_toc.yml

# Table of contents
# Learn more at https://jupyterbook.org/customize/toc.html

format: jb-book
root: book/intro
parts:
  - caption: Frontmatter
    chapters:
    # - file: frontmatter/toc
    - file: book/frontmatter/2025outline
  
  - caption: "Unit 1: Basic Programing"
    numbered: True
    chapters:
    - file: book/unit1/python
    - file: book/unit1/stat_variables
    - file: book/unit1/linux
    - file: book/unit1/sci_python
    - file: book/unit1/data_viz
    - file: book/unit1/r
  
  - caption: "Homework Unit 1"
    numbered: False
    chapters:
    - file: book/unit1/hw1

  - caption: "Unit 2: Basic Statistics"
    numbered: True
    chapters:
      - file: book/unit2/correlation_testing
      - file: book/unit2/pearson
      - file: book/unit2/fisher    # move to start of Unit 3
      - file: book/unit2/autocorrelation
      - file: book/unit2/hypothesis
      - file: book/unit2/pca
      # - file: book/unit2/stats   #why not this?
  
  - caption: "Homework Unit 2"
    numbered: False
    chapters:
    - file: book/unit2/hw2
    - file: book/unit2/hw3

  - caption: "Unit 3: Model Fitting"
    numbered: True
    chapters:
    - file: book/unit3/frequentist-v-bayesian
    - file: book/unit3/linear_regression
    - file: book/unit3/chi_square_ml_emcee
    - file: book/unit3/resampling    # move to unit 2?
    - file: book/unit3/goodness_of_fit
    - file: book/unit3/aic_bic
    - file: book/unit3/emcee
    - file: book/unit3/BHM
    - file: book/unit3/bayesian_model_compare
  
  - caption: "Homework Unit 3"
    numbered: False
    chapters:
    - file: book/unit3/hw4
    - file: book/unit3/hw5
    
  - caption: "Unit 4: Advanced Topics"
    numbered: True
    chapters:
      - file: book/unit4/scikit_learn
      - file: book/unit4/neural_network
      - file: book/unit4/deep_learning
      - file: book/unit4/two_point
      - file: book/unit4/clustering
  
  - caption: "References"
    numbered: False
    chapters:
    - file: book/bibliography
    - file: genindex