YSI Sweave Tutorial
Ross
2018-08-02
1 The why
Bottom line: Markdown is not LaTeX. It was designed for HTML instead of LaTeX.
(Yihui Xie Explaining Markdown, Pandoc, and LaTeX formatting power on SO )[https://stackoverflow.com/a/17648350/9115822]
2 Get the repo
git clone https://github.com/trendlock/picklerick.git3 Open a .Rnw. file
4 Basics
4.1 Function Syntax
\leads a function{}brackets are used instead of()
A simple form of a sweave document is:
\documentclass{article}
\begin{document}
Text
\end{document}5 Spacing / Page Breaks
In general sweave will behave smartly with images, tables and plots. But there are commands to manually adjust the behaviour.
- {
\clearpage} - plush all material and start a new page - {
\clearpage} - allow to break the line here - {
\newline} - request a new line - {
\newpage} - request a new page - {
\nolinebreak} - no line break should happen here - {
\nopagebreak} - no page break should happen here - {
\pagebreak} - encourage page break
Ie. the following will give two pages with the word Text on them
\documentclass{article}
\begin{document}
Text
\newpage
Text
\end{document}6 Typeface
6.1 Prior to \begin{document}
A font family is selected with :
\usepackage{<fontpkg>}6.2 In Body
Then a certain block of text is assigned a font with the wrapper:
{\fontfamily{<fontcode>}\selectfont <text> }6.3 Example
\documentclass{article}
\usepackage{tgadventor}
\begin{document}
{\fontfamily{qag}\selectfont
This document is a sample document to test font
families and font typefaces.
}
\end{document}
Some examples to choose from:
tibble::tribble(
~Font, ~"fontpkg", ~"fontcode", ~Example,
"Computer Modern Roman", NA, "cmr", "Typeface-cmr.png",
"Latin Modern Roman", "lmodern", "lmr", "Typeface-lmr.png",
"Latin Modern Dunhill", "lmodern", "lmdh", "Typeface-lmdh.png",
"TEX Gyre Termes", "tgtermes", "qtm", "Typeface-qtm.png",
"TEX Gyre Pagella", "tgpagella", "qpl", "Typeface-qpl.png",
"TEX Gyre Bonum", "tgbonum", "qbk", "Typeface-qbk.png",
"TEX Gyre Schola", "tgschola", "qcs", "Typeface-qsc.png",
"Times", "times", "ptm", "Typeface-ptm.png",
"Utopia / Fourier", "utopia / fourier", "put", "Typeface-put.png",
"Palatino", "palatino", "ppl", "Typeface-ppl.png",
"Bookman", "bookman", "pbk", "Typeface-pbk.png",
"Charter", "charter", "bch", "Typeface-bch.png",
"Computer Modern Sans Serif", NA, "cmss", "Typeface-cmss.png",
"Latin Modern Sans Serif", "lmodern", "lmss", "Typeface-lmss.png",
"TEX Gyre Adventor", "tgadventor", "qag", "Typeface-qag.png",
"TEX Gyre Heros", "tgheros", "qhv", "Typeface-qhv.png",
"Helvetica", "helvet", "phv", "Typeface-phv.png",
"Computer Modern Typewriter", NA, "cmtt", "Typeface-cmtt.png",
"Latin Modern Sans Typewriter", "lmodern", "lmtt", "Typeface-lmtt.png",
"TEX Gyre Cursor", "tgcursor", "qcr", "Typeface-qcr.png",
"Courier", "courier", "pcr", "Typeface-pcr.png"
) %>% select(-Example) %>%
kableExtra::kable()| Font | fontpkg | fontcode |
|---|---|---|
| Computer Modern Roman | NA | cmr |
| Latin Modern Roman | lmodern | lmr |
| Latin Modern Dunhill | lmodern | lmdh |
| TEX Gyre Termes | tgtermes | qtm |
| TEX Gyre Pagella | tgpagella | qpl |
| TEX Gyre Bonum | tgbonum | qbk |
| TEX Gyre Schola | tgschola | qcs |
| Times | times | ptm |
| Utopia / Fourier | utopia / fourier | put |
| Palatino | palatino | ppl |
| Bookman | bookman | pbk |
| Charter | charter | bch |
| Computer Modern Sans Serif | NA | cmss |
| Latin Modern Sans Serif | lmodern | lmss |
| TEX Gyre Adventor | tgadventor | qag |
| TEX Gyre Heros | tgheros | qhv |
| Helvetica | helvet | phv |
| Computer Modern Typewriter | NA | cmtt |
| Latin Modern Sans Typewriter | lmodern | lmtt |
| TEX Gyre Cursor | tgcursor | qcr |
| Courier | courier | pcr |
7 Table of Contents
Inserted after \begin{document}:
\tableofcontents
This will build a table of contents for that numbers all \section{} and \subsection{} elements.
8 Margin Control
Adjust:
\usepackage[margin=0.8in]{geometry}9 Footnotes
Footnotes can be inserted with the following function, and are self numbering:
\footnote{A footnote}10 Bibliographies
Now comes the fun… There are a few components to using a bibliography.
10.1 Prior to \begin{document}
Indicating a bib package to use. There are some arguments used here to specify the style of the citations and the sorting of the reference list. This particular combination was used for a report we did.
\usepackage[backend=bibtex, sorting=none, citestyle=authoryear]{biblatex}Alternatively a author - year style would be another typical requirement: citestyle=authoryear.
Documentation on sorting: biblatex 3.1.2
Secondly you must call a function to point to your bibliography file (.bib) which must be in the same directory. In this example my file is called refs.bib.
\bibliography{refs}10.2 In Body
Insert the function at end of your document but before the \end{}.
\printbibliography10.3 References
In the .bib file a reference might look like the following (the which can often be near the paper on google scholar if it is a academic paper, otherwise you will probably have to prepare them yourself):
@article{garland2005,
author={Bill Garland},
title = {Elementary Physics of Reactor Control Module - Fission Product Poisoning},
volume = {3},
url = {http://www.nuceng.ca/br_space/2017-09_4d03_6d03/misc_files/xenon_poisoning.pdf},
publisher = {Nuclear Engineering (Originally from McMaster University)},
year = {2005}
}11 Citations
11.2 Numeric
Try differnt options for numeric citations.
Tip: delete all the temp files in dir to clear bib settings.
\usepackage[backend=bibtex, sorting=none, citestyle=numeric]{biblatex}
12 Page Numbers
Are included by default. To nullify the inclusion of page numbers use:
\pagenumbering{gobble}13 R Chunks in Sweave
13.1 Syntax
Instead of the markdown usage of backticks and curly brackets, sweave uses the following syntax to define a chunk:
<<chunkname>>=
print(mtcars)
@13.2 Setup chunk
<<setup, include=FALSE, cache=FALSE, echo=FALSE>>=
opts_chunk$set(echo=F)
library(<pkgs>)
@13.3 Plotting
<<cars, warning=FALSE, message=F>>=
ggplot(mtcars, aes(disp, mpg, col = as.factor(gear))) +
geom_point()
@14 Using Figures
14.1 R Output
\begin{figure}
<<cars, warning=FALSE, message=F>>=
ggplot(mtcars, aes(disp, mpg, col = as.factor(gear))) +
geom_point()
@
\caption{The relationship between cylinder displacement and miles per gallon for each car.}
\label{fig:Cars}
\end{figure}14.2 Image from file
\begin{figure}
\includegraphics[width=\textwidth]{imgs/morty.jpg}
\caption{A caption about Morty}
\label{fig:morty}
\end{figure}
14.3 Advanced: Two figures side by side with a single caption
\usepackage{graphicx,caption}
\usepackage{subcaption}
\begin{document}
\begin{figure}
\begin{subfigure}{0.5\textwidth}
\includegraphics[width=0.9\linewidth]{imgs/rick.png}
\caption{}
\end{subfigure}
\begin{subfigure}{0.5\textwidth}
\includegraphics[width=0.9\linewidth]{imgs/morty.jpg}
\caption{}
\end{subfigure}
\caption{(a) Rick and (b) Morty}
\label{fig:rickmorty}
\end{figure}15 Referring to figures
Here is a sentence with reference to Figure \ref{fig:rickmorty}.16 Positioning of figures
[h]Place the float here, i.e., approximately at the same point it occurs in the source text (however, not exactly at the spot)[t]Position at the top of the page.[b]Position at the bottom of the page.[p]Put on a special page for floats only.[H]Places the float at precisely the location in the LaTeX code. Requires the float package (\usepackage{float}).
[Source][https://www.sharelatex.com/learn/Positioning_of_Figures]
17 Inline code
\Sexpr{Sys.Date()}(Stands for S expression. S being the precursor to R)