permute_pam {bamm}

R Documentation

permute_pam: Function to permute a Presence-Absence-Matrix.

Description

permute_pam: Function to permute a Presence-Absence-Matrix.

Usage

permute_pam(m, niter = NULL, as_sparse = FALSE)

Arguments

m	Presence-Absence-Matrix (PAM) or a binary matrix with columns representing species and rows sites.
niter	Number of iterations to permute the PAM.
as_sparse	If TRUE the PAM will be returned as a sparse matrix

Details

This function is an implementation of the curve ball algorithm following Strona et al. (2014).

Value

Returns a permuted matrix of the same dimensions of m (same number of rows and columns). Note that the sum of each row and column of this permuted matrix is equal to that of m. species.

Author(s)

Luis Osorio-Olvera & Jorge Soberón

References

Strona G, Nappo D, Boccacci F, Fattorini S, San-Miguel-Ayanz J (2014). “A fast and unbiased procedure to randomize ecological binary matrices with fixed row and column totals.” Nature Communications, 5(1), 1–9. ISSN 20411723, doi:10.1038/ncomms5114, https://www.r-project.org..

Examples

set.seed(111)
pam <- matrix(rbinom(100,1,0.3),nrow = 10,ncol = 10)
ppam <- bamm::permute_pam(m = pam,niter = NULL,as_sparse = FALSE)
# Check if matrices are different
all(pam == ppam)
# Check if row totals are the same
all(Matrix::rowSums(pam) == Matrix::rowSums(ppam))
# Check if column total are the same
all(Matrix::colSums(pam) == Matrix::colSums(ppam))

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