_site.yml

name: "Population genomics"
output_dir: "."
navbar:
  title: "Population genetics and genomics in R"
  left:
    - text: "Table of contents"
      href: "TOC.html"
    - text: "Part I"
      menu:
        - text: "Introduction"
          href: "Introduction.html"
        - text: "Getting ready to use R"
          href: "Getting_ready_to_use_R.html"
    - text: "Part II"
      menu:
        - text: "Data preparation"
          href: "Data_Preparation.html"
        - text: "First steps"
          href: "First_Steps.html"
        - text: "Population strata and clone correction"
          href: "Population_Strata.html"
        - text: "Locus-based statistics and missing data"
          href: "Locus_Stats.html"
        - text: "Genotypic evenness, richness, and diversity"
          href: "Genotypic_EvenRichDiv.html"
        - text: "Linkage disequilibrium"
          href: "Linkage_disequilibrium.html"
        - text: "Population structure"
          href: "Pop_Structure.html"
        - text: "Minimum Spanning Networks"
          href: "Minimum_Spanning_Networks.html"
        - text: "AMOVA"
          href: "AMOVA.html"
        - text: "Discriminant analysis of principal components (DAPC)"
          href: "DAPC.html"
    - text: "Part III"
      menu:
        - text: "Population genomics and HTS"
          href: "intro_vcf.html"
        - text: "Reading VCF data"
          href: "reading_vcf.html"
        - text: "Analysis of genomic data"
          href: "analysis_of_genome.html"
        - text: "Analysis of GBS data"
          href: "gbs_analysis.html"
        - text: "Clustering plot"
          href: "clustering_plot.html"
    - text: "Workshops"
      menu:
        - text: "ICPP"
          menu:
            - text: "Preparation"
              href: "workshop_icpp.html"
            - text: "Introduction"
              href: "intro_vcf.html"
            - text: "VCF data"
              href: "reading_vcf.html"
            - text: "Quality control"
              href: "quality_control.html"
            - text: "Analysis of GBS data"
              href: "gbs_analysis.html"
            - text: "Analysis of genome data"
              href: "analysis_of_genome.html"
        - text: "APS Southern Division"
          menu:
            - text: "Preparation"
              href: "workshop_southernAPS.html"
            - text: "Introduction"
              href: "intro_vcf.html"
            - text: "VCF data"
              href: "reading_vcf.html"
            - text: "Quality control"
              href: "quality_control.html"
            - text: "Analysis of GBS data"
              href: "gbs_analysis.html"
    - text: "About"
      menu:
        - text: "Authors"
          href: "Authors.html"
    - text: "Appendices"
      menu:
        - text: "Introduction to R"
          href: "intro_to_R.html"
        - text: "Data sets"
          href: "Data_sets.html"
        - text: "Function glossary"
          href: "funpendix.html"
        - text: "Background_functions"
          href: "background_functions.html"
        - text: "Source Code"
          href: https://github.com/grunwaldlab/Population_Genetics_in_R/
output:
  html_document:
    theme: sandstone
    highlight: tango
    includes:
      in_header: googlecode.html
      before_body: 
      after_body: 
    css: styles.css      
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