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

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Documentation for package ‘radEmu’ version 2.3.2.0

• 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.