{"Package":"nullcat","Type":"Package","Title":"Null Models for Categorical and Continuous Community Matrices","Version":"0.1.0","Authors@R":"person(\"Matthew\", \"Kling\",\nemail = \"mattkling@berkeley.edu\",\nrole = c(\"aut\", \"cre\", \"cph\"))","Description":"Provides null model algorithms for categorical and quantitative\ncommunity ecology data. Extends classic binary null models (e.g.,\n'curveball', 'swap') to work with categorical data. Provides a stratified\nrandomization framework for continuous data.","License":"MIT + file LICENSE","Encoding":"UTF-8","RoxygenNote":"7.3.2","LinkingTo":"Rcpp","Imports":"Rcpp","Suggests":"knitr, rmarkdown, testthat (>= 3.0.0), vegan","Config/testthat/edition":"3","URL":"https://github.com/matthewkling/nullcat,\nhttps://matthewkling.github.io/nullcat/","BugReports":"https://github.com/matthewkling/nullcat/issues","VignetteBuilder":"knitr","NeedsCompilation":"yes","Packaged":"2025-12-13 17:56:32 UTC; matthewkling","Author":"Matthew Kling [aut, cre, cph]","Maintainer":"Matthew Kling ","Repository":"CRAN","Date/Publication":"2025-12-18 14:30:07 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/nullcat_0.1.0.tar.gz","jsonAuthors":[{"name":"Matthew Kling","email":"mattkling@berkeley.edu","maintainer":true}],"readme":"\n\n\n\n[![R-CMD-check](https://github.com/matthewkling/nullcat/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/matthewkling/nullcat/actions/workflows/R-CMD-check.yaml)\n\n\n# nullcat $\"nullcat$ \n\n`nullcat` provides null model algorithms for categorical and\nquantitative community ecology data. It extends classic binary null\nmodels (e.g., curveball, swap) to work with categorical data, and\nintroduces a stratified randomization framework for continuous data that\naddresses limitations in existing methods for randomizing quantitative\nand count data.\n\n## Installation\n\n``` r\n# Install stable version from CRAN:\ninstall.packages(\"nullcat\")\n\n# Or dev version from GitHub:\n# install.packages(\"remotes\")\nremotes::install_github(\"matthewkling/nullcat\")\n```\n\n## Quick start\n\n#### Categorical null models\n\nGeneralize binary null models to matrices where cells contain integers\nrepresenting discrete categories:\n\n``` r\nlibrary(nullcat)\n\n# Create a categorical matrix\nset.seed(123)\ncat_matrix <- matrix(sample(1:4, 20*10, replace = TRUE), nrow = 20)\n\n# Randomize using curvecat (preserves row & column category multisets)\nrandomized <- curvecat(cat_matrix, n_iter = 1000)\n\n# Verify margins are preserved\nall.equal(sort(cat_matrix[1,]), sort(randomized[1,]))\n#> [1] TRUE\nall.equal(sort(cat_matrix[,1]), sort(randomized[,1]))\n#> [1] TRUE\n```\n\nAvailable algorithms: `curvecat()`, `swapcat()`, `tswapcat()`,\n`r0cat()`, `c0cat()`\n\n#### Quantitative null models\n\nApply stratified randomization to continuous community data:\n\n``` r\n# Create a quantitative community matrix\nset.seed(456)\ncomm <- matrix(rexp(50 * 30, rate = 0.5), nrow = 50)\n\n# Stratified randomization with 5 strata\nrand1 <- quantize(comm, n_strata = 5, n_iter = 2000)\n\n# Preserve row value multisets (row sums maintained)\nrand2 <- quantize(comm, n_strata = 5, fixed = \"row\", n_iter = 2000)\nall.equal(rowSums(comm), rowSums(rand2))\n#> [1] TRUE\n```\n\n## Learn more\n\nSee `vignette(\"nullcat\")` for comprehensive documentation including:\n\n- Categorical null model algorithms and their constraints\n- Quantitative null model workflow and stratification options\n- Convergence diagnostics and burn-in estimation\n- Efficient batch generation of null distributions\n- Integration with the vegan package\n\n**Package website:** \n\n**Report issues:** ","jobInfo":{"package":"nullcat","version":"0.1.0","parsingStatus":"success","parserVersion":2,"parsedAt":"2025-12-18T16:29:49+0000"}}

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