Package: LOCOM2 1.0

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>.

Authors:Yi-Juan Hu [aut, cre]

LOCOM2_1.0.tar.gz
LOCOM2_1.0.tar.gz(r-4.7-arm64)LOCOM2_1.0.tar.gz(r-4.7-x86_64)LOCOM2_1.0.tar.gz(r-4.6-arm64)LOCOM2_1.0.tar.gz(r-4.6-x86_64)
LOCOM2_1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
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:

On CRAN:

Conda:

openblascppopenmp

1.70 score 234 downloads 1 exports 79 dependencies

Last updated from:2bb5211708. Checks:6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK167
linux-devel-x86_64OK160
source / vignettesOK212
linux-release-arm64OK158
linux-release-x86_64OK156
wasm-releaseOK143

Exports:locom2

Dependencies:abindbackportsBHBiocParallelbootbroomcarcarDataclicodetoolscolorspacecowplotcpp11DerivdoBydplyrfarverforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsggplot2gluegtableisobandlabelinglambda.rlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmatrixStatsmgcvmicrobenchmarkminqamodelrnlmenloptrnnetnumDerivpbkrtestpermutepillarpkgconfigpurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangS7scalessnowSparseMstringistringrsurvivaltibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrzoo