Fast Agent-Based Epi Models

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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