_pkgdown.yml

url: https://somalogic.github.io/SomaDataIO

development:
  mode: auto

authors:
  Stu Field:
    href: https://github.com/stufield
  SomaLogic Operating Co., Inc.:
    href: http://www.somalogic.com
  footer:
    roles: [fnd]
    text: "was developed by the Bioinformatics Dept. at"
  sidebar:
    roles: [cre, fnd]
    before: "Special :pray: to:"
    after: ":dna:"
  before: "[SomaDataIO](https://github.com/SomaLogic/SomaDataIO/) is proudly brought to you by:"
  after: ":dna:"

footer:
  structure:
    left: [logo, package, developed_by]
    right: built_with
  components:
    logo: "<img src='../favicon-16x16.png'>"

template:
  bootstrap: 5
  package: tidytemplate
  bslib:
    #bg: "#202123"      # dark theme
    #fg: "#B8BCC2"      # dark theme
    primary: "#0054AD"
    border-radius: 0.5rem
    btn-border-radius: 0.25rem
    base_font: {google: "Roboto"}

home:
  sidebar:
    structure: [links, help, oss, license, citation, authors, dev, toc]
    components:
      oss:
        title: Other Software
        text: >
          [SomaPlotr](https://somalogic.github.io/SomaPlotr/) <br />
          [SomaScan.db](https://somalogic.github.io/SomaScan.db/) <br />
          [Canopy (Python)](https://github.com/SomaLogic/Canopy/) <br />
          [DataDelve Statistics](https://somalogic.com/datadelve-statistics/)
      help:
        title: Getting Help
        text: >
          [Ask a question](https://somalogic.github.io/SomaDataIO/SUPPORT.html) <br />
          [Report a bug](https://github.com/SomaLogic/SomaDataIO/issues)

  links:
  - text: Learn more about SomaScan
    href: http://www.somalogic.com
  - text: Read SomaScan tech notes
    href: http://www.somalogic.com/tech-notes/

navbar:
  structure:
    left: [intro, reference, articles, workflows, FAQs, news]
    right: [search, github]
  components:
    workflows:
      text: Workflows
      menu:
      - text: Difference Testing
      - text: Two-Group Comparison
        href: articles/stat-two-group-comparison.html
      - text: ANOVA Three-Group Analysis
        href: articles/stat-three-group-analysis-anova.html
      - text: ---

      - text: Making Predictions
      - text: Binary Classification
        href: articles/stat-binary-classification.html
      - text: Linear Regression
        href: articles/stat-linear-regression.html

    FAQs:
      text: Coming Soon
      menu:
      - text: SomaScan FAQs
      - text: ---
      - text: Standard Process
      - text: Best Practices
      - text: ----
      - text: Non-Standard Matrices
      - text: Limits of Detection (LoD)

articles:
  - title: Loading and Wrangling
    navbar: ~
    contents:
    - starts_with("articles/tips-")

  - title: Command Line Merge Tool
    navbar: ~
    contents:
    - articles/cli-merge-tool

  - title: Lifting and Bridging
    navbar: ~
    contents:
    - articles/lifting-and-bridging

  - title: Statistical Workflow Examples
    contents:
    - starts_with("articles/stat-")

reference:
  - title: Load an ADAT
    desc: >
      Load RFU (feature) data loaded into (and out of) an R session.
    contents:
    - read_adat
    - write_adat
    - soma_adat
    - loadAdatsAsList
    - parseHeader
    - rownames
    - Col.Meta
    - is_intact_attr
    - groupGenerics
    - reexports

  - title: ADAT Manipulation
    desc: >
      Functions that allow filtering, wrangling, and subset
      selection of ADAT objects.
    contents:
    - SeqId
    - is_seqFormat
    - starts_with("getAnalyte")
    - getMeta
    - diffAdats
    - merge_clin

  - title: Transform Between SomaScan Versions
    desc: >
      Functionality required to bridge between SomaScan versions,
      e.g. 11k -> 7k, sometimes referred to as "lifting".
    contents:
    - lift_adat
    - read_annotations
    - transform
    - starts_with("getSomaScan")
    - getSignalSpace

  - title: Expression Data
    desc: >
      Functions to convert objects to those familiar with `expression` data.
    contents:
    - adat2eSet
    - pivotExpressionSet

  - title: Helpers
    desc: >
      Accessor functions to add, modify, or retreive attribute information.
      Typically used internally but are exported for user convenience.
    contents:
    - addAttributes
    - addClass
    - cleanNames
    - getAdatVersion

  - title: Data Objects
    desc: Objects provided with `SomaDataIO`.
    contents:
    - SomaScanObjects

  - title: Parameters
    desc: Common parameter arguments to functions in `SomaDataIO`.
    contents:
    - params

  - title: Deprecated
    desc: >
      Functions that have been deprecated (sunset) in the
      current `SomaDataIO` release.
    contents:
    - SomaDataIO-deprecated

news:
  - one_page: true