More detailed explanation of Rmarkdown can be found at the RStudio Website or in the pandoc website (which is what R Markdown uses to convert to other documents).

This was the code shown for the session:

YAML Header

R Markdown files should have at the top a YAML header. YAML is just a series of settings to use for the document, like title, author, what document to create (Word, PDF, etc), where your bibliography is located etc.

---
title: "DNS session"
author: "Luke W. Johnston"
date: "November 30, 2016"
bibliography: sample.bib
csl: ama.csl
output: word_document
---

Code chunk

Code chunks allow you to insert R output (like results, plots, tables, numbers, etc) into the document. This is the primary strength of using R Markdown. Use Ctrl-Alt-I to insert a code chunk when using RStudio.

Headers

Inserting a header, such as Introductions or Methods, is easy:

# Header 1

## Header 2

### Header 3

Bolding and italics

To bold use **bold**. To italicize use *italicize*.

Some code used in the session:

library(captioner)
tab_nums <- captioner(prefix = "Table")
tab1 <- tab_nums("tab1", "This is the caption for table 1. Looking at the regression from the swiss dataset.")
#tab1

fig_nums <- captioner(prefix = "Figure")
fig1 <- fig_nums("fig1", "This is a caption for figure 1, showing a scatter plot.")

If you want to see the results, see Table 1.

library(pander)
pander(lm(Fertility ~ Education, data = swiss), caption = tab1, style = 'rmarkdown')

Table: Table 1: This is the caption for table 1. Looking at the regression from the swiss dataset.

Including Plots

You can also embed plots here (see Figure 1), for example:

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.

Inline numbers 70.14

Citations

library(curl)
curl_download("http://codeasmanuscript.github.io/code-along/misc/sample.bib", "sample.bib")
curl_download("https://raw.githubusercontent.com/citation-style-language/styles/master/american-medical-association.csl", "ama.csl")

According to certain authors blah blah [@Lash2007a]

These other authors say … [@An2013a; @Vandenbroucke2007a]

It’s good to have the last header be:

# References

… since the references will be inserted at the end.