Package: epiworldR 0.15.1-0
George Vega Yon
epiworldR: Fast Agent-Based Epi Models
A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.
Authors:
epiworldR_0.15.1-0.tar.gz
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epiworldR_0.15.1-0.tgz(r-4.6-emscripten)
|manual.html✨
card.svg |card.png
epiworldR/json (API)
NEWS
| # Install 'epiworldR' in R: |
| install.packages('epiworldR', repos = c('https://uofuepibio.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/uofuepibio/epiworldr/issues
Pkgdown/docs site:https://uofuepibio.github.io
abmagent-based-modelingcovid-19epidemicsepidemiologyr-programmingrpackrpkgseirseir-modelsimulationsirsir-modelquartocppopenmp
Last updated from:cfb016fec9. Checks:12 OK, 1 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
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| linux-devel-arm64 | OK | 206 | ||
| linux-devel-x86_64 | OK | 222 | ||
| source / vignettes | ERROR | 303 | ||
| linux-release-arm64 | OK | 196 | ||
| linux-release-x86_64 | OK | 194 | ||
| macos-release-arm64 | OK | 282 | ||
| macos-release-x86_64 | OK | 331 | ||
| macos-oldrel-arm64 | OK | 250 | ||
| macos-oldrel-x86_64 | OK | 292 | ||
| windows-devel | OK | 236 | ||
| windows-release | OK | 261 | ||
| windows-oldrel | OK | 244 | ||
| wasm-release | OK | 158 |
Exports:add_entities_from_dataframeadd_entityadd_globaleventadd_paramadd_stateadd_tooladd_tool_agentadd_tool_nadd_virusadd_virus_agentadd_virus_nagents_from_edgelistagents_sbmagents_smallworldchange_stateclone_modelcompute_reproduction_numbercompute_ts_ci_areadistribute_entity_randomlydistribute_entity_to_setdistribute_tool_randomlydistribute_tool_to_entitiesdistribute_tool_to_setdistribute_virus_randomlydistribute_virus_setdistribute_virus_to_entitiesdistribute_virus_to_setdraw_mermaiddraw_mermaid_from_datadraw_mermaid_from_filedraw_mermaid_from_filesdraw_mermaid_from_matrixentityentity_add_agententity_get_agentsepiworld_cpp_versionget_active_casesget_agentsget_agents_data_ncolsget_agents_statesget_agents_toolsget_all_accepted_kernel_scoresget_all_accepted_paramsget_all_accepted_statsget_all_sample_acceptanceget_all_sample_drawn_probget_all_sample_kernel_scoresget_all_sample_paramsget_all_sample_statsget_contact_matrixget_current_accepted_paramsget_current_accepted_statsget_current_proposed_paramsget_current_proposed_statsget_entitiesget_entity_nameget_entity_sizeget_generation_timeget_hist_toolget_hist_totalget_hist_transition_matrixget_hist_virusget_hospitalizationsget_initial_paramsget_mean_paramsget_mean_statsget_n_paramsget_n_replicatesget_n_samplesget_n_statsget_n_toolsget_n_virusesget_nameget_name_toolget_name_virusget_ndaysget_networkget_observed_statsget_outbreak_sizeget_paramget_reproductive_numberget_stateget_statesget_today_totalget_toolget_transition_probabilityget_transmissionsget_virusglobalaction_funglobalaction_set_paramsglobalaction_toolglobalaction_tool_logitglobalevent_funglobalevent_set_paramsglobalevent_toolglobalevent_tool_logithas_toolhas_virusinitial_statesLFMCMCload_agents_entities_tiesmake_saverModelModelDiffNetModelSEIRModelSEIRCONNModelSEIRDModelSEIRDCONNModelSEIRMixingModelSEIRMixingQuarantineModelSIRModelSIRCONNModelSIRDModelSIRDCONNModelSIRLogitModelSIRMixingModelSISModelSISDModelSURVplot_generation_timeplot_incidenceplot_multiple_transitionplot_reproductive_numberqueuing_offqueuing_onrm_entityrm_globaleventrm_toolrm_virusrunrun_lfmcmcrun_multiplerun_multiple_get_resultsset_agents_dataset_contact_matrixset_death_reductionset_death_reduction_funset_death_reduction_ptrset_distribution_entityset_distribution_toolset_distribution_virusset_incubationset_incubation_funset_incubation_ptrset_kernel_funset_nameset_name_toolset_name_virusset_observed_dataset_paramset_params_namesset_prob_deathset_prob_death_funset_prob_death_ptrset_prob_infectingset_prob_infecting_funset_prob_infecting_ptrset_prob_recoveryset_prob_recovery_funset_prob_recovery_ptrset_proposal_funset_recovery_enhancerset_recovery_enhancer_funset_recovery_enhancer_ptrset_simulation_funset_state_functionset_stats_namesset_summary_funset_susceptibility_reductionset_susceptibility_reduction_funset_susceptibility_reduction_ptrset_transmission_reductionset_transmission_reduction_funset_transmission_reduction_ptrsizetodaytooltool_fun_logitupdate_fun_rateupdate_fun_susceptibleuse_kernel_fun_gaussianuse_proposal_norm_reflectiveverbose_offverbose_onvirusvirus_fun_logitvirus_set_state
Dependencies:cpp11
Advanced Modeling - Multiple Diseases, Tools, and Events
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Building models with the model builder
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Getting started with epiworldR
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Implementation details of epiworldR
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Likelihood Free Markhov Chain Monte Carlo (LFMCMC)
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Mixing models
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Run Multiple
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Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add entities to a model according to a data.frame | add_entities_from_dataframe |
| Agents in epiworldR | agents epiworld_agent epiworld_agents get_agents get_agents.epiworld_model get_state print.epiworld_agent print.epiworld_agents [.epiworld_agents |
| Load agents to a model | add_tool_agent add_virus_agent agents_from_edgelist agents_smallworld change_state get_agents_states get_agents_tools get_network has_tool has_virus network |
| Compute a reproduction number from a daily contact matrix with group-specific infectiousness and susceptibility | compute_reproduction_number |
| Compute time-series confidence intervals area | compute_ts_ci_area |
| Get entities | add_entity distribute_entity_randomly distribute_entity_to_set entities entity entity_add_agent entity_get_agents get_entities get_entity_name get_entity_size load_agents_entities_ties rm_entity set_distribution_entity [.epiworld_entities |
| Generation time | epiworld-gentime epiworld_generation_time get_generation_time plot.epiworld_generation_time plot_generation_time |
| Model history and totals | epiworld-history epiworld_hist_tool epiworld_hist_total epiworld_hist_virus get_hist_tool get_hist_total get_hist_virus get_today_total plot.epiworld_hist |
| Hospitalizations by tool | epiworld-hospitalizations get_hospitalizations |
| Methods for epiworldR objects | add_param add_param.epiworld_model clone_model epiworld-methods epiworld_model get_agents_data_ncols get_name get_ndays get_n_replicates get_n_tools get_n_viruses get_param get_states get_tool get_virus initial_states queuing_off queuing_on run set_agents_data set_name set_param size summary.epiworld_model today verbose_off verbose_on |
| Reproductive number (Rt) | epiworld-repnum epiworld_repnum get_reproductive_number plot.epiworld_repnum plot_reproductive_number |
| Summary counts and probabilities | epiworld-summaries get_active_cases get_outbreak_size get_transition_probability |
| Transition dynamics and incidence | as.array.epiworld_hist_transition epiworld-transition epiworld_hist_transition get_hist_transition_matrix plot.epiworld_hist_transition plot_incidence |
| Transmission network | epiworld-transmissions get_transmissions |
| Get or set the contact matrix of a mixing model | get_contact_matrix set_contact_matrix |
| Global Events | actions add_globalevent epiworld_globalevent epiworld_globalevent_set_param epiworld_globalevent_tool epiworld_globalevent_tool_logit global-actions global-events globalevent_fun globalevent_set_params globalevent_tool globalevent_tool_logit rm_globalevent |
| Deprecated and removed functions in epiworldR | add_tool_n add_virus_n epiworldR-deprecated globalaction_fun globalaction_set_params globalaction_tool globalaction_tool_logit |
| Likelihood-Free Markhov Chain Monte Carlo (LFMCMC) | epiworld_lfmcmc get_all_accepted_kernel_scores get_all_accepted_params get_all_accepted_stats get_all_sample_acceptance get_all_sample_drawn_prob get_all_sample_kernel_scores get_all_sample_params get_all_sample_stats get_current_accepted_params get_current_accepted_stats get_current_proposed_params get_current_proposed_stats get_initial_params get_mean_params get_mean_stats get_n_params get_n_samples get_n_stats get_observed_stats LFMCMC print.epiworld_lfmcmc run_lfmcmc set_kernel_fun set_observed_data set_params_names set_proposal_fun set_simulation_fun set_stats_names set_summary_fun use_kernel_fun_gaussian use_proposal_norm_reflective verbose_off.epiworld_lfmcmc |
| Model building functions | add_state epiworld_update_fun Model model_builder set_state_function update_fun_rate update_fun_susceptible |
| Network Diffusion Model | epiworld_diffnet ModelDiffNet |
| Susceptible Exposed Infected Recovered model (SEIR) | epiworld_seir ModelSEIR |
| Susceptible Exposed Infected Removed model (SEIR connected) | epiworld_seirconn ModelSEIRCONN |
| Susceptible-Exposed-Infected-Recovered-Deceased model (SEIRD) | epiworld_seird ModelSEIRD |
| Susceptible Exposed Infected Removed Deceased model (SEIRD connected) | epiworld_seirdconn ModelSEIRDCONN |
| Susceptible Exposed Infected Removed model (SEIR) with mixing | epiworld_seirmixing ModelSEIRMixing |
| Susceptible Exposed Infected Removed model (SEIR) with mixing and quarantine | epiworld_seirmixingquarantine ModelSEIRMixingQuarantine |
| SIR model | epiworld_sir ModelSIR |
| Susceptible Infected Removed model (SIR connected) | epiworld_sirconn ModelSIRCONN |
| SIRD model | epiworld_sird ModelSIRD |
| Susceptible Infected Removed Deceased model (SIRD connected) | epiworld_sirdconn ModelSIRDCONN |
| SIR Logistic model | ModelSIRLogit |
| Susceptible Infected Removed model (SIR) with mixing | epiworld_sirmixing ModelSIRMixing |
| SIS model | epiworld_sis ModelSIS |
| SISD model | epiworld_sisd ModelSISD |
| SURV model | epiworld_surv ModelSURV |
| Network models in epiworld | agents_sbm agents_sbm.epiworld_model network-models |
| Plot transition matrices from 'run_multiple_get_results()' | plot_multiple_transition |
| Plot epidemic curves | plot.epiworld_model |
| Visualize results from 'run_multiple()' | plot.epiworld_multiple_save |
| Model Diagram | draw_mermaid draw_mermaid_from_data draw_mermaid_from_file draw_mermaid_from_files draw_mermaid_from_matrix epiworld-model-diagram plot.epiworld_diagram print.epiworld_diagram |
| Run multiple simulations at once | epiworld_saver make_saver run_multiple run_multiple_get_results |
| Tools in epiworld | add_tool epiworld_tool get_name_tool print.epiworld_agents_tools rm_tool set_death_reduction set_death_reduction_fun set_death_reduction_ptr set_name_tool set_recovery_enhancer set_recovery_enhancer_fun set_recovery_enhancer_ptr set_susceptibility_reduction set_susceptibility_reduction_fun set_susceptibility_reduction_ptr set_transmission_reduction set_transmission_reduction_fun set_transmission_reduction_ptr tool tool_fun_logit |
| Tool distribution functions | distribute_tool_randomly distribute_tool_to_entities distribute_tool_to_set set_distribution_tool tool-distribution |
| Virus design | add_virus epiworld_virus get_name_virus rm_virus set_incubation set_incubation_fun set_incubation_ptr set_name_virus set_prob_death set_prob_death_fun set_prob_death_ptr set_prob_infecting set_prob_infecting_fun set_prob_infecting_ptr set_prob_recovery set_prob_recovery_fun set_prob_recovery_ptr virus virus_fun_logit virus_set_state |
| Virus distribution functions | distribute_virus_randomly distribute_virus_set distribute_virus_to_entities distribute_virus_to_set set_distribution_virus virus-distribution |
