Package index • yersinia

All functions

analyze_outbreaks(): Analyze outbreak characteristics

animate_spatial_spread(): Create animated spatial plot over time

calculate_R0(): Calculate basic reproduction number (R0) for different model types

calculate_equilibrium(): Calculate equilibrium values for deterministic models

calculate_force_of_infection(): Calculate force of infection over time

calculate_outbreak_metrics(): Calculate outbreak summary statistics

calculate_spatial_correlation(): Calculate spatial correlation in infection levels

load_named_scenario(): Load named scenario parameters

load_scenario(): Load plague model scenario parameters

make_contact_matrix(): Calculate model statistics

model: Plague odin.dust models This is an odin.dust model.

new_plague_results(): Create a plague_results object

plot(<plague_results>): Plot method for plague_results

plot_comparison(): Create multi-panel comparison plot

plot_dynamics(): Plot compartment dynamics with uncertainty bands

plot_phase_portrait(): Plot phase portrait (S vs I)

plot_sensitivity(): Plot sensitivity analysis results

plot_spatial_heatmap(): Plot spatial heatmap for a single time point

plot_total_infected(): Generate seasonal forcing

print(<plague_outbreak_metrics>): Print method for outbreak metrics

print(<plague_results>): Print method for plague_results

print(<scenario_parameters>): Print method for plague_parameters

run_human_stochastic_model(): Run human stochastic model

run_plague_model(): Run plague model simulation

run_sensitivity_analysis(): Create simulation timepoints

run_stochastic_simulation(): Run stochastic simulation with given parameters

summarize_outbreak_metrics(): Summarize outbreak metrics across replicates

summary(<plague_results>): Summary method for plague_results

validate_parameters(): Validate plague model parameters