In Auburngrads/AFIT: Rmarkdown Templates For Academic Documents at Department of Defense Schools

library(knitcitations)
library(RefManageR)
library(xtable)
source('scripts/R/setup.R')
cite_options(citation_format = 'pandoc', 
             cite.style = "numeric")
bib <- read.bibtex('bibtex/my_bib.bib')
berger = citet('10.2307/2291285')
knitc <- citet(citation('knitcitations'))

Introduction

Welcome to Markdown!

\MakeUppercase{fIrSt ThInGs FiRsT} - \underline{this IS your thesis}. As you start writing your document, you will replace this example content with your own. This document is meant to serve as a shell for your thesis and a primer on how to use Markdown. Throughout this document, you will find several references and/or resources showing how to include

• text
• citations & bibliographies
• plots
• images
• tables
• quotes
• acronyms
• glossary terms
• symbols
• equations
• code chunks

What is Markdown and Why Should You Use it?

Markdown is intended to be as easy-to-read and easy-to-write as is feasible. This means that

There are many advantages to building your thesis in Rmarkdown, this paper advantage of r try(berger)

For a quick cheatsheet on how to build an Rmarkdown, you can visit https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf.

Tables

It's really easy to go from a matrix or a data.frame to a \LaTeX-style table in under 5 seconds. For information on how to build a table in R, you can visit http://www.cyclismo.org/tutorial/R/tables.html. The following resource will get you started on how to get your table in R ready for publication https://www.r-bloggers.com/making-publication-ready-tables-with-xtable.

Plots

Plots are a useful way to display data. Building plots in R is quick and easy. The following is an example using the data set mtcars.

plot(mtcars$mpg,mtcars$hp,
     main="Scatterplot",
     xlab="Miles per Gallon", 
     ylab="Horse Power", 
     col="blue")

For a detailed and in depth desriptions on how to make plots, and the different kinds that R is capable of creating, you can visit http://www.statmethods.net/graphs/scatterplot.html.

The ggplot2 package has the ability to offer many more plotting options than the plot() command. You can learn more about ggplot2 by going to http://docs.ggplot2.org/current/ggplot.html. Creating a plot with ggplot2 will allow you to add layers of data to a single plot, which can be helpful in certain situations.

Text

The purpose of this is to show stuff to you. And I want to show you some really cool stuff.

Equations

In-line equations are included within a line of text like this $y=mx^2+b$

Display Equations stand out from the rest of the text:

N <- 30
Y <- rnorm(n = N, sd = 1, mean = 0)
X <- rnorm(n = N, sd = 1, mean = 0)
plot(x = sort(X),
     y = sort(Y), 
     pch = 16,
     col = 'red',
     cex = 1.5,
     las = 1)

text, text, text

model  <- lm(Y~X)
xmodel <- xtable(summary(model), 
                 caption = 'Summary of Model')
print(xmodel, comment = F,
      include.rownames = F,
      caption.placement = 'top')

$$\bar{Y}=\frac{\sum_{i=1}^N Y_i}{N}=\frac{r sum(Y)}{r N}$$

Code Chunks

R gives you the ability to show the code that that was used for any plot, table, or function. You start a code chunk with r** and end a code chunk with **. Let's use the code chunk for building plots above as an example of what you would see in a code chunk.

plot(mtcars$mpg,mtcars$hp,
     main="Scatterplot",
     xlab="Miles per Gallon", ylab="Horse Power", col="blue")

Chunk Options

Code chunks have many options. You might choose to display a code chunk, like above. To do that you would add eval=FALSE. It would look like this ```r. For the purpose of displaying a plot you would add echo=FALSE in which case the code chunk would not be displayed at all. For a function, adding echo=FALSE would print only the answer to the function. For the function 2 + 2, it would look like this:

2+2

For a complete list of code chunk option, you can visit http://rmarkdown.rstudio.com/authoring_rcodechunks.html.

Headings

The purpose of this is to show stuff to you. And I want to show you some really cool stuff.

Quotes

The purpose of this is to show stuff to you. And I want to show you some really cool stuff.

Bibliography

The purpose of this is to show stuff to you. And I want to show you some really cool stuff.

Symbols

The purpose of this is to show stuff to you. And I want to show you some really cool stuff.

Images

The purpose of this is to show stuff to you. And I want to show you some really cool stuff.

Acronyms

The purpose of this is to show stuff to you. And I want to show you some really cool stuff.

Glossary

The purpose of this is to show stuff to you. And I want to show you some really cool stuff.

This template demonstrates some of the basic latex you'll need to know to create a JSS article.

Code formatting

Don't use markdown, instead use the more precise latex commands:

• \proglang{Java}
• \pkg{plyr}
• \code{print("abc")}

R code

This is a quote in markdown

Paragraph.

\begin{quote} This is a quote in \LaTeX \end{quote}

Can be inserted in regular R markdown blocks.

plot(rnorm(100), col = 2, pch = 16, las = 1)

Literature Review

Citing published journal articles

Published articles have a Digital Object Identifier, or doi associated with them. The knitcitations [r try(knitc)] package allows us to easily cite papers by simply providing the doi. Note: This requires an internet connection

Citing published books with an ISBN

ISBN

Methodology

The purpose of this is to show stuff to you. And I want to show you some really cool stuff.

Analysis And Results

The purpose of this is to show stuff to you. And I want to show you some really cool stuff.

Conclusion

write.bibtex(file = 'bibtex/final_bib.bib')

Auburngrads/AFIT documentation built on May 5, 2019, 8:13 a.m.