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Package index

Model-neutral diagnostics

Calculate and inspect influence diagnostics. The plot() and autoplot() methods here display influ_diag objects, including influence and CDI plots.

influ()
Calculate CPUE influence diagnostics
influ(<brmsfit>)
Influence diagnostics for brms models
influ(<gam>)
Influence diagnostics for generalised additive models
influ(<glm>)
Influence diagnostics for generalised linear models
influ(<glmmTMB>)
Influence diagnostics for glmmTMB models
influ(<merMod>) influ(<lmerMod>) influ(<glmerMod>)
Influence diagnostics for lme4 mixed models
influ(<sdmTMB>)
Influence diagnostics for sdmTMB models
influ(<tinyVAST>)
Influence diagnostics for tinyVAST models
influ_effects() influ_indices() influ_composition() influ_draws() influ_metrics()
Extract a table from an influence diagnostic
influ_families()
Families supported by the influence engine
plot(<influ_diag>) autoplot(<influ_diag>)
Plot a model-neutral influence diagnostic
plot_cdi()
Overlay coefficient, distribution, and influence diagnostics

Additional diagnostics and comparisons

Compare indices and model steps, and inspect sampling composition and data coverage. The plot() and autoplot() methods here display influ_steps objects.

plot_bubble()
Bubble plot of sampling composition
plot_compare()
Compare standardised CPUE indices
index_ratio() as.data.frame(<influ_index_ratio>) print(<influ_index_ratio>) summary(<influ_index_ratio>)
Calculate point-estimate ratios between stored annual indices
plot_index_ratio() plot(<influ_index_ratio>) autoplot(<influ_index_ratio>)
Plot a separate index-ratio diagnostic
influ_steps() print(<influ_steps>) summary(<influ_steps>)
Calculate a sequence of refitted year-effect contrasts
plot(<influ_steps>) autoplot(<influ_steps>)
Plot a stored step sequence
plot_step()
Display the effect of sequential model-standardisation steps
plot_data_extent()
Plot the completeness of variables through time

CPUE indices and assessment tables

Calculate standardised means or area-integrated totals. Use plot_index(), plot(), or autoplot() to display the resulting influ_index objects.

cpue_index() as.data.frame(<influ_index>) print(<influ_index>)
Calculate an assessment-ready CPUE index
integrate_index()
Calculate an area-integrated expected-response index
index_domain() as.data.frame(<influ_domain>) summary(<influ_domain>) print(<influ_domain>) plot(<influ_domain>) autoplot(<influ_domain>)
Diagnose prediction-domain support and index dependence
index_table()
Format a calculated index for assessment reporting
index_vcov() vcov(<influ_index>)
Extract covariance among calculated annual indices
plot_index() plot(<influ_index>) autoplot(<influ_index>)
Plot calculated CPUE indices
geo_mean()
Geometric mean

Residual diagnostics

Inspect generalised residual patterns, grouped departures, and quantile comparisons. The plot() and autoplot() methods here display influ_residuals objects.

check_cpue() print(<influ_check>) summary(<influ_check>) as.data.frame(<influ_check>)
Check a CPUE model, overall and term by term
plot(<influ_check>) autoplot(<influ_check>)
Plot stored CPUE model-check results
influ_residuals() print(<influ_residuals>)
Calculate compact simulation-based residual diagnostics
as_influ_residuals()
Diagnose externally simulated responses
plot(<influ_residuals>) autoplot(<influ_residuals>)
Plot a four-panel CPUE residual diagnostic
plot_implied_residuals() plot(<influ_implied>) autoplot(<influ_implied>)
Plot residual-implied annual effects
implied_effects() print(<influ_implied>) as.data.frame(<influ_implied>)
Calculate residual-implied effects by year and group
plot_grouped_residuals()
Plot generalised residual departures by year and group
plot_predicted_residuals()
Plot predictive means against generalised residuals

Model-specific criteria and constrained native refitting, with explicit comparison safeguards.

get_bayes_R2()
Summarise Bayesian R-squared for brms models
table_criterion()
Summarise criteria across CPUE model types
search_cpue() print(<influ_search>) summary(<influ_search>) as.data.frame(<influ_search>)
Search a constrained set of CPUE models
selected_model()
Retrieve the recommended model from a CPUE search
plot(<influ_search>) autoplot(<influ_search>)
Plot a stored CPUE model search

Data

Simulated data supplied with the package.

lobsters_per_pot
Simulated CPUE data

Package

influ2
Model-neutral influence diagnostics