Package index

All functions

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)

ModelDiffNet() plot(<epiworld_diffnet>)

Network Diffusion Model

ModelSEIR() plot(<epiworld_seir>)

Susceptible Exposed Infected Recovered model (SEIR)

ModelSEIRCONN() plot(<epiworld_seirconn>)

Susceptible Exposed Infected Removed model (SEIR connected)

ModelSEIRD() plot(<epiworld_seird>)

Susceptible-Exposed-Infected-Recovered-Deceased model (SEIRD)

ModelSEIRDCONN() plot(<epiworld_seirdconn>)

Susceptible Exposed Infected Removed Deceased model (SEIRD connected)

ModelSEIRMixing() plot(<epiworld_seirmixing>)

Susceptible Exposed Infected Removed model (SEIR) with mixing

ModelSIR() plot(<epiworld_sir>)

SIR model

ModelSIRCONN() plot(<epiworld_sirconn>)

Susceptible Infected Removed model (SIR connected)

ModelSIRD() plot(<epiworld_sird>)

SIRD model

ModelSIRDCONN() plot(<epiworld_sirdconn>)

Susceptible Infected Removed Deceased model (SIRD connected)

ModelSIRLogit()

SIR Logistic model

ModelSIRMixing() plot(<epiworld_sirmixing>)

Susceptible Infected Removed model (SIR) with mixing

ModelSIS() plot(<epiworld_sis>)

SIS model

ModelSISD() plot(<epiworld_sisd>)

SISD model

ModelSURV() plot(<epiworld_surv>)

SURV model

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_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_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()

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()

Methods for epiworldR objects

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

Deprecated and removed functions in epiworldR

epiworldR epiworldR-package

epiworldR

globalevent_tool() globalevent_tool_logit() globalevent_set_params() globalevent_fun() add_globalevent() rm_globalevent()

Global Events

run_multiple() run_multiple_get_results() make_saver()

Run multiple simulations at once

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()

Tools in epiworld

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_set()

Virus design