slide.qmd

---
title: "<br><br>- Knowledge Sharing - Data Access and Analysis Library<br>"
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---
## Intro
:::{.standard-slide style="font-size: 20px;"}
- [One Pager](https://loop.cloud.microsoft/p/eyJ1IjoiaHR0cHM6Ly9ibWdmLnNoYXJlcG9pbnQuY29tL3NpdGVzL2lkbWxlYWRlcnNoaXA%2FbmF2PWN6MGxNa1p6YVhSbGN5VXlSbWxrYld4bFlXUmxjbk5vYVhBbVpEMWlKVEl4UWxOYWRrZ3hia0ZtUlV0bFNWOUdNa2xZZWtWclluWlVWREZHWlUwM05VMTBaek5zV1VObmEwTXhTMkp4UzBZM1ZXOUhhMUZNZUd4NFVISlhUMnhtVkNabVBUQXhSRFJPV0VFMFFsTktVa00zUlZkRVEwRkdSRnBVVXpKSVRGUTFXVFpYTlZrbVl6MGxNa1ltWVQxTWIyOXdRWEJ3In0%3D)
<br>
Creating Repository of high-quality codes for data access and analysis, making sharing and understanding easier.
<br>
- [Project Website](https://institutefordiseasemodeling.github.io/data_access_library/)
<br>
![](./assets/slide_intro/dilbert.png){height=50% width=60% align=center}
:::

## Overview
:::{.standard-slide}
::: {.column width="60%" style="font-size: 32px;"}
- Problems and Challenges
- Project Goals and Concepts
- Technology Exploration
    + Quarto: A versatile publishing tool
    + Codespace: A easy-to-use cloud development environment
- Piloting workshop
- Q&A Discussions
:::

::: {.column width="40%" style="height: 100%;"}
<br><br>
![](./assets/slide_intro/salespitch.png){height=100% width=100% align=center}
:::
:::

## Problems / Challenges
:::{.standard-slide}

- **What are barriers to knowledge sharing and why is using Github repo not enough?**
   - Reproducibility
   - Interactivity
   - Collaboration
   - Learning curve

    ![](./assets/slide_intro/git_1.png){height=50% align="center"}
:::

## Data Access and Analysis Library
:::{.standard-slide}

- **Project Goals:**
  + Knowledge Sharing & Collaboration.
  + Reusability & Reproducibility.
  + High-Quality and Comprehensive Code.
  + Multilingual solution (R, Python, Julia etc.)

<br><br>
- **For More Details**
See: [One Pager](https://loop.cloud.microsoft/p/eyJ1IjoiaHR0cHM6Ly9ibWdmLnNoYXJlcG9pbnQuY29tL3NpdGVzL2lkbWxlYWRlcnNoaXA%2FbmF2PWN6MGxNa1p6YVhSbGN5VXlSbWxrYld4bFlXUmxjbk5vYVhBbVpEMWlKVEl4UWxOYWRrZ3hia0ZtUlV0bFNWOUdNa2xZZWtWclluWlVWREZHWlUwM05VMTBaek5zV1VObmEwTXhTMkp4UzBZM1ZXOUhhMUZNZUd4NFVISlhUMnhtVkNabVBUQXhSRFJPV0VFMFFsTktVa00zUlZkRVEwRkdSRnBVVXpKSVRGUTFXVFpYTlZrbVl6MGxNa1ltWVQxTWIyOXdRWEJ3In0%3D)
:::

## Knowledge Sharing <br>with Literate Programming Ideas

::: {.standard-slide style="font-size: 20px;"}
![](./assets/concept.png){height=90% align=right}
<br>
* More about [Donald E. Knuth](https://www-cs-faculty.stanford.edu/~knuth/)
<br>
* More about [Literate Programming](https://en.wikipedia.org/wiki/Literate_programming)
<br><br>
:::

## Technology Exploration
#### Quarto: A versatile publishing tool

:::{.standard-slide style="font-size: 26px;"}

- Why choose Quarto?

    + Open Source, actively developed and maintained by Posit Community.

    + Familiar Syntax & Workflow for Markdown Users.

    + Multilingual, support for R, Python, Javascript, and Julia…

    + Enables reproducible code, rich outputs, and seamless format conversion.

<iframe src="https://rdatatoolbox.github.io/course-quarto/#/literate-programming" width="100%" height="500px" align="center"></iframe>

:::
---

## Technology Exploration
#### Recap of Quarto Features
:::{.standard-slide style="font-size: 26px;"}
![](./assets/slide_intro/slide_7.png){width=50% height=50% align="right"}
<br>

| **Quarto** | **RMarkdown** |**Jupyter Notebook** |
|-------------|-------------|-------------|
| Natively supports Python, R, Julia, [Observable](https://observablehq.com/) and other programming languages. | Primarily uses R for dynamic content.| Python (default) but can extend using jupyter kernels (e.g. IRkernel for R) |
| Offers a wider range of publishing options, including articles, presentations, dashboards, websites, blogs, and books in HTML, PDF, MS Word, ePub, and more.  | Limited publishing format: HTML, PDF, and MS Word. | Need nbconvert to convert to other formats. |
| Supports a variety of authoring tools like [VS Code](https://marketplace.visualstudio.com/items?itemName=quarto.quarto), RStudio, [Jupyter Lab](https://quarto.org/docs/tools/jupyter-lab-extension.html), any text editor that supports markdown (including [Obsidian](https://github.com/danieltomasz/qmd-as-md-obsidian)). | Typically uses RStudio as its primary authoring environment.  |  Primarily designed for Python IDEs |
| Facilitates advanced interactivity with Jupyter Widgets, htmlwidgets for R, Observable JS, and Shiny. Quarto extensions simplifies the usage.  | Offers interactivity but require additional complicated setup. | Interactivity is available but requires extra libraries (ipywidgets, plotly etc). |


:::
## Technology Exploration
#### Quarto Markdown (.qmd) Examples

:::{.standard-slide style="font-size: 32px;"}

````markdown
---
title: "Quarto Document Example with Labeled Code"
author: "John Smith"
date: "2025-02-15"
format: html
---
# Introduction
This document demonstrates Quarto’s R code chunk.

## Basic Calculation Example
This section calculates the mean of a vector.
The code chunk below is labeled as `calculate_mean` for easier reference.

` ` `{r calculate_mean}
#| echo: true
#| eval: false
# This chunk calculates the mean of a vector of numbers
numbers <- c(1, 2, 3, 4, 5)
mean_value <- mean(numbers)
mean_value
` ` `
````
:::

---
## Technology Exploration
#### Control how your code runs: Execution Options

:::{.standard-slide style="font-size: 32px;"}

- `warning=FALSE`: Suppresses warnings.
- `include=FALSE`: Hides code and output but runs the code.
- `echo=FALSE`: Hides code but shows output, useful for report-style documents.
- `eval=FALSE`:Do not run the code. (some code may need special setup or prompts for credentials)

```markdown
` ` `{r warning=FALSE}

OR

` ` `{r}
#| warning: false

` ` `
````
- Check [here](https://quarto.org/docs/computations/execution-options.html) for more options.
:::

## Technology Exploration
#### Quarto Tables
:::{.standard-slide}
![](./assets/slide_intro/qmd_table.png){width=100% align=right}
:::

## Technology Exploration
#### Quarto Figures
:::{.standard-slide}
![](./assets/slide_intro/qmd_figure.png){width=100% height=60% align=right}
:::

## Technology Exploration
#### Quarto callouts
:::{.standard-slide}
![](./assets/slide_intro/qmd_callouts.png){width=100% height=60% align=right}
:::

## Technology Exploration
#### Rstudio Support
:::{.standard-slide}
![](./assets/slide_intro/slide_12.png){width=100% align=right}
:::

## Technology Exploration
#### Quarto for Python
:::{.standard-slide}
::: {.column width="50%"}
- Run Python code in Quarto document. <br>
![](./assets/slide_intro/qmd_python.png){align=right}
:::
::: {.column width="50%"}
- Run Python code in Jupyter notebook. <br>
![](./assets/slide_intro/qmd_jupyter.png){height=80% align=left}
:::
- For more information, visit [Quarto for Python](https://quarto.org/docs/computations/python.html)
- [VS code extension](https://marketplace.visualstudio.com/items?itemName=quarto.quarto) is available.
:::

## Technology Exploration
#### Quarto Extensions
:::{.standard-slide}

<iframe src="https://quarto.org/docs/gallery/" width="100%" height="800px"></iframe>

- For more information, visit [Quarto Extensions](https://quarto.org/docs/extensions/).
:::

## Technology Exploration
#### Reproducibility with Github Codespace
:::{.standard-slide}
![](./assets/slide_intro/c2.png){width=100% height=100% align=center}
:::

## Piloting Workshop
::: {.column width="60%" style="font-size: 26px;"}
- **Date**: 2024-12-10
- Participants tried out using Codespace and learned to use Quarto <br>
![](./assets/slide_intro/cs_usage.png){align=right height=250px}
- Active discussion between participants
    + Need [copilot enabled](https://docs.github.com/en/codespaces/reference/using-github-copilot-in-github-codespaces) IDE to trouble shoot scripts
    + Setup [quarto environment](https://quarto.org/docs/extensions/managing.html) and [package management](https://scientificcoder.com/comparing-package-management-in-python-r-julia-and-rust#heading-overview-table)
    + Need to work with private dataset or large dataset ([Tony Ting's](https://github.com/gatesfoundation/idm-azurestorage-codepsaces-example/) example using Azure blob storage)

:::
::: {.column width="40%"}
![](./assets/slide_intro/beta.png)
:::

## <font size=16px>Some examples contributed by team members participating in the workshop</font><br>
:::{.standard-slide style="font-size: 26px;"}
<details>
  <summary style="cursor: pointer; font-size: 1.2em; font-weight: bold; color: blue;">
    Simple Example using Quarto
  </summary>
  <iframe src="https://institutefordiseasemodeling.github.io/data_access_library/r/samples/simple_plot/simple_plot.html" width="100%" height="400px" style="border: none; margin-top: 10px;"></iframe>
</details>
<details>
  <summary style="cursor: pointer; font-size: 1.2em; font-weight: bold; color: blue;">
    SIR Model Simulation using Jupyter Notebook (Python)
  </summary>
  <iframe src="https://institutefordiseasemodeling.github.io/data_access_library/python/samples/sir/sir_model_simulation.html" width="100%" height="400px" style="border: none; margin-top: 10px;"></iframe>
</details>
<details>
  <summary style="cursor: pointer; font-size: 1.2em; font-weight: bold; color: blue;">
    Ying-yi's R script for visualizing logistic regression model results from Family planning survey
  </summary>
  <iframe src="https://institutefordiseasemodeling.github.io/data_access_library/r/samples/yl_DHS/simple_dhs_fp_plot.html" width="100%" height="400px" style="border: none; margin-top: 10px;"></iframe>
</details>
<details>
  <summary style="cursor: pointer; font-size: 1.2em; font-weight: bold; color: blue;">
    Hil shows a step-by-step data exploration for examining age structure and household age contacts
  </summary>
  <iframe src="https://institutefordiseasemodeling.github.io/data_access_library/r/samples/dhs_examples_pakistan.hl/dhs_example_pakistan_hl.html" width="100%" height="400px" style="border: none; margin-top: 10px;"></iframe>
</details>
<details>
  <summary style="cursor: pointer; font-size: 1.2em; font-weight: bold; color: blue;">
    Amelia used Quarto to create a website for a Data visualization workshop
  </summary>
  <iframe src="https://bertozzivill.github.io/Principles-and-Practice-of-Data-Visualization-in-R/" width="100%" height="400px" style="border: none; margin-top: 10px;"></iframe>
</details>