{"id":40545070,"url":"https://github.com/mooreryan/featuretable","last_synced_at":"2026-01-20T23:36:38.368Z","repository":{"id":37576889,"uuid":"290091320","full_name":"mooreryan/featuretable","owner":"mooreryan","description":null,"archived":false,"fork":false,"pushed_at":"2023-03-22T00:08:06.000Z","size":1657,"stargazers_count":1,"open_issues_count":10,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-10-10T17:14:50.969Z","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/mooreryan.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}},"created_at":"2020-08-25T02:26:05.000Z","updated_at":"2023-03-21T16:11:13.000Z","dependencies_parsed_at":"2022-08-29T09:41:01.600Z","dependency_job_id":"d9e876d1-0436-4817-86f2-12b35c8481cd","html_url":"https://github.com/mooreryan/featuretable","commit_stats":null,"previous_names":[],"tags_count":11,"template":false,"template_full_name":null,"purl":"pkg:github/mooreryan/featuretable","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mooreryan%2Ffeaturetable","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mooreryan%2Ffeaturetable/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mooreryan%2Ffeaturetable/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mooreryan%2Ffeaturetable/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mooreryan","download_url":"https://codeload.github.com/mooreryan/featuretable/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mooreryan%2Ffeaturetable/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28618803,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-20T22:24:05.405Z","status":"ssl_error","status_checked_at":"2026-01-20T22:20:31.342Z","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":[],"created_at":"2026-01-20T23:36:38.291Z","updated_at":"2026-01-20T23:36:38.357Z","avatar_url":"https://github.com/mooreryan.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# FeatureTable\n\n[![R-CMD-check](https://github.com/mooreryan/featuretable/actions/workflows/check-standard.yaml/badge.svg?branch=main)](https://github.com/mooreryan/featuretable/actions/workflows/check-standard.yaml)\n\n_Note: I still consider FeatureTable to be in the pre-release stage. The code itself is well tested and I use it in my own research, but the API has not stabalized and is still subject to breaking changes when I cut a new release._\n\n## Installing\n\nThe simplest was is probably by using the `remotes` package:\n\n```r\nremotes::install_github(\n  repo = \"mooreryan/featuretable\",\n  build_vignettes = TRUE, build = TRUE, force = TRUE, upgrade = \"never\",\n  # This will ensure that all suggested dependencies are installed as well.\n  dependencies = TRUE\n)\n```\n\n_Note: you can install a specific tag or relase by replacing this `\"mooreryan/featuretable\"` with something like this `\"mooreryan/featuretable@0.0.11\"`. (That would install tag 0.0.11.)_\n\nAlternatively, you could procure the code, and install with `devtools`. To obtain the code, either:\n\n- Go to the [Releases page](https://github.com/mooreryan/featuretable/releases) and click on the latest release,\n- Or, if you want to follow the main branch, clone this repository.\n\nThen install with devtools. (Ensure that you are running this from the root of the project's source directory.)\n\n```r\ndevtools::install(\n  build_vignettes = TRUE, build = TRUE, force = TRUE, upgrade = \"never\",\n  # This will ensure that all suggested dependencies are installed as well.\n  dependencies = TRUE\n)\n```\n\n## Dependencies\n\nHere is some info about the dependencies. Note that if you used one of the code snippets above, all the optional dependencies will be installed as well.\n\n### Required\n\nThese packages _must_ be installed to use `featuretable`.\n\n- `R6`\n- `rlang`\n\n### Suggested\n\n- If you want nice plots, I suggest you also install `ggplot2`, `ggrepel`, and `biplotr`.\n- If you want fancy zero replacement, you should install `zCompositions`.\n- If you need to import or export `phyloseq` objects, then you need to install `phyloseq`.\n- If you want to build the vignettes yourself, you will need `knitr` and `rmarkdown`. Also, some of the vignettes use `magrittr` to keep things clean.\n\n### Test suite dependencies\n\n- If you want to run the test suite locally, then you need to install `testthat`.\n- Some of the tests require additional packages. If you don't have them, those tests should be skipped.\n  - Testing plotting functions requires `vdiffr`.\n  - If you want to run the coverage report for yourself, then you will need to install `covr`.\n  - Some of the tests compare bespoke implementations of certain functions to their counterparts in `dplyr`, `tibble`, and `tidyr`.\n  - Property tests require the `hedgehog` package.\n\n## Usage\n\n### Vignettes\n\n`FeatureTable` comes with some detailed vignettes describing its usage. After installing, you can view them with the following command:\n\n```\nbrowseVignettes(\"featuretable\")\n```\n\n### Function docs\n\nAdditionally, each function has a lot of info in the help section. You can run `?featuretable` to get an overview of everything. Click on the links in there to get to individual function docs. You can also access function docs with the `?`, e.g., `?keep_samples`.\n\n## R v3 and v4 compatibility\n\n`R CMD CHECK`, which includes unit tests, are run via GitHub CI for the following versions:\n\n- MacOS, Windows, \u0026 Ubuntu\n  - Latest release\n- Ubuntu\n  - 4.1.3\n  - 4.0.5\n  - 3.6.3\n  - 3.5.3\n\nSo as long as that is passing (see the badge at the top of the README), then you can be (pretty) sure the package works with both R v3 and v4.\n\nNotes:\n\n- Each time `data.frame` or `as.data.frame` is called in the `FeatureTable` code and tests , `stringsAsFactors = TRUE` is passed in as an argument.\n  - So, if you need a specific stable sorting of your string-like data, you need to set the factor levels yourself.\n  - In theory, you should be fine passing in `data.frame`s that don't have their strings as factors, since `FeatureTable` will convert all strings to factors, but I should probably add tests for this.\n  - This behavior may change in the future though!\n- One thing to note is that `as.data.frame.FeatureTable` does not have a `stringsAsFactors` parameter. This shouldn't be a problem as string-esque data is not allowed in the `data` field anyway.\n\n## Hacking\n\nNotes for working on the code.\n\n- If you make an update to the core R6 class, make sure you regenerate the `.rda` files in `data`, using the scripts in `data-raw`.\n  - Note that generating the data files requires the [DivNet](https://github.com/adw96/DivNet) R package.\n  - You can use the recipe in the `justfile` for this.\n\n### Just\n\nJust go and install [just](https://just.systems/man/en/chapter_1.html). Then use the recipes in the `justfile`.\n\n### Default branch is now main\n\nThe default branch is now `main`, and the `master` branch no longer exists.\n\nIf you have a local clone using `master` as the default branch, you can [update](https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/managing-branches-in-your-repository/renaming-a-branch) it by running the following commands.\n\n```\ngit branch -m master main\ngit fetch origin\ngit branch -u origin/main main\ngit remote set-head origin -a\n```\n\nOptionally, run the following command to remove tracking references to the old branch name.\n\n```\ngit remote prune origin\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmooreryan%2Ffeaturetable","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmooreryan%2Ffeaturetable","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmooreryan%2Ffeaturetable/lists"}