cm010.Rmd

---
title: "A deep dive into R Markdown"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(cache=TRUE)
```

# cm010 - April 25, 2018

## Overview

* Review the importance of reproducibility in scientific research
* Identify the major components of R Markdown documents
* Explain how to use chunk options to customize output
* Demonstrate the value of caching
* Explain how to include in-line R code
* Introduce the different R Markdown document formats
* Practice writing R scripts (`.R`) versus R Markdown documents (`.Rmd`)

## Before class

* Read chapters 27, 29 in [R for Data Science](http://r4ds.had.co.nz) for more on R Markdown and document formats
* Review [chapter 6](http://r4ds.had.co.nz/workflow-scripts.html) in *R for Data Science* for more info on scripts

## Slides and links

* [Slides](extras/cm010_slides.html)
* [A dive into R Markdown](program_rmarkdown.html)

* [R Markdown](http://rmarkdown.rstudio.com/) - the official site for R Markdown. Lots of great explanations of the different formats and options available for each one.
* [`pipeline-example`](https://github.com/uc-cfss/pipeline-example) - a repo demonstrating how to combine and use R scripts and R Markdown documents. I recommend you fork/clone the repo to your computer, then explore and execute the different files to see how everything works together.

## What you need to do

* [Start homework 5](hw05-reproducible-research.html)