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miniLNM: Miniature Logistic-Normal Multinomial Models

Logistic-normal Multinomial (LNM) models are common in problems with multivariate count data. This package gives a simple implementation with a 30 line 'Stan' script. This lightweight implementation makes it an easy starting point for other projects, in particular for downstream tasks that require analysis of "compositional" data. It can be applied whenever a multinomial probability parameter is thought to depend linearly on inputs in a transformed, log ratio space. Additional utilities make it easy to inspect, create predictions, and draw samples using the fitted models. More about the LNM can be found in Xia et al. (2013) "A Logistic Normal Multinomial Regression Model for Microbiome Compositional Data Analysis" <doi:10.1111/biom.12079> and Sankaran and Holmes (2023) "Generative Models: An Interdisciplinary Perspective" <doi:10.1146/annurev-statistics-033121-110134>.

Version: 0.1.0
Depends: R (≥ 4.0.0)
Imports: Rcpp (≥ 0.12.0), RcppParallel (≥ 5.0.1), cli, dplyr, fansi, formula.tools, glue, methods, posterior, rstan (≥ 2.18.1), rstantools (≥ 2.4.0), tidyselect
LinkingTo: BH (≥ 1.66.0), Rcpp (≥ 0.12.0), RcppEigen (≥ 0.3.3.3.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.18.1), StanHeaders (≥ 2.18.0)
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0)
Published: 2024-09-13
DOI: 10.32614/CRAN.package.miniLNM
Author: Kris Sankaran ORCID iD [aut, cre]
Maintainer: Kris Sankaran <ksankaran at wisc.edu>
BugReports: https://github.com/krisrs1128/miniLNM/issues/
License: CC0
URL: https://github.com/krisrs1128/miniLNM/, https://krisrs1128.github.io/miniLNM/
NeedsCompilation: yes
SystemRequirements: GNU make
Materials: README
CRAN checks: miniLNM results

Documentation:

Reference manual: miniLNM.pdf
Vignettes: Example on Simulated Data (source, R code)

Downloads:

Package source: miniLNM_0.1.0.tar.gz
Windows binaries: r-devel: miniLNM_0.1.0.zip, r-release: miniLNM_0.1.0.zip, r-oldrel: miniLNM_0.1.0.zip
macOS binaries: r-release (arm64): miniLNM_0.1.0.tgz, r-oldrel (arm64): miniLNM_0.1.0.tgz, r-release (x86_64): miniLNM_0.1.0.tgz, r-oldrel (x86_64): miniLNM_0.1.0.tgz

Reverse dependencies:

Reverse imports: multimedia

Linking:

Please use the canonical form https://CRAN.R-project.org/package=miniLNM to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.