R: Fast Agent-Based Epi Models

# Fast Agent-Based Epi Models

## Documentation for package ‘epiworldR’ version 0.1-0

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

## Help Pages

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

epiworldR-package | epiworldR

## -- A --

actions | Global Actions
add_globalevent | Global Actions
add_tool | Tools in epiworld
add_tool_agent | Load agents to a model
add_tool_n | Tools in epiworld
add_virus | Virus design
add_virus_agent | Load agents to a model
add_virus_n | Virus design
agents | Load agents to a model
agents_from_edgelist | Load agents to a model
agents_smallworld | Load agents to a model
as.array.epiworld_hist_transition | Accessing the database of epiworld

## -- C --

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

## -- E --

epiworld-data | Accessing the database of epiworld
epiworld-methods | Methods for epiworldR objects
epiworldR | epiworldR
epiworldR-deprecated | Deprecated functions in epiworldR
epiworld_agent | Agents in epiworldR
epiworld_agents | Agents in epiworldR
epiworld_diffnet | Network Diffusion Model
epiworld_globalevent | Global Actions
epiworld_globalevent_set_param | Global Actions
epiworld_globalevent_tool | Global Actions
epiworld_globalevent_tool_logit | Global Actions
epiworld_hist_tool | Accessing the database of epiworld
epiworld_hist_total | Accessing the database of epiworld
epiworld_hist_variant | Accessing the database of epiworld
epiworld_hist_virus | Accessing the database of epiworld
epiworld_model | Methods for epiworldR objects
epiworld_repnum | Accessing the database of epiworld
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_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_sis | SIS model
epiworld_sisd | SISD model
epiworld_surv | SURV model
epiworld_tool | Tools in epiworld
epiworld_virus | Virus design

## -- G --

get_agents | 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_generation_time | Accessing the database of epiworld
get_hist_tool | Accessing the database of epiworld
get_hist_total | Accessing the database of epiworld
get_hist_transition_matrix | Accessing the database of epiworld
get_hist_virus | Accessing the database of epiworld
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_replicates | Methods for epiworldR objects
get_n_tools | Methods for epiworldR objects
get_n_viruses | Methods for epiworldR objects
get_param | Methods for epiworldR objects
get_reproductive_number | Accessing the database of epiworld
get_state | Agents in epiworldR
get_states | Methods for epiworldR objects
get_today_total | Accessing the database of epiworld
get_tool | Methods for epiworldR objects
get_transition_probability | Accessing the database of epiworld
get_transmissions | Accessing the database of epiworld
get_virus | Methods for epiworldR objects
global-actions | Global Actions
globalaction_fun | Deprecated functions in epiworldR
globalaction_set_params | Deprecated functions in epiworldR
globalaction_tool | Deprecated functions in epiworldR
globalaction_tool_logit | Deprecated functions in epiworldR
globalevent_fun | Global Actions
globalevent_set_params | Global Actions
globalevent_tool | Global Actions
globalevent_tool_logit | Global Actions

## -- H --

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

## -- I --

initial_states | Methods for epiworldR objects

## -- M --

make_saver | Run multiple simulations at once
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)
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
ModelSIS | SIS model
ModelSISD | SISD model
ModelSURV | SURV model

## -- N --

network | Load agents to a model

## -- P --

plot.epiworld_diffnet | Network Diffusion Model
plot.epiworld_generation_time | Accessing the database of epiworld
plot.epiworld_hist_transition | Accessing the database of epiworld
plot.epiworld_repnum | Accessing the database of epiworld
plot.epiworld_seir | Susceptible Exposed Infected Recovered model (SEIR)
plot.epiworld_seirconn | Susceptible Exposed Infected Removed model (SEIR connected)
plot.epiworld_seird | Susceptible-Exposed-Infected-Recovered-Deceased model (SEIRD)
plot.epiworld_seirdconn | Susceptible Exposed Infected Removed Deceased model (SEIRD connected)
plot.epiworld_sir | SIR model
plot.epiworld_sirconn | Susceptible Infected Removed model (SIR connected)
plot.epiworld_sird | SIRD model
plot.epiworld_sirdconn | Susceptible Infected Removed Deceased model (SIRD connected)
plot.epiworld_sis | SIS model
plot.epiworld_sisd | SISD model
plot.epiworld_surv | SURV model
plot_generation_time | Accessing the database of epiworld
plot_incidence | Accessing the database of epiworld
plot_reproductive_number | Accessing the database of epiworld
print.epiworld_agent | Agents in epiworldR
print.epiworld_agents | Agents in epiworldR
print.epiworld_agents_tools | Tools in epiworld

## -- Q --

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

## -- R --

rm_tool | Tools in epiworld
rm_virus | Virus design
run | Methods for epiworldR objects
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_incubation | Virus design
set_incubation_fun | Virus design
set_incubation_ptr | Virus design
set_name | Methods for epiworldR objects
set_name_tool | Tools in epiworld
set_name_virus | Virus design
set_param | Methods for epiworldR objects
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_recovery_enhancer | Tools in epiworld
set_recovery_enhancer_fun | Tools in epiworld
set_recovery_enhancer_ptr | Tools in epiworld
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 --

tool | Tools in epiworld
tool_fun_logit | Tools in epiworld

## -- V --

verbose_off | Methods for epiworldR objects
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