_pkgdown.yml

url: https://sahirbhatnagar.com/ggmix

template:
  params:
    bootswatch: cosmo
    docsearch:
      api_key: f8a14d62b00c65f3af4a90aa62a286b8
      index_name: ggmix

authors:
  Sahir Bhatnagar:
    href: https://sahirbhatnagar.com
  Karim Oualkacha:
    href: https://karimoualkacha.uqam.ca/
  Yi Yang:
    href: http://www.math.mcgill.ca/yyang/
  Celia Greenwood:
    href: https://www.mcgill.ca/statisticalgenetics/

development:
  mode: auto

reference:
  - title: Model Fitting
    desc: >
      Main functions for fitting the ggmix model
    contents:
    - ggmix
    - gic

  - title: Methods for objects of class ggmix_fit and ggmix_gic
    desc: >
      Method functions to extract relevant information from fitted objects
    contents:
    - predict.ggmix_fit
    - predict.ggmix_gic
    - print.ggmix_fit
    - coef.ggmix_fit
    - coef.ggmix_gic
    - plot.ggmix_fit
    - plot.ggmix_gic
    - ranef


  - title: Datasets
    desc: >
      Two datasets that ship with the package to illustrate usage
    contents:
    - karim
    - admixed


  - title: Diagnostic Plots
    desc: >
      Plots for assessing model fit
    contents:
    - plot.ggmix_gic


  - title: Simulate Data
    desc: >
      Simulate data with different geographies
    contents:
    - gen_structured_model

  - title: Internal Utility Functions
    desc: >
      Functions not really meant for the user
    contents:
    - logliklasso
    - lmmlasso
    - kkt_check
    - lambdalasso
    - sigma2lasso
    - gr_eta_lasso_fullrank
    - fn_eta_lasso_fullrank
    - ggmix_data_object

navbar:
  type: default
  left:
    - text: Home
      href: index.html
    - text: Vignettes
      menu:
      - text: Introduction to ggmix
        href: articles/introduction-to-ggmix.html
      - text: Prior annotation weights
        href: articles/prior-annotation-weights.html
      - text: Alternative input for population structure
        href: articles/alternative-kinship-input.html
    - text: Functions and data
      href: reference/index.html
    - text: News
      href: news/index.html
  twitter:
     icon: fa-lg fa-twitter
     href: http://twitter.com/syfi_24