Package: radEmu 2.3.2.1

Amy D Willis

radEmu: Using Relative Abundance Data to Estimate of Multiplicative Differences in Mean Absolute Abundance

A differential abundance method for the analysis of microbiome data. 'radEmu' estimates fold-differences in the abundance of taxa across samples relative to "typical" fold-differences. Notably, it does not require pseudocounts, nor choosing a denominator taxon. For more details, see Clausen et al. (2026) <doi:10.1093/biomet/asag009>.

Authors:David Clausen [aut], Amy D Willis [aut, cre], Sarah Teichman [aut]

radEmu_2.3.2.1.tar.gz
radEmu_2.3.2.1.zip(r-4.7)radEmu_2.3.2.1.zip(r-4.6)radEmu_2.3.2.1.zip(r-4.5)
radEmu_2.3.2.1.tgz(r-4.6-any)radEmu_2.3.2.1.tgz(r-4.5-any)
radEmu_2.3.2.1.tar.gz(r-4.7-any)radEmu_2.3.2.1.tar.gz(r-4.6-any)
radEmu_2.3.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
radEmu/json (API)
NEWS

# Install 'radEmu' in R:
install.packages('radEmu', repos = c('https://statdivlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/statdivlab/rademu/issues

Pkgdown/docs site:https://statdivlab.github.io

Datasets:
  • power_model - A fitted GLM model for the power of radEmu to reject a truly false null hypothesis
  • wirbel_otu - MOTU table from Wirbel et al. meta-analysis of fecal metagenomes.
  • wirbel_otu_small - Subset of mOTU table from Wirbel et al. meta-analysis of fecal metagenomes.
  • wirbel_sample - Covariates from Wirbel et al. meta-analysis of fecal metagenomes.
  • wirbel_sample_small - Covariates from Wirbel et al. meta-analysis of fecal metagenomes, for a subset of samples.
  • wirbel_taxonomy - Taxonomy information for mOTUs from Wirbel et al. meta analysis.

On CRAN:

Conda:

dametagenomicsmicrobiomestatistics

7.18 score 65 stars 72 scripts 244 downloads 10 exports 5 dependencies

Last updated from:a4125fb228. Checks:7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING325
source / vignettesERROR253
linux-release-x86_64WARNING309
macos-release-arm64WARNING239
macos-oldrel-arm64WARNING316
windows-develWARNING235
windows-releaseWARNING251
windows-oldrelWARNING235
wasm-releaseOK152

Exports:control_fndpseudohuber_median_dxdpsuedohuber_median_dxemuFitemuFit_micromake_design_matrixmake_reference_constraintspseudohuber_medianpsuedohuber_medianscore_test

Dependencies:latticemagrittrMASSMatrixrlang

Readme and manuals

Help Manual

Help pageTopics
Create list of control options (to pass to 'emuFit()')control_fn
Calculate the derivative to the pseudo-Huber smoothed mediandpseudohuber_median_dx dpsuedohuber_median_dx
Fit radEmu modelemuFit
Runs checks for appropriate arguments before running 'emuFit()'emuFit_check
Fit radEmu model. Called by emuFitemuFit_micro
Fit radEmu model with Firth penaltyemuFit_micro_penalized
fits model with B_kj constrained to equal g(B_k) for constraint fn gfit_null
fits model with B_kj constrained to equal g(B_k) for constraint fn g, for a symmetric constraint with a discrete designfit_null_discrete
fits model with B_kj constrained to equal g(B_k) for constraint fn g, for a single category constraintfit_null_scc
fits model with B_kj constrained to equal g(B_k) for constraint fn g, for a symmetric constraintfit_null_symmetric
fits model with B_kj constrained to equal g(B_k) for constraint fn g, for a symmetric constraintfit_null_symmetric_subset
Generates the design matrix for a given 'formula' and 'data' objectmake_design_matrix
makes plots to investigate convergence of estimation under null hypothesismake_diagnostics_plots
Make lists of constraint functions and their gradients when using a reference taxonmake_reference_constraints
Plotting functionplot.emuFit
A fitted GLM model for the power of radEmu to reject a truly false null hypothesispower_model
Print functionprint.emuFit
Calculate the pseudo-Huber smoothed medianpseudohuber_median psuedohuber_median
Run robust score testscore_test
Data simulation functionsimulate_data
mOTU table from Wirbel et al. meta-analysis of fecal metagenomes.wirbel_otu
subset of mOTU table from Wirbel et al. meta-analysis of fecal metagenomes.wirbel_otu_small
Covariates from Wirbel et al. meta-analysis of fecal metagenomes.wirbel_sample
Covariates from Wirbel et al. meta-analysis of fecal metagenomes, for a subset of samples.wirbel_sample_small
Taxonomy information for mOTUs from Wirbel et al. meta analysis.wirbel_taxonomy