{"id":19624219,"url":"https://github.com/bioconductor/sweave2rmd","last_synced_at":"2025-04-28T05:31:29.440Z","repository":{"id":38236670,"uuid":"492873550","full_name":"Bioconductor/sweave2rmd","owner":"Bioconductor","description":"A project for converting Bioconductor Sweave documents to Rmd","archived":false,"fork":false,"pushed_at":"2023-08-15T02:26:17.000Z","size":210,"stargazers_count":8,"open_issues_count":17,"forks_count":20,"subscribers_count":10,"default_branch":"main","last_synced_at":"2024-05-09T07:47:41.626Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-sa-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Bioconductor.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2022-05-16T14:35:00.000Z","updated_at":"2024-05-01T08:09:45.000Z","dependencies_parsed_at":"2023-02-14T03:55:18.774Z","dependency_job_id":null,"html_url":"https://github.com/Bioconductor/sweave2rmd","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fsweave2rmd","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fsweave2rmd/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fsweave2rmd/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fsweave2rmd/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Bioconductor","download_url":"https://codeload.github.com/Bioconductor/sweave2rmd/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224096915,"owners_count":17255189,"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":[],"created_at":"2024-11-11T11:37:19.879Z","updated_at":"2024-11-11T11:37:21.228Z","avatar_url":"https://github.com/Bioconductor.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Sweave2Rmd\n## Description of the project\n\nSweave2Rmd is a project to convert all [Bioconductor](https://bioconductor.org)\nSweave vignettes to Rmd.\n\nSee the project [Trello Board](https://trello.com/b/nJHqzR1j/bioconductor-vignettes-rnw-rmd-project)\nfor vignettes that need converting and the [Github Project](https://github.com/orgs/Bioconductor/projects/2)\nfor the status of vignettes being converted. \n\nIf you'd like to volunteer, see contribute.Rmd.\n\nIf you're a Bioconductor maintainer who needs help converting to `.Rmd`,\nopen an issue in your repository and ask `@Bioconductor/sweave2rmd` for\nhelp converting.\n\nThis project follows the [Bioconductor Code of\nConduct](https://bioconductor.github.io/bioc_coc_multilingual/).\n\n## Script to categorize vignettes\n\nThis is a script that will categorize a list of packages with Sweave vignettes.\nThe vignettes are categorized to determine which vignettes need work on the\nsweave2rmd project board. The script takes a list of vignettes for a given\nversion of Bioconductor for a given repo with respect to a threshold value\nprovided.\n\n### How to use the script\n\n#### Declare variables and settings\n\nDeclare the variables to be used in the script and call the relevant libraries.\n\n- **threshold**: the variable used to classify a package as a\nhigh-priority or low-priority package. The threshold is set to a certain number,\nexample in our script is 40, this means that any package that has a rank below\n40 is considered a high-priority package. The lower the rank number, the higher\nthe priority.\n\n- **version** : The Bioconductor version that will be used in the script.\n\n- **filepath** : Path to a file listing the full path of vignettes; e.g.,\n    ```\n    # Example data\n    ABSSeq/vignettes/ABSSeq.Rnw\n    ABarray/vignettes/ABarray.Rnw\n    ABarray/vignettes/ABarrayGUI.Rnw\n    ```\n\n- **repo**: Repository used in the script\n\n#### How to run the script\n\nRun this command in your terminal `Rscript categorize_vignettes.R`\n\nThe syntax remains same for Windows/MacOS/Linux/Ubuntu.\n\n**Note**: Open a Terminal from the location of the script for the command to work.\n\n#### Output of the script\n\nFor every package, their rank, priority, and status are computed. This is the\noutput that we want from the script, which will help us categorize the packages.\n\n-  **rank** : The rank of the package as compared to all other packages\n\n-  **priority** : Based on rank and the threshold given in the script, is the\npackage a high or low priority package.\n\n- **status**: Is the package ready for conversion or do additional steps, such \nas contacting the maintainer are needed.\n\nFor vignettes not in the specified version, the rank, priority and action are\nnot computed. Their status is specified as deprecated which helps know which\nvignettes are no longer maintained or used.\n\nThe results from the script are output as an excel file. The desired output is\nan excel file because it will be easy to use, export and also share.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fsweave2rmd","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioconductor%2Fsweave2rmd","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fsweave2rmd/lists"}