{"id":30019828,"url":"https://github.com/veupathdb/microbiomecomputations","last_synced_at":"2025-08-25T21:06:29.944Z","repository":{"id":38444115,"uuid":"421075378","full_name":"VEuPathDB/microbiomeComputations","owner":"VEuPathDB","description":null,"archived":false,"fork":false,"pushed_at":"2025-04-13T13:18:40.000Z","size":1674,"stargazers_count":1,"open_issues_count":15,"forks_count":0,"subscribers_count":20,"default_branch":"master","last_synced_at":"2025-08-06T09:50:43.293Z","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":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/VEuPathDB.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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}},"created_at":"2021-10-25T15:14:52.000Z","updated_at":"2023-09-30T14:35:58.000Z","dependencies_parsed_at":"2023-10-24T20:31:18.528Z","dependency_job_id":"c5bb7ba1-60de-48b7-b2a2-63559476d147","html_url":"https://github.com/VEuPathDB/microbiomeComputations","commit_stats":null,"previous_names":[],"tags_count":35,"template":false,"template_full_name":null,"purl":"pkg:github/VEuPathDB/microbiomeComputations","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2FmicrobiomeComputations","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2FmicrobiomeComputations/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2FmicrobiomeComputations/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2FmicrobiomeComputations/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/VEuPathDB","download_url":"https://codeload.github.com/VEuPathDB/microbiomeComputations/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VEuPathDB%2FmicrobiomeComputations/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":272131796,"owners_count":24878986,"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":"2025-08-25T02:00:12.092Z","response_time":1107,"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":"2025-08-06T01:21:41.330Z","updated_at":"2025-08-25T21:06:29.936Z","avatar_url":"https://github.com/VEuPathDB.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003e [!CAUTION]\n\u003e Maintenance of this repository was moved to [microbiomeDB](https://github.com/microbiomeDB) on 28 Feb 2024.\n\u003e Please see the [new location](https://github.com/microbiomeDB/microbiomeComputations) for the most recent version.\n\n\n\n\n# microbiomeComputations\n\nmicrobiomeComputations is an R package which provides helper functions for performing common analyses \non microbiome data. The results are available as json, or optionally in a `data.table`. This package is intended to be compliant with the API specified in the VEuPathDB EdaComputeService.\n\n## Installation\n\nUse the R package [remotes](https://cran.r-project.org/web/packages/remotes/index.html) to install microbiomeComputations. From the R command prompt:\n\n```R\nremotes::install_github('VEuPathDB/microbiomeComputations')\n```\n\n## Usage\n```\n# df is a data frame of abundance values with samples as rows. One column should hold the sample id, all other columns are assumed to be taxa\n# the 'recordIdColumn' is the name of the column that contains the sample ids.\n# 'method' can be 'simpson', 'shannon', or 'evenness'.\ndt \u003c- alphaDiv(df, recordIdColumn=\"entity.SampleID\", method='simpson')\n```\n\n## Testing\nThis package uses the testthat package for testing.\n\n## Contributing\nPull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.\n\nPlease make sure to update unit tests as appropriate. If making a change that affects the eda-verse, please conduct integration testing if possible.\n\n## License\n[Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0.txt)\n\n\n\u003c!-- badges: start --\u003e\n  [![R-CMD-check](https://github.com/VEuPathDB/microbiomeComputations/workflows/R-CMD-check/badge.svg)](https://github.com/VEuPathDB/microbiomeComputations/actions)\n  \u003c!-- badges: end --\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fveupathdb%2Fmicrobiomecomputations","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fveupathdb%2Fmicrobiomecomputations","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fveupathdb%2Fmicrobiomecomputations/lists"}