim4_f(), asim4(), asim5_f(), asim5(), asim6_f(), asim6(), asim7_f(), asim8_f(), asim8(), asim9_f(), asim9()

Examples

## Not run: 
amat <- rmat(20,12) # creates a random 20 x 12 abundance matrix
asim7(amat)         # performs proportional abundance resampling algorithm

## End(Not run)

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