# Fast Agent-Based Epi Models

## Documentation for package ‘epiworldR’ version 0.13.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A C D E G H I L M N P Q R S T U V misc

## -- A --

actions | Global Events
add_entities_from_dataframe | Add entities to a model according to a data.frame
add_entity | Get entities
add_globalevent | Global Events
add_param | Methods for epiworldR objects
add_param.epiworld_model | Methods for epiworldR objects
add_tool | Tools in epiworld
add_tool_agent | Load agents to a model
add_tool_n | Deprecated and removed functions in epiworldR
add_virus | Virus design
add_virus_agent | Load agents to a model
add_virus_n | Deprecated and removed functions in epiworldR
agents | Agents in epiworldR
agents_from_edgelist | Load agents to a model
agents_smallworld | Load agents to a model
as.array.epiworld_hist_transition | Transition dynamics and incidence

## -- C --

change_state | Load agents to a model
clone_model | Methods for epiworldR objects

## -- D --

distribute_entity_randomly | Get entities
distribute_entity_to_set | Get entities
distribute_tool_randomly | Tools in epiworld
distribute_tool_to_entities | Tools in epiworld
distribute_tool_to_set | Tools in epiworld
distribute_virus_randomly | Virus design
distribute_virus_set | Virus design
distribute_virus_to_entities | Virus design
distribute_virus_to_set | Virus design
draw_mermaid | Methods for epiworldR objects
draw_mermaid_from_data | Model Diagram
draw_mermaid_from_file | Model Diagram
draw_mermaid_from_files | Model Diagram
draw_mermaid_from_matrix | Model Diagram

## -- E --

entities | Get entities
entity | Get entities
entity_add_agent | Get entities
entity_get_agents | Get entities
epiworld-gentime | Generation time
epiworld-history | Model history and totals
epiworld-hospitalizations | Hospitalizations by tool
epiworld-methods | Methods for epiworldR objects
epiworld-model-diagram | Model Diagram
epiworld-repnum | Reproductive number (Rt)
epiworld-summaries | Summary counts and probabilities
epiworld-transition | Transition dynamics and incidence
epiworld-transmissions | Transmission network
epiworldR-deprecated | Deprecated and removed functions in epiworldR
epiworld_agent | Agents in epiworldR
epiworld_agents | Agents in epiworldR
epiworld_diffnet | Network Diffusion Model
epiworld_generation_time | Generation time
epiworld_globalevent | Global Events
epiworld_globalevent_set_param | Global Events
epiworld_globalevent_tool | Global Events
epiworld_globalevent_tool_logit | Global Events
epiworld_hist_tool | Model history and totals
epiworld_hist_total | Model history and totals
epiworld_hist_transition | Transition dynamics and incidence
epiworld_hist_virus | Model history and totals
epiworld_lfmcmc | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
epiworld_model | Methods for epiworldR objects
epiworld_repnum | Reproductive number (Rt)
epiworld_saver | Run multiple simulations at once
epiworld_seir | Susceptible Exposed Infected Recovered model (SEIR)
epiworld_seirconn | Susceptible Exposed Infected Removed model (SEIR connected)
epiworld_seird | Susceptible-Exposed-Infected-Recovered-Deceased model (SEIRD)
epiworld_seirdconn | Susceptible Exposed Infected Removed Deceased model (SEIRD connected)
epiworld_seirmixing | Susceptible Exposed Infected Removed model (SEIR) with mixing
epiworld_seirmixingquarantine | Susceptible Exposed Infected Removed model (SEIR) with mixing and quarantine
epiworld_sir | SIR model
epiworld_sirconn | Susceptible Infected Removed model (SIR connected)
epiworld_sird | SIRD model
epiworld_sirdconn | Susceptible Infected Removed Deceased model (SIRD connected)
epiworld_sirmixing | Susceptible Infected Removed model (SIR) with mixing
epiworld_sis | SIS model
epiworld_sisd | SISD model
epiworld_surv | SURV model
epiworld_tool | Tools in epiworld
epiworld_virus | Virus design

## -- G --

get_active_cases | Summary counts and probabilities
get_agents | Agents in epiworldR
get_agents.epiworld_model | Agents in epiworldR
get_agents_data_ncols | Methods for epiworldR objects
get_agents_states | Load agents to a model
get_agents_tools | Load agents to a model
get_all_accepted_kernel_scores | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_all_accepted_params | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_all_accepted_stats | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_all_sample_acceptance | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_all_sample_drawn_prob | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_all_sample_kernel_scores | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_all_sample_params | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_all_sample_stats | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_current_accepted_params | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_current_accepted_stats | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_current_proposed_params | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_current_proposed_stats | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_entities | Get entities
get_entity_name | Get entities
get_entity_size | Get entities
get_generation_time | Generation time
get_hist_tool | Model history and totals
get_hist_total | Model history and totals
get_hist_transition_matrix | Transition dynamics and incidence
get_hist_virus | Model history and totals
get_hospitalizations | Hospitalizations by tool
get_initial_params | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_mean_params | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_mean_stats | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_name | Methods for epiworldR objects
get_name_tool | Tools in epiworld
get_name_virus | Virus design
get_ndays | Methods for epiworldR objects
get_network | Load agents to a model
get_n_params | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_n_replicates | Methods for epiworldR objects
get_n_samples | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_n_stats | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_n_tools | Methods for epiworldR objects
get_n_viruses | Methods for epiworldR objects
get_observed_stats | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
get_outbreak_size | Summary counts and probabilities
get_param | Methods for epiworldR objects
get_reproductive_number | Reproductive number (Rt)
get_state | Agents in epiworldR
get_states | Methods for epiworldR objects
get_today_total | Model history and totals
get_tool | Methods for epiworldR objects
get_transition_probability | Summary counts and probabilities
get_transmissions | Transmission network
get_virus | Methods for epiworldR objects
global-actions | Global Events
global-events | Global Events
globalaction_fun | Deprecated and removed functions in epiworldR
globalaction_set_params | Deprecated and removed functions in epiworldR
globalaction_tool | Deprecated and removed functions in epiworldR
globalaction_tool_logit | Deprecated and removed functions in epiworldR
globalevent_fun | Global Events
globalevent_set_params | Global Events
globalevent_tool | Global Events
globalevent_tool_logit | Global Events

## -- H --

has_tool | Load agents to a model
has_virus | Load agents to a model

## -- I --

initial_states | Methods for epiworldR objects

## -- L --

LFMCMC | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
load_agents_entities_ties | Get entities

## -- M --

make_saver | Run multiple simulations at once
ModelDiffNet | Network Diffusion Model
ModelMeaslesMixing | Deprecated and removed functions in epiworldR
ModelMeaslesMixingRiskQuarantine | Deprecated and removed functions in epiworldR
ModelMeaslesQuarantine | Deprecated and removed functions in epiworldR
ModelMeaslesSchool | Deprecated and removed functions in epiworldR
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

## -- N --

network | Load agents to a model

## -- P --

plot.epiworld_diagram | Model Diagram
plot.epiworld_generation_time | Generation time
plot.epiworld_hist | Model history and totals
plot.epiworld_hist_transition | Transition dynamics and incidence
plot.epiworld_repnum | Reproductive number (Rt)
plot_generation_time | Generation time
plot_incidence | Transition dynamics and incidence
plot_reproductive_number | Reproductive number (Rt)
print.epiworld_agent | Agents in epiworldR
print.epiworld_agents | Agents in epiworldR
print.epiworld_agents_tools | Tools in epiworld
print.epiworld_diagram | Model Diagram
print.epiworld_lfmcmc | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)

## -- Q --

queuing_off | Methods for epiworldR objects
queuing_on | Methods for epiworldR objects

## -- R --

rm_entity | Get entities
rm_globalevent | Global Events
rm_tool | Tools in epiworld
rm_virus | Virus design
run | Methods for epiworldR objects
run_lfmcmc | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
run_multiple | Run multiple simulations at once
run_multiple_get_results | Run multiple simulations at once

## -- S --

set_agents_data | Methods for epiworldR objects
set_death_reduction | Tools in epiworld
set_death_reduction_fun | Tools in epiworld
set_death_reduction_ptr | Tools in epiworld
set_distribution_entity | Get entities
set_distribution_tool | Tools in epiworld
set_distribution_virus | Virus design
set_incubation | Virus design
set_incubation_fun | Virus design
set_incubation_ptr | Virus design
set_kernel_fun | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
set_name | Methods for epiworldR objects
set_name_tool | Tools in epiworld
set_name_virus | Virus design
set_observed_data | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
set_param | Methods for epiworldR objects
set_params_names | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
set_prob_death | Virus design
set_prob_death_fun | Virus design
set_prob_death_ptr | Virus design
set_prob_infecting | Virus design
set_prob_infecting_fun | Virus design
set_prob_infecting_ptr | Virus design
set_prob_recovery | Virus design
set_prob_recovery_fun | Virus design
set_prob_recovery_ptr | Virus design
set_proposal_fun | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
set_recovery_enhancer | Tools in epiworld
set_recovery_enhancer_fun | Tools in epiworld
set_recovery_enhancer_ptr | Tools in epiworld
set_simulation_fun | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
set_stats_names | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
set_summary_fun | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
set_susceptibility_reduction | Tools in epiworld
set_susceptibility_reduction_fun | Tools in epiworld
set_susceptibility_reduction_ptr | Tools in epiworld
set_transmission_reduction | Tools in epiworld
set_transmission_reduction_fun | Tools in epiworld
set_transmission_reduction_ptr | Tools in epiworld
size | Methods for epiworldR objects
summary.epiworld_model | Methods for epiworldR objects

## -- T --

today | Methods for epiworldR objects
tool | Tools in epiworld
tool_fun_logit | Tools in epiworld

## -- U --

use_kernel_fun_gaussian | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
use_proposal_norm_reflective | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)

## -- V --

verbose_off | Methods for epiworldR objects
verbose_off.epiworld_lfmcmc | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)
verbose_on | Methods for epiworldR objects
virus | Virus design
virus_fun_logit | Virus design
virus_set_state | Virus design

## -- misc --

[.epiworld_agents | Agents in epiworldR
[.epiworld_entities | Get entities