{"id":22151679,"url":"https://github.com/epiverse-trace/episoap","last_synced_at":"2025-07-26T05:31:45.948Z","repository":{"id":63002563,"uuid":"541612824","full_name":"epiverse-trace/episoap","owner":"epiverse-trace","description":"[Not published - under active development] A Store of Outbreak Analytics Pipelines Provided as Rmarkdown Report Templates","archived":false,"fork":false,"pushed_at":"2024-04-12T12:06:22.000Z","size":12084,"stargazers_count":4,"open_issues_count":42,"forks_count":2,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-04-12T23:37:36.352Z","etag":null,"topics":["automated-report","decision-support","epidemiology","epiverse","literate-programming","outbreak-analysis","pipelines","r","r-package","rmarkdown-templates"],"latest_commit_sha":null,"homepage":"https://epiverse-trace.github.io/episoap/","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/epiverse-trace.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2022-09-26T13:53:50.000Z","updated_at":"2024-04-15T10:26:36.481Z","dependencies_parsed_at":"2024-04-15T10:26:23.329Z","dependency_job_id":null,"html_url":"https://github.com/epiverse-trace/episoap","commit_stats":{"total_commits":187,"total_committers":4,"mean_commits":46.75,"dds":"0.11229946524064172","last_synced_commit":"c8bbd2d0344246dbc34f2cafa369b23b2f2753ba"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fepisoap","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fepisoap/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fepisoap/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fepisoap/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/epiverse-trace","download_url":"https://codeload.github.com/epiverse-trace/episoap/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":227652611,"owners_count":17799230,"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","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":["automated-report","decision-support","epidemiology","epiverse","literate-programming","outbreak-analysis","pipelines","r","r-package","rmarkdown-templates"],"created_at":"2024-12-02T00:35:37.554Z","updated_at":"2024-12-02T00:35:38.409Z","avatar_url":"https://github.com/epiverse-trace.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\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# episoap: A Store of Outbreak Analytics Pipelines \u003cimg src=\"man/figures/logo.svg\" align=\"right\" width=\"120\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![R-CMD-check](https://github.com/epiverse-trace/episoap/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/episoap/actions/workflows/R-CMD-check.yaml)\n[![Codecov test coverage](https://codecov.io/gh/epiverse-trace/episoap/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/episoap?branch=main)\n[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)\n\u003c!-- badges: end --\u003e\n\nThis package provides a store of curated outbreak analytics pipelines as \nrmarkdown reports.\n\n## Target audience\n\nThe analyses are largely automated, and should be of use to any outbreak\nanalyst. A basic R literacy will be required to adapt the report to other\ndatasets.\n\n## Installation\n\nYou can install the development version of soap from [GitHub](https://github.com/) with:\n\n``` r\n# install.packages(\"devtools\")\ndevtools::install_github(\"epiverse-trace/episoap\")\n```\n\n## Usage\n\nReports are provided a [rmarkdown templates](https://rstudio.github.io/rstudio-extensions/rmarkdown_templates.html). You can load them either via RStudio graphical interface\n\n![Graphical interface to open a soap rmarkdown template in RStudio](man/figures/template_rstudio.png)\n\nor by running:\n\n```{r, eval = FALSE}\nrmarkdown::draft(file = \"myreport.Rmd\", template = \"transmissibility\", package = \"episoap\")\n```\n\nTo get a list of the template reports available in this package, you can run:\n\n```{r}\nepisoap::list_templates()\n```\n\n### System dependencies\n\nYou may need to install system dependencies:\n\n```\n# macOS\nbrew install libsodium cmake\n\n# Linux (Debian based)\napt install libsodium-dev cmake\n```\n\n## Related projects\n\nThis project has some overlap with other R packages:\n\n- [`{sitrep}`](https://github.com/R4EPI/sitrep) from the Applied Epi\norganisation. While the stated goals and approaches can appear similar,\n`{episoap}` and `{sitrep}` are actually two very different projects. The\n`{sitrep}` reports are more specific (providing, e.g., reports for a specific\ndisease although a generic template is in development), and thus more detailed.\nThey are also more opinionated in the sense that they provide a single analysis\npath for each situation, based on the extensive experience of MSF. `{episoap}`\non the other hand offers a more generic approach, with the emphasis on\nalternative paths you can take within a single analysis.\n\n## Acknowledgements\n\n- Thanks to Sam Abbott for pointing out issues with the way EpiNow2 was used in the transmissibility pipeline (#35)\n- The package logo is a derivative from a [pipeline logo](https://www.flaticon.com/free-icon/pipeline_2082696), provided by [flaticon user \"Eucalyp\"](https://www.flaticon.com/authors/eucalyp) for free for personal and commercial use with attribution.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiverse-trace%2Fepisoap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fepiverse-trace%2Fepisoap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiverse-trace%2Fepisoap/lists"}