_pkgdown.yml

url: https://yjunechoe.github.io/jlmerclusterperm/

home:
  title: jlmerclusterperm
  description: Julia implementation of bootstrapped cluster-based permutation analysis for time series data

authors:
  June Choe:
    href: https://yjunechoe.github.io

template:
  bootstrap: 5
  bootswatch: flatly
  bslib:
    base_font: {google: "Atkinson Hyperlegible"}

reference:

- title: Julia setup
  desc: >
    Start a Julia session set up for jlmerclusterperm
  contents:
  - julia_setup_ok
  - jlmerclusterperm_setup

- title: Interface to Julia regression modelling
  desc: >
    Making a jlmer_spec object and fitting models in Julia
  contents:
  - make_jlmer_spec
  - jlmer
  - to_jlmer

- title: Cluster-based permutation analysis
- subtitle: Empirical clusters
  desc: >
    Detect empirical clusters from the observed data using timewise regression models
  contents:
  - compute_timewise_statistics
  - extract_empirical_clusters
- subtitle: Null distribution
  desc: >
    Construct a null distribution of cluster-mass statistics via bootstrapped permutation
  contents:
  - permute_by_predictor
  - permute_timewise_statistics
  - extract_null_cluster_dists
- subtitle: Significance test
  desc: >
    Test the probability of the observed cluster-mass statistic vs. null distribution
  contents:
  - calculate_clusters_pvalues
  - walk_threshold_steps
- subtitle: All in one go
  contents:
  - clusterpermute

- title: Tidiers
  desc: >
    Methods for collecting jlmerclusterperm objects as tidy data
  contents:
  - cluster_permutation_tidiers
  - julia_model_tidiers

- title: Interop utilities
  desc: >
    Set and get Julia options from R
  contents:
  - julia_rng
  - julia_progress

articles:
- title: Topics
  navbar: Topics
  contents:
  - articles/tidying-output
  - articles/julia-interface
  - articles/reproducibility
  - articles/asynchronous-cpa
  - articles/eyetrackingR-comparison
- title: Case Studies
  navbar: Case Studies
  contents:
  - articles/Garrison-et-al-2020
  - articles/Geller-et-al-2020
  - articles/deCarvalho-et-al-2021
  - articles/Ito-et-al-2018

news:
  - add_cran_date: TRUE

figures:
  dev: ragg::agg_png
  dpi: 96
  dev.args: []
  out.width: "100%"
  fig.ext: png
  fig.height: ~
  fig.retina: 2
  bg: "white"