{"id":23631138,"url":"https://github.com/jameel-institute/daedalus","last_synced_at":"2025-08-31T07:31:16.491Z","repository":{"id":247436675,"uuid":"825755318","full_name":"jameel-institute/daedalus","owner":"jameel-institute","description":"[UNDER DEVELOPMENT] R package implementing the DAEDALUS model for projecting and optimising health, social, and economic costs of a pandemic.","archived":false,"fork":false,"pushed_at":"2025-08-21T11:12:17.000Z","size":15342,"stargazers_count":6,"open_issues_count":22,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-08-21T11:52:15.103Z","etag":null,"topics":["decision-support","epidemiological-models","health-economics","pandemic-preparedness","public-health","r-package","rcpp","sdg-3"],"latest_commit_sha":null,"homepage":"https://jameel-institute.github.io/daedalus/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/jameel-institute.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2024-07-08T12:38:16.000Z","updated_at":"2025-08-19T09:36:42.000Z","dependencies_parsed_at":"2024-09-16T10:48:08.996Z","dependency_job_id":"eb7ca276-10f2-46b6-b5c8-a774e8dceb78","html_url":"https://github.com/jameel-institute/daedalus","commit_stats":null,"previous_names":["j-idea/daedalus","jameel-institute/daedalus"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/jameel-institute/daedalus","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jameel-institute%2Fdaedalus","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jameel-institute%2Fdaedalus/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jameel-institute%2Fdaedalus/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jameel-institute%2Fdaedalus/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jameel-institute","download_url":"https://codeload.github.com/jameel-institute/daedalus/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jameel-institute%2Fdaedalus/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":272953914,"owners_count":25021133,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-31T02:00:09.071Z","response_time":79,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["decision-support","epidemiological-models","health-economics","pandemic-preparedness","public-health","r-package","rcpp","sdg-3"],"created_at":"2024-12-28T02:48:44.896Z","updated_at":"2025-08-31T07:31:16.423Z","avatar_url":"https://github.com/jameel-institute.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\nbibliography: vignettes/resources/references.json\nlink-citations: true\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# daedalus: Model health, social, and economic costs of a pandemic\n\n\u003c!-- badges: start --\u003e\n[![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept)\n[![R build status](https://github.com/jameel-institute/daedalus/workflows/R-CMD-check/badge.svg)](https://github.com/jameel-institute/daedalus/actions/workflows/R-CMD-check.yaml)\n[![Codecov test coverage](https://codecov.io/gh/jameel-institute/daedalus/branch/main/graph/badge.svg)](https://app.codecov.io/gh/jameel-institute/daedalus?branch=main)\n[![CRAN status](https://www.r-pkg.org/badges/version/daedalus)](https://CRAN.R-project.org/package=daedalus)\n\u003c!-- badges: end --\u003e\n\n_daedalus_ implements the integrated epidemiological and economic model in @haw2022.\n\n![](vignettes/figures/daedalus.png)\n\n## Installation\n\nYou can install the development version of daedalus from this repository using the _pak_ package, or from the Jameel Institute R-universe.\n\n```r\n# install.packages(\"pak\")\npak::pak(\"jameel-institute/daedalus\", upgrade = FALSE)\n\n# installation from R-universe\ninstall.packages(\n  \"daedalus\", \n  repos = c(\n    \"https://jameel-institute.r-universe.dev\", \"https://cloud.r-project.org\"\n  )\n)\n```\n\n### Installation notes\n\n_daedalus_ is under active development. To use a version of _daedalus_ associated with major milestones, install a specific version from the list below.\n\n- IDM Thailand 2024: `pak::pak(\"jameel-institute/daedalus@v0.1.0\")`\n\n- IfG workshop 2025 (with real time modelling): `pak::pak(\"jameel-institute/daedalus@v0.2.0\")`\n\n### Known issues\n\nWe have found the following issues with released versions:\n\n1. `v0.1.0`: Consumer-worker contacts are not correctly handled, leading to higher and faster epidemic peaks.\n\n2. `v0.2.0`: Consumer-worker contacts are not included in the model, leading to lower and later epidemic peaks. The 'recovered' compartment does not include recoveries from hospitalisation. Please use the helper function `get_epidemic_summary()` to get epidemic sizes.\n\n## Quick start\n\nThe model can be run for any country or territory in the `country_names` list by passing the country name to the function.\nThis automatically pulls country-specific demographic and economic data, which is included in the package, into the model (see the ['Get started' vignette](https://jameel-institute.github.io/daedalus/articles/daedalus.html) for more details).\n\n```{r libraries}\nlibrary(daedalus)\n\n# run model for Canada\ndata \u003c- daedalus(\"Canada\", \"influenza_1918\")\n\n# get pandemic costs as a total in million dollars\nget_costs(data, \"total\")\n\n# disaggregate total for economic, education, and health costs\nget_costs(data, \"domain\")\n```\n\nUsers can select infection parameters from among seven epidemics caused by directly-transmitted viral respiratory pathogens, which are stored in the stand-alone helper package `daedalus.data`. These can be called as `daedalus.data::infection_data`, while epidemic identifiers are stored as `daedalus.data::epidemic_names`.\n\nUsers can override default country contact data and epidemic-specific infection arguments by passing custom classes to `daedalus()`; see the package website for more details.\n\nUsers can also model the implementation of pandemic response measures: for more on this see the documentation for the main model function `daedalus()`, and the vignette on modelling interventions on the package website.\n\n## Related projects\n\n_daedalus_ is an R implementation of the scenario model from a [project on the economics of pandemic preparedness](https://github.com/robj411/p2_drivers).\n\n[_daedalus.data_](https://github.com/jameel-institute/daedalus.data) is a stand-alone helper R package to handle input data for the _daedalus_ model. Its purpose is to allow users to flexibly manipulate or change epidemiological and economic data, without needing to modify the model itself.\n\n## References\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjameel-institute%2Fdaedalus","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjameel-institute%2Fdaedalus","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjameel-institute%2Fdaedalus/lists"}