This package is considered a duplicate. The official version of this package is found at:https://yijuanhu.r-universe.dev/LOCOM2

Package: LOCOM2 1.1

Yi-Juan Hu

LOCOM2: A Logistic Regression Model for Testing Microbial Differential Abundance

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>.

Authors:Yi-Juan Hu [aut, cre]

LOCOM2_1.1.tar.gz
LOCOM2_1.1.zip(r-4.7-x86_64)LOCOM2_1.1.zip(r-4.7-arm64)LOCOM2_1.1.zip(r-4.6-x86_64)LOCOM2_1.1.zip(r-4.6-arm64)
LOCOM2_1.1.tar.gz(r-4.7-arm64)LOCOM2_1.1.tar.gz(r-4.7-x86_64)LOCOM2_1.1.tar.gz(r-4.6-arm64)LOCOM2_1.1.tar.gz(r-4.6-x86_64)
LOCOM2_1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
LOCOM2/json (API)

# Install 'LOCOM2' in R:

install.packages('LOCOM2', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yijuanhu/locom2/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

meta.1 - Metadata for samples in otu.table.1
meta.2 - Metadata for samples in otu.table.2
otu.table.1 - Simulated OTU count table
otu.table.2 - Simulated OTU count table
throat.meta.filter - Metadata of the throat microbiome samples
throat.otu.table.filter - OTU count table from 16S sequencing of the throat microbiome samples
throat.otu.taxonomy - Taxonomy names for OTUs from 16S sequencing of the throat microbiome samples

On CRAN:

openblas cpp openmp

2.00 score 1 scripts 425 downloads 2 exports 78 dependencies

Last updated from:74554e3fdc. Checks:10 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	OK	134
linux-devel-x86_64	OK	175
source / vignettes	OK	248
linux-release-arm64	OK	130
linux-release-x86_64	OK	131
windows-devel-arm64	OK	234
windows-devel-x86_64	OK	173
windows-release-arm64	OK	256
windows-release-x86_64	OK	118
wasm-release	OK	142

Exports:com2seq locom2

Dependencies:abind backports BH BiocParallel boot broom car carData cli codetools colorspace cowplot cpp11 Deriv doBy dplyr farver forecast formatR Formula fracdiff futile.logger futile.options generics ggplot2 glue gtable isoband labeling lambda.r lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels matrixStats mgcv minqa modelr nlme nloptr nnet numDeriv pbkrtest permute pillar pkgconfig purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang S7 scales snow SparseM stringi stringr survival tibble tidyr tidyselect timeDate urca utf8 vctrs viridisLite withr zoo

Help page	Topics
com2seq: combining two sequencing datasets (e.g., from 16S marker-gene and shotgun metagenomic sequencing) for integrative analysis of differential abundance at both the genus and community levels	com2seq
A logistic regression model for testing differential abundance in compositional microbiome data (LOCOM2)	locom2
Metadata for samples in otu.table.1	meta.1
Metadata for samples in otu.table.2	meta.2
Simulated OTU count table	otu.table.1
Simulated OTU count table	otu.table.2
Metadata of the throat microbiome samples	throat.meta.filter
OTU count table from 16S sequencing of the throat microbiome samples	throat.otu.table.filter
Taxonomy names for OTUs from 16S sequencing of the throat microbiome samples	throat.otu.taxonomy

Package: LOCOM2 1.1

LOCOM2: A Logistic Regression Model for Testing Microbial Differential Abundance

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)