{"id":14069907,"url":"https://github.com/aaronpeikert/reproducible-research","last_synced_at":"2025-04-13T02:32:07.650Z","repository":{"id":36059595,"uuid":"206075650","full_name":"aaronpeikert/reproducible-research","owner":"aaronpeikert","description":"A Reproducible Data Analysis Workflow with R Markdown, Git, Make, and Docker","archived":false,"fork":false,"pushed_at":"2022-03-31T12:32:12.000Z","size":2547,"stargazers_count":124,"open_issues_count":1,"forks_count":17,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-03-26T20:21:16.757Z","etag":null,"topics":["containerization","dependency-management","literate-programming","open-science","r","reproducibility","version-management"],"latest_commit_sha":null,"homepage":"https://psyarxiv.com/8xzqy/","language":"TeX","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/aaronpeikert.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-09-03T12:48:03.000Z","updated_at":"2025-02-18T14:02:02.000Z","dependencies_parsed_at":"2022-08-08T13:01:06.975Z","dependency_job_id":null,"html_url":"https://github.com/aaronpeikert/reproducible-research","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aaronpeikert%2Freproducible-research","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aaronpeikert%2Freproducible-research/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aaronpeikert%2Freproducible-research/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aaronpeikert%2Freproducible-research/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/aaronpeikert","download_url":"https://codeload.github.com/aaronpeikert/reproducible-research/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248657793,"owners_count":21140842,"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":["containerization","dependency-management","literate-programming","open-science","r","reproducibility","version-management"],"created_at":"2024-08-13T07:07:19.585Z","updated_at":"2025-04-13T02:32:07.104Z","avatar_url":"https://github.com/aaronpeikert.png","language":"TeX","funding_links":[],"categories":["TeX"],"sub_categories":[],"readme":"---\noutput:\n  md_document:\n    variant: gfm\n---\n\n```{r setup, include=FALSE}\nknitr::opts_chunk$set(echo = TRUE)\nlibrary(here)\nlibrary(readr)\nlibrary(pander)\n```\n\nThis is the accompanying GitHub repository to a work in progress paper by Aaron Peikert[![ORCID iD](https://orcid.org/sites/default/files/images/orcid_16x16.png)](https://orcid.org/0000-0001-7813-818X) and Andreas M. Brandmaier [![ORCID iD](https://orcid.org/sites/default/files/images/orcid_16x16.png)](http://orcid.org/0000-0001-8765-6982).\n\n[![licensebuttons by](https://licensebuttons.net/l/by/3.0/88x31.png)](https://creativecommons.org/licenses/by/4.0) [![Ask Me Anything !](https://img.shields.io/badge/Ask%20me-anything-1abc9c.svg)](https://github.com/aaronpeikert/reproducible-research/issues/new) ![Open Source Love](https://badges.frapsoft.com/os/v2/open-source.svg?v=103)\n\n# Abstract\n\n```{r abstract, child = 'abstract.Rmd'}\n```\n\n```{r, echo=FALSE}\nknitr::include_graphics(\"Images/nutshell.svg\")\n```\n\n# Resources\n\n```{r, include=FALSE}\nresources \u003c- read_csv(here(\"data\", \"resources.csv\"), trim_ws = FALSE)\n```\n\n```{r, echo=FALSE, asis=TRUE}\npander(\n  resources,\n  split.tables = Inf,\n  split.cells = Inf,\n  missing = \"\",\n  keep.line.breaks = TRUE,\n  style = \"multiline\"\n)\n```\n\n\n# Compile\n\nThe following paragraphs describe how you can obtain a copy of the source files of our manuscript describing reproducible workflows, and create the PDF. Either, you can go the 'standard' way of downloading a local copy of the repository and knit the manuscript file in R, or you can use the reproducible workflow as suggested and use Make to create a container and build the final PDF file in exactly the same virtual computational environment that we used to render the PDF.\n\n## Standard Way\n\nRequires: `Git`, `RStudio`, `pandoc`, `pandoc-citeproc` \u0026 `rmarkdown`.\n\nOpen RStudio -\u003e File -\u003e New Project -\u003e Version Control -\u003e Git\n\nInsert:\n\n```\nhttps://github.com/aaronpeikert/reproducible-research.git\n```\n\nOpen `manuscript.Rmd` click on `Knit`.\n\n## Using a Reproducible Workflow\n\nDoes not require R or RStudio, but `make` \u0026 `docker`.\n\nExecute in Terminal:\n\n```{bash, eval=FALSE}\ngit clone https://github.com/aaronpeikert/reproducible-research.git\ncd reproducible-research\nmake build\nmake all DOCKER=TRUE\n```\n\n**Note: Windows user need to manually edit the `Makefile` and set current_path to the current directory and use `make all DOCKER=TRUE WINDOWS=TRUE`. We hope that future releases of Docker for Windows will not require that workaround.**\n\n## Rebuild Everything\n\nIn case you experience some unexpected behavior with this workflow, you should check that you have the most recent version (`git pull`), rebuild the docker image (`make build`) and force the rebuild of all targets (`make -B DOCKER`).\n\n```{bash, eval=FALSE}\ngit pull \u0026\u0026 make rebuild \u0026\u0026 make -B DOCKER=TRUE\n```\n\n# Session Info\n\n```{r}\nsessioninfo::session_info()\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faaronpeikert%2Freproducible-research","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faaronpeikert%2Freproducible-research","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faaronpeikert%2Freproducible-research/lists"}