_toc.yml

format: jb-book
root: intro
parts:
  - caption: About This Course
    chapters:
    - file: 1-intro/why
    - file: 1-intro/learning_objectives
    - file: syllabus
    - file: 1-intro/learning_approach
      sections:
      - file: 1-intro/actually_write_code
      - file: 1-intro/mindset
      - file: 1-intro/flipped_classroom
      - file: 1-intro/errors_debugging
      - file: 1-intro/ai
      - file: 1-intro/teamwork
    - file: 1-intro/pedagogy
      sections:
      - file: 1-intro/teaching_approach
      - file: 1-intro/authenticity
      - file: 1-intro/21st_cen_skills
      - file: 1-intro/constructivism
      - file: 1-intro/connectivism
    - file: 1-intro/open
      sections:
      - file: 1-intro/software
      - file: 1-intro/free_licenses
      - file: 1-intro/open_science
      - file: 1-intro/peer_review
      - file: 1-intro/for_profit
      - file: 1-intro/impact_factors
      - file: 1-intro/novelty
      - file: 1-intro/open_publishing
      - file: 1-intro/preregistration
      - file: 1-intro/open_methods
      - file: 1-intro/oer
      - file: 1-intro/oer_this_course
      - file: 1-intro/licenses

  - caption: Introduction to Data Science
    chapters:
    - file: 2-nds/introduction
    - file: 2-nds/learning_objectives
    - file: 2-nds/what_is_nds
      sections:
      - file: 2-nds/data
      - file: 2-nds/where
      - file: 2-nds/data_science
      - file: 2-nds/data_cleaning
    - file: 2-nds/tools_for_nds
      sections:
      - file: 2-nds/spreadsheets
      - file: 2-nds/spreadsheets_limits
      - file: 2-nds/reproducibility
      - file: 2-nds/sci_prog_lang
      - file: 2-nds/which_lang
      - file: 2-nds/libs
      - file: 2-nds/why_python
    - file: 2-nds/coding
      sections:
      - file: 2-nds/python
      - file: 2-nds/terminal
      - file: 2-nds/jupyter
      - file: 2-nds/markdown
      - file: 2-nds/vscode
      - file: 2-nds/github

  - caption: Set Up Your Computer for Data Science
    chapters:
    - file: 2b-setup/introduction
    - file: 2b-setup/learning_objectives
    - file: 2b-setup/first_steps
      sections:
      - file: 2b-setup/github
      - file: 2b-setup/codespaces
      - file: 2b-setup/github_classroom
    - file: 2b-setup/install_tools
      sections:
      - file: 2b-setup/anaconda
      - file: 2b-setup/miniconda
      - file: 2b-setup/vscode
      - file: 2b-setup/github_desktop
    - file: 2b-setup/first_repo
      sections:
      - file: 2b-setup/clone
      - file: 2b-setup/github_repo
      - file: 2b-setup/repo_in_vscode
      - file: 2b-setup/edit_commit_push
      - file: 2b-setup/edit_readme
      - file: 2b-setup/new_markdown_file
    - file: 2b-setup/getting_help
    - file: 2b-setup/submitting_assignments

  - caption: Introducing Python
    chapters:
    - file: 3-python/introduction
    - file: 3-python/learning_objectives
    - file: 3-python/preliminaries
      sections:
      - file: 3-python/jupyter_intro
      - file: 3-python/getting_help
    - file: 3-python/data_types
      sections:
      - file: 3-python/variables_assignment
      - file: 3-python/types_conversion
      - file: 3-python/builtin
      - file: 3-python/lists
      - file: 3-python/dictionaries
    - file: 3-python/flow_control
      sections:
      - file: 3-python/for_loops
      - file: 3-python/conditionals
    - file: 3-python/working_w_data
      sections:
      - file: 3-python/pandas_dataframes
      - file: 3-python/looping_data_files

  - caption: AI-Assisted Coding
    chapters:
    - file: 3b-ai_assisted/introduction
    - file: 3b-ai_assisted/ai_assisted
    - file: 3b-ai_assisted/rt_data
    - file: 3b-ai_assisted/pandas_copilot
    - file: 3b-ai_assisted/multi_data_files
      sections:
      - file: 3b-ai_assisted/multi_data_files_1
      - file: 3b-ai_assisted/multi_data_files_2
      - file: 3b-ai_assisted/multi_data_files_3

  - caption: Visualizing Data
    chapters:
    - file: 4-viz/introduction
    - file: 4-viz/learning_objectives
    - file: 4-viz/plotting
    - file: 4-viz/proc_vs_oo
    - file: 4-viz/subplots
    - file: 4-viz/plotting_types
    - file: 4-viz/seaborn
    - file: 4-viz/human_factors

  - caption: Exploratory Data Analysis
    chapters:
    - file: 5-eda/introduction
    - file: 5-eda/learning_objectives
    - file: 5-eda/repeated_measures
    - file: 5-eda/data_cleaning
    - file: 5-eda/ttests

  - caption: Single Unit Data
    chapters:
    - file: 6-single_unit/introduction
    - file: 6-single_unit/learning_objectives
    - file: 6-single_unit/single_unit_intro
      sections:
      - file: 6-single_unit/intro_spike_trains
      - file: 6-single_unit/ten_intensities
      - file: 6-single_unit/heat_maps
    - file: 6-single_unit/intro_multielec_data
      sections:
      - file: 6-single_unit/pandas_multielec
      - file: 6-single_unit/corr_spike_trains

  - caption: EEG Data
    chapters:
    - file: 7-eeg/introduction
    - file: 7-eeg/learning_objectives
    - file: 7-eeg/about_eeg
    - file: 7-eeg/approaches
      sections:
      - file: 7-eeg/time_freq
      - file: 7-eeg/erps
      - file: 7-eeg/components
    - file: 7-eeg/mne_python
      sections:
      - file: 7-eeg/mne_data_1
      - file: 7-eeg/mne_data_2
    - file: 7-eeg/erp_preprocessing
      sections:
      - file: 7-eeg/erp_filtering
      - file: 7-eeg/erp_artifacts
      - file: 7-eeg/erp_segmentation
      - file: 7-eeg/erp_avg_reref
    - file: 7-eeg/erp_group
      sections:
      - file: 7-eeg/erp_group_viz
      - file: 7-eeg/erp_group_stats

  - caption: MRI Data
    chapters:
    - file: 8-mri/introduction
    - file: 8-mri/learning_objectives
    - file: 8-mri/read_viz
    - file: 8-mri/nifti

  - caption: Machine Learning
    chapters:
    - file: 9-machine_learning/introduction

  - caption: References
    chapters:
    - file: zrefs