Markdown Guide

# Markdown for the Modern Researcher: Efficiency and Clarity ## Introduction - Overview of Markdown's relevance and utility in modern research. - How Markdown streamlines documentation in diverse scientific and coding environments. ## Participants **Ty Tuff** - Data Scientist - ESIIL - expert*** in turning complex data into actionable insights. He is a great teacher! **Bob Rabin** Research meteorologist - KBOCC and Ilisagvik College **Darryl Reano:** Acoma/Kewa; School of Earth and Space Exploration at Arizona State University; Geoscience Education Research **Mary Banner** - SUNY ESF Graduate student. Ponca and Ojibwe **Jason Tinant** *Oglala Lakota College* -- Fascinated by water... **Rachel Lieber**: ESIIL Community Engagement Specialist, CU Boulder **Cody O'Dale** - Environmental GIS Specialist - Shoshone-Bannock Tribes **Cynthia Sanders** *College of the Muscogee Nation* **Alex "Panda" Armendariz** Mescalero Apache - Graduate Student at Cal Poly Pomona - Research focused on Indigenous Food Systems **Byron Andrew: Jemez Pueblo/Yupik: Natural Resources Department, GIS Manager **Eva Weddell** *Ihanktunwan Dakota* - Conservation biology at Oglala Lakota College **Justina White Eyes** Dakota State ** Shannon Boldt Northwest Indian College **Summer Dupree** - Student at Oglala Lakota College **Cibele Amaral** - ESIIL Interim Analytics Director and Remote Sensing Scientist **William Blacksmith*** - *Sicangu Lakota Climate Center* - IT Specialist **Saima Shikesho** - Student at Dartmouth College ## Section 1: Mastering Markdown Syntax - **Objective:** Equip researchers with a thorough understanding of Markdown syntax and its diverse applications. - **Topics Covered:** - Fundamentals of Text Formatting (headings, lists, bold, italics) **vvv - Integrating Multimedia (image and video links) - Diagrams with Mermaid (creating flowcharts, mind maps, timvvvelines) - Interactive Elements (hyperlinks, embedding interactive content) - **Activities:** - Crafting a Markdown document with various formatting elements. - Developing diagrams using Mermaid for research presentations. - Embedding multimedia elements in a Markdown document for enhanced communication. ## Section 2: Markdown in Research Tools - **Objective:** Showcase the integration of Markdown in RStudio and Jupyter Notebooks for scientific documentation. - **Topics Covered:** - Implementing Markdown in RStudio (R Markdown, knitting to HTML/PDF) - Utilizing Markdown in Jupyter Notebooks (code and Markdown cells) - Best practices for documenting research code - Including code outputs and visualizations in documentation - **Activities:** - Creating and sharing an R Markdown document with annotated research data. - Building a comprehensive Jupyter Notebook with integrated Markdown annotations. ## Section 3: Disseminating Research with Markdown and GitHub Pages - **Objective:** Teach researchers how to publish and manage Markdown-based documentation as web pages. - **Topics Covered:** - Setting up a GitHub repository for hosting documentation - Transforming Markdown files into web-friendly formats - Customizing web page layouts and themes - Advanced features using Jekyll - Version control and content management for documentation - **Activities:** - Publishing a research project documentation on GitHub Pages. - Applying custom themes and layouts to enhance online documentation. ## Conclusion - Review of Markdown's role in enhancing research efficiency and clarity. - Encouraging the integration of Markdown into daily research activities for improved documentation and dissemination. ## Additional Resources - Curated list of advanced Markdown tutorials, guides for GitHub Pages, and Jekyll resources for researchers. ## Section 1: Mastering Markdown Syntax ### 1. Fundamentals of Text Formatting - **Headings**: Use `#` for different levels of headings. - # Heading Level 1 - ## Heading Level 2 - ### Heading Level 3 - **Lists**: Bulleted lists use asterisks, numbers for ordered lists. - Item 1 - Item 2 - Subitem 2.1 - Subitem 2.2 - 1. First item - 2. Second item - **Bold and Italics**: Use asterisks or underscores. - **Bold Text** - *Italic Text* ### 2. Advanced Structures - **Tables**: Create tables using dashes and pipes. - | Header 1 | Header 2 | Header 3 | |----------|----------|----------| | Row 1 | Data | Data | | Row 2 | Data | Data | - Add a ":"" to change text justification. Here the : is added on the left for left justification. | Header 1 | Header 2 | Header 3 | |---------:|--------- |----------| | Row 1 | Data | Data | | Row 2 | Data | Data | - | | | | | | | | | | | | | |---|---|---|---|---|---|---|---|---|---|---|---| | A | N | A | L | Y | T | I | C | S | E | N | R | | E | I | N | V | I | R | O | N | M | E | N | T | | V | E | L | O | P | M | O | C | O | M | U | N | | E | G | A | G | E | L | L | A | H | C | N | E | | R | A | T | A | D | E | V | E | L | O | P | W | | E | I | T | S | I | T | N | E | I | C | S | R | | S | O | I | G | O | L | O | I | B | H | T | L | | A | H | T | L | A | E | W | E | G | N | E | L | | T | I | T | S | I | T | N | E | I | C | S | N | | I | E | E | S | R | E | H | T | O | E | N | I | | C | S | L | L | A | H | C | E | G | L | A | N | | E | G | A | L | L | E | H | C | N | E | I | C | - If you hit the boundaries of Markdown's capabilities, you can start to add html directly. Remember, this entire exercisse is to translate to html. **Sudoku Puzzle** Fill in the blank cells with numbers from 1 to 9, such that each row, column, and 3x3 subgrid contains all the numbers from 1 to 9 without repetition. | | | | | | | | | | |---|---|---|---|---|---|---|---|---| | 5 | 3 | | | 7 | | | | | | 6 | | | 1 | 9 | 5 | | | | | | 9 | 8 | | | | | 6 | | | 8 | | | | 6 | | | | 3 | | 4 | | | 8 | | 3 | | | 1 | | 7 | | | | 2 | | | | 6 | | | 6 | | | | | 2 | 8 | | | | | | 4 | 1 | 9 | | | 5 | | | | | | 8 | | | 7 | 9 | <table> <tr><td style="color: blue;">5</td><td style="color: blue;">3</td><td style="color: grey;">4</td><td style="color: grey;">6</td><td style="color: blue;">7</td><td style="color: grey;">8</td><td style="color: grey;">9</td><td style="color: grey;">1</td><td style="color: grey;">2</td></tr> <tr><td style="color: blue;">6</td><td style="color: grey;">7</td><td style="color: grey;">2</td><td style="color: blue;">1</td><td style="color: blue;">9</td><td style="color: blue;">5</td><td style="color: grey;">3</td><td style="color: grey;">4</td><td style="color: grey;">8</td></tr> <tr><td style="color: grey;">1</td><td style="color: blue;">9</td><td style="color: blue;">8</td><td style="color: grey;">3</td><td style="color: grey;">4</td><td style="color: grey;">2</td><td style="color: grey;">5</td><td style="color: blue;">6</td><td style="color: grey;">7</td></tr> <tr><td style="color: blue;">8</td><td style="color: grey;">5</td><td style="color: grey;">9</td><td style="color: grey;">7</td><td style="color: blue;">6</td><td style="color: grey;">1</td><td style="color: grey;">4</td><td style="color: grey;">2</td><td style="color: blue;">3</td></tr> <tr><td style="color: blue;">4</td><td style="color: grey;">2</td><td style="color: grey;">6</td><td style="color: blue;">8</td><td style="color: grey;">5</td><td style="color: blue;">3</td><td style="color: grey;">7</td><td style="color: grey;">9</td><td style="color: blue;">1</td></tr> <tr><td style="color: blue;">7</td><td style="color: grey;">1</td><td style="color: grey;">3</td><td style="color: grey;">9</td><td style="color: blue;">2</td><td style="color: grey;">4</td><td style="color: grey;">8</td><td style="color: grey;">5</td><td style="color: blue;">6</td></tr> <tr><td style="color: grey;">9</td><td style="color: blue;">6</td><td style="color: grey;">1</td><td style="color: grey;">5</td><td style="color: grey;">3</td><td style="color: grey;">7</td><td style="color: blue;">2</td><td style="color: blue;">8</td><td style="color: grey;">4</td></tr> <tr><td style="color: grey;">2</td><td style="color: grey;">8</td><td style="color: grey;">7</td><td style="color: blue;">4</td><td style="color: blue;">1</td><td style="color: blue;">9</td><td style="color: grey;">6</td><td style="color: grey;">3</td><td style="color: blue;">5</td></tr> <tr><td style="color: grey;">3</td><td style="color: grey;">4</td><td style="color: grey;">5</td><td style="color: grey;">2</td><td style="color: blue;">8</td><td style="color: grey;">6</td><td style="color: grey;">1</td><td style="color: grey;">7</td><td style="color: blue;">9</td></tr> </table> - **Blockquotes**: Use `>` for blockquotes. - > This is a blockquote. - > It can span multiple lines. ### 3. Integrating Multimedia - **Images**: Add images using the format `![alt text](image_url)`. - ![Markdown Logo](https://example.com/markdown-logo.png) - **Videos**: Embed videos using HTML in Markdown. - `<iframe width="560" height="315" src="https://www.youtube.com/embed/dQw4w9WgXcQ" frameborder="0" allowfullscreen></iframe>` ### 4. Diagrams with Mermaid - **Flowcharts**: ```mermaid graph TD A[Start] --> B[Analyze Data] B --> C{Is Data Large?} C -->|Yes| D[Apply Big Data Solutions] C -->|No| E[Use Traditional Methods] D --> F[Machine Learning] E --> G[Statistical Analysis] F --> H{Model Accurate?} G --> I[Report Results] H -->|Yes| J[Deploy Model] H -->|No| K[Refine Model] J --> L[Monitor Performance] K --> F L --> M[End: Success] I --> N[End: Report Generated] style A fill:#f9f,stroke:#333,stroke-width:2px style M fill:#9f9,stroke:#333,stroke-width:2px style N fill:#9f9,stroke:#333,stroke-width:2px ``` - **Mind Maps**: ```mermaid mindmap root((ESIIL)) section Data Sources Satellite Imagery ::icon(fa fa-satellite) Remote Sensing Data Drones Aircraft On-ground Sensors Weather Stations IoT Devices Open Environmental Data Public Datasets ::icon(fa fa-database) section Research Focus Climate Change Analysis Ice Melt Patterns Sea Level Rise Biodiversity Monitoring Species Distribution Habitat Fragmentation Geospatial Analysis Techniques Machine Learning Models Predictive Analytics section Applications Conservation Strategies ::icon(fa fa-leaf) Urban Planning Green Spaces Disaster Response Flood Mapping Wildfire Tracking section Tools and Technologies GIS Software QGIS ArcGIS Programming Languages Python R Cloud Computing Platforms AWS Google Earth Engine Data Visualization D3.js Tableau ``` - **Timelines**: ```mermaid gantt title ESIIL Year 2 Project Schedule dateFormat YYYY-MM-DD section CI Sovereign OASIS via private jupiterhubs :2024-08-01, 2024-10-30 OASIS documentation :2024-09-15, 70d Data cube OASIS via cyverse account :2024-09-15, 100d Integrate with ESIIL User Management system :2024-08-01, 2024-11-30 Build badges to deploy DE from mkdoc :2024-09-01, 2024-12-15 Streamline Github ssh key management :2024-10-01, 2024-12-31 Cyverse support (R proxy link) :2024-11-01, 2024-12-31 Cyverse use summary and statistics :2024-08-01, 2024-12-15 section CI Consultation and Education Conferences/Invited talks :2024-08-01, 2024-12-31 Office hours :2024-08-15, 2024-12-15 Proposals :2024-09-01, 2024-11-15 Private lessons :2024-09-15, 2024-11-30 Pre-event trainings :2024-10-01, 2024-12-15 Textbook development w/ education team :2024-08-01, 2024-12-15 Train the trainers / group lessons :2024-08-15, 2024-11-30 Tribal engagement :2024-09-01, 2024-12-15 Ethical Space training :2024-09-15, 2024-12-31 section CI Design and Build Data library (repository) :2024-08-01, 2024-10-30 Analytics library (repository) :2024-08-15, 2024-11-15 Containers (repository) :2024-09-01, 2024-11-30 Cloud infrastructure templates (repository) :2024-09-15, 2024-12-15 Tribal resilience Data Cube :2024-10-01, 2024-12-31 ``` ```mermaid %%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}} }%% gitGraph commit id: "Start from template" branch c1 commit id: "Set up SSH key pair" commit id: "Modify _config.yml for GitHub Pages" commit id: "Initial website structure" commit id: "Add new markdown pages" commit id: "Update navigation tree" commit id: "Edit existing pages" commit id: "Delete old markdown pages" commit id: "Finalize website updates" commit id: "Add new markdown pages" commit id: "Update navigation tree" checkout c1 branch b1 commit commit checkout c1 merge b1 ``` ` ```mermaid %%{init: {"quadrantChart": {"chartWidth": 400, "chartHeight": 400}, "themeVariables": {"quadrant1TextFill": "#ff0000"} }}%% quadrantChart x-axis Urgent --> Not Urgent y-axis Not Important --> "Important ❤" quadrant-1 Plan quadrant-2 Do quadrant-3 Delegate quadrant-4 Delete ``` ```mermaid timeline title Major Events in Environmental Science and Data Science section Environmental Science 19th century : Foundations in Ecology and Conservation 1962 : Publication of 'Silent Spring' by Rachel Carson 1970 : First Earth Day 1987 : Brundtland Report introduces Sustainable Development 1992 : Rio Earth Summit 2015 : Paris Agreement on Climate Change section Data Science 1960s-1970s : Development of Database Management Systems 1980s : Emergence of Data Warehousing 1990s : Growth of the World Wide Web and Data Mining 2000s : Big Data and Predictive Analytics 2010s : AI and Machine Learning Revolution 2020s : Integration of AI in Environmental Research ``` ```mermaid erDiagram CAR ||--o{ NAMED-DRIVER : allows CAR { string registrationNumber string make string model } PERSON ||--o{ NAMED-DRIVER : is PERSON { string firstName string lastName int age } ``` ```mermaid --- config: sankey: showValues: false --- sankey-beta NASA Data,Big Data Harmonization,100 Satellite Imagery,Big Data Harmonization,80 Open Environmental Data,Big Data Harmonization,70 Remote Sensing Data,Big Data Harmonization,90 Big Data Harmonization, Data Analysis and Integration,340 Data Analysis and Integration,Climate Change Research,100 Data Analysis and Integration,Biodiversity Monitoring,80 Data Analysis and Integration,Geospatial Mapping,60 Data Analysis and Integration,Urban Planning,50 Data Analysis and Integration,Disaster Response,50 ``` ### 5. Interactive Elements - **Hyperlinks**: Use the format `[link text](URL)`. - [Google](https://www.google.com) - [Play Tetris](https://tetris.com/play-tetris) - **Embedding Interactive Content**: Use HTML tags or specific platform embed codes. - `<iframe src="https://example.com/interactive-content" width="600" height="400"></iframe>` ### 6. Math Notation Markdown can be combined with LaTeX for mathematical notation, useful in environmental data science for expressing statistical distributions, coordinate systems, and more. This requires a Markdown renderer with LaTeX support (like MathJax or KaTeX). - **Inline Math**: Use single dollar signs for inline math expressions. Representing the normal distribution. Example: The probability density function of the normal distribution is given by $f(x|\mu,\sigma) = \frac{1}{\sigma\sqrt{2\pi}}e^{-\frac{1}{2}\left(\frac{x-\mu}{\sigma}\right)^2}$.` - **Display Math**: Use double dollar signs for standalone equations. Example: $$ f(x|\mu,\sigma) = \frac{1}{\sigma\sqrt{2\pi}}e^{-\frac{1}{2}\left(\frac{x-\mu}{\sigma}\right)^2} $$ - **Common LaTeX Elements for Environmental Data Science**: - **Statistical Distributions**: - Normal Distribution: `\frac{1}{\sigma\sqrt{2\pi}}e^{-\frac{1}{2}\left(\frac{x-\mu}{\sigma}\right)^2}` for $\frac{1}{\sigma\sqrt{2\pi}}e^{-\frac{1}{2}\left(\frac{x-\mu}{\sigma}\right)^2}$ - Poisson Distribution: `P(k; \lambda) = \frac{\lambda^k e^{-\lambda}}{k!}` for $P(k; \lambda) = \frac{\lambda^k e^{-\lambda}}{k!}$ - **Coordinate Systems**: - Spherical Coordinates: `(r, \theta, \phi)` for $(r, \theta, \phi)$ - Cartesian Coordinates: `(x, y, z)` for $(x, y, z)$ - **Geospatial Equations**: - Haversine Formula for Distance: `a = \sin^2\left(\frac{\Delta\phi}{2}\right) + \cos(\phi_1)\cos(\phi_2)\sin^2\left(\frac{\Delta\lambda}{2}\right)` for $a = \sin^2\left(\frac{\Delta\phi}{2}\right) + \cos(\phi_1)\cos(\phi_2)\sin^2\left(\frac{\Delta\lambda}{2}\right)$ Note: The rendering of these equations as formatted math will depend on your Markdown viewer's LaTeX capabilities. ### 7. Effective Citations in Markdown ## Inline Citations - **Objective:** Learn how to use inline citations in Markdown. - **Example Usage:** - Inline citation of a single work: - Some text with an inline citation. [@jones:envstudy:2020] - Inline citation with specific page or section: - More text with a specific section cited. [See @jones:envstudy:2020, §4.2] - Contrasting views: - Discussion of a topic with a contrasting view. [Contra @smith:climatechange:2019, p. 78] ## Footnote Citations - **Objective:** Understand how to use footnote citations in Markdown. - **Example Usage:** - Citing with a footnote: - Some statement in the text.[^1] - Multiple references to the same footnote: - Another statement referring to the same source.[^1] - A different citation: - Additional comment with a new citation.[^2] ## Creating Footnotes - **Example Syntax:** - [^1]: First reference details. Example: Emma Jones, "Environmental Study," Nature Journal, May 2020, https://nature-journal.com/envstudy2020. - [^2]: Second reference details. Example: David Smith, "Climate Change Controversies," Science Daily, August 2019, https://sciencedaily.com/climatechange2019.

Syntax	Example	Reference
# Header	Header	基本排版
- Unordered List	Unordered List
1. Ordered List	Ordered List
- [ ] Todo List	Todo List
> Blockquote	Blockquote
Bold font	Bold font
Italics font	Italics font
~~Strikethrough~~	~~Strikethrough~~
19^th^	19^th
H~2~O	H₂O
++Inserted text++	Inserted text
==Marked text==	Marked text
[link text](https:// "title")	Link
![image alt](https:// "title")	Image
`Code`	`Code`	在筆記中貼入程式碼
```javascript var i = 0; ```	`var i = 0;`
:smile:		Emoji list
{%youtube youtube_id %}	Externals
$L^aT_eX$	L^aT_eX
:::info This is a alert area. :::	This is a alert area.