{"id":14069123,"url":"https://github.com/rostools/prodigenr","last_synced_at":"2025-10-22T03:32:20.531Z","repository":{"id":42663150,"uuid":"42332547","full_name":"rostools/prodigenr","owner":"rostools","description":"Project directory generator R package","archived":false,"fork":false,"pushed_at":"2024-12-14T13:50:41.000Z","size":3416,"stargazers_count":43,"open_issues_count":1,"forks_count":13,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-10-10T12:36:45.107Z","etag":null,"topics":["cran","devtools","open-science","open-source","project-management","reproducibility","reproducible-research","reproducible-science","rstats","rstudio","usethis"],"latest_commit_sha":null,"homepage":"https://rostools.github.io/prodigenr/","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/rostools.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2015-09-11T21:14:30.000Z","updated_at":"2025-10-06T09:17:34.000Z","dependencies_parsed_at":"2025-10-22T03:31:14.531Z","dependency_job_id":null,"html_url":"https://github.com/rostools/prodigenr","commit_stats":null,"previous_names":[],"tags_count":14,"template":false,"template_full_name":null,"purl":"pkg:github/rostools/prodigenr","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rostools%2Fprodigenr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rostools%2Fprodigenr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rostools%2Fprodigenr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rostools%2Fprodigenr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rostools","download_url":"https://codeload.github.com/rostools/prodigenr/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rostools%2Fprodigenr/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280374621,"owners_count":26320077,"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":"2025-10-22T02:00:06.515Z","response_time":63,"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":["cran","devtools","open-science","open-source","project-management","reproducibility","reproducible-research","reproducible-science","rstats","rstudio","usethis"],"created_at":"2024-08-13T07:06:37.925Z","updated_at":"2025-10-22T03:32:20.516Z","avatar_url":"https://github.com/rostools.png","language":"R","funding_links":[],"categories":["R"],"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# Create projects with prodigenr \u003cimg src=\"man/figures/logo.png\" style=\"text-align: right;\" width=\"70\"/\u003e\n\n\u003c!-- badges: start --\u003e\n\n[![CRAN Status\nBadge](http://www.r-pkg.org/badges/version/prodigenr)](https://cran.r-project.org/package=prodigenr)\n[![R-CMD-check](https://github.com/rostools/prodigenr/workflows/R-CMD-check/badge.svg)](https://github.com/rostools/prodigenr/actions)\n[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)\n[![CRAN RStudio mirror\ndownloads](http://cranlogs.r-pkg.org/badges/prodigenr)](https://www.r-pkg.org:443/pkg/prodigenr)\n\n\u003c!-- badges: end --\u003e\n\nThis package has a simple aim of being a project directory generator\n(prodigenr), with a simple focus on:\n\n1.  Creating a standardized project folder structure with a few template\n    files needed for beginning a data analysis project.\n2.  Following a \"one project, one (main) output\" principle, such as a\n    report/manuscript in the case of scientific output or a book or\n    website for things like courses or workshops.\n3.  Adhering to established best practices that make it easier for the\n    project to be reproducible and open.\n\nThis standardized approach to how a scientific project is structured\nhelps ensure that the final code and documents are fairly modular,\nself-contained, easy to share and make public, and be as reproducible as\npossible. The structure also makes use of the existing and established\napplications and workflows ([RStudio](https://posit.co/),\n[devtools](https://CRAN.R-project.org/package=devtools), and\n[usethis](https://CRAN.R-project.org/package=usethis)).\n\n## Installation\n\nYou can install the released version of prodigenr from\n[CRAN](https://cran.r-project.org) with:\n\n``` r\ninstall.packages(\"prodigenr\")\n```\n\nAnd the development version from [GitHub](https://github.com/) with:\n\n``` r\n# install.packages(\"pak\")\npak::pak(\"rostools/prodigenr\")\n```\n\n## Usage\n\nThere are two ways of creating a new project: using the R console or\nusing the RStudio \"New Project\" menu option.\n\nThrough the console, use the `setup_project()` command. So, for\ninstance, if you want a manuscript project, type out:\n\n``` r\nlibrary(prodigenr)\nsetup_project(\"~/Desktop/DiseaseDiet\")\n```\n\nThis then creates a directory tree, with template files for starting\nyour analysis! Open the newly created project via the `.Rproj` file. For\nthe RStudio approach, go to \"File -\\\u003e New Project\", then \"New directory\"\nand find the prodigenr project in the list.\n\nOnce in the project, you can add a manuscript/report\n[Quarto](https://quarto.org/) file using:\n\n``` r\ncreate_report() \n```\n\nThe main secondary function is the `template_list` command, which lists\nthe available template files:\n\n```{r, include=FALSE}\nlibrary(prodigenr)\n```\n\n```{r}\ntemplate_list\n```\n\nFor a more detailed tutorial, see the introduction vignette:\n\n``` r\nvignette('prodigenr', 'prodigenr')\n```\n\n## Related packages or projects\n\nThere are several existing packages for creating projects, each of which\nhas it's own pros and cons. Check out the last section of the\n`vignette(\"prodigenr\")` for more details. Try them out and see which you\nlike!\n\nprodigenr tries to use ideas from R\npackages/[devtools](https://CRAN.R-project.org/package=devtools) while\nstill being as simple as possible and to be more specific to academic\nresearchers primarily in biomedical/non-computer science fields.\nHowever, it can always improve! I welcome any suggestions, just submit a\n[GitHub issue](https://github.com/rostools/prodigenr/issues).\n\n## Interested in contributing?\n\nSee the [contributing\ndocumentation](https://rostools.github.io/prodigenr/CONTRIBUTING.html)\nfor information on how to contribute. Please note that this project is\nreleased with a [Contributor Code of\nConduct](https://rostools.github.io/prodigenr/CODE_OF_CONDUCT.html). By\nparticipating in this project you agree to abide by its terms.\n\nSpecial thanks to Zhila Semnani for creating the logo!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frostools%2Fprodigenr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frostools%2Fprodigenr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frostools%2Fprodigenr/lists"}