---
title: Reproducible Research Using Jupyter Notebook
subtitle: Biostat/Biomath M257
author: Dr. Hua Zhou @ UCLA
date: today
format:
  html:
    theme: cosmo
    embed-resources: true
    number-sections: true
    toc: true
    toc-depth: 4
    toc-location: left
    code-fold: false
jupyter:
  jupytext:
    formats: 'ipynb,qmd'
    text_representation:
      extension: .qmd
      format_name: quarto
      format_version: '1.0'
      jupytext_version: 1.14.5
  kernelspec:
    display_name: Julia 1.8.5
    language: julia
    name: julia-1.8
---

> An article about computational science in a scientific publication is **not** the scholarship itself, it is merely **advertising** of the scholarship. The actual scholarship is the complete software development environment and the complete set of instructions which generated the figures.
> 
> -- Buckheit and Donoho (1995)

* For background and history of reproducible research in statistics/data science, see [lecture notes](https://ucla-biostat-203b.github.io/2023winter/slides/03-repres/repres.html) in 203B.

* This course assumes familiarity with Git/GitHub and Jupyter Notebook. Your homework should be authored using Jupyter Notebook and submitted via Git/GitHub.

    For an introduction to Git/GitHub, see [lecture notes](https://ucla-biostat-203b.github.io/2023winter/slides/04-git/git.html) in 203B.

## Jupyter Notebook

* IPython notebook (precursor of Jupyter notebook) is a powerful tool for authoring dynamic document in Python, which combines code, formatted text, math, and multimedia in a single document.  

* [Jupyter](http://jupyter.org) is the current development that emcompasses multiple languages including **Ju**lia, **Pyt**hon, and **R**. 

* Julia uses Jupyter notebook through the [IJulia.jl](https://github.com/JuliaLang/IJulia.jl) package.

* In this course, you are required to write your homework reports using Jupyter Notebook.

* For each homework, you need to submit your Jupyter Notebook (.e.g, `hw1.ipynb`), html (e.g., `hw1.html`), along with all code and data that are necessary to reproduce the results.

* You can start with the Jupyter Notebook for the lectures.  

### Installation

Installing the IJulia.jl package will install a minimal Python/Jupyter distribution that is private to Julia.
```julia
using Pkg
Pkg.add("IJulia")
```
We can also tell IJulia to use a Jupyter program already installed in our system:
```julia
ENV["JUPYTER"] = "path_to_jupyter_executable"
Pkg.build("IJulia")
```

### Usage

* We can invoke Jupyter notebook within Julia by
```julia
using IJulia
notebook() # using home as working directory 
```
or, using current directory as the working directory, by
```julia
notebook(dir = pwd()) # using current directory as working directory 
```

* Notebook can be stopped by hitting `Ctrl+c` in Julia REPL.

* Useful to know some keyboard shortcuts. I frequently use
    * `shift + return`: execute current cell. 
    * `b`: create a cell below current cell.
    * `a`: create a cell above current cell.  
    * `y`: change cell to code.  
    * `m`: change cell to Markdown.  
    Check more shortcuts in menu `Help` -> `Keyboard Shortcuts`.

* **Notebook extensions** offer many utilities for productivity. They can be installed by
```julia
#Pkg.add("Conda")
using Conda
Conda.add_channel("conda-forge")
Conda.add("jupyter_contrib_nbextensions")
```

* Notebook can be **converted to other formats** such as html, LaTeX, Markdown, Julia code, and many others, via menu `File` -> `Download as`. For your homework, please submit both notebook (ipynb) and html.

* **Mathematical formula** can can be typeset as LaTeX in Markdown cells. For example, inline math: $e^{i \pi} + 1 = 0$ and displayed math
$$
    e^x = \sum_{i=0}^\infty \frac{1}{i!} x^i.
$$
For multiline displayed math:
\begin{eqnarray*}
    e^x &=& \sum_{i=0}^\infty \frac{1}{i!} x^i \\
    &\approx& 1 + x + \frac{x^2}{2}.
\end{eqnarray*}

* If you have a lot of commonly used LaTeX macros, put them in a `.tex` file and load them using the notebook extension `Load TeX macros`. 

## JupyterLab

- JupyterLab (more IDE-like) is supposed to replace Jupyter Notebook after it reaches v1.0.

- To invoke JupyterLab:
```julia
using IJulia

jupyterlab() # use home as working directory
```
or
```julia
jupyterlab(dir = pwd()) # use current directory as working directory
```

- To install extensions for JupyterLab, `Settings` -> `Enable Extension Manager (experimental)` then click the extension icon on the left to search, install, and uninstall extensions.

## Quarto

* [Quarto](https://quarto.org/), developed by Posit (formerly RStudio), is an open-source scientific and technical publishing system.

* We can use [Jupytext](https://jupytext.readthedocs.io/en/latest/) to maintain parallel synchronized versions of .qmd and .ipynb files.