_pkgdown.yml

url: https://eyeris.shawnschwartz.com/

news:
    cran_dates: true
    releases:
    - text: "LATEST STABLE RELEASE"
    - text: "v3.2.0 (CRAN)"
      href: news/index.html#eyeris-320-lumpy-space-princess-lumpy-space-princess
    - text: -------
    - text: "v3.1.0 (CRAN)"
      href: news/index.html#eyeris-310-lumpy-space-princess-lumpy-space-princess
    - text: "v3.0.1 (CRAN)"
      href: news/index.html#eyeris-301-lumpy-space-princess-lumpy-space-princess
    - text: "v3.0.0 (CRAN)"
      href: news/index.html#eyeris-300-lumpy-space-princess-lumpy-space-princess
    - text: "Previous Releases"
    - text: "v2.1.1 (CRAN)"
      href: news/index.html#eyeris-211-lumpy-space-princess-lumpy-space-princess
    - text: "v2.1.0 (CRAN)"
      href: news/index.html#eyeris-210-lumpy-space-princess-lumpy-space-princess
    - text: "v2.0.0 (CRAN)"
      href: news/index.html#eyeris-200-lumpy-space-princess-lumpy-space-princess
    - text: "v1.2.1 (CRAN)"
      href: news/index.html#eyeris-121-tree-trunks-tree-trunks
    - text: "v1.2.0 (CRAN)"
      href: news/index.html#eyeris-120-tree-trunks-tree-trunks
    - text: "v1.1.0 (CRAN)"
      href: news/index.html#eyeris-110-princess-bubblegum-princess-bubblegum
    - text: "v1.0.1 (devel)"
      href: news/index.html#eyeris-101-ice-king-ice-king
    - text: "v1.0.0 (CRAN)"
      href: news/index.html#eyeris-100-ice-king-ice-king
    - text: "v0.1.1.9000 (devel)"
      href: news/index.html#eyeris-0119000-jake-the-dog-jake-the-dog
    - text: "v0.1.0.9000 (devel)"
      href: news/index.html#eyeris-0109000-jake-the-dog-jake-the-dog
    - text: "v0.0.0.9000 (devel)"
      href: news/index.html#eyeris-0009000-finn-the-human-finn-the-human

home:
  sidebar:
    structure: [authors, citation, links, license, dev]

navbar:
  structure:
    left:  [intro, reference, articles, news, preprint]
    right: [search, github, bluesky, lightswitch]
  components:
    bluesky:
      icon: fa-twitter
      href: http://bsky.app/profile/shawnschwartz.bsky.social
      aria-label: Bluesky
    preprint:
      text: "bioRxiv Preprint"
      href: http://www.biorxiv.org/content/10.1101/2025.06.01.657312v1
      aria-label: Preprint

template:
  bootstrap: 5
  light-switch: false
  theme: breeze-light
  math-rendering: mathjax
  includes:
    in_header: |
      <script async src="https://cdn.seline.com/seline.js" data-token="dec3c94d0af2ccd"></script>
  bslib:
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      pkgdown-nav-height: 100px
      primary: "#820000"

footer:
  structure:
    left: developed_by
    right: [built_with, legal]
  components:
    legal: Provided without **any warranty**.<br />The funders had no role in study design, data collection, and interpretation, or the decision to submit the work for publication.

authors:
  Shawn Schwartz:
      href: "http://shawnschwartz.com"
  footer:
      roles: [cre]
      text: "Made with ♥ in Palo Alto by"
  sidebar:
      roles: [aut, fnd, ctb]

reference:
  - title: "🧠 Core Pipeline"
    desc: >
      Start here with the full pipeline wrapper to quickly and easily call and customize the opinionated `glassbox` pipeline in `eyeris`.
    contents:
      - glassbox
      - eyelogger

  - title: "⏱️ Epoching Pupil Data"
    desc: >
      Conveniently extract tidy trial-based epochs with optional baseline correction.
    contents:
      - epoch

  - title: "📤 Export & Visualize"
    desc: >
      Save out BIDS-style derivatives, generate diagnostic HTML reports, and interactively plot and explore your pupil data.
    contents:
      - bidsify
      - boilerplate
      - summarize_confounds
      - plot.eyeris
      - plot_gaze_heatmap
      - plot_binocular_correlation
      - eyeris_color_palette

  - title: "🗄 Database Storage & Analysis"
    desc: >
      High-performance database storage and querying powered by DuckDB. Scalable alternative to CSV files for large studies, cloud computing, and collaborative research.
    contents:
      - eyeris_db_collect
      - eyeris_db_summary
      - eyeris_db_connect
      - eyeris_db_disconnect
      - eyeris_db_read
      - eyeris_db_list_tables
      - eyeris_db_to_chunked_files
      - eyeris_db_to_parquet
      - read_eyeris_parquet
      - process_chunked_query
      - eyeris_db_split_for_sharing
      - eyeris_db_reconstruct_from_chunks

  - title: "🔧 Preprocessing Steps"
    desc: >
      Modular functions used by the `glassbox` pipeline for cleaning and transforming pupil data.
    contents:
      - load_asc
      - load_generic
      - resample
      - deblink
      - detransient
      - interpolate
      - lpfilt
      - downsample
      - bin
      - detrend
      - zscore

  - title: "🧩 Build Your Own Extensions"
    desc: >
      Advanced tools for creating custom steps that plug into the glassbox pipeline.
    contents:
      - pipeline_handler

  - title: "🧪 Simulate Pupil Data"
    desc: >
      Generate synthetic, pipeline-compatible pupil time series with known ground truth for testing, demonstrations, and reproducible examples.
    contents:
      - simulate_eyeris
      - sim_params
      - print.eyeris_sim_params

  - title: "📈 Demo Datasets"
    desc: >
      Example eye-tracking / pupil datasets for testing and demonstrating pipeline functionality.
    contents:
      - eyelink_asc_demo_dataset
      - eyelink_asc_binocular_demo_dataset

articles:
  - title: Start Here
    navbar: Start Here
    contents:
    - complete-pipeline
    - epoching-bids-reports
    - multiple-runs-separate-files
  - title: Pupil Data Quality Control
    navbar: Pupil Data Quality Control
    contents:
    - reports
  - title: Advanced Topics
    navbar: Advanced Topics
    contents:
    - anatomy
    - custom-extensions
    - database-guide
    - chunked-database-export
    - internal-api
  - title: For AI Coding Agents
    navbar: For AI Coding Agents
    contents:
    - agents