{ "_id": "6acd0e31a14063b82c3aad6e", "Package": "epiworldR", "Type": "Package", "Title": "Fast Agent-Based Epi Models", "Version": "0.19.0-0", "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=\"Niko\", family=\"Speybroeck\", role=c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-3322-3502\",\nwhat = \"Design of the social bubbles intervention\")),\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", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "SystemRequirements": "C++17", "VignetteBuilder": "quarto", "Config/roxygen2/version": "8.1.0", "Repository": "https://uofuepibio.r-universe.dev", "Date/Publication": "2026-10-12 15:47:46 UTC", "RemoteUrl": "https://github.com/UofUEpiBio/epiworldR", "RemoteRef": "HEAD", "RemoteSha": "5a138cfdd864e4e5b7a0c5358ca6705782e8cba4", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-12 16:01:52 UTC", "User": "root" }, "Author": "George Vega Yon [aut, cre] (ORCID:\n),\nDerek Meyer [aut] (ORCID: ),\nAndrew Pulsipher [aut] (ORCID: ),\nNiko Speybroeck [aut] (ORCID: ,\nwhat: Design of the social bubbles intervention),\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_0.19.0-0.tar.gz", "_fileid": "https://r2.ropensci.org/bbff1b671e88395c3c7ec739ee8261332179b44e406f8a687905450ec77348ac", "_filesize": 2480714, "_sha256": "bbff1b671e88395c3c7ec739ee8261332179b44e406f8a687905450ec77348ac", "_expires": "2027-01-20T16:43:25.000Z", "_created": "2026-10-12T16:01:52.000Z", "_published": "2026-10-12T16:43:29.334Z", "_buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/38273882149", "_status": "failure", "_host": "GitHub-Actions", "_jobs": [ { "job": 114897400829, "time": 187, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11758363178" }, { "job": 114897400728, "time": 215, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11758263649" }, { "job": 114897400906, "time": 218, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11758268521" }, { "job": 114897400813, "time": 165, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11758157908" }, { "job": 114897400973, "time": 223, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11759874496" }, { "job": 114897400769, "time": 419, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11759447553" }, { "job": 114897400837, "time": 204, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11760035654" }, { "job": 114897400974, "time": 523, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11759658831" }, { "job": 114894627028, "time": 413, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "11759110565" }, { "job": 114897400767, "time": 150, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11758532724" }, { "job": 114897401030, "time": 497, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11758672682" }, { "job": 114897401037, "time": 303, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11759305308" }, { "job": 114897401253, "time": 296, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11758063486" }, { "job": 114897400948, "time": 582, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11759097710" }, { "job": 114897401011, "time": 283, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11758088321" } ], "_upstream": "https://github.com/UofUEpiBio/epiworldR", "_commit": { "id": "5a138cfdd864e4e5b7a0c5358ca6705782e8cba4", "author": "George G. Vega Yon ", "committer": "GitHub ", "message": "usescout: serve data from the `usescout` branch; rename from whouses (#214)\n\n- The tool was renamed from whouses to usescout (gvegayon/usescout).\n- Data, report and badge live on a dedicated `usescout` branch (was\n `whouses-data`); main stays protected and untouched.\n- Rename the config (.usescout.yml) and workflow (usescout.yml).\n- .Rbuildignore: ignore .usescout.yml.\n- README.qmd / README.md: badge reads the usescout branch, plus a short\n \"Who uses epiworldR?\" section that points to the report.\n\nCo-authored-by: Claude Sonnet 5.5 ", "time": 1791820066 }, "_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": "2025-42", "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": 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"covid-19", "epidemics", "epidemiology", "r-programming", "rpack", "rpkg", "seir", "seir-model", "simulation", "sir", "sir-model", "quarto", "cpp", "openmp" ], "_stars": 14, "_contributors": [ { "user": "gvegayon", "count": 275, "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": 13 }, "_downloads": { "count": 720, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/epiworldR" }, "_devurl": "https://github.com/uofuepibio/epiworldr", "_pkgdown": "https://uofuepibio.github.io/epiworldR/", "_searchresults": 210, "_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_target_tool", "add_tool", "add_tool_agent", "add_tool_n", "add_virus", "add_virus_agent", "add_virus_n", "agents_from_edgelist", "agents_sbm", "agents_smallworld", "bubbles", "change_state", "clear_targets_tool", "clone_epi", "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_last_transmission_mode", "get_lineage_virus", "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_targets_tool", "get_today_total", "get_tool", "get_transition_probability", "get_transmission_kappa", "get_transmission_mode", "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", "sample_household_sizes", "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_targets_tool", "set_transmission_mode", "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": "bubbles", "title": "Social bubbles intervention for network models", "concept": [ "global-events" ], "topics": [ "bubbles", "sample_household_sizes" ] }, { "page": "clone_epi", "title": "Copy epiworld objects", "topics": [ "clone_epi", "clone_epi.epiworld_model", "clone_epi.epiworld_tool", "clone_epi.epiworld_virus" ] }, { "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", "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", 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