├── .Rbuildignore ├── .github ├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ └── issue_template.md ├── SUPPORT.md ├── pull_request_template.md └── workflows │ ├── check.yaml │ ├── on-release.yml │ ├── pr_build.yml │ └── test-coverage.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── calculate.R ├── plot.R ├── read_dist.R ├── read_tax.R ├── reexports.R ├── rmd_helpers.R ├── schtools.R ├── shared.R ├── snakemake.R └── utils.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── conda-env └── schtools-dev.yml ├── cran-comments.md ├── docs ├── 404.html ├── CODE_OF_CONDUCT.html ├── CONTRIBUTING.html ├── LICENSE-text.html ├── LICENSE.html ├── SUPPORT.html ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── articles │ ├── 1F4A9_color.png │ ├── 1F527_color.png │ ├── 1F528_color.png │ ├── articles │ │ ├── 1F4A9_color.png │ │ ├── 1F527_color.png │ │ ├── 1F528_color.png │ │ ├── logo.html │ │ ├── logo_files │ │ │ ├── figure-html │ │ │ │ ├── emojis-1.png │ │ │ │ └── logo-1.png │ │ │ └── header-attrs-2.11 │ │ │ │ └── header-attrs.js │ │ ├── poo-hammer.png │ │ └── schtools-logo.png │ ├── index.html │ ├── introduction.html │ ├── introduction_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ ├── figure-html │ │ │ ├── italic-genus-1.png │ │ │ └── unnamed-chunk-2-1.png │ │ ├── header-attrs-2.10 │ │ │ └── header-attrs.js │ │ └── header-attrs-2.11 │ │ │ └── header-attrs.js │ ├── logo.html │ ├── logo_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ └── figure-html │ │ │ ├── emojis-1.png │ │ │ └── logo-1.png │ ├── poo-hammer.png │ └── schtools-logo.png ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── deps │ ├── bootstrap-5.1.0 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-5.1.3 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-5.2.2 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── data-deps.txt │ └── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map ├── dev │ ├── CODE_OF_CONDUCT.html │ ├── CONTRIBUTING.html │ ├── LICENSE-text.html │ ├── LICENSE.html │ ├── SUPPORT.html │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── articles │ │ ├── 1F4A9_color.png │ │ ├── 1F527_color.png │ │ ├── 1F528_color.png │ │ ├── articles │ │ │ └── logo.html │ │ ├── index.html │ │ ├── introduction.html │ │ ├── introduction_files │ │ │ ├── accessible-code-block-0.0.1 │ │ │ │ └── empty-anchor.js │ │ │ └── figure-html │ │ │ │ └── italic-genus-1.png │ │ ├── logo.html │ │ ├── logo_files │ │ │ ├── accessible-code-block-0.0.1 │ │ │ │ └── empty-anchor.js │ │ │ └── figure-html │ │ │ │ ├── emojis-1.png │ │ │ │ └── logo-1.png │ │ ├── poo-hammer.png │ │ └── schtools-logo.png │ ├── authors.html │ ├── deps │ │ ├── bootstrap-5.1.0 │ │ │ ├── bootstrap.bundle.min.js │ │ │ ├── bootstrap.bundle.min.js.map │ │ │ └── bootstrap.min.css │ │ ├── bootstrap-5.1.3 │ │ │ ├── bootstrap.bundle.min.js │ │ │ ├── bootstrap.bundle.min.js.map │ │ │ └── bootstrap.min.css │ │ ├── bootstrap-5.2.2 │ │ │ ├── bootstrap.bundle.min.js │ │ │ ├── bootstrap.bundle.min.js.map │ │ │ └── bootstrap.min.css │ │ ├── data-deps.txt │ │ └── jquery-3.6.0 │ │ │ ├── jquery-3.6.0.js │ │ │ ├── jquery-3.6.0.min.js │ │ │ └── jquery-3.6.0.min.map │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ ├── favicon.ico │ ├── index.html │ ├── link.svg │ ├── logo.png │ ├── news │ │ └── index.html │ ├── pkgdown.js │ ├── pkgdown.yml │ ├── pull_request_template.html │ ├── reference │ │ ├── Rplot001.png │ │ ├── calc_relabun.html │ │ ├── close_enough.html │ │ ├── figures │ │ │ └── logo.png │ │ ├── format_number.html │ │ ├── get_wildcards_tbl.html │ │ ├── index.html │ │ ├── inline_hook.html │ │ ├── is_nearly_whole.html │ │ ├── is_nondesc.html │ │ ├── load_deps.html │ │ ├── log_snakemake.html │ │ ├── parse_tax.html │ │ ├── paste_oxford_list.html │ │ ├── pool_taxon_counts.html │ │ ├── read_dist.html │ │ ├── read_tax.html │ │ ├── reexports.html │ │ ├── schtools.html │ │ ├── set_knitr_opts.html │ │ ├── theme_lucas-1.png │ │ ├── theme_lucas.html │ │ ├── theme_sovacool-1.png │ │ └── theme_sovacool.html │ ├── search.json │ └── sitemap.xml ├── docsearch.css ├── docsearch.js ├── favicon-16x16.png ├── favicon-32x32.png ├── favicon.ico ├── index.html ├── link.svg ├── logo.png ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── pull_request_template.html ├── reference │ ├── Rplot001.png │ ├── calc_relabun.html │ ├── close_enough.html │ ├── figures │ │ └── logo.png │ ├── format_number.html │ ├── get_wildcards_tbl.html │ ├── index.html │ ├── inline_hook.html │ ├── is_nearly_whole.html │ ├── is_nondesc.html │ ├── load_deps.html │ ├── log_snakemake.html │ ├── parse_tax.html │ ├── paste_oxford_list.html │ ├── pool_taxon_counts.html │ ├── read_dist.html │ ├── read_tax.html │ ├── reexports.html │ ├── schtools-package.html │ ├── schtools.html │ ├── set_knitr_opts.html │ ├── theme_lucas-1.png │ ├── theme_lucas.html │ ├── theme_sovacool-1.png │ └── theme_sovacool.html ├── search.json └── sitemap.xml ├── inst ├── CITATION └── extdata │ ├── sample.final.thetayc.0.03.lt.ave.dist │ ├── test.shared │ └── test.taxonomy ├── man ├── calc_relabun.Rd ├── close_enough.Rd ├── figures │ └── logo.png ├── format_number.Rd ├── get_wildcards_tbl.Rd ├── inline_hook.Rd ├── is_nearly_whole.Rd ├── is_nondesc.Rd ├── load_deps.Rd ├── log_snakemake.Rd ├── parse_tax.Rd ├── paste_oxford_list.Rd ├── pool_taxon_counts.Rd ├── read_dist.Rd ├── read_tax.Rd ├── reexports.Rd ├── schtools-package.Rd ├── set_knitr_opts.Rd ├── theme_lucas.Rd └── theme_sovacool.Rd ├── pkgdown └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── schtools.Rproj ├── tests ├── testthat.R └── testthat │ ├── test-calculate.R │ ├── test-plot.R │ ├── test-read_dist.R │ ├── test-read_tax.R │ ├── test-rmd_helpers.R │ ├── test-shared.R │ ├── test-snakemake.R │ └── test-utils.R └── vignettes ├── .gitignore ├── articles ├── 1F4A9_color.png ├── 1F527_color.png ├── 1F528_color.png ├── logo.Rmd ├── poo-hammer.png └── schtools-logo.png └── introduction.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SchlossLab/schtools/HEAD/.Rbuildignore 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