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  "Title": "Plague Transmission Models for Epidemiological Research",
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  "Description": "A toolkit for plague transmission modeling using\nstochastic compartmental models. Implements carcass-based\ntransmission dynamics (Didelot et al. 2017) with spatial\nstructure and multi-host dynamics for epidemiological research.",
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    "ca_step",
    "calculate_equilibrium",
    "calculate_force_of_infection",
    "calculate_outbreak_metrics",
    "calculate_R0",
    "cohort_data",
    "cohort_obs_period",
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    "hero_ui",
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    "lab_fit_assemble",
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    "lab_fit_run",
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    "load_scenario",
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    "model_accordion_server",
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    "outbreak_summary",
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    "plague_stochastic_humans",
    "plague_stochastic_metapop",
    "plot_comparison",
    "plot_dynamics",
    "plot_phase_portrait",
    "plot_sensitivity",
    "prior_bounds",
    "prior_default",
    "prior_density",
    "prior_families",
    "prior_to_dsl",
    "priors_accordion_server",
    "priors_accordion_ui",
    "priors_default",
    "priors_to_bounds",
    "priors_to_dsl",
    "run_ca",
    "run_diagnostics",
    "run_plague_metapop_model",
    "run_plague_model",
    "status_bar_server",
    "status_bar_ui",
    "summarize_outbreak_metrics",
    "with_alpha_seasonal",
    "with_briere_seasonal",
    "with_per_group_fixed",
    "with_R0_to_beta_r"
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      "title": "Historical plague outbreak data",
      "object": "outbreaks",
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        "tbl",
        "data.frame"
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      "fields": [
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        "location",
        "year",
        "population",
        "day",
        "deaths"
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      "table": true,
      "tojson": true
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      "title": "Names of bundled scenario YAML files.",
      "topics": [
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      "title": "Advance the CA one tick",
      "topics": [
        "ca_step"
      ]
    },
    {
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      "title": "Calculate equilibrium values for deterministic models",
      "topics": [
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      "title": "Calculate force of infection over time",
      "topics": [
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      "topics": [
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      "topics": [
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      ]
    },
    {
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      "topics": [
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    },
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      "title": "Per-outbreak population values (K_h / K_r when fixed).",
      "topics": [
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      ]
    },
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      "title": "Cohort module — server.",
      "topics": [
        "cohort_server"
      ]
    },
    {
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      "title": "Cohort module — UI.",
      "topics": [
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      "topics": [
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    },
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      "title": "Temperature-dependent multiplier for delta_R (rate of loss of carcass infectiousness in a Didelot-style plague model)",
      "topics": [
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      "topics": [
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      "title": "Diagnostics strip module — UI.",
      "topics": [
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      "topics": [
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    {
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      "topics": [
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      "title": "Detect low NegBinomial dispersion ('kappa').",
      "topics": [
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    },
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      "title": "Hero plot module — server.",
      "topics": [
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    },
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      "title": "Hero plot module — UI.",
      "topics": [
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    },
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      "title": "Posterior predictive forward simulation from a Lab fit.",
      "topics": [
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    },
    {
      "page": "lab_fit_run",
      "title": "Run a deterministic-pilot fit assembled by 'lab_fit_assemble()'.",
      "topics": [
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      ]
    },
    {
      "page": "lab_fit_run_production",
      "title": "Run a stochastic production fit on top of a deterministic pilot.",
      "topics": [
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    },
    {
      "page": "lab_session_from_list",
      "title": "Reconstruct a LabSession from a saved state list.",
      "topics": [
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    },
    {
      "page": "LabSession",
      "title": "LabSession R6 class — Virtual Lab session state.",
      "topics": [
        "LabSession"
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    },
    {
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      "title": "Load named scenario parameters",
      "topics": [
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    {
      "page": "load_scenario",
      "title": "Load plague model scenario parameters",
      "topics": [
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    },
    {
      "page": "make_hex_lattice",
      "title": "Build a hexagonal CA lattice",
      "topics": [
        "make_hex_lattice"
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    },
    {
      "page": "make_lookups",
      "title": "Build CA transition-probability lookups",
      "topics": [
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    },
    {
      "page": "make_square_grid",
      "title": "Build a square-lattice CA grid",
      "topics": [
        "make_square_grid"
      ]
    },
    {
      "page": "model_accordion_server",
      "title": "Model accordion module — server.",
      "topics": [
        "model_accordion_server"
      ]
    },
    {
      "page": "model_accordion_ui",
      "title": "Model accordion module — UI.",
      "topics": [
        "model_accordion_ui"
      ]
    },
    {
      "page": "model_config_default",
      "title": "Default model configuration for a fresh Virtual Lab session.",
      "topics": [
        "model_config_default"
      ]
    },
    {
      "page": "model_config_resolve",
      "title": "Resolve a model config to per-parameter scope and value.",
      "topics": [
        "model_config_resolve"
      ]
    },
    {
      "page": "new_plague_results",
      "title": "Create a plague_results object",
      "topics": [
        "new_plague_results"
      ]
    },
    {
      "page": "outbreak_summary",
      "title": "Per-outbreak summary table for the cohort picker.",
      "topics": [
        "outbreak_summary"
      ]
    },
    {
      "page": "outbreaks",
      "title": "Historical plague outbreak data",
      "topics": [
        "outbreaks"
      ]
    },
    {
      "page": "plague_fit_filter",
      "title": "Build a particle filter for the humans plague model.",
      "topics": [
        "plague_fit_filter"
      ]
    },
    {
      "page": "plague_fit_fitted_names",
      "title": "Default fitted parameter names for plague humans fits.",
      "topics": [
        "plague_fit_fitted_names"
      ]
    },
    {
      "page": "plague_fit_fixed_pars",
      "title": "Build the fixed (non-fitted) parameter list for a plague humans fit.",
      "topics": [
        "plague_fit_fixed_pars"
      ]
    },
    {
      "page": "plague_fit_prior",
      "title": "Default prior over the fitted plague humans parameters (monty DSL).",
      "topics": [
        "plague_fit_prior"
      ]
    },
    {
      "page": "plague_fit_setup",
      "title": "Assemble everything needed to call 'monty::monty_sample()' on a plague fit.",
      "topics": [
        "plague_fit_setup"
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    },
    {
      "page": "plague_fit_vcv",
      "title": "Default diagonal VCV for the random-walk sampler.",
      "topics": [
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    },
    {
      "page": "plague_stochastic_humans",
      "title": "Stochastic humans plague model (carcass formulation)",
      "topics": [
        "plague_stochastic_humans"
      ]
    },
    {
      "page": "plague_stochastic_metapop",
      "title": "Stochastic metapopulation plague model (rat dispersal between patches)",
      "topics": [
        "plague_stochastic_metapop"
      ]
    },
    {
      "page": "plot_comparison",
      "title": "Create multi-panel comparison plot",
      "topics": [
        "plot_comparison"
      ]
    },
    {
      "page": "plot_dynamics",
      "title": "Plot compartment dynamics with uncertainty bands",
      "topics": [
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      ]
    },
    {
      "page": "plot_phase_portrait",
      "title": "Plot phase portrait (S vs I)",
      "topics": [
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      ]
    },
    {
      "page": "plot_sensitivity",
      "title": "Plot parameter sensitivity results",
      "topics": [
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    {
      "page": "plot.plague_results",
      "title": "Plot method for plague_results",
      "topics": [
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    {
      "page": "print.plague_outbreak_metrics",
      "title": "Print method for outbreak metrics",
      "topics": [
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    {
      "page": "print.plague_results",
      "title": "Print method for plague_results",
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    {
      "page": "print.scenario_parameters",
      "title": "Print method for plague_parameters",
      "topics": [
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    {
      "page": "prior_bounds",
      "title": "Hard-bound interval implied by a prior, for piling detection.",
      "topics": [
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      ]
    },
    {
      "page": "prior_default",
      "title": "Default prior for a single fittable parameter.",
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