_pkgdown.yml

url: https://bayer-group.github.io/drcHelper/index.html
template:
  math-rendering: mathjax
  bootstrap: 5
  params:
    bootswatch: flatly
search:
  exclude: news/index.html
repo:
  url:
    home: https://github.com/Bayer-Group/drcHelper
    source: https://github.com/Bayer-Group/drcHelper/blob/main/
    issue: https://github.com/Bayer-Group/drcHelper/issues/
    user: https://github.com/
news:
  cran_dates: yes
development:
  mode: release  # Change from 'auto' to 'release' sot that the articles are always built to /docs/ instead of /docs/dev/, making your current navigation URLs work correctly.
  version_label: default
authors:
  before: We define *authors* as those who are actively maintaining the code base,
    and *contributors* as those who made a significant contribution in the past. For
    all acknowledgements, see the section in the [Home Page](https://bayer-group.github.io/drcHelper).
  footer:
    roles:
    - aut
    - ctb
    - cre
    - fnd
    text: Developed by
  sidebar:
    roles: aut

navbar:
  structure:
    left:
    - getstarted
    - reference
    - tutorials
    - articles
    - validation
    - news
    right:
    - search
    - newissue
    - github
  components:
    getstarted:
      text: Get Started
      menu:
      - text: Introduction
        href: articles/Introduction.html
      - text: Example ECx Helper Functions Usage
        href: articles/drcHelper.html
      - text: Example NOEC Helper Functions Usage
        href: articles/Dunnetts_Test_for_Data_with_Hierarchical_Structure.html
      - text: Using DRC and BMD
        href: articles/Examples_drc.html
      - text: Example DRC - OECD 201
        href: articles/Examples_oecd201.html
    reference:
      text: Reference
      href: reference/
    tutorials:
      text: Regulatory Stats
      menu:
      - text: NOEC Calculations
        href: articles/NOEC_Methods.html
      - text: Limit Test Calculations
        href: articles/Limit-Test.html
      - text: EFSA Criteria and Other Reliability Criteria
        href: articles/EFSA-Criteria.html
      - text: RSCABS
        href: articles/Example_RSCABS.html
      - text: Trend Testing
        href: articles/Trend-Testing.html
      - text: NOEC ECx and BMD
        href: articles/NOEC_ECx_BMD.html
      - text: MDD in Regulatory Context
        href: articles/MDD-in-Regulatory-Context.html
    articles:
      text: Articles
      menu:
      - text: Core Statistical Methods Overview
        href: articles/core_statistical_methods.html
      - text: Quantal Data Analysis
        href: articles/Quantal-Data.html
      - text: Ordinal Data Analysis
        href: articles/Ordinal-Data.html
      - text: Count Data Analysis
        href: articles/Count_Data.html
      - text: LMM, GLMM, and GAMM Models
        href: articles/LMM-GLMM-and-GAMM.html
      - text: "-------------"
      - text: Advanced Topics Overview
        href: articles/advanced_topics.html
      - text: Normality Checks
        href: articles/Normality-Check.html
      - text: Binomial Extra Variance
        href: articles/Binomial_Extra_Variance.html
      - text: Equivalence Testing
        href: articles/Equivalence-Testing.html
      - text: "-------------"
      - text: Alternative Methods Overview
        href: articles/alternative_methods.html
      - text: NLS Examples
        href: articles/Examples using NLS.html
      - text: DRDA Examples
        href: articles/Examples_using_drda.html
      - text: TSK Method
        href: articles/TSK_method.html
      - text: MQJT
        href: articles/MQJT.html
      - text: Biphasic Dose Response Models
        href: articles/Advanced_Fitting-a-biphasic-dose-reponse-model.html
    validation:
      text: Validation
      menu:
      - text: System Testing
        href: articles/System_Testing.html
      - text: ED Calculation Consistency
        href: articles/val_ED_plus.html
      - text: TSK and Probit Model
        href: articles/TSK-and-Probit-Models.html
      - text: Which JT test to use
        href: articles/Verification_which_JT.html
      - text: Verification of CA test
        href: articles/Verification_CA_test.html
      - text: Validation of MCP tests
        href: articles/Validation_MCP_tests.html
      - text: Study Types and Templates
        href: articles/Test-Guidelines.html
    newissue:
      icon: fa-bug
      href: https://github.com/Bayer-Group/drcHelper/issues/new?template=Blank+issue
      aria-label: New Issue

# Article index page section organization
articles:
  - title: "Get Started"
    desc: >
      Introduction to the package and basic usage
    contents:
      - Introduction
      - drcHelper
      - Dunnetts_Test_for_Data_with_Hierarchical_Structure
      - Example_Analysis_Workflow

  - title: "Core Statistical Methods"
    desc: >
      These articles cover the foundational statistical methods implemented in drcHelper
    contents:
      - core_statistical_methods
      - articles/Quantal-Data
      - articles/Ordinal-Data
      - articles/Count_Data
      - articles/LMM-GLMM-and-GAMM

  - title: "Advanced Topics"
    desc: >
      These articles cover more advanced statistical concepts and techniques
    contents:
      - advanced_topics
      - articles/Normality-Check
      - articles/Binomial_Extra_Variance
      - articles/Equivalence-Testing
      - articles/A-Notes-on-Power

  - title: "Alternative Methods"
    desc: >
      These articles explore alternative statistical methods and approaches
    contents:
      - alternative_methods
      - "articles/Examples using NLS"
      - articles/Examples_using_drda
      - articles/TSK_method
      - articles/MQJT
      - articles/Advanced_Fitting-a-biphasic-dose-reponse-model

  - title: "Regulatory Statistics"
    desc: >
      Statistical methods for regulatory assessments
    contents:
      - articles/NOEC_Methods
      - articles/Limit-Test
      - articles/EFSA-Criteria
      - articles/Example_RSCABS
      - articles/Trend-Testing
      - articles/NOEC_ECx_BMD
      - articles/OECD_ED_Assays
      - articles/Test-Guidelines
      - articles/MDD-in-Regulatory-Context

  - title: "Validation"
    desc: >
      Validation of statistical methods in the package
    contents:
      - articles/System_Testing
      - articles/val_ED_plus
      - articles/TSK-and-Probit-Models
      - articles/Verification_which_JT
      - articles/Validation_MCP_tests
      - articles/Verification_CA_test
      - articles/Verification-of-Williams-Test

  - title: "Examples"
    desc: >
      Example applications of the package
    contents:
      - articles/Examples_drc
      - articles/Examples_oecd201