_quarto.yml

project:
  type: book

book:
  title: "EEB313: Quantitative Methods in R for Biology"
  author: "Mete K. Yuksel & Zoë Humphries"
  date: today
  chapters:
    - index.qmd
    - about-us.qmd
    - downloadingR.qmd
    - part: "Lectures"
      chapters:
      - lectures/lec01-r_and_rstudio.qmd
      - lectures/lec02-basic-r.qmd
      - lectures/lec03-command_git.qmd
      - lectures/lec04-data-wrangling.qmd
      - lectures/lec05-data-visualization.qmd
      - lectures/lec06-exploratory-data-analysis.qmd
      - lectures/lec07-self-directed-analysis.qmd
      - lectures/lec08-intro-inference-1.qmd
      - lectures/lec09-intro-inference-2.qmd
      - lectures/lec10-linear-models-1.qmd
      - lectures/lec11-linear-models-2.qmd
      - lectures/lec12-model-selection.qmd
      - lectures/lec13-intro-to-multivariate-stats.qmd
      - lectures/lec14-mathematical-models-1.qmd
      - lectures/lec15-mathematical-models-2.qmd
    - part: "Assignments"
      chapters:
      - assignments/assignment-00.qmd
      - assignments/assignment-01.qmd
      - assignments/assignment-02.qmd
      - assignments/assignment-03.qmd
      - assignments/assignment-04.qmd
      - assignments/assignment-05.qmd
      - assignments/challenge-assignment.qmd
    - part: "Project"
      chapters:
      - projects.qmd
      - projects_databases.qmd
    - part: "Datasets"
      chapters:
        - text: "portal_data.csv"
          href: lectures/data/portal_data.csv
        - text: "pseudo.ara.busco"
          href: lectures/data/pseudo.ara.busco
        - text: "pseudo.LTRs"
          href: lectures/data/pseudo.LTRs
        - text: "disease_distance.csv"
          href: lectures/data/disease_distance.csv
        - text: "SSDinMammals.csv"
          href: lectures/data/SSDinMammals.csv
        - text: "medicago.csv"
          href: lectures/data/medicago.csv
        - text: "bmr.csv"
          href: lectures/data/bmr.csv
        - text: "Pigot2020.csv"
          href: lectures/data/Pigot2020.csv
        - text: "influenza_cities.csv"
          href: lectures/data/influenza_cities.csv
        - text: "meas.csv"
          href: lectures/data/meas.csv
        - text: "satellites.csv"
          href: lectures/data/satellites.csv
        - text: "WF_inference_data.csv"
          href: lectures/data/WF_inference_data.csv
    - part: "Miscellaneous notes"
      chapters:
      - review-for-challenge.qmd
  repo-url: https://github.com/EEB313/eeb313.github.io
  sidebar:
    search: true
    border: true

format:
  html:
    theme:
      light: [cosmo, format/_light.scss]
    code-copy: true
    code-fold: false
    code-overflow: wrap

extra_files:
  - assignment-00.Rmd
  - assignment-01.Rmd
  - assignment-02.Rmd
  - assignment-03.Rmd
  - assignment-04.Rmd
  - assignment-05.Rmd
  - assignment-00.qmd
  - assignment-01.qmd
  - assignment-02.qmd
  - assignment-03.qmd
  - assignment-04.qmd
  - assignment-05.qmd
  - challenge-assignment.qmd
  - challenge-assignment.Rmd
  - lec07-self-directed-analysis.qmd
  - lec07-self-directed-analysis.Rmd
  - review-for-challenge.qmd
  - review-for-challenge.Rmd
  - portal_data.csv
  - pseudo.ara.busco
  - pseudo.LTRs
  - pseudoMol_Kdist.txt
  - SSDinMammals.csv
  - disease_distance.csv
  - medicago.csv
  - bmr.csv
  - Pigot2020.csv
  - influenza_cities.csv
  - meas.csv
  - satellites.csv
  - WF_inference_data.csv