Package: epiworldR 0.5-0
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_0.5-0.tar.gz
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epiworldR.pdf |epiworldR.html✨
epiworldR/json (API)
NEWS
| # Install 'epiworldR' in R: |
| install.packages('epiworldR', repos = c('https://epiverse-connect.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/uofuepibio/epiworldr/issues
abmagent-based-modelingcovid-19epidemicsepidemiologyr-programmingrpackrpkgseirseir-modelsimulationsirsir-modelcppopenmp
Last updated 1 days agofrom:174263f5f6. Checks:OK: 9. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 25 2024 |
| R-4.5-win-x86_64 | OK | Nov 25 2024 |
| R-4.5-linux-x86_64 | OK | Nov 25 2024 |
| R-4.4-win-x86_64 | OK | Nov 25 2024 |
| R-4.4-mac-x86_64 | OK | Nov 25 2024 |
| R-4.4-mac-aarch64 | OK | Nov 25 2024 |
| R-4.3-win-x86_64 | OK | Nov 25 2024 |
| R-4.3-mac-x86_64 | OK | Nov 25 2024 |
| R-4.3-mac-aarch64 | OK | Nov 25 2024 |
Exports:add_entityadd_globaleventadd_paramadd_tooladd_tool_agentadd_tool_nadd_virusadd_virus_agentadd_virus_nagents_from_edgelistagents_smallworldchange_stateclone_modeldistribute_entity_randomlydistribute_entity_to_setdistribute_tool_randomlydistribute_tool_to_setdistribute_virus_randomlydistribute_virus_setentityentity_add_agententity_get_agentsget_accepted_paramsget_accepted_statsget_agentsget_agents_data_ncolsget_agents_statesget_agents_toolsget_entitiesget_entity_nameget_entity_sizeget_generation_timeget_hist_toolget_hist_totalget_hist_transition_matrixget_hist_virusget_n_parametersget_n_replicatesget_n_samplesget_n_statisticsget_n_toolsget_n_virusesget_nameget_name_toolget_name_virusget_ndaysget_networkget_paramget_params_meanget_reproductive_numberget_stateget_statesget_statistics_histget_stats_meanget_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_saverModelDiffNetModelSEIRModelSEIRCONNModelSEIRDModelSEIRDCONNModelSEIRMixingModelSIRModelSIRCONNModelSIRDModelSIRDCONNModelSIRLogitModelSIRMixingModelSISModelSISDModelSURVplot_generation_timeplot_incidenceplot_reproductive_numberqueuing_offqueuing_onrm_entityrm_globaleventrm_toolrm_virusrunrun_lfmcmcrun_multiplerun_multiple_get_resultsset_agents_dataset_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_par_namesset_paramset_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_stats_namesset_summary_funset_susceptibility_reductionset_susceptibility_reduction_funset_susceptibility_reduction_ptrset_transmission_reductionset_transmission_reduction_funset_transmission_reduction_ptrsizetodaytooltool_fun_logituse_kernel_fun_gaussianuse_proposal_norm_reflectiveverbose_offverbose_onvirusvirus_fun_logitvirus_set_state
Dependencies:cpp11
Getting started with epiworldR
Rendered fromgetting-started.Rmdusingknitr::rmarkdownon Nov 25 2024.Last update: 2024-10-07
Started: 2023-04-21
Implementation details of epiworldR
Rendered fromimplementation.Rmdusingknitr::rmarkdownon Nov 25 2024.Last update: 2024-10-07
Started: 2023-07-05
Likelihood Free Markhov Chain Monte Carlo (LFMCMC)
Rendered fromlikelihood-free-mcmc.Rmdusingknitr::rmarkdownon Nov 25 2024.Last update: 2024-11-20
Started: 2024-11-05
Mixing models
Rendered frommixing.Rmdusingknitr::rmarkdownon Nov 25 2024.Last update: 2024-10-07
Started: 2024-08-01
Run Multiple
Rendered fromrun-multiple.Rmdusingknitr::rmarkdownon Nov 25 2024.Last update: 2024-10-07
Started: 2023-05-02
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| epiworldR | epiworldR-package epiworldR |
| 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 |
| 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 |
| Accessing the database of epiworld | as.array.epiworld_hist_transition epiworld-data epiworld_hist_tool epiworld_hist_total epiworld_hist_variant epiworld_hist_virus epiworld_repnum get_generation_time get_hist_tool get_hist_total get_hist_transition_matrix get_hist_virus get_reproductive_number get_today_total get_transition_probability get_transmissions plot.epiworld_generation_time plot.epiworld_hist_transition plot.epiworld_repnum plot_generation_time plot_incidence plot_reproductive_number |
| 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 |
| Deprecated and removed functions in epiworldR | add_tool_n add_virus_n epiworldR-deprecated globalaction_fun globalaction_set_params globalaction_tool globalaction_tool_logit |
| 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 |
| Likelihood-Free Markhov Chain Monte Carlo (LFMCMC) | epiworld_lfmcmc get_accepted_params get_accepted_stats get_n_parameters get_n_samples get_n_statistics get_params_mean get_statistics_hist get_stats_mean LFMCMC print.epiworld_lfmcmc run_lfmcmc set_kernel_fun set_observed_data set_par_names set_proposal_fun set_simulation_fun set_stats_names set_summary_fun use_kernel_fun_gaussian use_proposal_norm_reflective |
| Network Diffusion Model | epiworld_diffnet ModelDiffNet plot.epiworld_diffnet |
| Susceptible Exposed Infected Recovered model (SEIR) | epiworld_seir ModelSEIR plot.epiworld_seir |
| Susceptible Exposed Infected Removed model (SEIR connected) | epiworld_seirconn ModelSEIRCONN plot.epiworld_seirconn |
| Susceptible-Exposed-Infected-Recovered-Deceased model (SEIRD) | epiworld_seird ModelSEIRD plot.epiworld_seird |
| Susceptible Exposed Infected Removed Deceased model (SEIRD connected) | epiworld_seirdconn ModelSEIRDCONN plot.epiworld_seirdconn |
| Susceptible Exposed Infected Removed model (SEIR) with mixing | epiworld_seirmixing ModelSEIRMixing plot.epiworld_seirmixing |
| SIR model | epiworld_sir ModelSIR plot.epiworld_sir |
| Susceptible Infected Removed model (SIR connected) | epiworld_sirconn ModelSIRCONN plot.epiworld_sirconn |
| SIRD model | epiworld_sird ModelSIRD plot.epiworld_sird |
| Susceptible Infected Removed Deceased model (SIRD connected) | epiworld_sirdconn ModelSIRDCONN plot.epiworld_sirdconn |
| SIR Logistic model | ModelSIRLogit |
| Susceptible Infected Removed model (SIR) with mixing | epiworld_sirmixing ModelSIRMixing plot.epiworld_sirmixing |
| SIS model | epiworld_sis ModelSIS plot.epiworld_sis |
| SISD model | epiworld_sisd ModelSISD plot.epiworld_sisd |
| SURV model | epiworld_surv ModelSURV plot.epiworld_surv |
| Run multiple simulations at once | epiworld_saver make_saver run_multiple run_multiple_get_results |
| Tools in epiworld | add_tool distribute_tool_randomly distribute_tool_to_set epiworld_tool get_name_tool print.epiworld_agents_tools rm_tool set_death_reduction set_death_reduction_fun set_death_reduction_ptr set_distribution_tool 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 |
| Virus design | add_virus distribute_virus_randomly distribute_virus_set epiworld_virus get_name_virus rm_virus set_distribution_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 |
