_site.yml

name: "vcfR"
output_dir: "."
navbar:
  title: "vcfR"
  left:
    - text: "Home"
      href: index.html
    - text: "R language"
      href: rlanguage.html
    - text: "Tutorial"
      menu:
        - text: "A quick introduction"
          href: "quick_intro.html"
        - text: "VCF data"
          href: "vcf_data.html"
        - text: "vcfR objects"
          href: "vcfR_object.html"
        - text: "How much memory"
          href: "how_much_memory.html"
        - text: "Extracting matrices"
          href: "matrices.html"
        - text: "Tidy vcfR"
          href: "tidy_vcfR.html"
        - text: "chromR objects"
          href: "chromR_object.html"
        - text: "Visualization 1"
          href: "visualization_1.html"
        - text: "Visualization 2"
          href: "visualization_2.html"
        - text: "Sequence coverage"
          href: "sequence_coverage.html"
        - text: "Filtering data"
          href: "filtering_data.html"
        - text: "Ranking data"
          href: "ranking_data.html"
        - text: "Windowing"
          href: "windowing.html"          
        - text: "Genetic differentiation"
          href: "genetic_differentiation.html"
    - text: "GBS class"
      menu:
        - text: "GBS class"
          href: "gbs_class.html"
        - text: "VCF data"
          href: "vcf_data.html"
        - text: "Extract data"
          href: "extract_data.html"
        - text: "Depth plot"
          href: "depth_plot.html"
        - text: "Missing data"
          href: "missing_data.html"
        - text: "Censoring data"
          href: "censoring_data.html"
        - text: "Omitting data"
          href: "omitting_data.html"
        - text: "Apply"
          href: "apply.html"
    - text: "Ploidy"
      menu:
        - text: "Ploidy"
          href: "ploidy.html"
        - text: "Determining ploidy 1"
          href: "determining_ploidy_1.html"
        - text: "Determining ploidy 2"
          href: "determining_ploidy_2.html"
    - text: "Export"
      menu:
        - text: "Overview"
          href: "export.html"
        - text: "Export to *vcf.gz"
          href: "export_vcfgz.html"
        - text: "Genind and Genclone"
          href: "export_genind_genclone.html"
        - text: "Genlight and SNPclone"
          href: "export_genlight_snpclone.html"
        - text: "DNAbin"
          href: "dnabin.html"
    - text: "FAQ"
      menu:
        - text: "Subset to 1 chromosome"
          href: "subset_data_to_1chrom.html"
        - text: "Missing data"
          href: "missing_data.html"
        - text: "VCF software"
          href: "vcf_software.html"
        - text: "Haploidizing diploid data"
          href: "dip_to_hap.html"
        - text: "Compiling vcfR"
          href: "compiling_vcfR.html"
        - text: "Reporting an issue"
          href: "reporting_issue.html"
output:
  html_document:
    theme: sandstone
    highlight: textmate
    include:
      in_header: googlecode.html
      before_body: header.html
      after_body: footer.html
    css: styles.css