asim5: Resampling with occurrences and row/column abundances fixed

In irhoppe/cooccur: Abundance Matrix Randomizations

Description

Randomizes an abundance matrix by assigning individuals to nonempty cells, with probabilities proportional to observed row and column abundance totals. Individuals are sequentially assigned to the matrix in this way until, for each row and column, total abundances are reached.

Usage

asim5(speciesData)

Arguments

speciesData

species-by-site abundance matrix

Details

Resamples total abundance conditional on and constrained by marginal sums; equivalent to algorithm OF in Ulrich and Gotelli (2010), and to the Fortran subroutine of in Ulrich (2008).

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(), asim6_f(), asim6(), asim7_f(), asim7(), asim8_f(), asim8(), asim9_f(), asim9()

Examples

## Not run: 
amat <- rmat(20,12) # creates a random 20 x 12 abundance matrix
asim5(amat)         # performs proportional abundance resampling algorithm

## End(Not run)

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