Package: yersinia 0.1.0

Nick Gauthier

yersinia: Plague Transmission Models for Epidemiological Research

A toolkit for plague transmission modeling using stochastic compartmental models. Implements carcass-based transmission dynamics (Didelot et al. 2017) with spatial structure and multi-host dynamics for epidemiological research.

Authors:Nick Gauthier [aut, cre], Nich Martin [aut]

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 |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
yersinia/json (API)

# Install 'yersinia' in R:
install.packages('yersinia', repos = c('https://flmnh-ai.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/flmnh-ai/yersinia/issues

Pkgdown/docs site:https://flmnh-ai.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On CRAN:

Conda:

cppopenmp

2.86 score 16 scripts 69 exports 29 dependencies

Last updated from:55e29c328d. Checks:12 ERROR, 1 OK. Indexed: yes.

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linux-devel-x86_64ERROR236
source / vignettesERROR339
linux-release-arm64ERROR222
linux-release-x86_64ERROR210
macos-release-arm64ERROR173
macos-release-x86_64ERROR491
macos-oldrel-arm64ERROR171
macos-oldrel-x86_64ERROR266
windows-develERROR253
windows-releaseERROR221
windows-oldrelERROR237
wasm-releaseOK216

Exports:available_scenariosca_stepcalculate_equilibriumcalculate_force_of_infectioncalculate_outbreak_metricscalculate_R0cohort_datacohort_obs_periodcohort_populationcohort_servercohort_uiconfigurable_param_namesdiag_strip_serverdiag_strip_uidiagnose_bound_pilingdiagnose_chain_stuckdiagnose_low_kappahero_serverhero_uilab_applab_fit_assemblelab_fit_forward_simlab_fit_runlab_fit_run_productionlab_session_from_listLabSessionload_scenariomake_hex_latticemake_lookupsmake_square_gridmodel_accordion_servermodel_accordion_uimodel_config_defaultmodel_config_resolvenew_plague_resultsoutbreak_summaryplague_fit_filterplague_fit_fitted_namesplague_fit_fixed_parsplague_fit_priorplague_fit_setupplague_fit_vcvplague_stochastic_humansplague_stochastic_metapopplot_comparisonplot_dynamicsplot_phase_portraitplot_sensitivityprior_boundsprior_defaultprior_densityprior_familiesprior_to_dslpriors_accordion_serverpriors_accordion_uipriors_defaultpriors_to_boundspriors_to_dslrun_carun_diagnosticsrun_plague_metapop_modelrun_plague_modelstatus_bar_serverstatus_bar_uisummarize_outbreak_metricswith_alpha_seasonalwith_briere_seasonalwith_per_group_fixedwith_R0_to_beta_r

Dependencies:backportscheckmateclicpp11cubelyrdplyrdust2genericsgluelatticelifecyclemagrittrMatrixmontyodin2pillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithryaml

Readme and manuals

Help Manual

Help pageTopics
Names of bundled scenario YAML files.available_scenarios
Advance the CA one tickca_step
Calculate equilibrium values for deterministic modelscalculate_equilibrium
Calculate force of infection over timecalculate_force_of_infection
Calculate outbreak summary statisticscalculate_outbreak_metrics
Calculate basic reproduction number (R0) for different model typescalculate_R0
Long-format cohort data with NA-padded synchronized time grid.cohort_data
Per-outbreak observation period (must be consistent across the cohort).cohort_obs_period
Per-outbreak population values (K_h / K_r when fixed).cohort_population
Cohort module — server.cohort_server
Cohort module — UI.cohort_ui
Names of model parameters configurable from the Virtual Lab UI.configurable_param_names
Temperature-dependent multiplier for delta_R (rate of loss of carcass infectiousness in a Didelot-style plague model)delta_R_multiplier
Diagnostics strip module — server.diag_strip_server
Diagnostics strip module — UI.diag_strip_ui
Detect posterior mass piling against prior bounds.diagnose_bound_piling
Detect non-mixing chains via R-hat.diagnose_chain_stuck
Detect low NegBinomial dispersion ('kappa').diagnose_low_kappa
Hero plot module — server.hero_server
Hero plot module — UI.hero_ui
Launch the yersinia Virtual Lab Shiny app.lab_app
Assemble a deterministic-pilot fit from a LabSession.lab_fit_assemble
Posterior predictive forward simulation from a Lab fit.lab_fit_forward_sim
Run a deterministic-pilot fit assembled by 'lab_fit_assemble()'.lab_fit_run
Run a stochastic production fit on top of a deterministic pilot.lab_fit_run_production
Reconstruct a LabSession from a saved state list.lab_session_from_list
LabSession R6 class — Virtual Lab session state.LabSession
Load named scenario parametersload_named_scenario
Load plague model scenario parametersload_scenario
Build a hexagonal CA latticemake_hex_lattice
Build CA transition-probability lookupsmake_lookups
Build a square-lattice CA gridmake_square_grid
Model accordion module — server.model_accordion_server
Model accordion module — UI.model_accordion_ui
Default model configuration for a fresh Virtual Lab session.model_config_default
Resolve a model config to per-parameter scope and value.model_config_resolve
Create a plague_results objectnew_plague_results
Per-outbreak summary table for the cohort picker.outbreak_summary
Historical plague outbreak dataoutbreaks
Build a particle filter for the humans plague model.plague_fit_filter
Default fitted parameter names for plague humans fits.plague_fit_fitted_names
Build the fixed (non-fitted) parameter list for a plague humans fit.plague_fit_fixed_pars
Default prior over the fitted plague humans parameters (monty DSL).plague_fit_prior
Assemble everything needed to call 'monty::monty_sample()' on a plague fit.plague_fit_setup
Default diagonal VCV for the random-walk sampler.plague_fit_vcv
Stochastic humans plague model (carcass formulation)plague_stochastic_humans
Stochastic metapopulation plague model (rat dispersal between patches)plague_stochastic_metapop
Create multi-panel comparison plotplot_comparison
Plot compartment dynamics with uncertainty bandsplot_dynamics
Plot phase portrait (S vs I)plot_phase_portrait
Plot parameter sensitivity resultsplot_sensitivity
Plot method for plague_resultsplot.plague_results
Print method for outbreak metricsprint.plague_outbreak_metrics
Print method for plague_resultsprint.plague_results
Print method for plague_parametersprint.scenario_parameters
Hard-bound interval implied by a prior, for piling detection.prior_bounds
Default prior for a single fittable parameter.prior_default
Evaluate a prior's density on a grid for plotting.prior_density
Registry of supported prior distribution families.prior_families
Convert one prior to a monty-DSL expression.prior_to_dsl
Priors accordion module — server.priors_accordion_server
Priors accordion module — UI.priors_accordion_ui
Build a default priors list for a set of fitted parameters.priors_default
Bounds for every parameter in a packer, including per-group decorations.priors_to_bounds
Convert a full priors list to a list of monty-DSL expressions.priors_to_dsl
Run a CA from 'n_seeds' seed cells for 'n_ticks'run_ca
Run all v1 diagnostics on a fit.run_diagnostics
Run human stochastic model (dust2/odin2 backend)run_human_stochastic_model
Run plague metapopulation modelrun_plague_metapop_model
Run plague model simulationrun_plague_model
Status bar module — server.status_bar_server
Status bar module — UI.status_bar_ui
Summarize outbreak metrics across replicatessummarize_outbreak_metrics
Summary method for plague_resultssummary.plague_results
Modulate per-group seasonal forcing by a fitted alpha exponent.with_alpha_seasonal
Compute per-group seasonal forcing from temperature via Brière.with_briere_seasonal
Splice per-group fixed parameters into a grouped packer.with_per_group_fixed
Convert R0 to beta_r per group during unpack.with_R0_to_beta_r