Package: epiworldR 0.3-2

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:George Vega Yon [aut, cre], Derek Meyer [aut], Susan Holmes [rev], Abinash Satapathy [rev], Carinogurjao [rev], Centers for Disease Control and Prevention [fnd]

epiworldR_0.3-2.tar.gz
epiworldR_0.3-2.tar.gz(r-4.5-noble)epiworldR_0.3-2.tar.gz(r-4.4-noble)
epiworldR_0.3-2.tgz(r-4.4-emscripten)epiworldR_0.3-2.tgz(r-4.3-emscripten)
epiworldR.pdf |epiworldR.html
epiworldR/json (API)
NEWS

# Install 'epiworldR' in R:
install.packages('epiworldR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/uofuepibio/epiworldr/issues

Pkgdown:https://uofuepibio.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

4.97 score 1 packages 52 scripts 428 downloads 129 exports 1 dependencies

Last updated 2 months agofrom:f1d0b846ab. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 08 2024
R-4.5-linux-x86_64OKNov 08 2024

Exports:add_entityadd_globaleventadd_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_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_replicatesget_n_toolsget_n_virusesget_nameget_name_toolget_name_virusget_ndaysget_networkget_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_statesload_agents_entities_tiesmake_saverModelDiffNetModelSEIRModelSEIRCONNModelSEIRDModelSEIRDCONNModelSEIRMixingModelSIRModelSIRCONNModelSIRDModelSIRDCONNModelSIRLogitModelSIRMixingModelSISModelSISDModelSURVplot_generation_timeplot_incidenceplot_reproductive_numberqueuing_offqueuing_onrm_entityrm_toolrm_virusrunrun_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_nameset_name_toolset_name_virusset_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_recovery_enhancerset_recovery_enhancer_funset_recovery_enhancer_ptrset_susceptibility_reductionset_susceptibility_reduction_funset_susceptibility_reduction_ptrset_transmission_reductionset_transmission_reduction_funset_transmission_reduction_ptrsizetooltool_fun_logitverbose_offverbose_onvirusvirus_fun_logitvirus_set_state

Dependencies:cpp11

Getting started with epiworldR

Rendered fromgetting-started.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2024-10-08
Started: 2023-06-09

Implementation details of epiworldR

Rendered fromimplementation.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2024-10-08
Started: 2023-06-21

Mixing models

Rendered frommixing.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2024-10-08
Started: 2024-10-08

Run Multiple

Rendered fromrun-multiple.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2024-10-08
Started: 2023-06-09

Readme and manuals

Help Manual

Help pageTopics
epiworldRepiworldR-package epiworldR
Agents in epiworldRagents epiworld_agent epiworld_agents get_agents get_agents.epiworld_model get_state print.epiworld_agent print.epiworld_agents [.epiworld_agents
Load agents to a modeladd_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 entitiesadd_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 epiworldas.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 objectsclone_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 verbose_off verbose_on
Deprecated and removed functions in epiworldRadd_tool_n add_virus_n epiworldR-deprecated globalaction_fun globalaction_set_params globalaction_tool globalaction_tool_logit
Global Actionsactions add_globalevent epiworld_globalevent epiworld_globalevent_set_param epiworld_globalevent_tool epiworld_globalevent_tool_logit global-actions globalevent_fun globalevent_set_params globalevent_tool globalevent_tool_logit
Network Diffusion Modelepiworld_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 mixingepiworld_seirmixing ModelSEIRMixing plot.epiworld_seirmixing
SIR modelepiworld_sir ModelSIR plot.epiworld_sir
Susceptible Infected Removed model (SIR connected)epiworld_sirconn ModelSIRCONN plot.epiworld_sirconn
SIRD modelepiworld_sird ModelSIRD plot.epiworld_sird
Susceptible Infected Removed Deceased model (SIRD connected)epiworld_sirdconn ModelSIRDCONN plot.epiworld_sirdconn
SIR Logistic modelModelSIRLogit
Susceptible Infected Removed model (SIR) with mixingepiworld_sirmixing ModelSIRMixing plot.epiworld_sirmixing
SIS modelepiworld_sis ModelSIS plot.epiworld_sis
SISD modelepiworld_sisd ModelSISD plot.epiworld_sisd
SURV modelepiworld_surv ModelSURV plot.epiworld_surv
Run multiple simulations at onceepiworld_saver make_saver run_multiple run_multiple_get_results
Tools in epiworldadd_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 designadd_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