rmd_mwe.Rmd

---
title: "RMarkdown for writing scientific papers: A minimal working example"
author: "Mike Frank"
date: "`r Sys.Date()`"
output: 
  html_document:
    toc: true
    number_sections: true
bibliography: mwe.bib
---
  
# Introduction

This is a minimal working example of using RMarkdown to write prose with code. 

First load packages. 

```{r}
rm(list=ls())
library(knitr)
library(ggplot2)
```

Now, here are some of the startup options I often use. Caching can be very helpful for large files, but can also cause problems when there are external dependencies that change. 

```{r}
opts_chunk$set(fig.width=8, fig.height=5, 
                      echo=TRUE, warning=FALSE, message=FALSE, cache=TRUE)
```

And you can use various local and glbal chunk options like `echo=FALSE` to suppress showing the code (better for papers). 

# Analysis

Now on to the meat of the analysis. 

## Graphs

It's really easy to include graphs, like this one.

```{r}
qplot(hp, mpg, col = factor(cyl), data = mtcars)
```

## Statistics

It's also really easy to include statistical tests of various types. 

For this I really like the `broom` package, which formats the outputs of various tests really nicely. Paired with knitr's `kable` you can make very simple tables. 

```{r}
library(broom)
mod <- lm(mpg ~ hp + cyl, data = mtcars)
kable(tidy(mod), digits = 3)
```

Of course, cleaning these up can take some work. For example, we'd need to rename a bunch of fields to make this table have the labels we wanted (e.g., to turn `hp` into `Horsepower`). 

I also do a lot of APA-formatted statistics. We can compute them first, and then print them inline.

```{r}
ts <- with(mtcars,t.test(hp[cyl==4], hp[cyl==6]))
```

There's a statistically-significant difference in horsepower for 4- and 6-cylinder cars  ($t(`r  round(ts$parameter,2)`) = `r  round(ts$statistic,2)`$, $p = `r round(ts$p.value,3)`$). To insert these stats inline I wrote e.g. `round(ts$parameter, 2)` inside an inline code block.

Note that rounding can get you in trouble here, because it's very easy to have an output of $p = 0$ when in fact $p$ can never be exactly equal to 0. 

# Conclusions

It's also possible to include references using `bibtex`, by using `@ref` syntax. So in conclusion, and as described by @xie2013dynamic, `knitr` is really amazing! 

# Bibliography