Package index • epiworldR

General Models

Standard epidemiological models including SIR, SEIR, SIS, and their variants.

ModelDiffNet(): Network Diffusion Model
ModelSEIR(): Susceptible Exposed Infected Recovered model (SEIR)
ModelSEIRCONN(): Susceptible Exposed Infected Removed model (SEIR connected)
ModelSEIRD(): Susceptible-Exposed-Infected-Recovered-Deceased model (SEIRD)
ModelSEIRDCONN(): Susceptible Exposed Infected Removed Deceased model (SEIRD connected)
ModelSEIRMixing(): Susceptible Exposed Infected Removed model (SEIR) with mixing
ModelSEIRMixingQuarantine(): Susceptible Exposed Infected Removed model (SEIR) with mixing and quarantine
ModelSIR(): SIR model
ModelSIRCONN(): Susceptible Infected Removed model (SIR connected)
ModelSIRD(): SIRD model
ModelSIRDCONN(): Susceptible Infected Removed Deceased model (SIRD connected)
ModelSIRLogit(): SIR Logistic model
ModelSIRMixing(): Susceptible Infected Removed model (SIR) with mixing
ModelSIS(): SIS model
ModelSISD(): SISD model
ModelSURV(): SURV model

Measles Models

Specialized measles models with mixing, quarantine, and vaccination features.

ModelMeaslesMixing(): Measles model with mixing
ModelMeaslesMixingRiskQuarantine(): Measles model with mixing and risk-based quarantine
ModelMeaslesSchool(): Measles model with quarantine

Likelihood-Free MCMC

Functions for performing Likelihood-Free Markov Chain Monte Carlo simulations.

LFMCMC() run_lfmcmc() set_observed_data() set_proposal_fun() use_proposal_norm_reflective() set_simulation_fun() set_summary_fun() set_kernel_fun() use_kernel_fun_gaussian() get_mean_params() get_mean_stats() get_initial_params() get_current_proposed_params() get_current_accepted_params() get_current_proposed_stats() get_current_accepted_stats() get_observed_stats() get_all_sample_params() get_all_sample_stats() get_all_sample_acceptance() get_all_sample_drawn_prob() get_all_sample_kernel_scores() get_all_accepted_params() get_all_accepted_stats() get_all_accepted_kernel_scores() get_n_samples() get_n_stats() get_n_params() verbose_off(<epiworld_lfmcmc>) set_params_names() set_stats_names() print(<epiworld_lfmcmc>): Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)

Model Utility Functions

Functions for manipulating models, running simulations, and extracting results.

get_agents() `[`(<epiworld_agents>) print(<epiworld_agent>) print(<epiworld_agents>) get_state(): Agents in epiworldR
agents_smallworld() agents_from_edgelist() get_network() get_agents_states() add_virus_agent() add_tool_agent() has_virus() has_tool() change_state() get_agents_tools(): Load agents to a model
get_hist_total() get_today_total() get_hist_virus() get_hist_tool() get_transition_probability() get_reproductive_number() plot(<epiworld_repnum>) plot_reproductive_number() get_hist_transition_matrix() as.array(<epiworld_hist_transition>) plot_incidence() plot(<epiworld_hist_transition>) get_transmissions() get_generation_time() plot(<epiworld_generation_time>) plot_generation_time(): Accessing the database of epiworld
queuing_on() queuing_off() verbose_off() verbose_on() run() summary(<epiworld_model>) get_states() get_param() add_param() set_param() set_name() get_name() get_n_viruses() get_n_tools() get_ndays() today() get_n_replicates() size() set_agents_data() get_agents_data_ncols() get_virus() get_tool() initial_states() clone_model() draw_mermaid(): Methods for epiworldR objects
print(<epiworld_diagram>) plot(<epiworld_diagram>) draw_mermaid_from_data() draw_mermaid_from_matrix() draw_mermaid_from_file() draw_mermaid_from_files(): Model Diagram
run_multiple() run_multiple_get_results() make_saver(): Run multiple simulations at once

Virus Functions

Functions for creating and manipulating virus objects in models.

virus() set_name_virus() get_name_virus() add_virus() virus_set_state() rm_virus() virus_fun_logit() set_prob_infecting() set_prob_infecting_ptr() set_prob_infecting_fun() set_prob_recovery() set_prob_recovery_ptr() set_prob_recovery_fun() set_prob_death() set_prob_death_ptr() set_prob_death_fun() set_incubation() set_incubation_ptr() set_incubation_fun() set_distribution_virus() distribute_virus_randomly() distribute_virus_to_set() distribute_virus_set(): Virus design

Tool Functions

Functions for creating and managing tools (e.g., vaccines, interventions).

tool() set_name_tool() get_name_tool() add_tool() rm_tool() tool_fun_logit() set_susceptibility_reduction() set_susceptibility_reduction_ptr() set_susceptibility_reduction_fun() set_transmission_reduction() set_transmission_reduction_ptr() set_transmission_reduction_fun() set_recovery_enhancer() set_recovery_enhancer_ptr() set_recovery_enhancer_fun() set_death_reduction() set_death_reduction_ptr() set_death_reduction_fun() print(<epiworld_agents_tools>) set_distribution_tool() distribute_tool_randomly() distribute_tool_to_set(): Tools in epiworld

Entity Functions

Functions for working with entities in mixing models.

get_entities() `[`(<epiworld_entities>) entity() get_entity_size() get_entity_name() entity_add_agent() rm_entity() add_entity() load_agents_entities_ties() entity_get_agents() distribute_entity_randomly() distribute_entity_to_set() set_distribution_entity(): Get entities

Global Events

Functions for defining and managing global events in simulations.

globalevent_tool() globalevent_tool_logit() globalevent_set_params() globalevent_fun() add_globalevent() rm_globalevent(): Global Events