ps_quantize: Stratified randomization of a phylospatial object

In phylospatial: Spatial Phylogenetic Analysis

Stratified randomization of a phylospatial object

Description

Generates a randomized version of a phylospatial object by extracting the tip community matrix, permuting it using nullcat::quantize(), and rebuilding the phylospatial object using the permuted tip matrix.

Usage

ps_quantize(ps, ...)

Arguments

ps	Object of class phylospatial
...	Additional arguments passed to quantize.

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.

For repeated randomizations to generate a null distribution, it is more efficient to use ps_rand(fun = "quantize"), which is structured to avoid unnecessarily recomputing overhead that is shared across randomizations.

Value

A rendomized version of ps

Examples

if (requireNamespace("nullcat", quietly = TRUE)) {
  ps <- ps_simulate(data_type = "prob")
  ps_rand <- ps_quantize(ps, n_strata = 4,
    n_iter = 1000, # note: you'd want higher n_iter for a real analysis
    method = "curvecat", fixed = "cell")
}

phylospatial documentation built on Dec. 24, 2025, 1:06 a.m.