{ "_id": "6a59dfea09eb0996dd68ef9b", "Package": "epiworldR", "Type": "Package", "Title": "Fast Agent-Based Epi Models", "Version": "0.15.1-0", "Authors@R": "c(\nperson(given=\"George\", family=\"Vega Yon\", role=c(\"aut\", \"cre\"),\nemail=\"g.vegayon@gmail.com\", comment = c(ORCID = \"0000-0002-3171-0844\")),\nperson(given=\"Derek\", family=\"Meyer\", role=c(\"aut\"),\nemail=\"derekmeyer37@gmail.com\", comment = c(ORCID = \"0009-0005-1350-6988\")),\nperson(given=\"Andrew\", family=\"Pulsipher\", role=c(\"aut\"),\nemail=\"pulsipher.a@gmail.com\", comment = c(ORCID = \"0000-0002-0773-3210\")),\nperson(given=\"Susan\", family=\"Holmes\", role = \"rev\", comment =\nc(what = \"JOSS reviewer\", ORCID=\"0000-0002-2208-8168\")),\nperson(given=\"Abinash\", family=\"Satapathy\", role = \"rev\", comment =\nc(what = \"JOSS reviewer\", ORCID=\"0000-0002-2955-2744\")),\nperson(given=\"Carinogurjao\", role = \"rev\"),\nperson(\"Centers for Disease Control and Prevention\", role=\"fnd\", comment = \"Award number 1U01CK000585; 75D30121F00003\"\n))", "Description": "A flexible framework for Agent-Based Models (ABM), the\n'epiworldR' package provides methods for prototyping disease\noutbreaks and transmission models using a 'C++' backend, making\nit very fast. It supports multiple epidemiological models,\nincluding the Susceptible-Infected-Susceptible (SIS),\nSusceptible-Infected-Removed (SIR),\nSusceptible-Exposed-Infected-Removed (SEIR), and others,\ninvolving arbitrary mitigation policies and multiple-disease\nmodels. Users can specify infectiousness/susceptibility rates\nas a function of agents' features, providing great complexity\nfor the model dynamics. Furthermore, 'epiworldR' is ideal for\nsimulation studies featuring large populations.", "URL": "https://github.com/UofUEpiBio/epiworldR,\nhttps://uofuepibio.github.io/epiworldR/,\nhttps://uofuepibio.github.io/epiworldR-workshop/", "BugReports": "https://github.com/UofUEpiBio/epiworldR/issues", "License": "MIT + file LICENSE", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "SystemRequirements": "C++17", "VignetteBuilder": "quarto", "Repository": "https://uofuepibio.r-universe.dev", "Date/Publication": "2026-07-17 05:33:30 UTC", "RemoteUrl": "https://github.com/UofUEpiBio/epiworldR", "RemoteRef": "HEAD", "RemoteSha": "85a8317e64404ef0246b5d0f34e5099f25939969", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-17 07:45:47 UTC", "User": "root" }, "Author": "George Vega Yon [aut, cre] (ORCID:\n),\nDerek Meyer [aut] (ORCID: ),\nAndrew Pulsipher [aut] (ORCID: ),\nSusan Holmes [rev] (what: JOSS reviewer, ORCID:\n),\nAbinash Satapathy [rev] (what: JOSS reviewer, ORCID:\n),\nCarinogurjao [rev],\nCenters for Disease Control and Prevention [fnd] (Award number\n1U01CK000585; 75D30121F00003)", "Maintainer": "George Vega Yon ", "_user": "uofuepibio", "_type": "src", "_file": "epiworldR_0.15.1-0.tar.gz", "_fileid": "https://r2.ropensci.org/a3004753d94106ee7b640435fe4df478dc4bda8f80cbaa5642a35e5ae29c23be", "_filesize": 3484347, "_sha256": "a3004753d94106ee7b640435fe4df478dc4bda8f80cbaa5642a35e5ae29c23be", "_expires": "2026-10-25T07:55:19.000Z", "_created": "2026-07-17T07:45:47.000Z", "_published": "2026-07-17T07:55:22.055Z", "_jobs": [ { "job": 87833045665, "time": 208, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8400522066" }, { "job": 87833045614, "time": 223, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8400526242" }, { "job": 87833045722, "time": 209, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8400522065" }, { "job": 87833045680, "time": 220, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8400524960" }, { "job": 87833045701, "time": 249, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8400534354" }, { "job": 87833045743, "time": 454, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8400605643" }, { "job": 87833045707, "time": 208, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8400520583" }, { "job": 87833045650, "time": 388, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8400582971" }, { "job": 87831958802, "time": 380, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "8400446344" }, { "job": 87833045591, "time": 151, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8400500985" }, { "job": 87833045621, "time": 235, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8400530406" }, { "job": 87833045675, "time": 272, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8400542873" }, { "job": 87833045700, "time": 240, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8400531232" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/29563834950", "_status": "failure", "_upstream": "https://github.com/UofUEpiBio/epiworldR", "_commit": { "id": "85a8317e64404ef0246b5d0f34e5099f25939969", "author": "George G. Vega Yon ", "committer": "George G. Vega Yon ", "message": "Minor update\n", "time": 1784266410 }, "_maintainer": { "name": "George Vega Yon", "email": "g.vegayon@gmail.com", "login": "gvegayon", "bluesky": "@gvegayon.bsky.social", "linkedin": "in/georgevegayon", "description": "Scientist at @UofUEpiBio modeling complex systems using statistical computing. Lots of time at @CDCgov.", "uuid": 893619, "orcid": "0000-0002-3171-0844" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "cpp11", "role": "LinkingTo" }, { "package": "utils", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "quarto", "role": "Suggests" }, { "package": "tinytest", "role": "Suggests" }, { "package": "netplot", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" }, { "package": "data.table", "role": "Suggests" }, { "package": "DiagrammeR", "role": "Suggests" } ], "_owner": "uofuepibio", "_selfowned": true, "_usedby": 2, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-42", "n": 3 }, { "week": "2025-43", "n": 1 }, { "week": "2025-45", "n": 4 }, { "week": "2025-46", "n": 3 }, { "week": "2025-47", "n": 1 }, { "week": "2025-50", "n": 3 }, { "week": "2025-51", "n": 4 }, { "week": "2026-02", "n": 1 }, { "week": "2026-03", "n": 1 }, { "week": "2026-07", "n": 3 }, { "week": "2026-08", "n": 1 }, { "week": "2026-11", "n": 1 }, { "week": "2026-13", "n": 3 }, { "week": "2026-16", "n": 1 }, { "week": "2026-17", "n": 4 }, { "week": "2026-18", "n": 2 }, { "week": "2026-20", "n": 2 }, { "week": "2026-29", "n": 1 } ], "_tags": [ { "name": "v0.10.0.0", "date": "2025-11-13" }, { "name": "v0.11.0.0", "date": "2026-01-09" }, { "name": "v0.11.0.1", "date": "2026-01-14" }, { "name": "v0.11.2.0", "date": "2026-02-10" }, { "name": "v0.12.0.0", "date": "2026-02-18" }, { "name": "v0.13.0.0", "date": "2026-03-12" }, { "name": "v0.14.0.0", "date": "2026-03-28" } ], "_topics": [ "abm", "agent-based-modeling", "covid-19", "epidemics", "epidemiology", "r-programming", "rpack", "rpkg", "seir", "seir-model", "simulation", "sir", "sir-model", "quarto", "cpp", "openmp" ], "_stars": 14, "_contributors": [ { "user": "gvegayon", "count": 249, "uuid": 893619 }, { "user": "derekmeyer37", "count": 123, "uuid": 105825983 }, { "user": "apulsipher", "count": 25, "uuid": 45372570 }, { "user": "copilot", "count": 6, "uuid": 198982749 }, { "user": "abinashbunty", "count": 1, "uuid": 25522048 } ], "_userbio": { "uuid": 89941410, "type": "organization", "name": "Divisions of Epidemiology and Biostatistics at the U", "followers": 11 }, "_downloads": { "count": 524, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/epiworldR" }, "_devurl": "https://github.com/uofuepibio/epiworldr", "_pkgdown": "https://uofuepibio.github.io/epiworldR/", "_searchresults": 156, "_quarto": true, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/epiworldR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/uofuepibio/epiworldr", "_realowner": "uofuepibio", "_cranurl": true, "_releases": [ { "version": "0.0-1", "date": "2023-06-09" }, { "version": "0.0-2", "date": "2023-06-22" }, { "version": "0.0-3", "date": "2023-09-08" }, { "version": "0.0-4", "date": "2024-02-09" }, { "version": "0.1-0", "date": "2024-04-08" }, { "version": "0.3-2", "date": "2024-10-08" }, { "version": "0.6.0.0", "date": "2025-01-17" }, { "version": "0.6.1.0", "date": "2025-01-28" }, { "version": "0.8.1.0", "date": "2025-04-22" }, { "version": "0.8.2.0", "date": "2025-05-13" }, { "version": "0.8.3.0", "date": "2025-06-12" }, { "version": "0.10.0.0", "date": "2025-11-14" }, { "version": "0.11.0.0", "date": "2025-12-22" }, { "version": "0.11.0.1", "date": "2026-01-14" }, { "version": "0.11.2.0", "date": "2026-02-03" }, { "version": "0.12.0.0", "date": "2026-02-21" }, { "version": "0.13.0.0", "date": "2026-03-12" }, { "version": "0.14.0.0", "date": "2026-03-28" } ], "_exports": [ "add_entities_from_dataframe", "add_entity", "add_globalevent", "add_param", "add_state", "add_tool", "add_tool_agent", "add_tool_n", "add_virus", "add_virus_agent", "add_virus_n", "agents_from_edgelist", "agents_sbm", "agents_smallworld", "change_state", "clone_model", "compute_reproduction_number", "compute_ts_ci_area", "distribute_entity_randomly", "distribute_entity_to_set", "distribute_tool_randomly", "distribute_tool_to_entities", "distribute_tool_to_set", "distribute_virus_randomly", "distribute_virus_set", "distribute_virus_to_entities", "distribute_virus_to_set", "draw_mermaid", "draw_mermaid_from_data", "draw_mermaid_from_file", "draw_mermaid_from_files", "draw_mermaid_from_matrix", "entity", "entity_add_agent", "entity_get_agents", "epiworld_cpp_version", "get_active_cases", "get_agents", "get_agents_data_ncols", "get_agents_states", "get_agents_tools", "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_contact_matrix", "get_current_accepted_params", "get_current_accepted_stats", "get_current_proposed_params", "get_current_proposed_stats", "get_entities", "get_entity_name", "get_entity_size", "get_generation_time", "get_hist_tool", "get_hist_total", "get_hist_transition_matrix", "get_hist_virus", "get_hospitalizations", "get_initial_params", "get_mean_params", "get_mean_stats", "get_n_params", "get_n_replicates", "get_n_samples", "get_n_stats", "get_n_tools", "get_n_viruses", "get_name", "get_name_tool", "get_name_virus", "get_ndays", "get_network", "get_observed_stats", "get_outbreak_size", "get_param", "get_reproductive_number", "get_state", "get_states", "get_today_total", "get_tool", "get_transition_probability", "get_transmissions", "get_virus", "globalaction_fun", "globalaction_set_params", "globalaction_tool", "globalaction_tool_logit", "globalevent_fun", "globalevent_set_params", "globalevent_tool", "globalevent_tool_logit", "has_tool", "has_virus", "initial_states", "LFMCMC", "load_agents_entities_ties", "make_saver", "Model", "ModelDiffNet", "ModelSEIR", "ModelSEIRCONN", "ModelSEIRD", "ModelSEIRDCONN", "ModelSEIRMixing", "ModelSEIRMixingQuarantine", "ModelSIR", "ModelSIRCONN", "ModelSIRD", "ModelSIRDCONN", "ModelSIRLogit", "ModelSIRMixing", "ModelSIS", "ModelSISD", "ModelSURV", "plot_generation_time", "plot_incidence", "plot_multiple_transition", "plot_reproductive_number", "queuing_off", "queuing_on", "rm_entity", "rm_globalevent", "rm_tool", "rm_virus", "run", "run_lfmcmc", "run_multiple", "run_multiple_get_results", "set_agents_data", "set_contact_matrix", "set_death_reduction", "set_death_reduction_fun", "set_death_reduction_ptr", "set_distribution_entity", "set_distribution_tool", "set_distribution_virus", "set_incubation", "set_incubation_fun", "set_incubation_ptr", "set_kernel_fun", "set_name", "set_name_tool", "set_name_virus", "set_observed_data", "set_param", "set_params_names", "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", "set_proposal_fun", "set_recovery_enhancer", "set_recovery_enhancer_fun", "set_recovery_enhancer_ptr", "set_simulation_fun", "set_state_function", "set_stats_names", "set_summary_fun", "set_susceptibility_reduction", "set_susceptibility_reduction_fun", "set_susceptibility_reduction_ptr", "set_transmission_reduction", "set_transmission_reduction_fun", "set_transmission_reduction_ptr", "size", "today", "tool", "tool_fun_logit", "update_fun_rate", "update_fun_susceptible", "use_kernel_fun_gaussian", "use_proposal_norm_reflective", "verbose_off", "verbose_on", "virus", "virus_fun_logit", "virus_set_state" ], "_help": [ { "page": "add_entities_from_dataframe", "title": "Add entities to a model according to a data.frame", "concept": [ "entity-functions" ], "topics": [ "add_entities_from_dataframe" ] }, { "page": "agents", "title": "Agents in epiworldR", "concept": [ "model-utility-functions" ], "topics": [ "agents", "epiworld_agent", "epiworld_agents", "get_agents", "get_agents.epiworld_model", "get_state", "print.epiworld_agent", "print.epiworld_agents", "[.epiworld_agents" ] }, { "page": "agents_smallworld", "title": "Load agents to a model", "concept": [ "model-utility-functions" ], "topics": [ "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" ] }, { "page": "compute_reproduction_number", "title": "Compute a reproduction number from a daily contact matrix with group-specific infectiousness and susceptibility", "topics": [ "compute_reproduction_number" ] }, { "page": "compute_ts_ci_area", "title": "Compute time-series confidence intervals area", "concept": [ "misc-functions" ], "topics": [ "compute_ts_ci_area" ] }, { "page": "entities", "title": "Get entities", "concept": [ "entity-functions" ], "topics": [ "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" ] }, { "page": "epiworld-gentime", "title": "Generation time", "concept": [ "Epidemiological metrics", "model-utility-functions" ], "topics": [ "epiworld-gentime", "epiworld_generation_time", "get_generation_time", "plot.epiworld_generation_time", "plot_generation_time" ] }, { "page": "epiworld-history", "title": "Model history and totals", "concept": [ "History", "model-utility-functions" ], "topics": [ "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" ] }, { "page": "epiworld-hospitalizations", "title": "Hospitalizations by tool", "concept": [ "Summaries", "model-utility-functions" ], "topics": [ "epiworld-hospitalizations", "get_hospitalizations" ] }, { "page": "epiworld-methods", "title": "Methods for epiworldR objects", "concept": [ "model-utility-functions" ], "topics": [ "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" ] }, { "page": "epiworld-repnum", "title": "Reproductive number (Rt)", "concept": [ "Epidemiological metrics", "model-utility-functions" ], "topics": [ "epiworld-repnum", "epiworld_repnum", "get_reproductive_number", "plot.epiworld_repnum", "plot_reproductive_number" ] }, { "page": "epiworld-summaries", "title": "Summary counts and probabilities", "concept": [ "Summaries", "model-utility-functions" ], "topics": [ "epiworld-summaries", "get_active_cases", "get_outbreak_size", "get_transition_probability" ] }, { "page": "epiworld-transition", "title": "Transition dynamics and incidence", "concept": [ "Transition dynamics", "model-utility-functions" ], "topics": [ "as.array.epiworld_hist_transition", "epiworld-transition", "epiworld_hist_transition", "get_hist_transition_matrix", "plot.epiworld_hist_transition", "plot_incidence" ] }, { "page": "epiworld-transmissions", "title": "Transmission network", "concept": [ "Network outputs", "model-utility-functions" ], "topics": [ "epiworld-transmissions", "get_transmissions" ] }, { "page": "get_contact_matrix", "title": "Get or set the contact matrix of a mixing model", "concept": [ "mixing-models" ], "topics": [ "get_contact_matrix", "set_contact_matrix" ] }, { "page": "global-events", "title": "Global Events", "concept": [ "global-events" ], "topics": [ "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" ] }, { "page": "epiworldR-deprecated", "title": "Deprecated and removed functions in epiworldR", "concept": [ "deprecated-functions" ], "topics": [ "add_tool_n", "add_virus_n", "epiworldR-deprecated", "globalaction_fun", "globalaction_set_params", "globalaction_tool", "globalaction_tool_logit" ] }, { "page": "LFMCMC", "title": "Likelihood-Free Markhov Chain Monte Carlo (LFMCMC)", "concept": [ "fmcmc" ], "topics": [ "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" ] }, { "page": "model_builder", "title": "Model building functions", "concept": [ "model-building-functions" ], "topics": [ "add_state", "epiworld_update_fun", "Model", "model_builder", "set_state_function", "update_fun_rate", "update_fun_susceptible" ] }, { "page": "ModelDiffNet", "title": "Network Diffusion Model", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_diffnet", "ModelDiffNet" ] }, { "page": "ModelSEIR", "title": "Susceptible Exposed Infected Recovered model (SEIR)", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_seir", "ModelSEIR" ] }, { "page": "ModelSEIRCONN", "title": "Susceptible Exposed Infected Removed model (SEIR connected)", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_seirconn", "ModelSEIRCONN" ] }, { "page": "ModelSEIRD", "title": "Susceptible-Exposed-Infected-Recovered-Deceased model (SEIRD)", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_seird", "ModelSEIRD" ] }, { "page": "ModelSEIRDCONN", "title": "Susceptible Exposed Infected Removed Deceased model (SEIRD connected)", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_seirdconn", "ModelSEIRDCONN" ] }, { "page": "ModelSEIRMixing", "title": "Susceptible Exposed Infected Removed model (SEIR) with mixing", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_seirmixing", "ModelSEIRMixing" ] }, { "page": "ModelSEIRMixingQuarantine", "title": "Susceptible Exposed Infected Removed model (SEIR) with mixing and quarantine", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_seirmixingquarantine", "ModelSEIRMixingQuarantine" ] }, { "page": "ModelSIR", "title": "SIR model", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_sir", "ModelSIR" ] }, { "page": "ModelSIRCONN", "title": "Susceptible Infected Removed model (SIR connected)", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_sirconn", "ModelSIRCONN" ] }, { "page": "ModelSIRD", "title": "SIRD model", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_sird", "ModelSIRD" ] }, { "page": "ModelSIRDCONN", "title": "Susceptible Infected Removed Deceased model (SIRD connected)", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_sirdconn", "ModelSIRDCONN" ] }, { "page": "ModelSIRLogit", "title": "SIR Logistic model", "concept": [ "Models", "general-models" ], "topics": [ "ModelSIRLogit" ] }, { "page": "ModelSIRMixing", "title": "Susceptible Infected Removed model (SIR) with mixing", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_sirmixing", "ModelSIRMixing" ] }, { "page": "ModelSIS", "title": "SIS model", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_sis", "ModelSIS" ] }, { "page": "ModelSISD", "title": "SISD model", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_sisd", "ModelSISD" ] }, { "page": "ModelSURV", "title": "SURV model", "concept": [ "Models", "general-models" ], "topics": [ "epiworld_surv", "ModelSURV" ] }, { "page": "network-models", "title": "Network models in epiworld", "topics": [ "agents_sbm", "agents_sbm.epiworld_model", "network-models" ] }, { "page": "plot_multiple_transition", "title": "Plot transition matrices from 'run_multiple_get_results()'", "concept": [ "epiworld-model-diagrams" ], "topics": [ "plot_multiple_transition" ] }, { "page": "plot.epiworld_model", "title": "Plot epidemic curves", "concept": [ "plot-epidemic-curves" ], "topics": [ "plot.epiworld_model" ] }, { "page": "plot.epiworld_multiple_save", "title": "Visualize results from 'run_multiple()'", "concept": [ "plot-epidemic-curves" ], "topics": [ "plot.epiworld_multiple_save" ] }, { "page": "epiworld-model-diagram", "title": "Model Diagram", "concept": [ "epiworld-model-diagrams" ], "topics": [ "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" ] }, { "page": "run_multiple", "title": "Run multiple simulations at once", "concept": [ "model-utility-functions" ], "topics": [ "epiworld_saver", "make_saver", "run_multiple", "run_multiple_get_results" ] }, { "page": "tool", "title": "Tools in epiworld", "concept": [ "tool-functions" ], "topics": [ "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" ] }, { "page": "tool-distribution", "title": "Tool distribution functions", "concept": [ "tool-distribution" ], "topics": [ "distribute_tool_randomly", "distribute_tool_to_entities", "distribute_tool_to_set", "set_distribution_tool", "tool-distribution" ] }, { "page": "virus", "title": "Virus design", "concept": [ "virus-functions" ], "topics": [ "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" ] }, { "page": "virus-distribution", "title": "Virus distribution functions", "concept": [ "virus-distribution" ], "topics": [ "distribute_virus_randomly", "distribute_virus_set", "distribute_virus_to_entities", "distribute_virus_to_set", "set_distribution_virus", "virus-distribution" ] } ], "_pkglogo": "https://github.com/UofUEpiBio/epiworldR/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/UofUEpiBio/epiworldR/raw/HEAD/README.md", "_rundeps": [ "cpp11" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "advanced-modeling.qmd", "filename": "advanced-modeling.html", "title": "Advanced Modeling - Multiple Diseases, Tools, and Events", "engine": "quarto::html", "headings": [ "Introduction", "Example Scenario: Simultaneous COVID-19 and Flu Outbreaks", "Model Setup", "Add the Flu Virus", "Add a Tool (Vaccine)", "Add Events", "Full Model Summary", "Reproductive Numbers" ], "created": "2026-03-26 17:38:22", "modified": "2026-03-26 17:38:22", "commits": 1 }, { "source": "model-builder.qmd", "filename": "model-builder.html", "title": "Building models with the model builder", "engine": "quarto::html", "headings": [ "Introduction", "A minimal model built from scratch", "Extending the model to SEIRD" ], "created": "2026-04-17 07:02:36", "modified": "2026-04-24 04:51:26", "commits": 2 }, { "source": "getting-started.qmd", "filename": "getting-started.html", "title": "Getting started with epiworldR", "engine": "quarto::html", "headings": [ "Example 1: Simulating an SIR model", "Setup and running the model", "Plot", "Extracting information", "Adding more viruses/viruses", "Tools" ], "created": "2026-03-26 17:38:22", "modified": "2026-03-26 17:38:22", "commits": 1 }, { "source": "implementation.qmd", "filename": "implementation.html", "title": "Implementation details of epiworldR", "engine": "quarto::html", "headings": [ "Introduction", "General flow of the models", "Computing probabilities", "Transmission probability", "Adjusted probabilities", "Transmission in connected models[^models]" ], "created": "2026-03-26 17:38:22", "modified": "2026-03-26 17:38:22", "commits": 1 }, { "source": "likelihood-free-mcmc.qmd", "filename": "likelihood-free-mcmc.html", "title": "Likelihood Free Markhov Chain Monte Carlo (LFMCMC)", "engine": "quarto::html", "headings": [ "Introduction", "Setup The SIR Model", "Setup LFMCMC", "Run LFMCMC Simulation", "Results" ], "created": "2026-03-26 17:38:22", "modified": "2026-03-26 17:38:22", "commits": 1 }, { "source": "mixing.qmd", "filename": "mixing.html", "title": "Mixing models", "engine": "quarto::html", "headings": [ "Introduction", "An SEIR model with mixing", "Investigating the history" ], "created": "2026-03-26 17:38:22", "modified": "2026-04-17 07:02:36", "commits": 2 }, { "source": "run-multiple.qmd", "filename": "run-multiple.html", "title": "Run Multiple", "engine": "quarto::html", "headings": [ "Introduction", "Example: Simulating a SEIRCONN Model 50 Times", "Setup and Running Model", "Generating a Saver", "Plotting" ], "created": "2026-03-26 17:38:22", "modified": "2026-03-26 17:38:22", "commits": 1 } ], "_score": 9.542285521047411, "_indexed": true, "_nocasepkg": "epiworldr", "_universes": [ "uofuepibio", "gvegayon" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.15.1-0", "date": "2026-07-17T07:49:29.000Z", "distro": "resolute", "arch": "aarch64", "commit": "85a8317e64404ef0246b5d0f34e5099f25939969", "fileid": "https://r2.ropensci.org/f3e81d578e5e44cd1ffacdc3e1f9664e6be11b204748eeb3ea47ebbe5c9de42a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/29563834950" }, { "r": "4.7.0", "os": "linux", "version": "0.15.1-0", "date": "2026-07-17T07:49:26.000Z", "distro": "resolute", "arch": "x86_64", "commit": "85a8317e64404ef0246b5d0f34e5099f25939969", "fileid": "https://r2.ropensci.org/7ab4d9871a9fa4405fce435c4119737bfd3fc8e1cea0ec2069fd996f185b28d0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/29563834950" }, { "r": "4.6.1", "os": "linux", "version": "0.15.1-0", "date": "2026-07-17T07:49:26.000Z", "distro": "resolute", "arch": "aarch64", "commit": "85a8317e64404ef0246b5d0f34e5099f25939969", "fileid": "https://r2.ropensci.org/a92f5c4eac13fc9c91e00fb55cbb0b45075ccfef1b700c97958a992e540eeddb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/29563834950" }, { "r": "4.6.1", "os": "linux", "version": "0.15.1-0", "date": "2026-07-17T07:49:23.000Z", "distro": "resolute", "arch": "x86_64", "commit": "85a8317e64404ef0246b5d0f34e5099f25939969", "fileid": "https://r2.ropensci.org/0db853467559cb6bb75c5024c9c6f94bfd79c58a0609e46f2ea288193f898b67", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/29563834950" }, { "r": "4.5.3", "os": "mac", "version": "0.15.1-0", "date": "2026-07-17T07:49:46.000Z", "arch": "aarch64", "commit": "85a8317e64404ef0246b5d0f34e5099f25939969", "fileid": "https://r2.ropensci.org/269d93986edecb334e94124213b37811afa5679ce29e8c24a2f84fd2fa7d2157", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/29563834950" }, { "r": "4.5.3", "os": "mac", "version": "0.15.1-0", "date": "2026-07-17T07:51:02.000Z", "arch": "x86_64", "commit": "85a8317e64404ef0246b5d0f34e5099f25939969", "fileid": "https://r2.ropensci.org/6823e1c6676dc805002ec24212e92dda65ccc6dd6ab6648c068e2cf7db0b33f4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/29563834950" }, { "r": "4.6.1", "os": "mac", "version": "0.15.1-0", "date": "2026-07-17T07:49:19.000Z", "arch": "aarch64", "commit": "85a8317e64404ef0246b5d0f34e5099f25939969", "fileid": "https://r2.ropensci.org/7f05284ad60915b1f5bf30a8166af0c054b7071e6c459609d4ca0163be3b816c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/29563834950" }, { "r": "4.6.1", "os": "mac", "version": "0.15.1-0", "date": "2026-07-17T07:50:51.000Z", "arch": "x86_64", "commit": "85a8317e64404ef0246b5d0f34e5099f25939969", "fileid": "https://r2.ropensci.org/cec73d738b8336dff998fa358c2926614094ffac73bd2e3c3f65274b781a0bcc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/29563834950" }, { "r": "4.6.0", "os": "wasm", "version": "0.15.1-0", "date": "2026-07-17T07:49:07.000Z", "arch": "emscripten", "commit": "85a8317e64404ef0246b5d0f34e5099f25939969", "fileid": "https://r2.ropensci.org/c75b2ad249fc6ec7111f385d696bce2a7bfe459219f65280a52b413b055dd074", "status": "success", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/29563834950" }, { "r": "4.7.0", "os": "win", "version": "0.15.1-0", "date": "2026-07-17T07:48:43.000Z", "arch": "x86_64", "commit": "85a8317e64404ef0246b5d0f34e5099f25939969", "fileid": "https://r2.ropensci.org/794274f745b43bb7cdaf77e986866e87b96a527233be983e9730464e04ee36ce", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/29563834950" }, { "r": "4.5.3", "os": "win", "version": "0.15.1-0", "date": "2026-07-17T07:49:18.000Z", "arch": "x86_64", "commit": "85a8317e64404ef0246b5d0f34e5099f25939969", "fileid": "https://r2.ropensci.org/8b2a71395a0efd9908dcbd8182cafe10933a870bba56d88dc50a342c5b1a9efa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/29563834950" }, { "r": "4.6.1", "os": "win", "version": "0.15.1-0", "date": "2026-07-17T07:48:35.000Z", "arch": "x86_64", "commit": "85a8317e64404ef0246b5d0f34e5099f25939969", "fileid": "https://r2.ropensci.org/d4366ce1744ef65dcbe2248fb8919ccc3433dbd422601dad7c350bd3e9fb3537", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/29563834950" } ] }