Skip to contents

nullcat

nullcat provides null model algorithms for categorical and quantitative community ecology data. It extends classic binary null models (e.g., curveball, swap) to work with categorical data, and introduces a stratified randomization framework for continuous data that addresses limitations in existing methods for randomizing quantitative and count data.

Installation 

# Install stable version from CRAN:
install.packages("nullcat")

# Or dev version from GitHub:
# install.packages("remotes")
remotes::install_github("matthewkling/nullcat")

Quick start

Categorical null models

Generalize binary null models to matrices where cells contain integers representing discrete categories:

library(nullcat)

# Create a categorical matrix
set.seed(123)
cat_matrix <- matrix(sample(1:4, 20*10, replace = TRUE), nrow = 20)

# Randomize using curvecat (preserves row & column category multisets)
randomized <- curvecat(cat_matrix, n_iter = 1000)

# Verify margins are preserved
all.equal(sort(cat_matrix[1,]), sort(randomized[1,]))
#> [1] TRUE
all.equal(sort(cat_matrix[,1]), sort(randomized[,1]))
#> [1] TRUE

Available algorithms: curvecat(), swapcat(), tswapcat(), r0cat(), c0cat()

Quantitative null models

Apply stratified randomization to continuous community data:

# Create a quantitative community matrix
set.seed(456)
comm <- matrix(rexp(50 * 30, rate = 0.5), nrow = 50)

# Stratified randomization with 5 strata
rand1 <- quantize(comm, n_strata = 5, n_iter = 2000)

# Preserve row value multisets (row sums maintained)
rand2 <- quantize(comm, n_strata = 5, fixed = "row", n_iter = 2000)
all.equal(rowSums(comm), rowSums(rand2))
#> [1] TRUE

Learn more

See vignette("nullcat") for comprehensive documentation including:

  • Categorical null model algorithms and their constraints
  • Quantitative null model workflow and stratification options
  • Convergence diagnostics and burn-in estimation
  • Efficient batch generation of null distributions
  • Integration with the vegan package

Package website: https://matthewkling.github.io/nullcat/

Report issues: https://github.com/matthewkling/nullcat/issues