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Testing differential abundance at individual taxa and in a whole microbial community. The tests are based on the log-ratio of relative abundances. The tests accommodate continuous, discrete (binary, categorical), and multivariate traits, and allow adjustment of confounders. For more details see He (2026) <doi:10.64898/2026.04.07.716976>. This package also includes the 'com2seq' function that combines two sequencing datasets (e.g., from 16S marker-gene and shotgun sequencing) for integrative analysis of differential abundance. For more details see <doi:10.1080/01621459.2025.2516205>.
| Version: | 1.1 |
| Depends: | R (≥ 3.5.0) |
| Imports: | Rcpp (≥ 1.0.11), stats, permute, parallel, BiocParallel, matrixStats, abind, car |
| LinkingTo: | Rcpp, RcppArmadillo |
| Suggests: | testthat, survival |
| Published: | 2026-10-29 |
| DOI: | 10.32614/CRAN.package.LOCOM2 |
| Author: | Yi-Juan Hu [aut, cre] |
| Maintainer: | Yi-Juan Hu <yijuanhu at bicmr.pku.edu.cn> |
| BugReports: | https://github.com/yijuanhu/LOCOM2/issues |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | https://github.com/yijuanhu/LOCOM2 |
| NeedsCompilation: | yes |
| Materials: | README |
| CRAN checks: | LOCOM2 results |
| Reference manual: | LOCOM2.html , LOCOM2.pdf |
| Package source: | LOCOM2_1.1.tar.gz |
| Windows binaries: | r-devel: LOCOM2_1.0.zip, r-release: LOCOM2_1.1.zip, r-oldrel: LOCOM2_1.1.zip |
| macOS binaries: | r-release (arm64): LOCOM2_1.1.tgz, r-oldrel (arm64): LOCOM2_1.1.tgz, r-release (x86_64): LOCOM2_1.1.tgz, r-oldrel (x86_64): LOCOM2_1.1.tgz |
| Old sources: | LOCOM2 archive |
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These binaries (installable software) and packages are in development.
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