{ "_id": "6ad9fa6dc9cc1e56bbac4a1a", "Package": "yersinia", "Title": "Plague Transmission Models for Epidemiological Research", "Version": "0.1.0", "Authors@R": "c(\nperson(\"Nick\", \"Gauthier\", , \"nicolas.gauthier@ufl.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-2225-5827\")),\nperson(\"Nich\", \"Martin\", , \"n.martin@ufl.edu\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-9539-250X\")))", "Description": "A toolkit for plague transmission modeling using\nstochastic compartmental models. Implements carcass-based\ntransmission dynamics (Didelot et al. 2017) with spatial\nstructure and multi-host dynamics for epidemiological research.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "URL": "https://github.com/flmnh-ai/yersinia,\nhttps://flmnh-ai.github.io/yersinia/", "BugReports": "https://github.com/flmnh-ai/yersinia/issues", "Remotes": [ "mrc-ide/odin2", "mrc-ide/dust2", "mrc-ide/monty" ], "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "LazyData": "true", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://flmnh-ai.r-universe.dev", "Date/Publication": "2026-09-22 20:13:43 UTC", "RemoteUrl": "https://github.com/flmnh-ai/yersinia", "RemoteRef": "HEAD", "RemoteSha": "8be6bf3bf15560884691b2d8e153a407ac71363e", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-22 11:33:50 UTC", "User": "root" }, "Author": "Nick Gauthier [aut, cre] (ORCID:\n),\nNich Martin [aut] (ORCID: )", "Maintainer": "Nick Gauthier ", "_user": "flmnh-ai", "_type": "src", "_file": "yersinia_0.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/bdde9b6c70075f338fe23ee0f3168191927c72b46280dadc876a8085bfbd950a", "_filesize": 2150667, "_sha256": "bdde9b6c70075f338fe23ee0f3168191927c72b46280dadc876a8085bfbd950a", "_expires": "2027-01-30T11:58:35.000Z", "_created": "2026-10-22T11:33:50.000Z", "_published": "2026-10-22T11:58:36.849Z", "_upstream": "https://github.com/flmnh-ai/yersinia", "_status": "failure", "_maintainer": { "name": "Nick Gauthier", "email": "nicolas.gauthier@ufl.edu", "login": "nick-gauthier", "twitter": "@nick_gaut", "description": "Assistant Curator, AI for Bio/Cultural Diversity", "uuid": 12808168, "orcid": "0000-0002-2225-5827" }, "_jobs": [ { "job": 119800493112, "time": 250, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "12422398078" }, { "job": 119800493281, "time": 278, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "12423191428" }, { "job": 119800493121, "time": 369, "config": "linux-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "12422374374" }, { "job": 119800493140, "time": 321, "config": "linux-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "12422509152" }, { "job": 119800493145, "time": 218, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "12424365093" }, { "job": 119800493167, "time": 536, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "12423867562" }, { "job": 119800493290, "time": 218, "config": "macos-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "12423553483" }, { "job": 119800493174, "time": 472, "config": "macos-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "12422962930" }, { "job": 119796967333, "time": 494, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "12422527929" }, { "job": 119800493083, "time": 401, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12423670142" }, { "job": 119800493327, "time": 473, "config": "windows-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "12423036622" }, { "job": 119800493287, "time": 334, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "12423131056" }, { "job": 119800493158, "time": 260, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "12422981182" }, { "job": 119800493385, "time": 446, "config": "windows-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "12422398549" }, { "job": 119800493205, "time": 521, "config": "windows-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "12422234160" } ], "_buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923", "_commit": { "id": "8be6bf3bf15560884691b2d8e153a407ac71363e", "author": "Nick Gauthier ", "committer": "Nick Gauthier ", "message": "Archive delta_R-forcing vignettes; exclude standalone notebooks from build\n\n- Remove the seven monty vignettes that forced carcass decay through\n the (now removed) `seasonal` input: monty-seasonal, -london, -algiers,\n the three Barcelona fits and multicity-mechanistic. Superseded by\n thermal forcing on transmission; kept locally in archive/.\n- .Rbuildignore the two standalone rstan notebooks and the\n reference-deterministic-models vignette (depends on odin v1), so\n R CMD check does not need rstan or odin.\n- Update references to the removed vignettes in yersinia-intro,\n app_fit.R and app_priors.R.\n", "time": 1790108023 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "cpp11", "role": "LinkingTo" }, { "package": "dust2", "role": "LinkingTo" }, { "package": "monty", "role": "LinkingTo" }, { "package": "odin2", "role": "Imports" }, { "package": "dust2", "role": "Imports" }, { "package": "monty", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "yaml", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "checkmate", "role": "Imports" }, { "package": "glue", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "withr", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "posterior", "role": "Suggests" }, { "package": "bayesplot", "role": "Suggests" }, { "package": "sf", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "scales", "role": "Suggests" }, { "package": "R6", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" }, { "package": "bslib", "role": "Suggests" }, { "package": "DT", "role": "Suggests" } ], "_owner": "flmnh-ai", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-11", "n": 1 }, { "week": "2026-16", "n": 1 }, { "week": "2026-19", "n": 6 }, { "week": "2026-23", "n": 1 }, { "week": "2026-24", "n": 1 }, { "week": "2026-39", "n": 9 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "nick-gauthier", "count": 74, "uuid": 12808168 }, { "user": "nichmartin", "count": 6, "uuid": 74326322 } ], "_userbio": { "uuid": 116828111, "type": "organization", "name": "AI at the Florida Museum of Natural History", "followers": 9, "description": "Code repository for the AI for Human Ecology Lab at the Florida Museum of Natural History, University of Florida" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/yersinia" }, "_devurl": "https://github.com/flmnh-ai/yersinia", "_pkgdown": "https://flmnh-ai.github.io/yersinia/", "_searchresults": 11, "_topics": [ "cpp", "openmp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/yersinia.html", "LICENSE" ], "_cranurl": false, "_exports": [ "available_scenarios", "ca_step", "calculate_equilibrium", "calculate_force_of_infection", "calculate_outbreak_metrics", "calculate_R0", "cohort_check_fittable", "cohort_data", "cohort_obs_period", "cohort_population", "cohort_server", "cohort_ui", "configurable_param_names", "diag_strip_server", "diag_strip_ui", "diagnose_bound_piling", "diagnose_chain_stuck", "diagnose_low_kappa", "explore_server", "explore_ui", "hero_server", "hero_ui", "lab_app", "lab_compare_draws", "lab_compare_expand_stages", "lab_compare_max", "lab_compare_trajectories", "lab_fit_assemble", "lab_fit_forward_sim", "lab_fit_run", "lab_fit_run_production", "lab_library_autosave", "lab_library_delete", "lab_library_dir", "lab_library_last", "lab_library_list", "lab_library_load", "lab_library_promote", "lab_library_save", "lab_session_from_list", "LabSession", "load_scenario", "make_hex_lattice", "make_lookups", "make_square_grid", "model_accordion_server", "model_accordion_ui", "model_config_default", "model_config_resolve", "new_plague_results", "outbreak_label", "outbreak_resolve_id", "outbreak_summary", "param_label", "plague_fit_filter", "plague_fit_fitted_names", "plague_fit_fixed_pars", "plague_fit_prior", "plague_fit_setup", "plague_fit_vcv", "plague_stochastic_humans", "plague_stochastic_metapop", "plot_comparison", "plot_dynamics", "plot_phase_portrait", "plot_sensitivity", "prior_bounds", "prior_default", "prior_density", "prior_families", "prior_to_dsl", "priors_accordion_server", "priors_accordion_ui", "priors_default", "priors_to_bounds", "priors_to_dsl", "run_ca", "run_diagnostics", "run_plague_metapop_model", "run_plague_model", "status_bar_server", "status_bar_ui", "summarize_outbreak_metrics", "thermal_response", "with_per_group_fixed", "with_R0_to_beta_r", "with_thermal_beta" ], "_datasets": [ { "name": "outbreak_aliases", "title": "Pre-2026-09 outbreak identifiers", "object": "outbreak_aliases", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "legacy_id", "outbreak_id" ], "rows": 9, "table": true, "tojson": true }, { "name": "outbreaks", "title": "Historical plague outbreak data", "object": "outbreaks", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "outbreak_id", "label", "location", "year", "population", "day", "deaths", "obs_period", "krauer_id", "start_date", "date", "calendar", "interval", "country", "lat", "lon", "source", "population_source", "type", "complete", "sourcetype", "total_deaths", "attack_rate", "fittable", "unfit_reason", "attack_flag" ], "rows": 1584, "table": true, "tojson": true }, { "name": "outbreaks_all", "title": "Krauer's full plague-outbreak catalogue", "object": "outbreaks_all", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "outbreak_id", "label", "location", "year", "population", "day", "deaths", "obs_period", "krauer_id", "start_date", "date", "calendar", "interval", "country", "lat", "lon", "source", "population_source", "type", "complete", "sourcetype", "total_deaths", "attack_rate", "fittable", "unfit_reason", "attack_flag" ], "rows": 11559, "table": true, "tojson": true } ], "_help": [ { "page": "available_scenarios", "title": "Names of bundled scenario YAML files.", "topics": [ "available_scenarios" ] }, { "page": "ca_step", "title": "Advance the CA one tick", "topics": [ "ca_step" ] }, { "page": "calculate_equilibrium", "title": "Calculate equilibrium values for deterministic models", "topics": [ "calculate_equilibrium" ] }, { "page": "calculate_force_of_infection", "title": "Calculate force of infection over time", "topics": [ "calculate_force_of_infection" ] }, { "page": "calculate_outbreak_metrics", "title": "Calculate outbreak summary statistics", "topics": [ "calculate_outbreak_metrics" ] }, { "page": "calculate_R0", "title": "Calculate basic reproduction number (R0) for different model types", "topics": [ "calculate_R0" ] }, { "page": "cohort_check_fittable", "title": "Stop early when a cohort contains outbreaks that cannot be fitted.", "topics": [ "cohort_check_fittable" ] }, { "page": "cohort_data", "title": "Long-format cohort data with NA-padded synchronized time grid.", "topics": [ "cohort_data" ] }, { "page": "cohort_obs_period", "title": "Per-outbreak observation period (must be consistent across the cohort).", "topics": [ "cohort_obs_period" ] }, { "page": "cohort_population", "title": "Per-outbreak population values (K_h / K_r when fixed).", "topics": [ "cohort_population" ] }, { "page": "cohort_server", "title": "Cohort module — server.", "topics": [ "cohort_server" ] }, { "page": "cohort_ui", "title": "Cohort module — UI.", "topics": [ "cohort_ui" ] }, { "page": "configurable_param_names", "title": "Names of model parameters configurable from the Virtual Lab UI.", "topics": [ "configurable_param_names" ] }, { "page": "diag_strip_server", "title": "Diagnostics strip module — server.", "topics": [ "diag_strip_server" ] }, { "page": "diag_strip_ui", "title": "Diagnostics strip module — UI.", "topics": [ "diag_strip_ui" ] }, { "page": "diagnose_bound_piling", "title": "Detect posterior mass piling against prior bounds.", "topics": [ "diagnose_bound_piling" ] }, { "page": "diagnose_chain_stuck", "title": "Detect non-mixing chains via R-hat.", "topics": [ "diagnose_chain_stuck" ] }, { "page": "diagnose_low_kappa", "title": "Detect low NegBinomial dispersion ('kappa').", "topics": [ "diagnose_low_kappa" ] }, { "page": "explore_server", "title": "Outbreak explorer — server.", "topics": [ "explore_server" ] }, { "page": "explore_ui", "title": "Outbreak explorer — UI.", "topics": [ "explore_ui" ] }, { "page": "hero_server", "title": "Hero plot module — server.", "topics": [ "hero_server" ] }, { "page": "hero_ui", "title": "Hero plot module — UI.", "topics": [ "hero_ui" ] }, { "page": "lab_app", "title": "Launch the yersinia Virtual Lab Shiny app.", "topics": [ "lab_app" ] }, { "page": "lab_compare_draws", "title": "Marginal posterior draws for several saved fits.", "topics": [ "lab_compare_draws" ] }, { "page": "lab_compare_expand_stages", "title": "Expand a selection so stochastic entries contribute both stages.", "topics": [ "lab_compare_expand_stages" ] }, { "page": "lab_compare_max", "title": "Maximum number of fits comparable at once.", "topics": [ "lab_compare_max" ] }, { "page": "lab_compare_trajectories", "title": "Posterior predictive trajectories for several saved fits.", "topics": [ "lab_compare_trajectories" ] }, { "page": "lab_fit_assemble", "title": "Assemble a deterministic-pilot fit from a LabSession.", "topics": [ "lab_fit_assemble" ] }, { "page": "lab_fit_forward_sim", "title": "Posterior predictive forward simulation from a Lab fit.", "topics": [ "lab_fit_forward_sim" ] }, { "page": "lab_fit_run", "title": "Run a deterministic-pilot fit assembled by 'lab_fit_assemble()'.", "topics": [ "lab_fit_run" ] }, { "page": "lab_fit_run_production", "title": "Run a stochastic production fit on top of a deterministic pilot.", "topics": [ "lab_fit_run_production" ] }, { "page": "lab_library_autosave", "title": "Autosave a completed fit.", "topics": [ "lab_library_autosave" ] }, { "page": "lab_library_delete", "title": "Delete a saved fit from the library.", "topics": [ "lab_library_delete" ] }, { "page": "lab_library_dir", "title": "Directory backing the saved-fit library.", "topics": [ "lab_library_dir" ] }, { "page": "lab_library_last", "title": "Slug of the most recently saved fit.", "topics": [ "lab_library_last" ] }, { "page": "lab_library_list", "title": "List saved fits in the library.", "topics": [ "lab_library_list" ] }, { "page": "lab_library_load", "title": "Load a saved fit into a live session.", "topics": [ "lab_library_load" ] }, { "page": "lab_library_promote", "title": "Promote an autosaved entry to a named keeper.", "topics": [ "lab_library_promote" ] }, { "page": "lab_library_save", "title": "Save the current session to the fit library.", "topics": [ "lab_library_save" ] }, { "page": "lab_session_from_list", "title": "Reconstruct a LabSession from a saved state list.", "topics": [ "lab_session_from_list" ] }, { "page": "LabSession", "title": "LabSession R6 class — Virtual Lab session state.", "topics": [ "LabSession" ] }, { "page": "load_named_scenario", "title": "Load named scenario parameters", "topics": [ "load_named_scenario" ] }, { "page": "load_scenario", "title": "Load plague model scenario parameters", "topics": [ "load_scenario" ] }, { "page": "make_hex_lattice", "title": "Build a hexagonal CA lattice", "topics": [ "make_hex_lattice" ] }, { "page": "make_lookups", "title": "Build CA transition-probability lookups", "topics": [ "make_lookups" ] }, { "page": "make_square_grid", "title": "Build a square-lattice CA grid", "topics": [ "make_square_grid" ] }, { "page": "model_accordion_server", "title": "Model accordion module — server.", "topics": [ "model_accordion_server" ] }, { "page": "model_accordion_ui", "title": "Model accordion module — UI.", "topics": [ "model_accordion_ui" ] }, { "page": "model_config_default", "title": "Default model configuration for a fresh Virtual Lab session.", "topics": [ "model_config_default" ] }, { "page": "model_config_resolve", "title": "Resolve a model config to per-parameter scope and value.", "topics": [ "model_config_resolve" ] }, { "page": "new_plague_results", "title": "Create a plague_results object", "topics": [ "new_plague_results" ] }, { "page": "outbreak_aliases", "title": "Pre-2026-09 outbreak identifiers", "topics": [ "outbreak_aliases" ] }, { "page": "outbreak_label", "title": "Display labels for outbreak identifiers.", "topics": [ "outbreak_label" ] }, { "page": "outbreak_resolve_id", "title": "Resolve outbreak identifiers, translating pre-2026-09 ids.", "topics": [ "outbreak_resolve_id" ] }, { "page": "outbreak_summary", "title": "Per-outbreak summary table for the outbreak explorer.", "topics": [ "outbreak_summary" ] }, { "page": "outbreaks", "title": "Historical plague outbreak data", "topics": [ "outbreaks" ] }, { "page": "outbreaks_all", "title": "Krauer's full plague-outbreak catalogue", "topics": [ "outbreaks_all" ] }, { "page": "param_label", "title": "Human-readable label for a model parameter.", "topics": [ "param_label" ] }, { "page": "plague_fit_filter", "title": "Build a particle filter for the humans plague model.", "topics": [ "plague_fit_filter" ] }, { "page": "plague_fit_fitted_names", "title": "Default fitted parameter names for plague humans fits.", "topics": [ "plague_fit_fitted_names" ] }, { "page": "plague_fit_fixed_pars", "title": "Build the fixed (non-fitted) parameter list for a plague humans fit.", "topics": [ "plague_fit_fixed_pars" ] }, { "page": "plague_fit_prior", "title": "Default prior over the fitted plague humans parameters (monty DSL).", "topics": [ "plague_fit_prior" ] }, { "page": "plague_fit_setup", "title": "Assemble everything needed to call 'monty::monty_sample()' on a plague fit.", "topics": [ "plague_fit_setup" ] }, { "page": "plague_fit_vcv", "title": "Default diagonal VCV for the random-walk sampler.", "topics": [ "plague_fit_vcv" ] }, { "page": "plague_stochastic_humans", "title": "Stochastic humans plague model (carcass formulation)", "topics": [ "plague_stochastic_humans" ] }, { "page": "plague_stochastic_metapop", "title": "Stochastic metapopulation plague model (rat dispersal between patches)", "topics": [ "plague_stochastic_metapop" ] }, { "page": "plot_comparison", "title": "Create multi-panel comparison plot", "topics": [ "plot_comparison" ] }, { "page": "plot_dynamics", "title": "Plot compartment dynamics with uncertainty bands", "topics": [ "plot_dynamics" ] }, { "page": "plot_phase_portrait", "title": "Plot phase portrait (S vs I)", "topics": [ "plot_phase_portrait" ] }, { "page": "plot_sensitivity", "title": "Plot parameter sensitivity results", "topics": [ "plot_sensitivity" ] }, { "page": "plot.plague_results", "title": "Plot method for plague_results", "topics": [ "plot.plague_results" ] }, { "page": "print.plague_outbreak_metrics", "title": "Print method for outbreak metrics", "topics": [ "print.plague_outbreak_metrics" ] }, { "page": "print.plague_results", "title": "Print method for plague_results", "topics": [ "print.plague_results" ] }, { "page": "print.scenario_parameters", "title": "Print method for plague_parameters", "topics": [ "print.scenario_parameters" ] }, { "page": "prior_bounds", "title": "Hard-bound interval implied by a prior, for piling detection.", "topics": [ "prior_bounds" ] }, { "page": "prior_default", "title": "Default prior for a single fittable parameter.", "topics": [ "prior_default" ] }, { "page": "prior_density", "title": "Evaluate a prior's density on a grid for plotting.", "topics": [ "prior_density" ] }, { "page": "prior_families", "title": "Registry of supported prior distribution families.", "topics": [ "prior_families" ] }, { "page": "prior_to_dsl", "title": "Convert one prior to a monty-DSL expression.", "topics": [ "prior_to_dsl" ] }, { "page": "priors_accordion_server", "title": "Priors accordion module — server.", "topics": [ "priors_accordion_server" ] }, { "page": "priors_accordion_ui", "title": "Priors accordion module — UI.", "topics": [ "priors_accordion_ui" ] }, { "page": "priors_default", "title": "Build a default priors list for a set of fitted parameters.", "topics": [ "priors_default" ] }, { "page": "priors_to_bounds", "title": "Bounds for every parameter in a packer, including per-group decorations.", "topics": [ "priors_to_bounds" ] }, { "page": "priors_to_dsl", "title": "Convert a full priors list to a list of monty-DSL expressions.", "topics": [ "priors_to_dsl" ] }, { "page": "run_ca", "title": "Run a CA from 'n_seeds' seed cells for 'n_ticks'", "topics": [ "run_ca" ] }, { "page": "run_diagnostics", "title": "Run all v1 diagnostics on a fit.", "topics": [ "run_diagnostics" ] }, { "page": "run_human_stochastic_model", "title": "Run human stochastic model (dust2/odin2 backend)", "topics": [ "run_human_stochastic_model" ] }, { "page": "run_plague_metapop_model", "title": "Run plague metapopulation model", "topics": [ "run_plague_metapop_model" ] }, { "page": "run_plague_model", "title": "Run plague model simulation", "topics": [ "run_plague_model" ] }, { "page": "status_bar_server", "title": "Status bar module — server.", "topics": [ "status_bar_server" ] }, { "page": "status_bar_ui", "title": "Status bar module — UI.", "topics": [ "status_bar_ui" ] }, { "page": "summarize_outbreak_metrics", "title": "Summarize outbreak metrics across replicates", "topics": [ "summarize_outbreak_metrics" ] }, { "page": "summary.plague_results", "title": "Summary method for plague_results", "topics": [ "summary.plague_results" ] }, { "page": "thermal_response", "title": "Thermal response on transmission (Brière, visible coordinates)", "topics": [ "thermal_response" ] }, { "page": "with_per_group_fixed", "title": "Splice per-group fixed parameters into a grouped packer.", "topics": [ "with_per_group_fixed" ] }, { "page": "with_R0_to_beta_r", "title": "Convert R0 to beta_r per group during unpack.", "topics": [ "with_R0_to_beta_r" ] }, { "page": "with_thermal_beta", "title": "Compute per-group thermal forcing on transmission.", "topics": [ "with_thermal_beta" ] } ], "_readme": "https://github.com/flmnh-ai/yersinia/raw/HEAD/README.md", "_rundeps": [ "backports", "checkmate", "cli", "cpp11", "dplyr", "dust2", "generics", "glue", "lattice", "lifecycle", "magrittr", "Matrix", "monty", "odin2", "pillar", "pkgconfig", "purrr", "R6", "rlang", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "yaml" ], "_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" } ], "_score": 2.5185139398778875, "_indexed": true, "_nocasepkg": "yersinia", "_universes": [ "flmnh-ai", "nick-gauthier" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-10-22T11:38:15.000Z", "distro": "resolute", "arch": "aarch64", "commit": "8be6bf3bf15560884691b2d8e153a407ac71363e", "fileid": "https://r2.ropensci.org/ed5c27ee36286d110d636fbc14334807c76edff04c2033f989ec4dce867a9e4a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923" }, { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-10-22T11:38:33.000Z", "distro": "resolute", "arch": "x86_64", "commit": "8be6bf3bf15560884691b2d8e153a407ac71363e", "fileid": "https://r2.ropensci.org/cf2aa6026cb31c792b297f249826b9abbb5de47de856019bb13cb2969de2448f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923" }, { "r": "4.6.1", "os": "linux", "version": "0.1.0", "date": "2026-10-22T11:40:17.000Z", "distro": "resolute", "arch": "aarch64", "commit": "8be6bf3bf15560884691b2d8e153a407ac71363e", "fileid": "https://r2.ropensci.org/ca052bb9c14afa3491025406586da3afebfe2abc7388a05cc4717a752ca1566b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923" }, { "r": "4.6.1", "os": "linux", "version": "0.1.0", "date": "2026-10-22T11:39:39.000Z", "distro": "resolute", "arch": "x86_64", "commit": "8be6bf3bf15560884691b2d8e153a407ac71363e", "fileid": "https://r2.ropensci.org/9d4fc00ba6c62973cc4d0297006121ea5ce1e48028e330f35965dc9088cbd59d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923" }, { "r": "4.5.3", "os": "mac", "version": "0.1.0", "date": "2026-10-22T11:53:32.000Z", "arch": "aarch64", "commit": "8be6bf3bf15560884691b2d8e153a407ac71363e", "fileid": "https://r2.ropensci.org/a80d0b8ce865840df8aa735693ea22faa3f06b5630e4222ab92b87053233dded", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923" }, { "r": "4.5.3", "os": "mac", "version": "0.1.0", "date": "2026-10-22T11:55:44.000Z", "arch": "x86_64", "commit": "8be6bf3bf15560884691b2d8e153a407ac71363e", "fileid": "https://r2.ropensci.org/8de8592dbdd1c55b022ce8e61f8662fbd9c68206dd6ce986bbe7fb197db7c448", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923" }, { "r": "4.6.1", "os": "mac", "version": "0.1.0", "date": "2026-10-22T11:57:06.000Z", "arch": "aarch64", "commit": "8be6bf3bf15560884691b2d8e153a407ac71363e", "fileid": "https://r2.ropensci.org/7c1e8a67fdf186bc0199cbfa8ce9416b0d9e87a36fc3bef1e91709cd2faeacc2", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923" }, { "r": "4.6.1", "os": "mac", "version": "0.1.0", "date": "2026-10-22T11:47:16.000Z", "arch": "x86_64", "commit": "8be6bf3bf15560884691b2d8e153a407ac71363e", "fileid": "https://r2.ropensci.org/b8bccb4db13c87e9db28b2bd8ce9e911644c3ac6ed8f4f1736f2d90e7c321988", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.0", "date": "2026-10-22T11:41:34.000Z", "arch": "emscripten", "commit": "8be6bf3bf15560884691b2d8e153a407ac71363e", "fileid": "https://r2.ropensci.org/479578f1c8258f01825b7176893f17483340c8fda44d49185683631a832b70ee", "status": "success", "buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923" }, { "r": "4.7.0", "os": "win", "version": "0.1.0", "date": "2026-10-22T11:41:36.000Z", "arch": "aarch64", "commit": "8be6bf3bf15560884691b2d8e153a407ac71363e", "fileid": "https://r2.ropensci.org/24aea7a9d259fcc88f1916a10c4f22be1bf5fd5fc9199d7f9426dc3e5d6c43af", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923" }, { "r": "4.7.0", "os": "win", "version": "0.1.0", "date": "2026-10-22T11:38:24.000Z", "arch": "x86_64", "commit": "8be6bf3bf15560884691b2d8e153a407ac71363e", "fileid": "https://r2.ropensci.org/ebe9c316a6a6041b050243e5dae5d0a4c51af88a409fe2f24a47f6370c795576", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923" }, { "r": "4.5.3", "os": "win", "version": "0.1.0", "date": "2026-10-22T11:37:51.000Z", "arch": "x86_64", "commit": "8be6bf3bf15560884691b2d8e153a407ac71363e", "fileid": "https://r2.ropensci.org/5ae0c7aadb66c1e740e67356111cee8084de1f7c079a3254c6bda60e2319d6e2", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923" }, { "r": "4.6.1", "os": "win", "version": "0.1.0", "date": "2026-10-22T11:41:15.000Z", "arch": "aarch64", "commit": "8be6bf3bf15560884691b2d8e153a407ac71363e", "fileid": "https://r2.ropensci.org/b584f828457191aaf5d13675c605977aad648781ebcb1131eff12ddf7e015346", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923" }, { "r": "4.6.1", "os": "win", "version": "0.1.0", "date": "2026-10-22T11:42:01.000Z", "arch": "x86_64", "commit": "8be6bf3bf15560884691b2d8e153a407ac71363e", "fileid": "https://r2.ropensci.org/bec8d367556ff1692f4de03a10c4bb984f4f39817cb99df2a643f1f84df5701e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/flmnh-ai/actions/runs/39770582923" } ] }