nullcat (version 0.1.0)

nullcat_batch: Generate a batch of null matrices using nullcat()

Description

Runs the categorical null model implemented in nullcat() repeatedly, generating a batch of randomized matrices or, optionally, a batch of summary statistics computed from those matrices. This is the categorical analog of quantize_batch().

Usage

nullcat_batch(x, n_reps = 999L, stat = NULL, n_cores = 1L, seed = NULL, ...)

Value

If stat is NULL, returns a 3D array (rows × cols × n_reps). If stat is not NULL, returns a numeric array of statistic values (dimensionality depends on stat).

Arguments

x

Community matrix (sites × species) or any categorical matrix of integers.

n_reps

Number of randomizations to generate. Default is 999.

stat

Optional summary function taking a matrix and returning a numeric statistic. If NULL (default), the function returns the full set of randomized matrices.

n_cores

Number of compute cores to use for parallel processing. Default is 1.

seed

Integer used to seed random number generator, for reproducibility.

...

Additional arguments passed to nullcat() (e.g. method, n_iter, output).

Examples

set.seed(123)
x <- matrix(sample(1:4, 100, replace = TRUE), nrow = 10)

# Generate 99 randomized matrices
nulls <- nullcat_batch(x, n_reps = 99, method = "curvecat", n_iter = 100)

# Or compute a statistic on each
row_sums <- nullcat_batch(x, n_reps = 99, stat = rowSums,
                          method = "curvecat", n_iter = 100)

# Specify multiple cores for parallel processing
nulls <- nullcat_batch(x, n_reps = 99, n_iter = 100, n_cores = 2)