Package index • chlaa

Reference

chlaa_as_fit(): Coerce an object into class `chlaa_fit`
chlaa_case_study_setup(): Build A Shared Paper-Aligned Cholera Case Study Setup
chlaa_ceac(): Cost-effectiveness acceptability table from scenario simulations
chlaa_compare_scenarios(): Compare scenario outcomes against a baseline
chlaa_counterfactual_grid(): Build a counterfactual grid of AA-like scenarios
chlaa_econ_defaults(): Load default economics parameters
chlaa_econ_sources(): Load Economics Assumption Source Metadata
chlaa_fit_density_trace(): Extract Likelihood (Log-Density) Trace From A Fit
chlaa_fit_draws(): Extract posterior draws from a fit object
chlaa_fit_metadata(): Extract fit metadata (packer, prior, start parameters, data)
chlaa_fit_pmcmc(): Fit the cholera model to incidence data using pMCMC (monty + dust2)
chlaa_fit_report(): Summarise fit diagnostics and posterior summaries
chlaa_fit_select_iterations(): Select iterations from a posterior draws matrix
chlaa_fit_trace(): Extract a long trace data frame from posterior draws
chlaa_forecast_from_fit(): Forecast summary from a fitted posterior
chlaa_forecast_scenarios_from_fit(): Forecast multiple scenarios from a fitted posterior
chlaa_generate_example_outbreak_data(): Generate A Synthetic Cholera Outbreak Time Series
chlaa_health_econ(): Health economic outputs from scenario simulations
chlaa_make_aa_scenarios(): Build a standard set of anticipatory action scenarios
chlaa_make_aa_scenarios_from_fit(): Create AA scenario set using a fitted posterior baseline
chlaa_optimise_budget(): Optimise intervention allocation under a budget constraint
chlaa_parameter_info(): Parameter metadata table for the cholera model
chlaa_parameters(): Create a parameter list for the cholera model
chlaa_parameters_print(): Print a parameter table
chlaa_parameters_validate(): Validate a cholera parameter list
chlaa_plot_ce_plane(): Plot a cost-effectiveness plane from scenario comparisons
chlaa_plot_difference_vs_baseline(): Plot Scenario Differences Versus Baseline Through Time
chlaa_plot_forecast(): Plot a forecast summary
chlaa_plot_incidence(): Plot daily incidence summary for a variable
chlaa_plot_likelihood_density(): Plot Distribution Of Likelihood Values
chlaa_plot_likelihood_trace(): Plot The Likelihood Trace
chlaa_plot_parameter_pairs(): Plot Pairwise Posterior Parameter Densities
chlaa_plot_parameter_vs_likelihood(): Plot Parameters Against Sampled Likelihood
chlaa_plot_ppc(): Posterior predictive check plot for observed cases
chlaa_plot_scenario_forecasts(): Plot scenario forecast summaries
chlaa_plot_scenario_overlay(): Plot Scenario Trajectories On A Shared Axis
chlaa_plot_scenarios(): Plot scenario comparison bars for a chosen metric
chlaa_plot_trace(): Plot fit traces for selected parameters
chlaa_plot_trajectories(): Plot trajectories of selected model variables
chlaa_posterior_summary(): Posterior summary table for a fit
chlaa_prepare_data(): Prepare and validate incidence data for model fitting
chlaa_run_counterfactual_grid(): Run a counterfactual grid (convenience)
chlaa_run_scenarios(): Run multiple scenarios
chlaa_run_scenarios_from_snapshot(): Run Multiple Scenarios From A Shared Snapshot
chlaa_scenario(): Create a counterfactual scenario
chlaa_scenario_report(): Produce a compact scenario analysis report object
chlaa_scenario_summary(): Summarise scenario outcomes with uncertainty and baseline deltas
chlaa_scenarios_from_grid(): Convert a counterfactual grid to scenario objects
chlaa_simulate(): Simulate the cholera model
chlaa_simulate_from_snapshot(): Simulate Forward From A Snapshot
chlaa_simulate_posterior(): Posterior predictive simulation
chlaa_snapshot_create(): Create A Simulation Snapshot At A Given Time
chlaa_standard_scenarios(): Build standard operational scenario templates
chlaa_trigger_time_from_sim(): Derive an anticipatory action trigger time from a simulation
chlaa_update_from_fit(): Update a parameter list using posterior information from a fit