{"id":16284421,"url":"https://github.com/nuest/reproducible-research-at-giscience","last_synced_at":"2026-01-20T06:04:54.096Z","repository":{"id":49164041,"uuid":"245433508","full_name":"nuest/reproducible-research-at-giscience","owner":"nuest","description":null,"archived":false,"fork":false,"pushed_at":"2021-06-28T08:12:29.000Z","size":2569,"stargazers_count":2,"open_issues_count":1,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-09T00:04:45.260Z","etag":null,"topics":["giscience","research-compendium"],"latest_commit_sha":null,"homepage":"https://nuest.github.io/reproducible-research-at-giscience/","language":"TeX","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nuest.png","metadata":{"files":{"readme":"README.Rmd","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":"2020-03-06T13:58:29.000Z","updated_at":"2021-06-28T08:12:13.000Z","dependencies_parsed_at":"2022-09-21T08:53:18.889Z","dependency_job_id":null,"html_url":"https://github.com/nuest/reproducible-research-at-giscience","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/nuest/reproducible-research-at-giscience","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nuest%2Freproducible-research-at-giscience","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nuest%2Freproducible-research-at-giscience/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nuest%2Freproducible-research-at-giscience/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nuest%2Freproducible-research-at-giscience/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nuest","download_url":"https://codeload.github.com/nuest/reproducible-research-at-giscience/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nuest%2Freproducible-research-at-giscience/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28597087,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-20T02:08:49.799Z","status":"ssl_error","status_checked_at":"2026-01-20T02:08:44.148Z","response_time":117,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["giscience","research-compendium"],"created_at":"2024-10-10T19:19:29.905Z","updated_at":"2026-01-20T06:04:54.068Z","avatar_url":"https://github.com/nuest.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\ntitle: Reproducible research at the GIScience conference\n---\n\nThis repository is the reproducibility package for the article _\"Reproducible research and GIScience: an evaluation using GIScience conference papers\"_.\nThis repository is based on a previous analysis of [AGILE conference](https://agile-online.org/conference) submissions, see [https://github.com/nuest/reproducible-research-and-giscience](https://github.com/nuest/reproducible-research-and-giscience) ([10.5281/zenodo.1227260](https://doi.org/10.5281/zenodo.1227260)).\nFind the preprint and a deposition of this repository via the badges below.\n\n\u003c!--\n[![Article DOI](https://img.shields.io/badge/PUBLISHER-https%3A%2F%2Fdoi.org%2FDOI-brightgreen.svg)](https://doi.org/)\n--\u003e\n\n[![Earth ArXiv Preprint\nDOI](https://img.shields.io/badge/%F0%9F%8C%8D%F0%9F%8C%8F%F0%9F%8C%8E%20EarthArXiv-doi.org%2F10.31223%2FX5ZK5V-%23FF7F2A)](https://doi.org/10.31223/X5ZK5V) [![Zenodo\nDOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4032875.svg)](https://doi.org/10.5281/zenodo.4032875) [![CI rendering of PDF](https://img.shields.io/badge/PDF-CI%20rendering-informational)](https://nightly.link/nuest/reproducible-research-at-giscience/workflows/pdf/master/reproducible-research-at-giscience.zip)\n\n## Reproduce online\n\nClick the \"Binder\" button below to open an interactive editing environment with all required software installed on [MyBinder.org](https://mybinder.org/).\nIt uses the current version of the branch `master` in the repository, but you can also enter the Zenodo DOI (see above) in the MyBinder user interface to open a preserved release version.\n\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/nuest/reproducible-research-at-giscience/master?urlpath=rstudio)\n\nYou can start RStudio for the text analysis and figures via \"New \u003e RStudio\" or open the Jupyter Notebook for the bibliographic analysis in the folder `author_analysis`.\nYou can navigate to the R Markdown notebook files (see [list of files below](#files-in-this-repository)) to inspect and execute the code for the text analysis and reproduce the figures as described in [Reproduce locally](#reproduce-analyses), except that local installation of required packages is not required.\n\nUse [this link](https://mybinder.org/v2/zenodo/10.5281/zenodo.4032875/?filepath=author_analysis/BibTex_handling.ipynb) to directly open the Jupyter Notebook.\n\nUse [this link](https://mybinder.org/v2/gh/nuest/reproducible-research-at-giscience/master?urlpath=rstudio) to directly open RStudio.\n\n## Reproduce analyses\n\nOpen one of the two _R Markdown analysis files_ (`.Rmd`) with [RStudio](https://www.rstudio.com/products/rstudio/).\nThen select \"Knit \u003e Knit to PDF\" to render the document.\nIf you have errors rendering the whole PDF, try running each [chunk](https://rmarkdown.rstudio.com/authoring_rcodechunks.html) to locate the problem or use \"Knit to HTML\".\nDepending on the [R Markdown parameters](https://bookdown.org/yihui/rmarkdown/parameterized-reports.html), the historic tex analysis tries to download proceedings PDFs from a private share and requires a login.\nThis download does not work with knitting the whole document - please execute the chunk `data_download_drive` manually.\n\nThe documents do _not_ include code to install required packages.\nRun the code in the file `install.R` to install all dependencies.\nYou can skip the installation of LaTeX (recommended to use [`tinytex`](https://yihui.org/tinytex/)) and installation of LaTeX packages if you knit to HTML or run the chunks directly from RStudio.\n\n## Reproduce locally with Docker\n\nInstall [Docker CE](https://www.docker.com/community-edition) or a compatible tool for building an image based on a `Dockerfile` and running a container based on the image.\nThe `Dockerfile` uses the Rocker image [`rocker/binder:3.6.3`](https://hub.docker.com/r/rocker/binder), providing R version `3.6.3` with a CRAN mirror timestamp of July 5th 2019.\n\nDownload the project files, open a command line in the root directory (where this file is), and run the commands as documented at the end of the `Dockerfile`.\n\nIf you have [`repo2docker`](https://repo2docker.readthedocs.io), you can also run `repo2docker .` and use the `--editable` option to edit the workflows.\n_The `repo2docker` option is the only way the original authors worked on the analysis to ensure the computing environment is properly managed._\nYou can most easily achieve it using the included `Makefile`, just run\n\n```bash\nmake\n```\n\n## Files in this repository\n\n- `paper/reproducible-research-at-giscience.Rmd`: The paper manuscript; it uses the data from the directories `results` and `author_analysis`, which is generated by the other Rmd and Jupyter notebooks (see below).\n- `paper/reproducible-research-at-giscience-appendix.Rmd`: Appendix for the manuscript with the assessment results table.\n- `results/paper_assessment.csv`: Results of manual paper evaluation.\n- `results/text_analysis_{topwordstems,keywordstems}.csv`: Results of automated text analysis.\n- `results/figure_[...].{pdf,png}`: Figures and plots from text analysis and paper assessment; the plots are also created as part of the manuscript.\n- `giscience-reproducibility-assessment.Rmd`: R Markdown document with the visualisations about the assessment of paper reproducibility.\n- `giscience-historic-text-analysis.Rmd`: R Markdown document with the text analysis of historic GIScience proceedings.\n- `Dockerfile`: A recipe for the computational environment using [Docker](https://en.wikipedia.org/wiki/Docker_(software)).\n- `install.R`: R script file executed during creation of the Docker image to install required dependencies.\n- `author_analysis/*`: Data, code, and results simple comparison of authors' last names of the compared conferences based on a Jupyter Notebook; the contents of the file `author_counts.csv` are used in the article manuscript.\n- `docs/*`: Prerendered HTML files of the analysis documents hosted online at [https://nuest.github.io/reproducible-research-at-giscience/](https://nuest.github.io/reproducible-research-at-giscience/); files can be rendered with `make docs`\n\n## Deposition on Zenodo\n\nThis repository is archived on Zenodo: **https://doi.org/10.5281/zenodo.4032875**\n\nThe deposited archive was created using the [GitHub-Zenodo-integration](https://guides.github.com/activities/citable-code/) and includes all source files and the appendix as PDF.\n\nYou can open the Zenodo deposit directly on Binder: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/zenodo/10.5281/zenodo.4032875/)\n\n## License\n\nThe documents in this repository are licensed under a [Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0/).\n\nAll contained code is licensed under the [Apache License 2.0](https://choosealicense.com/licenses/apache-2.0/).\n\nThe data used is licensed under a [Open Data Commons Attribution License](https://opendatacommons.org/licenses/by/).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnuest%2Freproducible-research-at-giscience","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnuest%2Freproducible-research-at-giscience","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnuest%2Freproducible-research-at-giscience/lists"}