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

Model Methods

Core functions for manipulating models, running simulations, and extracting results.

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

run_multiple() run_multiple_get_results() make_saver()

Run multiple simulations at once

Model Diagrams

Functions for creating and visualizing model state transition diagrams.

print(<epiworld_diagram>) plot(<epiworld_diagram>) draw_mermaid_from_data() draw_mermaid_from_matrix() draw_mermaid_from_file() draw_mermaid_from_files()

Model Diagram

Agents

Functions for creating, inspecting, and manipulating agents in models.

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

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 History

Functions to extract simulation history at total, variant, and tool levels.

get_hist_total() get_today_total() plot(<epiworld_hist>) get_hist_virus() get_hist_tool()

Model history and totals

Transition Dynamics & Incidence

Transition counts by day, incidence plots, and array conversion.

get_hist_transition_matrix() as.array(<epiworld_hist_transition>) plot_incidence() plot(<epiworld_hist_transition>)

Transition dynamics and incidence

Reproductive Number (Rt)

Extraction and plotting of Rt by virus over time.

get_reproductive_number() plot(<epiworld_repnum>) plot_reproductive_number()

Reproductive number (Rt)

compute_reproduction_number()

Compute a reproduction number from a daily contact matrix with group-specific infectiousness and susceptibility

Generation Time

Extraction and plotting of generation time by virus over time.

get_generation_time() plot(<epiworld_generation_time>) plot_generation_time()

Generation time

plot(<epiworld_model>)

Plot epidemic curves

Network functions

Random graphs, transmission edges, including seeded infections.

get_transmissions()

Transmission network

agents_sbm()

Network models in epiworld

Summaries

Active cases, outbreak size, and transition probability snapshots.

get_transition_probability() get_active_cases() get_outbreak_size()

Summary counts and probabilities

Hospitalizations

Weighted hospitalization tracking when agents have multiple tools.

get_hospitalizations()

Hospitalizations by tool

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()

Virus design

Virus Distribution

Functions for assigning viruses across agents at initialization.

set_distribution_virus() distribute_virus_randomly() distribute_virus_to_set() distribute_virus_set() distribute_virus_to_entities()

Virus distribution functions

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>)

Tools in epiworld

Tool Distribution

Functions for assigning tools across agents at initialization.

set_distribution_tool() distribute_tool_randomly() distribute_tool_to_set() distribute_tool_to_entities()

Tool distribution functions

Entity Functions and Mixing Models

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

get_contact_matrix() set_contact_matrix()

Get or set the contact matrix of a mixing model

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

Model building

Functions for constructing models from components and running simulations.

Model() add_state() update_fun_susceptible() update_fun_rate() set_state_function()

Model building functions

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