{"id":47225337,"url":"https://github.com/bmaitner/r_citations","last_synced_at":"2026-03-13T19:30:34.378Z","repository":{"id":184279535,"uuid":"526320931","full_name":"bmaitner/R_citations","owner":"bmaitner","description":null,"archived":false,"fork":false,"pushed_at":"2024-08-22T20:37:16.000Z","size":49921,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-09T17:41:28.050Z","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":"cc0-1.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bmaitner.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,"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":"2022-08-18T18:02:22.000Z","updated_at":"2024-08-28T08:46:41.000Z","dependencies_parsed_at":"2025-09-09T16:36:11.792Z","dependency_job_id":null,"html_url":"https://github.com/bmaitner/R_citations","commit_stats":null,"previous_names":["bmaitner/r_citations"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/bmaitner/R_citations","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bmaitner%2FR_citations","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bmaitner%2FR_citations/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bmaitner%2FR_citations/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bmaitner%2FR_citations/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bmaitner","download_url":"https://codeload.github.com/bmaitner/R_citations/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bmaitner%2FR_citations/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30473274,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-13T17:15:31.527Z","status":"ssl_error","status_checked_at":"2026-03-13T17:15:22.394Z","response_time":60,"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":[],"created_at":"2026-03-13T19:30:29.683Z","updated_at":"2026-03-13T19:30:34.363Z","avatar_url":"https://github.com/bmaitner.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Overview\nThis repository contains code for investigating how often manuscripts in Ecology and Evolutionary Biology that cite the R software language make their R code available. The R scripts that this work relies upon are contained in the folder 'R_scripts'.  The data generated by this work (which includes both scripted and manual components) are stored in the 'data' folder.  The 'figures' folder contains figures produced for a related manuscript (in review). For more information, see the preprint at: https://www.authorea.com/doi/full/10.22541/au.170003886.68548206/v1\n\n# Important Data\n\n## Citation Data\nThe main data file in this repository is [cite_data.RDS](https://github.com/bmaitner/R_citations/blob/main/data/cite_data.RDS). This is an RDS file containing information on citation counts for R files and associated predictor variables.  Many of the variables are returned from the Rscopus package (https://cran.r-project.org/web/packages/rscopus/index.html) using the scopus API (https://dev.elsevier.com/sc_apis.html). Metadata on fields returned by the scopus API is available at https://dev.elsevier.com/sc_apis.html.  Below, we provide information on fields which are NOT returned by the scopus API (i.e., data which we collected).\n\n* uid = A unique ID assigned to each record.\n* r_scripts_available = A binary variable (yes/no) describing whether any R code was shared as part of the publication.\n* r_used = A binary variable (yes/no) describing whether R was used in the publication (as opposed to simply referenced without being used).\n* data_available = A binary variable (yes/no) describing whether the full data underlying the publication were included.\n* comments = Unstructured comments about the record.  This may contain information about why a judgement was made or where code was found.\n* code location = Text string describing where the code was located, options include:  NA, \"SI\", \"figshare\", \"website\", \"appendix\", \"dryad\", \"github\", \"Github\", \"zenodo\", \"environmental data initiative\", \"sciencebase.gov\", \"mendeley data\", \"osf\", \"bitbucket\"   \n* code format = Text string describing the format a code was shared in, options include: NA, \"word\", \"pdf\", \"R\", \"typeset text\", \"rtf\", \"txt\", \"rmd\"  \n* code license = Text string describing the license for the shared code, if any. Note that \"NA\" means that a license was not specified, where NA means we did not check. Options include: NA, \"NA\", \"GPL\", \"CC0\", \"CC-BY\", \"MIT\", \"Open\", \"copyright\" \n* n = A numeric index variable used to stratify randomization.\n\nSee https://dev.elsevier.com/sc_apis.html for information on the following fields:\n* title\n* author\n* year\n* doi\n* journal\n* issn\n* volume\n* pages\n* date\n* display_date\n* citations\n* article_type\n* open_access\n\n## Impact Factor Data\nThe other important data file in this repository is [impact_factor.csv](https://github.com/bmaitner/R_citations/blob/main/data/manual_downloads/impact_factors.csv). This is a CSV file containing information on the impact factors of journals used in this work, as recorded on June 16, 2023. This information on impact factor was provided by the R package \"scholar\" (https://cran.r-project.org/web/packages/scholar/index.html). Below we provide information on the fields included.\n\n* needed_journals = The list of journals submitted to the scholar R package. These were extracted from the \"journal\" field of the file cite_data.RDS (see above).\n* Journal = The journal title matched by scholar.\n* Cites = The number of citations of that journal.\n* ImpactFactor = The journal's impact factor.\n* Eigenfactor = The journal's Eigenfactor.\n* dist = The distance between the submitted journal name and the returned journal name, as calcualted by scholar.\n\n# Important Code\n\nThere are two important R scripts in this repository: [1_data_collection.R](https://github.com/bmaitner/R_citations/blob/main/R_scripts/1_data_collection.R) and [2_analyses_and_figures.R](https://github.com/bmaitner/R_citations/blob/main/R_scripts/2_analyses_and_figures.R). The former file was used to select publications for the study (along with relevant metadata). The latter file contains code underlying analyses and visualizations.\n\n\n[![DOI](https://zenodo.org/badge/526320931.svg)](https://zenodo.org/badge/latestdoi/526320931)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbmaitner%2Fr_citations","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbmaitner%2Fr_citations","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbmaitner%2Fr_citations/lists"}