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 
[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:
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