Fast Agent-Based Epi Models
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Documentation for package ‘epiworldR’ version 0.6.1.0
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A C D E G H I L M N P Q R S T U V misc
| epiworldR-package | epiworldR |
-- A --
| actions | Global Events |
| 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 | Accessing the database of epiworld |
-- 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_set | Tools in epiworld |
| distribute_virus_randomly | Virus design |
| distribute_virus_set | Virus design |
-- E --
| entities | Get entities |
| entity | Get entities |
| entity_add_agent | Get entities |
| entity_get_agents | Get entities |
| epiworld-data | Accessing the database of epiworld |
| epiworld-methods | Methods for epiworldR objects |
| epiworldR | epiworldR |
| epiworldR-deprecated | Deprecated and removed functions in epiworldR |
| epiworld_agent | Agents in epiworldR |
| epiworld_agents | Agents in epiworldR |
| epiworld_diffnet | Network Diffusion Model |
| epiworld_globalevent | Global Events |
| epiworld_globalevent_set_param | Global Events |
| epiworld_globalevent_tool | Global Events |
| epiworld_globalevent_tool_logit | Global Events |
| 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_lfmcmc | Likelihood-Free Markhov Chain Monte Carlo (LFMCMC) |
| 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_seirmixing | Susceptible Exposed Infected Removed model (SEIR) with mixing |
| 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_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 | 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_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_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 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 |
| 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 |
| 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_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_seirmixing | Susceptible Exposed Infected Removed model (SEIR) with mixing |
| 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_sirmixing | Susceptible Infected Removed model (SIR) with mixing |
| 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 |
| 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 |