Package index

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

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() get_active_cases() get_outbreak_size()

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() distribute_virus_to_entities()

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() distribute_tool_to_entities()

Tools in epiworld

Entity Functions

Functions for working with entities in mixing models.

add_entities_from_dataframe()

Add entities to a model according to a data.frame

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

Deprecated Functions

Functions that have been renamed or deprecated in recent versions.

globalaction_tool() globalaction_tool_logit() globalaction_set_params() globalaction_fun() add_tool_n() add_virus_n()

Deprecated and removed functions in epiworldR