session_extra_04.Rmd

---
title: Extra - Project Template
date: "November 5"
output:
  html_document:
    toc: yes
    toc_float: yes
---


```{r setup, include=FALSE}
knitr::opts_chunk$set(comment = "", prompt = TRUE)
set.seed(42)
```

## Project Template

### Why Use a Project Template?

**Your collaborators** and **future you** will thank you:

- Easier to jump into someone else's project

- Easier to share code

- Feel more confident about your results

- Which script did I run to import the data?

- If I update the data, how do I re-run the processing?

- Which script do I tweak to make an adjustment?

- Where did I *get* the data from in the first place?


### What Goes into a Typical Project?

Jump into our [Google Doc whiteboard](https://docs.google.com/document/d/1WXVLBVE3J4EOWhc0m0S2uvTD8HyWiY4BP95OygBEs8Q/edit?usp=sharing).

### Project Principles

1. Use common folder names to put things in a consistent place

1. Never overwrite your source data

1. Document your process with **code** or **words**

1. If you have multiple scripts, use `00_`, `01_`, etc. to indicate the order they should run.

### Project Template Layout

<details><summary>Project Template Starter</summary>

- <i class="em em-open_file_folder"></i> New Project
  - <i class="em em-file_folder"></i> code
  - <i class="em em-open_file_folder"></i> data
    - <i class="em em-file_folder"></i> raw
    - <i class="em em-file_folder"></i> processed
  - <i class="em em-file_folder"></i> deliverable
  - <i class="em em-bookmark_tabs"></i> README.Rmd
    - Analyst and Requester
    - Data Request
    - Document external data sources
    - Document project process

</details>

## Project

Create a new project and use it to complete the following task.

> **Data Request:** The PI would like to know the number of injections by drug that each patient received for injections given starting in 2010.

Use the data from our [Excel sheets of diagnsoses and therapies](session_extra_03.html#data).

```
https://git.io/fpez6
```

<details><summary>Import Data Starter Script</summary>

```r
library(tidyverse)
library(readxl)
library(lubridate)

diagnoses <- read_excel(_____, sheet = "Diagnoses") %>% 
  mutate(`Birth Date` = mdy_hms(`Birth Date`))
  
therapies <- read_excel(_____, sheet = "Therapies")
```

</details>

|    MRN|CHEMOCAT    |  n|
|------:|:-----------|--:|
| 161623|BELIMUMAB   |  2|
| 105705|LEUCOVORIN  |  1|
| 106355|ABARELIX    |  1|
| 133111|CARFILZOMIB |  1|
| 161623|ALEMTUZUMAB |  1|

Table: Example of requested data output.