diff --git a/docs/resources/first_meeting_notes.md b/docs/resources/first_meeting_notes.md index 4a7ee2a..b4e16b0 100644 --- a/docs/resources/first_meeting_notes.md +++ b/docs/resources/first_meeting_notes.md @@ -1,434 +1,89 @@ -# Markdown for the Modern Researcher: Efficiency and Clarity +# Primary Meeting 1 -## Introduction +# Day 1-5: Project Kickoff and Strategy -- Overview of Markdown's relevance and utility in modern research. -- How Markdown streamlines documentation in diverse scientific and coding environments. +## Meeting Details +- **Dates:** +- **Times:** +- **Location:** +- **Facilitator:** -## Section 1: Mastering Markdown Syntax +## Attendees +- List of attendees -- **Objective:** Equip researchers with a thorough understanding of Markdown syntax and its diverse applications. -- **Topics Covered:** - - Fundamentals of Text Formatting (headings, lists, bold, italics) - - Advanced Structures (tables, blockquotes) - - Integrating Multimedia (image and video links) - - Diagrams with Mermaid (creating flowcharts, mind maps, timelines) - - 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. +## Daily Agenda -## Section 2: Markdown in Research Tools +### Day 1: Setting the Stage -- **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. +#### Opening Remarks +- Welcoming speech and outline of the week's objectives. -## Section 3: Disseminating Research with Markdown and GitHub Pages +#### Project Overview +- Presentation of the project goals and significance. -- **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. +#### Theoretical Framework +- Discussion on the theoretical underpinnings of the project. -## Conclusion +#### Data Overview +- Review available data and any gaps that need addressing. -- 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. +### Day 2-4: Deep Dives -## Additional Resources +#### Daily Goals +- Outline specific goals for each day. -- Curated list of advanced Markdown tutorials, guides for GitHub Pages, and Jekyll resources for researchers. +#### Task Assignments +- Assign tasks and areas of responsibility to team members. +#### Theory and Data Synthesis +- Host focused discussions on how theory will inform data analysis. +- Explore different methodological approaches and data integration strategies. +#### Evening Social and Soft Work Sessions +- Casual gatherings to further discuss ideas and foster team bonding. +### Day 5: Roadmap and Closure -## Section 1: Mastering Markdown Syntax +#### Project Roadmap +- Draft a detailed plan of action for the project going forward. -### 1. Fundamentals of Text Formatting +#### Responsibilities +- Confirm individual responsibilities and deadlines. -- **Headings**: Use `#` for different levels of headings. - - # Heading Level 1 - - ## Heading Level 2 - - ### Heading Level 3 +#### Review and Feedback +- Reflect on the week's discussions and adjust the project plan as needed. -- **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 +#### Closing Remarks +- Summarize achievements and express appreciation for the team's efforts. -- **Bold and Italics**: Use asterisks or underscores. - - **Bold Text** - - *Italic Text* +## Detailed Notes -### 2. Advanced Structures +### Day 1 Notes +- Summary of discussions, decisions, and key points. -- **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 | +### Day 2 Notes +- ... - - | | | | | | | | | | | | | - |---|---|---|---|---|---|---|---|---|---|---|---| - | 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 | +### Day 3 Notes +- ... - - 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. +### Day 4 Notes +- ... -**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. +### Day 5 Notes +- ... -| | | | | | | | | | -|---|---|---|---|---|---|---|---|---| -| 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 | +## Action Items +- [ ] Specific task: Assigned to - Deadline +- [ ] Specific task: Assigned to - Deadline +- ... +## Reflections and Comments +- (Space for any additional thoughts, insights, or personal reflections on the meeting.) +## Next Steps +- Schedule for follow-up meetings or checkpoints. +- Outline of expected progress before the next primary meeting. - - - - - - - - - - - -
534678912
672195348
198342567
859761423
426853791
713924856
961537284
287419635
345286179
- - - - - -- **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. - - `` - -### 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. - - `` - - - - -### 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. - - +## Additional Documentation +- (Include or link to any additional documents, charts, or resources that were created or referenced during the meeting.) diff --git a/mkdocs.yml b/mkdocs.yml index 9e68ae6..b619479 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -28,9 +28,7 @@ nav: - References: - Notes from readings: resources/notes_from_readings.md - Citations: resources/citations.md - - Manuscript drafts: - - Manuscript: resources/manuscript_1.md - + # Configuration theme: