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mkdocs.yml
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118 lines (111 loc) · 3.54 KB
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site_name: KABR Tools Documentation
site_description: Tools for working with data for annotating animal behavior
site_author: Imageomics KABR Team
site_url: https://imageomics.github.io/kabr-tools
repo_name: Imageomics/kabr-tools
repo_url: https://github.com/Imageomics/kabr-tools
edit_uri: edit/main/docs/
theme:
name: material
logo: images/logo_128.png
favicon: images/logo_128.png
palette:
# Palette toggle for light mode
- scheme: default
accent: amber
toggle:
icon: material/brightness-7
name: Switch to dark mode
# Palette toggle for dark mode
- scheme: slate
accent: amber
toggle:
icon: material/brightness-4
name: Switch to light mode
features:
- navigation.tabs
- navigation.tabs.sticky
- navigation.sections
- navigation.expand
- navigation.top
- search.highlight
- search.suggest
- content.code.copy
- content.code.select
- content.tabs.link
extra_css:
- stylesheets/extra.css
plugins:
- search
- mkdocs-jupyter:
execute: false
include_source: true
show_input: true
ignore_h1_titles: true
- glightbox:
touchNavigation: true
loop: false
effect: zoom
slide_effect: slide
width: 100%
height: auto
zoomable: true
draggable: true
skip_classes:
- custom-skip-class-name
auto_caption: false
caption_position: bottom
markdown_extensions:
- pymdownx.highlight:
anchor_linenums: true
line_spans: __span
pygments_lang_class: true
- pymdownx.inlinehilite
- pymdownx.snippets
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
- pymdownx.tabbed:
alternate_style: true
- pymdownx.details
- admonition
- attr_list
- md_in_html
- tables
- toc:
permalink: true
nav:
- Home: index.md
- Pipeline:
- Overview: pipeline/overview.md
- Video Data Collection: pipeline/data-collection.md
- Pre-processing with CVAT: pipeline/preprocessing.md
- Behavior Labeling: pipeline/behavior-labeling.md
- Ecological Analysis: pipeline/analysis.md
- Optional Steps: pipeline/optional-steps.md
- Worked Example: pipeline/worked-example.md
- CVAT Guide:
- Setup and Usage: cvat/cvat-guide.md
- Data Management: cvat/cvat-data-management.md
- Methodology Comparisons:
- Overview: methodology_comparison/overview.md
- KABR Dataset Analysis: methodology_comparison/kabr_dataset/data_analysis.ipynb
- Focal Sampling vs Drone:
- Comparison: methodology_comparison/focalvsdrone/analysis/cm-focal-vs-drone.ipynb
- Gantt Charts: methodology_comparison/focalvsdrone/analysis/gantt_chart.ipynb
- By Species: methodology_comparison/scanvsfocal/analysis/cm-scan-vs-focal-by-species.ipynb
- Case Studies:
- Overview: case_studies/overview.md
- "0: Time Budget Analysis": case_studies/0_time_budget/time_budget.ipynb
- "1: Grevy's Landscape of Fear":
- "Visualizations": case_studies/1_grevys_landscape/grevys_landscape_graphs.ipynb
- "Linear Regression": case_studies/1_grevys_landscape/grevys_landscape_lr.ipynb
- "2: Zebra Behavior Transitions": case_studies/2_zebra_transition/behaviortransitionsheatmap.ipynb
- "3: Mixed Species Social": case_studies/3_mixed_species_social/mixed_species_overlap.ipynb
- Acknowledgements: acknowledgements.md
extra:
social:
- icon: fontawesome/brands/github
link: https://github.com/Imageomics/kabr-tools