_pkgdown.yml

# Website URL
url: https://cafferychen777.github.io/MicrobiomeStat/

# Website title and description
title: MicrobiomeStat
description: Comprehensive Statistical and Visualization Methods for Microbiome and Multi-Omics Data

# Enhanced template configuration
template:
  bootstrap: 5
  bootswatch: cosmo  # Modern theme
  bslib:
    primary: "#2E7D32"      # Deep green for biology theme
    secondary: "#558B2F"    # Light green
    success: "#4CAF50"      
    info: "#00ACC1"         # Cyan for information
    warning: "#FFB300"      
    danger: "#E53935"       
    base_font: {google: "Inter"}
    code_font: {google: "JetBrains Mono"}
  includes:
    in_header: |
      <link rel="stylesheet" href="extra.css">
      <link rel="stylesheet" href="../extra.css">
      <link rel="preconnect" href="https://fonts.googleapis.com">
      <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
      <link href="https://fonts.googleapis.com/css2?family=Inter:wght@300;400;600;700&family=JetBrains+Mono:wght@400;600&display=swap" rel="stylesheet">
    after_body: |
      <script src="extra.js"></script>
      <script src="../extra.js"></script>

# Enhanced navigation bar
navbar:
  type: default
  structure:
    left: [reference, articles, news]
    right: [search, github, twitter, discord]
  
  components:
    reference:
      text: "Functions"
      icon: fa-code
      href: reference/index.html
    
    articles:
      text: "Tutorials"
      icon: fa-book
      menu:
        - text: "Getting Started"
          href: articles/MicrobiomeStat.html
        - text: "-------"
        - text: "Analysis Workflows"
        - text: "Longitudinal Analysis"
          href: articles/longitudinal-analysis.html
    
    news:
      text: "News"
      icon: fa-newspaper
      href: news/index.html
    
    github:
      icon: fa-github fa-lg
      href: https://github.com/cafferychen777/MicrobiomeStat
      aria-label: GitHub
    
    twitter:
      icon: fa-twitter fa-lg
      href: https://twitter.com/cafferychen777
      aria-label: Twitter
    
    discord:
      icon: fa-discord fa-lg
      href: https://discord.gg/U6vNamyk
      aria-label: Discord

# Enhanced home page
home:
  title: MicrobiomeStat
  description: |
    **Comprehensive R package for advanced longitudinal microbiome and multi-omics data analysis**
    
    MicrobiomeStat provides a complete toolkit for microbiome data analysis, supporting cross-sectional, 
    paired sample, and longitudinal study designs with beautiful visualizations and automated reporting.
  
  strip_header: false
  
  links:
  - text: Get Started
    href: https://www.microbiomestat.wiki
    icon: fa-rocket
  - text: Browse Functions
    href: reference/index.html
    icon: fa-code
  - text: View Tutorials
    href: https://www.microbiomestat.wiki
    icon: fa-graduation-cap

# Enhanced reference page with better organization
reference:
  - title: "🚀 Unified Interface"
    desc: "Simplified high-level functions for common analyses"
    contents:
      - MicrobiomeStat-unified
      - plot_alpha
      - plot_beta
      - plot_taxa
      - test_alpha
      - test_beta
      - test_taxa

  - title: "📊 Alpha Diversity Analysis"
    desc: "Functions for analyzing within-sample diversity"
    contents:
      - plot_alpha_diversity
      - starts_with("generate_alpha")
      - mStat_calculate_alpha_diversity
      - mStat_calculate_adjusted_alpha_diversity
      - is_rarefied

  - title: "🌐 Beta Diversity Analysis"
    desc: "Functions for analyzing between-sample diversity"
    contents:
      - plot_beta_diversity
      - starts_with("generate_beta")
      - mStat_calculate_beta_diversity
      - mStat_calculate_adjusted_distance
      - mStat_calculate_PC
      - starts_with("mStat_subset")

  - title: "🦠 Taxonomic Analysis"
    desc: "Functions for taxonomic composition and differential abundance"
    contents:
      - plot_feature_diversity
      - starts_with("generate_taxa")
      - mStat_aggregate_by_taxonomy
      - mStat_aggregate_by_taxonomy2
      - mStat_aggregate_data
      - build_mStat_tax_table

  - title: "📈 Statistical Testing"
    desc: "Core statistical methods including LinDA"
    contents:
      - linda
      - linda2
      - linda.plot
  
  - title: "📁 Data Import & Conversion"
    desc: "Import data from various microbiome analysis platforms"
    contents:
      - starts_with("mStat_import")
      - starts_with("mStat_convert")
  
  - title: "🔧 Data Processing"
    desc: "Data manipulation and preprocessing utilities"
    contents:
      - mStat_normalize_data
      - mStat_rarefy_data
      - mStat_filter
      - mStat_subset_data
      - mStat_remove_feature
      - mStat_validate_data
      - mStat_update_meta_data
      - mStat_update_sample_name
      - mStat_combine_data
      - mStat_process_time_variable
      - mStat_identify_time_varying_vars
      - mStat_summarize_data_obj
  
  - title: "📝 Automated Reports"
    desc: "Generate comprehensive analysis reports"
    contents:
      - mStat_generate_report_single
      - mStat_generate_report_pair
      - mStat_generate_report_long
  
  - title: "🎨 Visualization Utilities"
    desc: "Helper functions for customizing plots"
    contents:
      - mStat_get_palette
      - mStat_get_theme
      - is_categorical
      - is_continuous_numeric
  
  - title: "📚 Example Datasets"
    desc: "Built-in datasets for testing and learning"
    contents:
      - ecam.obj
      - peerj32.obj
      - smokers
      - subset_T2D.obj
      - subset_pairs.obj

# Footer customization
footer:
  structure:
    left: developed_by
    right: built_with

# Development mode settings
development:
  mode: auto
  version_label: default
  version_tooltip: "Development version"