{
  "_id": "6a27b53a24555f66ed5386f4",
  "Package": "schtools",
  "Title": "Schloss Lab Tools for Reproducible Microbiome Research",
  "Version": "0.4.1.9000",
  "Date": "2023-08-21",
  "Authors@R": "c(person(given = \"Kelly\",\nfamily = \"Sovacool\",\nrole = c(\"aut\", \"cre\"),\nemail = \"sovacool@umich.edu\",\ncomment = c(ORCID = \"0000-0003-3283-829X\")),\nperson(given = \"Nicholas\",\nfamily = \"Lesniak\",\nrole = \"aut\",\nemail = \"nlesniak@umich.edu\",\ncomment = c(ORCID = \"0000-0001-9359-5194\")),\nperson(given = \"Sarah\",\nfamily = \"Lucas\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-1676-5801\")),\nperson(given = \"Courtney\",\nfamily = \"Armour\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-5250-1224\")),\nperson(given = \"Patrick\",\nfamily = \"Schloss\",\nrole = \"aut\",\nemail = \"pschloss@umich.edu\"),\nperson(given = \"Jacqueline\",\nfamily = \"Moltzau\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-1398-5980\")),\nperson(given = \"Andrew\",\nfamily = \"Hannah\",\nrole = \"ctb\"),\nperson(given = \"Nielson\",\nfamily = \"Baxter\",\nrole = \"ctb\"),\nperson(given = \"Alyxandria\",\nfamily = \"Schubert\",\nrole = \"ctb\"),\nperson(given = \"Kathryn\",\nfamily = \"Iverson\",\nrole = \"ctb\"))",
  "Description": "A collection of useful functions and example code created\nand used by the Schloss Lab for reproducible microbiome\nresearch. Perform common tasks like read files created by\nmothur <https://mothur.org/>, tidy up your microbiome data, and\nformat R Markdown documents for publication.  See the website\n<http://www.schlosslab.org/schtools/> for more information,\ndocumentation, and examples.",
  "License": "MIT + file LICENSE",
  "URL": "http://www.schlosslab.org/schtools/,\nhttps://github.com/SchlossLab/schtools",
  "BugReports": "https://github.com/SchlossLab/schtools/issues",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.3",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://kelly-sovacool.r-universe.dev",
  "Date/Publication": "2023-08-22 01:30:59 UTC",
  "RemoteUrl": "https://github.com/SchlossLab/schtools",
  "RemoteRef": "HEAD",
  "RemoteSha": "b066acf96bb43e80adfe00edb17d02206e704c45",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-09 06:19:06 UTC",
    "User": "root"
  },
  "Author": "Kelly Sovacool [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3283-829X>),\nNicholas Lesniak [aut] (ORCID: <https://orcid.org/0000-0001-9359-5194>),\nSarah Lucas [aut] (ORCID: <https://orcid.org/0000-0003-1676-5801>),\nCourtney Armour [aut] (ORCID: <https://orcid.org/0000-0002-5250-1224>),\nPatrick Schloss [aut],\nJacqueline Moltzau [ctb] (ORCID:\n<https://orcid.org/0000-0003-1398-5980>),\nAndrew Hannah [ctb],\nNielson Baxter [ctb],\nAlyxandria Schubert [ctb],\nKathryn Iverson [ctb]",
  "Maintainer": "Kelly Sovacool <sovacool@umich.edu>",
  "MD5sum": "357c7e214d08937fe3aa80df4e6991e7",
  "_user": "kelly-sovacool",
  "_type": "src",
  "_file": "schtools_0.4.1.9000.tar.gz",
  "_fileid": "8b52c4ff0375f1b0bdeb473b24898baba26779742e62a954859ac26f6d264042",
  "_filesize": 1663606,
  "_sha256": "8b52c4ff0375f1b0bdeb473b24898baba26779742e62a954859ac26f6d264042",
  "_created": "2026-06-09T06:19:06.000Z",
  "_published": "2026-06-09T06:39:54.762Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 80260573124,
      "time": 164,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7499986470"
    },
    {
      "job": 80260573117,
      "time": 154,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7499983763"
    },
    {
      "job": 80260573130,
      "time": 107,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7500267418"
    },
    {
      "job": 80260573110,
      "time": 104,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7500254118"
    },
    {
      "job": 80260107744,
      "time": 212,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7499942187"
    },
    {
      "job": 80260573125,
      "time": 129,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7499977086"
    },
    {
      "job": 80260573137,
      "time": 95,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7499967497"
    },
    {
      "job": 80260573121,
      "time": 93,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7499967055"
    },
    {
      "job": 80260573115,
      "time": 95,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7499967480"
    }
  ],
  "_buildurl": "https://github.com/r-universe/kelly-sovacool/actions/runs/27187646497",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/SchlossLab/schtools",
  "_commit": {
    "id": "b066acf96bb43e80adfe00edb17d02206e704c45",
    "author": "Kelly Sovacool <kellysovacool@gmail.com>",
    "committer": "Kelly Sovacool <kellysovacool@gmail.com>",
    "message": "Bump dev version\n",
    "time": 1692667859
  },
  "_maintainer": {
    "name": "Kelly Sovacool",
    "email": "sovacool@umich.edu",
    "login": "kelly-sovacool",
    "mastodon": "@kelly_sovacool@mastodon.social",
    "bluesky": "@kelly.sova.cool",
    "linkedin": "in/kelly-sovacool",
    "orcid": "0000-0003-3283-829X",
    "description": "Bioinformatics Software Engineer",
    "uuid": 17768269
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "formatR",
      "role": "Imports"
    },
    {
      "package": "glue",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "cowplot",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "ggtext",
      "role": "Suggests"
    },
    {
      "package": "here",
      "role": "Suggests"
    },
    {
      "package": "hexSticker",
      "role": "Suggests"
    },
    {
      "package": "hrbrthemes",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "purrr",
      "role": "Suggests"
    },
    {
      "package": "readr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "showtext",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "schlosslab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "microbiome",
    "mothur"
  ],
  "_stars": 32,
  "_contributors": [
    {
      "user": "kelly-sovacool",
      "count": 395,
      "uuid": 17768269
    },
    {
      "user": "ahanna",
      "count": 19,
      "uuid": 4356047
    },
    {
      "user": "nlesniak",
      "count": 11,
      "uuid": 11355896
    },
    {
      "user": "kdiverson",
      "count": 6,
      "uuid": 263221
    },
    {
      "user": "sklucas",
      "count": 6,
      "uuid": 9704436
    },
    {
      "user": "courtneyarmour",
      "count": 3,
      "uuid": 37886512
    },
    {
      "user": "nbaxter13",
      "count": 2,
      "uuid": 5519445
    },
    {
      "user": "jmoltzau",
      "count": 1,
      "uuid": 63260200
    },
    {
      "user": "pschloss",
      "count": 1,
      "uuid": 1264132
    }
  ],
  "_userbio": {
    "uuid": 17768269,
    "type": "user",
    "name": "Kelly Sovacool, PhD",
    "description": "Bioinformatics Software Engineer"
  },
  "_downloads": {
    "count": 40,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/schtools"
  },
  "_devurl": "https://github.com/schlosslab/schtools",
  "_pkgdown": "http://www.schlosslab.org/schtools/",
  "_searchresults": 35,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/schtools.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2021-11-22"
    },
    {
      "version": "0.1.1",
      "date": "2022-03-11"
    },
    {
      "version": "0.2.1",
      "date": "2022-05-12"
    },
    {
      "version": "0.3.0",
      "date": "2022-10-06"
    },
    {
      "version": "0.3.1",
      "date": "2022-11-16"
    },
    {
      "version": "0.4.0",
      "date": "2023-01-16"
    },
    {
      "version": "0.4.1",
      "date": "2023-08-21"
    }
  ],
  "_exports": [
    ".data",
    "%>%",
    "calc_relabun",
    "close_enough",
    "format_number",
    "get_wildcards_tbl",
    "inline_hook",
    "is_nearly_whole",
    "is_nondesc",
    "load_deps",
    "log_snakemake",
    "parse_tax",
    "paste_oxford_list",
    "pool_taxon_counts",
    "read_dist",
    "read_tax",
    "set_knitr_opts",
    "theme_lucas",
    "theme_sovacool"
  ],
  "_help": [
    {
      "page": "calc_relabun",
      "title": "Calculate OTU relative abundances from a shared file",
      "topics": [
        "calc_relabun"
      ]
    },
    {
      "page": "close_enough",
      "title": "Check whether two numeric vectors are close enough",
      "topics": [
        "close_enough"
      ]
    },
    {
      "page": "format_number",
      "title": "Format human-readable numbers.",
      "topics": [
        "format_number"
      ]
    },
    {
      "page": "get_wildcards_tbl",
      "title": "Get the Snakemake wildcards as a tibble",
      "topics": [
        "get_wildcards_tbl"
      ]
    },
    {
      "page": "inline_hook",
      "title": "Inline hook for knitr to paste human-readable numbers and nice lists.",
      "topics": [
        "inline_hook"
      ]
    },
    {
      "page": "is_nearly_whole",
      "title": "Checks whether a number is near to a whole number",
      "topics": [
        "is_nearly_whole"
      ]
    },
    {
      "page": "is_nondesc",
      "title": "Check whether all elements given are sorted in non-descending order",
      "topics": [
        "is_nondesc"
      ]
    },
    {
      "page": "load_deps",
      "title": "Install & load packages",
      "topics": [
        "load_deps"
      ]
    },
    {
      "page": "log_snakemake",
      "title": "Save output, messages, warnings, and errors to the Snakemake log file",
      "topics": [
        "log_snakemake"
      ]
    },
    {
      "page": "parse_tax",
      "title": "Convert taxonomy strings into dataframe of labels based on taxonomic classification",
      "topics": [
        "parse_tax"
      ]
    },
    {
      "page": "paste_oxford_list",
      "title": "Create a prose string from a list or vector",
      "topics": [
        "paste_oxford_list"
      ]
    },
    {
      "page": "pool_taxon_counts",
      "title": "Pool OTU counts at a particular taxonomic level",
      "topics": [
        "pool_taxon_counts"
      ]
    },
    {
      "page": "read_dist",
      "title": "Read in lower left triangular matrix from file",
      "topics": [
        "read_dist"
      ]
    },
    {
      "page": "read_tax",
      "title": "Read in a taxonomy file and parse it to a wide dataframe",
      "topics": [
        "read_tax"
      ]
    },
    {
      "page": "set_knitr_opts",
      "title": "Set knitr chunk options & inline hook",
      "topics": [
        "set_knitr_opts"
      ]
    },
    {
      "page": "theme_lucas",
      "title": "Sarah's go-to theme for ggplot2",
      "topics": [
        "theme_lucas"
      ]
    },
    {
      "page": "theme_sovacool",
      "title": "Kelly's go-to theme for ggplot2",
      "topics": [
        "theme_sovacool"
      ]
    }
  ],
  "_pkglogo": "https://github.com/SchlossLab/schtools/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/SchlossLab/schtools/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "dplyr",
    "formatR",
    "generics",
    "glue",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "rlang",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "introduction.Rmd",
      "filename": "introduction.html",
      "title": "Introduction to schtools",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Handling mothur data",
        "Calculate relative abundances",
        "Taxonomy files",
        "Pooling OTU counts at different taxonomic levels",
        "Distance files",
        "R Markdown helpers for scientific writing",
        "Who doesn't love an Oxford comma?",
        "Human-readable numbers"
      ],
      "created": "2020-09-04 12:22:52",
      "modified": "2022-11-15 15:57:18",
      "commits": 10
    }
  ],
  "_score": 5.6512780139981444,
  "_indexed": false,
  "_nocasepkg": "schtools",
  "_universes": [
    "kelly-sovacool"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.4.1.9000",
      "date": "2026-06-09T06:21:39.000Z",
      "distro": "noble",
      "commit": "b066acf96bb43e80adfe00edb17d02206e704c45",
      "fileid": "9d020bfb2c48a046e84094605f84db570af0ac1b23c8130be151cacd93d2069d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kelly-sovacool/actions/runs/27187646497"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.4.1.9000",
      "date": "2026-06-09T06:21:30.000Z",
      "distro": "noble",
      "commit": "b066acf96bb43e80adfe00edb17d02206e704c45",
      "fileid": "00840cff486289c0668c7449086de64000f0d023ed2bef94de31f8bfe6548ebc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kelly-sovacool/actions/runs/27187646497"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.4.1.9000",
      "date": "2026-06-09T06:39:12.000Z",
      "commit": "b066acf96bb43e80adfe00edb17d02206e704c45",
      "fileid": "d9bd94123ead27e1945e6b2e91330d246d526b06861da1e523a539391d0018ac",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kelly-sovacool/actions/runs/27187646497"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.4.1.9000",
      "date": "2026-06-09T06:38:18.000Z",
      "commit": "b066acf96bb43e80adfe00edb17d02206e704c45",
      "fileid": "1908b6bc38dbce021909e7448c5b1dbe0fd498bf4f7f8f9fed128db7a1fb011c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kelly-sovacool/actions/runs/27187646497"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.4.1.9000",
      "date": "2026-06-09T06:21:31.000Z",
      "commit": "b066acf96bb43e80adfe00edb17d02206e704c45",
      "fileid": "c883ccc134f8f5031e5b71fbda87f62ae7e1436090f7400bc64780d3b0256958",
      "status": "success",
      "buildurl": "https://github.com/r-universe/kelly-sovacool/actions/runs/27187646497"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.4.1.9000",
      "date": "2026-06-09T06:20:23.000Z",
      "commit": "b066acf96bb43e80adfe00edb17d02206e704c45",
      "fileid": "83c02dbc4e3fe3dfd171bf0eb81f2130617084c983f2e900f5e7a1e1fc12f8de",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kelly-sovacool/actions/runs/27187646497"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.4.1.9000",
      "date": "2026-06-09T06:20:22.000Z",
      "commit": "b066acf96bb43e80adfe00edb17d02206e704c45",
      "fileid": "7fa73680aa8c6f675e00657d95fcd279197dbf1875de3a41fab10ffcf4f9e5cb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kelly-sovacool/actions/runs/27187646497"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.4.1.9000",
      "date": "2026-06-09T06:20:23.000Z",
      "commit": "b066acf96bb43e80adfe00edb17d02206e704c45",
      "fileid": "12f4bf0746ccd6229b49fbcc578436ea6ac1d684f9b40c25a36c47cc5385466f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kelly-sovacool/actions/runs/27187646497"
    }
  ]
}