nullCom: Generate a set of null communities based on functions in the...
In ECGen/ComGenR: Functions for COMmunity GENetics analyses in R

Description Usage Arguments Details Value Author(s) Examples

This function produces a set of permuted matrices based on an input species abundance or presence-absence matrix.

1	nullCom(com, method = "r1", nits = 5000, burn = 500, thin = 10)

`com`	Community matrix with species abundances or presence-absences. Values are converted to presence-absence regardless of input.
`method`	Permutation method. Options include: r00 = fully random, r0 = maintain site frequencies, r1 = maintain both site and species frequencies. For more options see the oecosimu function in the vegan package.
`nits`	Number of iterations to conduct.
`burn`	The number permutations to conduct prior to recording matrices.
`thin`	The number of discarded matrices between iterations.

Provides high level access to the oecosimu function in vegan.

Returns a set of permuted matrices to be used for null modeling. The default null model is the most constrained version (i.e. both species and observation marginal totals are restricted).

Matthew K. Lau

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (com, method = "r1", nits = 5000, burn = 500, thin = 10) 
{
    com[com != 0] <- 1
    for (i in 1:burn) {
        post.burn <- commsimulator(x = com, method = method, 
            thin = thin)
    }
    out <- list()
    for (i in 1:nits) {
        out[[i]] <- commsimulator(x = post.burn, method = method, 
            thin = thin)
    }
    return(out)
  }