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

## Documentation for package ‘radEmu’ version 2.3.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

control_fn | Create list of control options (to pass to 'emuFit()')
dpseudohuber_median_dx | Calculate the derivative to the pseudo-Huber smoothed median
dpsuedohuber_median_dx | Calculate the derivative to the pseudo-Huber smoothed median
emuFit | Fit radEmu model
emuFit_check | Runs checks for appropriate arguments before running 'emuFit()'
emuFit_micro | Fit radEmu model. Called by emuFit
emuFit_micro_penalized | Fit radEmu model with Firth penalty
fit_null | fits model with B_kj constrained to equal g(B_k) for constraint fn g
fit_null_discrete | fits model with B_kj constrained to equal g(B_k) for constraint fn g, for a symmetric constraint with a discrete design
fit_null_scc | fits model with B_kj constrained to equal g(B_k) for constraint fn g, for a single category constraint
fit_null_symmetric | fits model with B_kj constrained to equal g(B_k) for constraint fn g, for a symmetric constraint
fit_null_symmetric_subset | fits model with B_kj constrained to equal g(B_k) for constraint fn g, for a symmetric constraint
make_design_matrix | Generates the design matrix for a given 'formula' and 'data' object
make_diagnostics_plots | makes plots to investigate convergence of estimation under null hypothesis
make_reference_constraints | Make lists of constraint functions and their gradients when using a reference taxon
plot.emuFit | Plotting function
power_model | A fitted GLM model for the power of radEmu to reject a truly false null hypothesis
print.emuFit | Print function
pseudohuber_median | Calculate the pseudo-Huber smoothed median
psuedohuber_median | Calculate the pseudo-Huber smoothed median
score_test | Run robust score test
simulate_data | Data simulation function
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.