Package: LOCOM2 1.0

Yi-Juan Hu

LOCOM2: A Logistic Regression Model for Testing Differential Abundance in Compositional Microbiome Data

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 allows adjustment of confounders.

Authors:Yi-Juan Hu [aut, cre]

LOCOM2_1.0.tar.gz
LOCOM2_1.0.zip(r-4.7-x86_64)LOCOM2_1.0.zip(r-4.7-arm64)LOCOM2_1.0.zip(r-4.6-x86_64)LOCOM2_1.0.zip(r-4.6-arm64)LOCOM2_1.0.zip(r-4.5-x86_64)
LOCOM2_1.0.tgz(r-4.6-x86_64)LOCOM2_1.0.tgz(r-4.6-arm64)LOCOM2_1.0.tgz(r-4.5-x86_64)LOCOM2_1.0.tgz(r-4.5-arm64)
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✨
DESCRIPTION
card.svg |card.png
LOCOM2/json (API)

# Install 'LOCOM2' in R:

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

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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

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:

cpp

3.00 score 2 stars 1 scripts 532 downloads 1 exports 78 dependencies

Last updated from:c038cb499f. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	177
linux-devel-x86_64	OK	197
source / vignettes	OK	243
linux-release-arm64	OK	168
linux-release-x86_64	OK	228
macos-release-arm64	OK	156
macos-release-x86_64	OK	534
macos-oldrel-arm64	OK	159
macos-oldrel-x86_64	OK	531
windows-devel-arm64	OK	356
windows-devel-x86_64	OK	189
windows-release-arm64	OK	357
windows-release-x86_64	OK	117
windows-oldrel-x86_64	OK	180
wasm-release	OK	137

Exports: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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A logistic regression model for testing differential abundance in compositional microbiome data (LOCOM2)	locom2
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