Package index

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Run a complete audit, summarize risk, plan downstream analysis, and visualize key diagnostics.

moat()

Audit a microbiome study design

summary(<moat_audit>)

Print a MOAT audit summary

autoplot(<moat_audit>)

Plot a MOAT audit risk dashboard

plan_analysis()

Generate a downstream analysis plan from a MOAT audit

report()

Render a MOAT audit HTML report

module_risks()

Extract module-level audit risks

as.data.frame(<moat_audit>)

Coerce a MOAT audit to a compact data frame

audit_reasons()

Extract audit risk reasons

audit_recommendations()

Extract audit recommendations

risk_thresholds()

Risk threshold reference

plot_design()

Plot outcome distribution across a design variable

plot_ordination()

Plot PCoA ordination coordinates from a batch audit

plot_variance()

Plot PERMANOVA variance explained by audited terms

Design And Correction Audits

Audit metadata confounding and evaluate whether batch adjustment is identifiable.

check_design()

Check experimental design metadata associations with the outcome

check_metadata_predictability()

Check whether metadata alone predicts the outcome

check_continuous_design()

Check continuous metadata associations with the outcome

check_balance()

Check batch-by-outcome balance

check_model_matrix()

Check model matrix identifiability

check_correction()

Check batch correction feasibility

Microbiome Distances And Batch Effects

Transform microbiome data, compute distances, and audit distance-based batch effects.

transform_biome()

Transform a feature-by-sample microbiome matrix

compute_biome_distance()

Compute distances between microbiome samples

check_permanova()

Check PERMANOVA variation explained by metadata variables

check_dispersion()

Check multivariate dispersion differences across metadata variables

check_feature_batch()

Check feature-level batch associations

check_batch()

Check microbiome batch effects across distances

Leakage Audits

Detect repeated-measure and metadata-driven validation leakage risks.

check_repeated_measures()

Check repeated-measure leakage risk

check_leakage()

Check validation leakage risk

Data And Audit Objects

Example data and lightweight audit object helpers.

toy_moat

Toy MOAT Microbiome Dataset

is_moat_audit()

Test if an object is a moat_audit

Package Helpers

`%>%`

Pipe operator