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Sarah Teichman
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basics for software page
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‎.Rbuildignore‎

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^.*\.Rproj$
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^\.Rproj\.user$
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^LICENSE\.md$
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^doc$
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^Meta$

‎.github/workflows/pkgdown.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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release:
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types: [published]
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workflow_dispatch:
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name: pkgdown
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jobs:
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pkgdown:
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runs-on: ubuntu-latest
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# Only restrict concurrency for non-PR jobs
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concurrency:
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group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::pkgdown, local::.
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needs: website
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- name: Build site
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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shell: Rscript {0}
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- name: Deploy to GitHub pages 🚀
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if: github.event_name != 'pull_request'
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uses: JamesIves/github-pages-deploy-action@v4.5.0
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with:
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clean: false
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branch: gh-pages
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folder: docs

‎.gitignore‎

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*.DS_Store
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inst/doc
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.Rproj.user
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/doc/
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/Meta/
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.Rhistory

‎DESCRIPTION‎

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Package: software
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Type: Package
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Title: StatDivLab Software Page
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Version: 0.0.0.9000
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Authors@R:
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as.person(c(
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"Amy Willis <adwillis@uw.edu> [aut, cre]",
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"Sarah Teichman [aut]"
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))
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Description: This is a way to host the software page for the Statistical Diversity Lab.
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License: MIT + file LICENSE
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 7.3.2
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Depends: DiagrammeR
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Suggests:
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knitr,
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rmarkdown
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VignetteBuilder: knitr
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URL: https://statdivlab.github.io/software.html, https://statdivlab.github.io/software/

‎LICENSE‎

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YEAR: 2025
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COPYRIGHT HOLDER: software authors

‎LICENSE.md‎

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# MIT License
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Copyright (c) 2025 software authors
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎NAMESPACE‎

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# Generated by roxygen2: do not edit by hand
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‎software.Rproj‎

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Version: 1.0
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RestoreWorkspace: Default
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SaveWorkspace: Default
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AlwaysSaveHistory: Default
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EnableCodeIndexing: Yes
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UseSpacesForTab: Yes
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NumSpacesForTab: 2
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Encoding: UTF-8
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RnwWeave: Sweave
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LaTeX: pdfLaTeX

‎vignettes/.gitignore‎

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*.html
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*.R

‎vignettes/software_page.Rmd‎

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---
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title: "StatDivLab Software"
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output: rmarkdown::html_vignette
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vignette: >
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%\VignetteIndexEntry{StatDivLab Software}
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%\VignetteEngine{knitr::rmarkdown}
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%\VignetteEncoding{UTF-8}
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---
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## Software!!
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Something about us
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Table with all software
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## Flowchart
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```{r, echo = FALSE}
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library(DiagrammeR)
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grViz("
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digraph flowchart {
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graph [layout = dot, rankdir = TB]
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node [style=filled, fillcolor=white]
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// Define shapes
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node [shape = none]
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Q1 [label = 'I care about...']
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Q2 [label = 'What do you want to estimate?']
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node [shape = ellipse]
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A1 [label = 'diversity estimation']
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A2 [label = 'differential abundance analysis']
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A3 [label = 'phylogenetics']
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A4 [label = 'other microbiome questions']
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A5 [label = 'other statistical tools']
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A6 [label = 'Richness']
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A7 [label = <&alpha;/&beta; Diversity>]
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node [shape = box]
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S1 [label = 'breakaway', URL=\"https://github.com/adw96/breakaway\"]
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S2 [label = 'DivNet', URL=\"https://github.com/adw96/DivNet\"]
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// Connect nodes
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Q1 -> A1
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Q1 -> A2
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Q1 -> A3
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A1 -> Q2
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Q2 -> A4
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Q2 -> A5
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A4 -> S1
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A5 -> S2
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}
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")
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```

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