_quarto.yml

project:
  type: website
  preview:
    port: 3434
  render:
  - '*.qmd'
  - '!myresources/'
  - '!renv/'
  - '!files/'
  resources: '*.xlsx'
execute:
  freeze: auto
description-meta: Modern Applied Data Analysis (MADA) course
engine: knitr
format:
  html:
    theme:
    - yeti
    - MADAstyle.scss
    author:
    - name: Andreas Handel
    date-modified: last-modified
    date-format: iso
    toc: true
    toc_depth: 3
    toc_float:
      collapsed: false
    link-external-newwindow: true
    fig-align: center
    highlight-style: a11y
    grid:
      content-mode: full
      sidebar-width: 300px
      body-width: 900px
    css: include/webex.css
    include-after-body: include/webex.js
lightbox:
  desc-position: right
  match: auto
  effect: zoom
  loop: false
website:
  title: MADA Course
  description: Modern Applied Data Analysis (MADA) course
  site-url: https://andreashandel.github.io/MADAcourse/
  repo-url: https://github.com/andreashandel/MADAcourse/
  favicon: media/MADAlogo.png
  page-navigation: true
  navbar:
    pinned: true
    background: '#81AF8E'
    foreground: dark
    logo: media/MADAlogo.png
    left:
    - text: General Information
      file: courseinfo/course-overview.qmd
    - text: Content
      file: content/content-overview.qmd
    - text: Assessments
      file: courseinfo/assessments-overview.qmd
    - text: Project
      file: project/project-overview.qmd
    - text: Resources
      file: resources/resources-overview.qmd
    right:
    - icon: github
      file: https://github.com/andreashandel/MADAcourse
  sidebar:
  - title: General Information
    style: docked
    collapse-level: 1
    background: '#e3e2db'
    contents:
    - text: Course Overview
      file: courseinfo/course-overview.qmd
    - text: Syllabus
      file: courseinfo/course-syllabus.qmd
    - text: Schedule
      file: courseinfo/course-schedule.qmd
    - text: Communication
      file: courseinfo/course-communication.qmd
  - title: Content
    contents:
    - text: Content Overview
      file: content/content-overview.qmd
    - section: 1. Course and Tools Introduction
      contents:
      - text: Course Introduction
        file: content/module-intro-tools/introduction-course.qmd
      - text: R and Rstudio
        file: content/module-intro-tools/tools-randrstudio.qmd
      - text: GitHub Introduction
        file: content/module-intro-tools/tools-github-introduction.qmd
      - text: GitHub and R Workflow
        file: content/module-intro-tools/tools-github-r-workflow.qmd
      - text: Quarto & Co
        file: content/module-intro-tools/tools-quarto.qmd
      - text: AI Tools
        file: content/module-intro-tools/tools-ai.qmd
      - text: Reference Management
        file: content/module-intro-tools/tools-reference-management.qmd
      - text: Guidance and Tips for R/RStudio/GitHub
        file: content/module-intro-tools/tools-tips-guidance.qmd
    - section: 2A. Data Analysis Introduction
      contents:
      - text: Motivating Examples
        file: content/module-data-analysis/data-analysis-motivation.qmd
      - text: Data Analysis Overview
        file: content/module-data-analysis/data-analysis-overview.qmd
    - section: 2B. READy Workflows
      contents:
      - text: READy Workflows Overview
        file: content/module-ready-workflow/ready-overview.qmd
      - text: READy Introduction
        file: content/module-ready-workflow/ready-introduction/ready-introduction.qmd
      - text: Project Organization
        file: content/module-ready-workflow/ready-organization/ready-organization.qmd
      - text: Project Management
        file: content/module-ready-workflow/ready-project-management/ready-project-management.qmd
      - text: Software Management
        file: content/module-ready-workflow/ready-software-management/ready-software-management.qmd
      - text: Project Documentation
        file: content/module-ready-workflow/ready-documentation/ready-documentation.qmd
      - text: Tools for a READy workflow
        file: content/module-ready-workflow/ready-tools/ready-tools.qmd
      - text: Open Research
        file: content/module-ready-workflow/ready-open/ready-open.qmd
    - section: 3. R Coding Basics
      contents:
      - text: R Coding Basics
        file: content/module-coding-basics/rcoding-basics.qmd
      - text: Tidyverse and Friends
        file: content/module-coding-basics/rcoding-tidyverse.qmd
    - section: 4A. Data Introduction
      contents:
      - text: Data Overview
        file: content/module-data/data-overview.qmd
      - text: Basic Data Types
        file: content/module-data/data-types-basic/data-types-basic.qmd
      - text: Complex Data Types
        file: content/module-data/data-types-complex/data-types-complex.qmd
      - text: Data Storage Formats
        file: content//module-data/data-storage-formats/data-storage-formats.qmd
      - text: Data Formats in R
        file: content//module-data/data-formats-r/data-formats-r.qmd
      - text: Data Generation 
        file: content//module-data/data-generation-process/data-generation-process.qmd
    - section: 4B. Synthetic Data
      contents:
      - text: Synthetic Data Overview
        file: content/module-synthetic-data/synthetic-data-overview.qmd
      - text: Introduction and Motivation
        file: content/module-synthetic-data/synthetic-data-introduction/synthetic-data-introduction.qmd
      - text: Creating new Data
        file: content/module-synthetic-data/synthetic-data-new-r/synthetic-data-new-r.qmd
      - text: Creating new data based on existing data
        file: content/module-synthetic-data/synthetic-data-new-existing-r/synthetic-data-new-existing-r.qmd
      - text: Scrambling existing Data
        file: content/module-synthetic-data/synthetic-data-existing-r/synthetic-data-existing-r.qmd
      - text: R packages for data creation
        file: content/module-synthetic-data/synthetic-data-r-packages/synthetic-data-r-packages.qmd
      - text: Use synthetic data with AI tools
        file: content/module-synthetic-data/synthetic-data-ai-tools-r/synthetic-data-ai-tools-r.qmd
      - text: Use synthetic data to test models
        file: content/module-synthetic-data/synthetic-data-model-testing-r/synthetic-data-model-testing-r.qmd
    - section: 5. Data Processing
      contents:
      - text: Data Processing Overview
        file: content/module-data-processing/data-processing-overview.qmd
      - text: Data Processing Introduction
        file: content/module-data-processing/data-processing-introduction/data-processing-introduction.qmd
      - text: Data loading
        file: content/module-data-processing/data-loading/data-loading.qmd
      - text: Dealing with missing data
        file: content/module-data-processing/missing-data/missing-data.qmd
      - text: Dealing with outliers
        file: content/module-data-processing/outliers/outliers.qmd
      - text: Feature Engineering
        file: content/module-data-processing/feature-engineering/feature-engineering.qmd
      - text: Merging data
        file: content/module-data-processing//merging-data/merging-data.qmd
    - section: 6. Presenting Data and Results
      contents:
      - text: Presenting Results Overview
        file: content/module-data-presentation/presenting-results-overview.qmd
      - text: Visualization Overview
        file: content/module-data-presentation/visualization-introduction.qmd
      - text: Visualization in R
        file: content/module-data-presentation/visualization-in-r.qmd
      - text: Tables in R
        file: content/module-data-presentation/tables-in-r.qmd
    - section: 7. Statistical Analysis Overview
      contents:
      - text: Statistical Analysis Introduction
        file: content/module-stats-overview/statistical-analysis-introduction.qmd
      - text: Some Statistical Model Fitting Terminology
        file: content/module-stats-overview/statistical-terminology.qmd
      - text: Descriptive and preliminary analysis
        file: content/module-stats-overview/descriptive-analysis.qmd
    - section: 8. Model Fitting
      contents:
      - text: Model Fitting Overview
        file: content/model-fitting/model-fitting-overview.qmd
      - text: Model Fitting Introduction
        file: content/model-fitting/model-fitting-introduction/model-fitting-introduction.qmd
      - text: Fitting Basic Models
        file: content/model-fitting/basic-statistical-models/basic-statistical-models.qmd
      - text: Model performance metrics
        file: content/model-fitting/model-evaluation/model-evaluation.qmd
      - text: Fitting Models in R
        file: content/model-fitting/model-fitting-r/model-fitting-r.qmd
    - section: 9. Model Assessment
      contents:
      - text: Model Assessment Overview
        file: content/model-assessment/model-assessment-overview.qmd
      - text: Model Assessment Introduction
        file: content/model-assessment/model-assessment-introduction/model-assessment-introduction.qmd
      - text: Reality-based assessment
        file: content/model-assessment/reality-based-assessment/reality-based-assessment.qmd
      - text: Model performance revisited
        file: content/model-assessment/model-performance-revisited/model-performance-revisited.qmd
      - text: Model evaluation with cross-validation
        file: content/model-assessment/external-data-assessment/external-data-assessment.qmd
      - text: Model evaluation with Information Criteria
        file: content/model-assessment/information-criteria-assessment/information-criteria-assessment.qmd
      - text: Model diagnostics
        file: content/model-assessment/diagnostics-assessment/diagnostics-assessment.qmd
      - text: Model uncertainty
        file: content/model-assessment/uncertainty-assessment/uncertainty-assessment.qmd
    - section: 10. Model Improvement
      contents:
      - text: Model Improvement Overview
        file: content/model-improvement/model-improvement-overview.qmd
      - text: Model Improvement Introduction
        file: content/model-improvement/model-improvement-introduction/model-improvement-introduction.qmd
      - text: Subset Selection
        file: content/model-improvement/model-improvement-subset/model-improvement-subset.qmd
      - text: Regularization
        file: content/model-improvement/model-improvement-regularization/model-improvement-regularization.qmd
      - text: Model Tuning
        file: content/model-improvement/model-improvement-tuning/model-improvement-tuning.qmd
    - section: 11. Machine Learning Models I
      contents:
      - text: ML Models Overview
        file: content/module-model-ml-1/ml-models-overview.qmd
      - text: Polynomial and Spline Models
        file: content/module-model-ml-1/polynomial-spline-models.qmd
      - text: Decision Trees
        file: content/module-model-ml-1/decision-trees.qmd
      - text: Many-Tree Models
        file: content/module-model-ml-1/many-tree-models.qmd
    - section: 12. Machine Learning Models II
      contents:
      - text: Support Vector Machine Models
        file: content/module-model-ml-2/svm-models.qmd
      - text: Discriminant Analysis Models
        file: content/module-model-ml-2/da-models.qmd
      - text: Some More ML models
        file: content/module-model-ml-2/more-ml-models.qmd
    - section: 13. Complete Analysis Workflow
      contents:
      - text: Complete Data Analysis Workflow
        file: content/module-workflow/complete-data-analysis-workflow.qmd
    - section: AI
      contents:
      - text: AI Overview
        file: content/module-ai/ai-overview.qmd
      - text: Introduction to AI
        file: content/module-ai/ai-introduction/ai-introduction.qmd
      - text: Introduction to LLM AI tools
        file: content/module-ai/ai-llm-introduction/ai-llm-introduction.qmd
      - text: AI Concepts
        file: content/module-ai/ai-conceptual/ai-conceptual.qmd
      - text: Current AI Tools
        file: content/module-ai/ai-tools/ai-tools.qmd
      - text: Write code with AI
        file: content/module-ai/ai-write-code-r/ai-write-code-r.qmd
      - text: Fix code with AI
        file: content/module-ai/ai-fix-code-r/ai-fix-code-r.qmd
      - text: Explore data with AI
        file: content/module-ai/ai-eda-r/ai-eda-r.qmd
      - text: Analyze data with AI
        file: content/module-ai/ai-analysis-r/ai-analysis-r.qmd
      - text: AI Resources
        file: content/module-ai/ai-resources/ai-resources.qmd
  - title: Assessments
    contents:
    - text: Assessments Overview
      file: courseinfo/assessments-overview.qmd
    - text: 1. Course and Tools Introduction
      file: content/module-intro-tools/assessment-course-tools-introduction.qmd
    - text: 2. Data Analysis Introduction & READy Workflow
      file: content/module-data-analysis/assessment-data-analysis.qmd
    - text: 3. R Coding Basics
      file: content/module-coding-basics/assessment-coding.qmd
    - text: 4. Data Introduction & Synthetic Data
      file: content/module-data/assessment-data.qmd
    - text: 5. Processing Data
      file: content/module-data-processing/assessment-data-processing.qmd
    - text: 6. Presenting Data and Results
      file: content/module-data-presentation/assessment-presenting-results.qmd
    - text: 7. Statistical Analysis Overview
      file: content/module-stats-overview/assessment-statistical-analysis.qmd
    - text: 8. Model Fitting
      file: content/model-fitting/assessment-model-fitting.qmd
    - text: 9. Model Assessment
      file: content/model-assessment/assessment-model-assessment.qmd
    - text: 10. Model Improvement
      file: content/model-improvement/assessment-model-improvement.qmd
    - text: 11. Machine Learning Models I
      file: content/module-model-ml-1/assessment-ml-models-1.qmd
    - text: 12. Machine Learning Models II
      file: content/module-model-ml-2/assessment-ml-models-2.qmd
    - text: 13. Complete Analysis Workflow
      file: content/module-workflow/assessment-complete-workflow.qmd
  - title: Project
    contents:
    - text: Project Overview
      file: project/project-overview.qmd
    - text: Project Details
      file: project/project-details.qmd
    - text: Project Review
      file: project/project-review.qmd
    - text: Project Examples
      file: project/project-examples.qmd
  - title: Resources
    contents:
    - text: Resources Overview
      file: resources/resources-overview.qmd
    - text: Course Resources
      file: resources/resources-course.qmd
    - text: General Resources
      file: resources/resources-general.qmd
    - text: Glossary
      file: resources/resources-glossary.qmd