{"id":29639190,"url":"https://github.com/neotomadb/qsr_manuscript","last_synced_at":"2026-02-25T20:02:06.665Z","repository":{"id":72351485,"uuid":"88179177","full_name":"NeotomaDB/QSR_Manuscript","owner":"NeotomaDB","description":"Repository for scripts and figures associated with Neotoma ms. to be submitted to QSR","archived":false,"fork":false,"pushed_at":"2025-04-05T06:46:31.000Z","size":1429,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-08-12T17:52:56.995Z","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":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/NeotomaDB.png","metadata":{"files":{"readme":"README.md","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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2017-04-13T15:24:22.000Z","updated_at":"2025-04-05T06:46:32.000Z","dependencies_parsed_at":null,"dependency_job_id":"cbc09ed6-6303-4a68-9d33-82c63686e39a","html_url":"https://github.com/NeotomaDB/QSR_Manuscript","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/NeotomaDB/QSR_Manuscript","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NeotomaDB%2FQSR_Manuscript","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NeotomaDB%2FQSR_Manuscript/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NeotomaDB%2FQSR_Manuscript/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NeotomaDB%2FQSR_Manuscript/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/NeotomaDB","download_url":"https://codeload.github.com/NeotomaDB/QSR_Manuscript/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NeotomaDB%2FQSR_Manuscript/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274748361,"owners_count":25341942,"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":"2025-09-12T02:00:09.324Z","response_time":60,"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":[],"created_at":"2025-07-21T20:08:22.261Z","updated_at":"2026-02-25T20:02:06.567Z","avatar_url":"https://github.com/NeotomaDB.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003c!-- badges: start --\u003e\n\n[![lifecycle](https://img.shields.io/badge/lifecycle-archived-orange.svg)](https://doi.org/10.1017/qua.2017.105)\n\n\u003c!-- badges: end --\u003e\n\n\n# QSR_Manuscript\nRepository for scripts and figures associated with Neotoma ms. to be submitted to QSR\n\n## Scraping Data from Neotoma\nOutcome: This process will generate a flat csv text file with six columns: datasetID, levels (rows in count matrix), taxa (columns in count matrix), occs (rows * columns in count matrix), date (of submission to NeotomaDB), dataset type. \n\n- Open a terminal/shell with python in the path\n- ```cd``` in the ```/scripts``` directory. \n- ```python get_neotoma_ds_summaries.py /name/of/file/to/dump/into.csv```. 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Warning: this will erase and overwrite the file if it already exists. \n\n## Summarizing and Cleaning the Data\nOutcome: This process will generate a CSV with cumulative sums for each year in the dataset\n\n- Open RStudio \n- Open the file ```summarize_records.R```\n- Set the working directory \n- Set the input file to the file you generated in step 1\n- Run the script\n\n## Plotting the data\nOutcome: This will produce a stacked line chart of the data in the summaries, generated during step 2.\n\n- Open RStudio\n- Open the file ```plot_summaries.R```\n- Set the working directory\n- Run the script.\n- Save the output from the graphics window in RStudio.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneotomadb%2Fqsr_manuscript","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fneotomadb%2Fqsr_manuscript","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneotomadb%2Fqsr_manuscript/lists"}