Brief presentation to faculty on integrating R and knitr in LaTeX for dynamic document/manuscript generation.

1. Department of!
Psychology!
University of Mary Hardin-Baylor!
Integrating R, knitr,
and LaTeX via
RStudio!
!
Aaron R. Baggett!
February15, 2013!

2. Introduction!
• R is a free, open-source statistical and data visualization
software application
• Open source = large community of developers
• Increasing in popularity
(Muenchen, 2012)
Aaron R. Baggett | 02/15/2013! 2!
R!

3. Introduction!
• Programming language
• Can interface with many other programs
• Object oriented language
a <- 15
b <- 15
a + b
[1] 30
Aaron R. Baggett | 02/15/2013! 3!
R!

4. > Response <- c("Not too happy", "Pretty happy", "Very happy")
> lt20k <- c(17.2, 60.5, 22.2)
> lt49k <- c(13, 56.8, 30.2)
> lt89k <- c(7.7, 50.3, 41.9)
> gt90k <- c(5.3, 51.8, 42.9)
>
> (happy <- data.frame(Response, lt20k, lt49k, lt89k, gt90k))
Response lt20k lt49k lt89k gt90k
1 Not too happy 17.2 13.0 7.7 5.3
2 Pretty happy 60.5 56.8 50.3 51.8
3 Very happy 22.2 30.2 41.9 42.9
> happy$Response <- NULL
> happy
lt20k lt49k lt89k gt90k
1 17.2 13.0 7.7 5.3
2 60.5 56.8 50.3 51.8
3 22.2 30.2 41.9 42.9
>
> (test <- chisq.test(happy))
Pearson's Chi-squared test
data: happy
X-squared = 17.73, df = 6, p-value = 0.00694
> test$expected
lt20k lt49k lt89k gt90k
[1,] 10.79 10.81 10.79 10.81
[2,] 54.82 54.88 54.82 54.88
[3,] 34.28 34.32 34.28 34.32

5. Introduction!
• Flexible and versatile
• 4,336 user contributed packages
o Statistics and data analysis
o Psychometrics
o Graphics
o Economics and finance
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R!

6. Introduction!
• Free graphical user interface (GUI) for R
o http://www.rstudio.com/
o https://twitter.com/rstudioapp
• Still requires use of syntax
o e.g., reg.fit <- lm(y ~ x1 + x2 + x3, data = df)
• Not limited by point and click interface
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RStudio!

7. Introduction!
• Consolidated work environment
o Four window panes
1. R Console
2. Script
3. Workspace
4. Utility tabs
a. Files
b. Plots
c. Packages
d. R Help
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Advantages of RStudio!

9. Introduction!
• Templates for document preparation
o knitr: http://yihui.name/knitr/
o Sweave: http://goo.gl/gMkqo
o R Markdown: http://goo.gl/YHBB1
• LaTeX integration
o knitr works best for me
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Advantages of RStudio!

10. Document Preparation!
• Pronounced “Lah-Tek”
• Document preparation system
• Sections, cross-references, bibliographies
• Equation/math typesetting
• Stability
• Like R, large, active community
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LaTeX http://www.latex-project.org/

11. LaTeX!
documentclass[11pt, oneside]{article}
usepackage{geometry}
geometry{letterpaper}
usepackage[parfill]{parskip}
usepackage{graphicx}
title{Brief Article}
author{The Author}
date{today}
begin{document}
maketitle
%section{}
%subsection{}
end{document}
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Standard Preamble!

12. Brief Article
The Author
February 15, 2013
1

13. Document Preparation!
• Comprehensive package for generating “Elegant,
flexible and fast, dynamic report generation with R.”
• Easily handles embedding R code directly in LaTeX
documents
• Tutorial video from knitr developers:
http://www.screenr.com/qcv8
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knitr!

15. knitr!
• All inline R code begins with: <<>>=
• And ends with: @
Aaron R. Baggett | 02/15/2013! 15!
knitr Code!
<<tidy = TRUE>>=
library(ggplot2)
names(diamonds) #Returns variable names
head(diamonds) #Returns first six rows of dataset
with(diamonds, summary(carat)) #Summarize 'carat' variable
with(diamonds, cor(carat, price)) #Correlate 'carat' and 'price’.
@
<<fig.width = 6, fig.height = 6, tidy = FALSE>>=
qplot(carat, data = diamonds, fill = color, geom = ‘histogram’,
binwidth = 0.4, xlim = c(0,3),
main = ‘Stacked Histogram of Diamond Carat Weight by Color’,
xlab = ‘Carat Weight’, ylab = ‘Count’)
@

16. knitr!
Aaron R. Baggett | 02/15/2013! 16!
knitr Code!
<<box, fig.width=5.5, fig.height=5.5, fig.align='center', tidy=FALSE>>=
plot(Sex, Extrov, main =
"Box-Whisker Plot of Variancen(Extroversion by Sex)”,
col = "dodgerblue3", ylab = "Extroversion")
@
newpage
setlengthparindent{0pt}textbf{large{5). Test to see if there is a
mean difference in Extroversion between males and females (make sure
you test the assumption of homogeneity of variance and set up your t-
test appropriately)}}
vspace*{-.55in}

18. knitr!
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knitr efficiency!

19. Conclusion!
• Efficient document markup
• Dynamic and attractive reports
• Stability
• Open source
• Free
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Benefits!

20. Aaron Baggett!
abaggett@umhb.edu
Aaron R. Baggett | 02/15/2013! 20!
Questions?!