random_shuffle: Generate individual or sample-based random shuffle...

In mcglinnlab/vario: Community variograms and associated null models

Generate individual or sample-based random shuffle statistical null expectations for variograms.

Description

Generate individual or sample-based random shuffle statistical null expectations for variograms.

Usage

random_shuffle(x, vobject, swap, nperm, npar, coords = NULL, breaks = NA)

Arguments

x	is either an output of class 'sim' that is the output of 'sim.neut.uni' OR an site x species matrix
vobject	is the output of 'vario', this informs the function of what parameterization of vario to use specifically it indiates if the pos.neg components and median should be calculated
swap	two options: 'indiv' or 'quad' for individual or quadrat-based shuffling repsectively.
nperm	is the number of permutations
npar	is the number of processors to run the analysis over
coords	the spatial coordinates of the sites, not needed if x is of class 'sim'
breaks	what spatial breaks to use

Note

The sample-based shuffling the mean of the null distribution is the same as the average variance across all distance classes. So shuffling is only useful in deriving the variance around that expectation.

if x is a presence-absence matrix then the individual and sample-based approaches will generate identical within-species variograms

this function requires snowfall and rlecuyer packages are loaded

mcglinnlab/vario documentation built on Feb. 22, 2023, 1:49 p.m.