ulrb: Unsupervised Learning Based Definition of Microbial Rare Biosphere
A tool to define rare biosphere. 'ulrb' solves the problem of the definition of rarity by replacing arbitrary thresholds with an unsupervised machine learning algorithm (partitioning around medoids, or k-medoids). This algorithm works for any type of microbiome data, provided there is an abundance table. For validation of this method to different abundance tables, see Pascoal et al, 2025. This method also works for non-microbiome data.
| Version: | 0.1.6 |
| Depends: | R (≥ 2.10) |
| Imports: | cluster, dplyr, ggplot2, purrr, rlang, stats, tidyr, clusterSim, gridExtra |
| Suggests: | knitr, rmarkdown, stringr, testthat (≥ 3.0.0), vegan |
| Published: | 2025-04-07 |
| DOI: | 10.32614/CRAN.package.ulrb |
| Author: | Francisco Pascoal 
[aut, cre],
Paula Branco
[aut],
Luís Torgo [aut],
Rodrigo Costa
[aut],
Catarina Magalhães
[aut] |
| Maintainer: | Francisco Pascoal <fpascoal1996 at gmail.com> |
| BugReports: | https://github.com/pascoalf/ulrb/issues |
| License: | GPL (≥ 3) |
| URL: | https://pascoalf.github.io/ulrb/ |
| NeedsCompilation: | no |
| Citation: | ulrb citation info |
| Materials: | README |
| CRAN checks: | ulrb results |
Documentation:
| Reference manual: | ulrb.pdf |
| Vignettes: |
Glossary (source, R code) Integration of ulrb in a simple microbial ecology workflow (source, R code) Alternative classifications with ulrb (source, R code) Tutorial to define rare biosphere with ulrb (source, R code) |
Downloads:
| Package source: | ulrb_0.1.6.tar.gz |
| Windows binaries: | r-devel: ulrb_0.1.6.zip, r-release: ulrb_0.1.5.zip, r-oldrel: ulrb_0.1.6.zip |
| macOS binaries: | r-devel (arm64): ulrb_0.1.6.tgz, r-release (arm64): ulrb_0.1.6.tgz, r-oldrel (arm64): ulrb_0.1.6.tgz, r-devel (x86_64): ulrb_0.1.6.tgz, r-release (x86_64): ulrb_0.1.6.tgz, r-oldrel (x86_64): ulrb_0.1.6.tgz |
| Old sources: | ulrb archive |
Linking:
Please use the canonical form https://CRAN.R-project.org/package=ulrb to link to this page.