Stratified randomization of community matrix

This is a simple wrapper around nullcat::quantize(), included in phylospatial mainly for backward compatibility.

Usage

quantize(x, ...)

Arguments

x

Community matrix with species in rows, sites in columns, and nonnegative quantities in cells.

...

Additional arguments passed to nullcat::quantize().

Value

A randomized version of x.

Details

The nullcat quantize routine involves three steps: converting a quantitative matrix to categorical strata, permuting the resulting categorical matrix using one of several categorical null model algorithms, and mapping the randomized categories back to quantitative values. Supply arguments via ... to control options for each of these stages.

Examples

if (requireNamespace("nullcat", quietly = TRUE)) {
      # example quantitative community matrix
      comm <- matrix(runif(2500), 50)

      # examples of different quantize usage
      rand <- quantize(comm)
      rand <- quantize(comm, n_strata = 4, transform = sqrt, fixed = "row")
      rand <- quantize(comm, method = "swapcat", n_iter = 500)
}