Package index • radEmu

All functions

control_fn(): Create list of control options (to pass to emuFit())

dpseudohuber_median_dx() 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_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

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() 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.