DDR-Yihui-Xie-Chap1-3.Rnw

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@


\title{Dynamic Documents with R and knitr}


\author{Yihui Xie}

\maketitle
\pagenumbering{gobble}


\chapter*{Note}

\pagenumbering{roman}

\thispagestyle{empty}~

This PDF document only contains the first three chapters, released
with permission of Chapman \& Hall. The complete book is available
on Amazon (\url{http://www.amazon.com/gp/product/1482203537}).

For those who are interested in writing a book with Chapman \& Hall,
the \LyX{} and Rnw source files are freely available in the repository
\url{https://github.com/yihui/knitr-book}. Hopefully this template
can help beginners eliminate 90\% of the possible \LaTeX{} problems,
e.g.,
\begin{itemize}
\item make odd-numbered pages recto, and even-numbered pages verso
\item leave a desired number of blank pages (note that eventually you should
remove this page, since this page is here only for trim marks to be
correctly generated on blank pages)
\item different page numbering styles
\item correct order of the items in the table of contents
\item blank pages after each chapter
\item ...
\end{itemize}
\newpage{}

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\newpage{}

\thispagestyle{empty}~

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\begin{center}
{\Large{To my parents\bigskip{}
}}\\
{\Large{Shaobai Xie }}\emph{\Large{and}}{\Large{ Guolan Xie}}
\par\end{center}{\Large \par}

\newpage{}

\tableofcontents{}


\chapter*{Preface}

\addcontentsline{toc}{chapter}{Preface}We import a dataset into a
statistical software package, run a procedure to get all results,
then copy and paste selected pieces into a typesetting program, add
a few descriptions, and finish a report. This is a common practice
of writing statistical reports. There are obvious dangers and disadvantages
in this process:
\begin{enumerate}
\item it is error-prone due to too much manual work;
\item it requires lots of human effort to do tedious jobs such as copying
results across documents;
\item the workflow is barely recordable especially when it involves GUI
(Graphical User Interface) operations, therefore it is difficult to
reproduce;
\item a tiny change of the data source in the future will require the author(s)
to go through the same procedure again, which can take nearly the
same amount of time and effort;
\item the analysis and writing are separate, so close attention has to be
paid to the synchronization of the two parts.
\end{enumerate}
In fact, a report can be generated dynamically from program code.
Just like a software package has its source code, a dynamic document
is the source code of a report. It is a combination of computer code
and the corresponding narratives. When we compile the dynamic document,
the program code in it is executed and replaced with the output; we
get a final report by mixing the code output with the narratives.
Because we only manage the source code, we are free of all the possible
problems above. For example, we can change a single parameter in the
source code, and get a different report on the fly.

In this book, \emph{dynamic documents} refer to the kind of source
documents containing both program code and narratives. Sometimes we
may just call them \emph{source documents} since ``dynamic'' may
sound confusing and ambiguous to some people (it does not mean interactivity
or animations). We also use the term \emph{report} frequently throughout
the book, which really means the output document compiled from a dynamic
document.


\section*{Who Should Read This Book}

This book is written for both beginners and advanced users. The main
goal is to make writing reports easier: the ``report'' here can
range from student homework or project reports, exams, books, blogs,
and web pages to virtually any documents related to statistical graphics,
computing, and data analysis.

For beginners, Chapter \ref{chap:intro} to \ref{chap:cache} should
be enough for basic applications (which have already covered many
features); for power users, Chapter \ref{chap:reference} to \ref{chap:engines}
can be helpful for understanding the extensibility of the \textbf{knitr}
package.

Familiarity with \LaTeX{} and HTML can be helpful, but is not required
at all; once we get the basic idea, we can write reports in simple
languages such as Markdown. Unless otherwise noted, all features apply
to all document formats, although we primarily use \LaTeX{} for examples.

We recommend the readers to take a look at the Web site RPubs (\url{http://rpubs.com}),
which contains a large number of user-contributed documents. Hopefully
they are convincing enough to show it is quick and easy to write dynamic
documents.


\section*{Software Information and Conventions}

The main tools we introduce in this book are the R language \citep{R-base}
and the \textbf{knitr} package \citep{R-knitr}, with which this book
was written, but the language in the documents is not restricted to
R; for example, we can also integrate Python, awk, and shell scripts,
etc., into the reports. For document formats, we mainly use \LaTeX{},
HTML, and Markdown.

Both R and \textbf{knitr} are available on CRAN (Comprehensive R Archive
Network) as free and open-source software: \url{http://cran.r-project.org}.
Their version information for this book can be found in the session
information:

<<session-info, cache=FALSE>>=
print(sessionInfo(), FALSE)
@

The \textbf{knitr} package is documented on the Web site \url{http://yihui.name/knitr/},
and the most important page is perhaps \url{http://yihui.name/knitr/options},
where we can find the complete reference for chunk options (Section
\ref{sub:chunk-options}). The development version is hosted on Github:
\url{https://github.com/yihui/knitr}; you can always check out the
latest development version, file issues/feature requests, or even
participate in the development by forking the repository and making
changes by yourself. There are plenty of examples in the repository
\url{https://github.com/yihui/knitr-examples}, including both minimal
and advanced examples. There is also a wiki page maintained by Frank
Harrell \emph{et al.} from the Department of Biostatistics, Vanderbilt
University, which introduced several tricks and useful experience
of using \textbf{knitr}: \url{http://biostat.mc.vanderbilt.edu}.

Unlike many other books on R, we do not add prompts to R source code
in this book, and we comment out the text output by two hashes \texttt{\#\#}
by default, as you can see above. The reason for this convention is
explained in Chapter \ref{chap:text}. Package names are in bold text
(e.g., \textbf{rpart}), function names in italic (e.g., \emph{paste()}),
inline code is formatted in a typewriter font (e.g., \texttt{mean(1:10,
trim = 0.1)}), and filenames are in sans serif fonts (e.g., \textsf{figure/foo.pdf}).


\section*{Structure of the Book}

Chapter \ref{chap:intro} is an overview of dynamic documents, introducing
the idea of literate programming; Chapter \ref{chap:rr} explains
why dynamic documents are important to scientific research from the
viewpoint of reproducible research; Chapter \ref{chap:first} gives
a first complete example that covers basic concepts and what we can
do with \textbf{knitr}; Chapter \ref{chap:editors} introduces a few
common text editors that support \textbf{knitr}, so that it is easier
to compile reports from source documents; and Chapter \ref{chap:formats}
describes the syntax for different document formats such as \LaTeX{},
HTML, and Markdown.

Chapter \ref{chap:text} to \ref{chap:engines} explain the core functionality
of the package. Chapter \ref{chap:text} and \ref{chap:graphics}
present how to control text and graphics output from \textbf{knitr},
respectively; Chapter \ref{chap:cache} talks about the caching mechanism
that may significantly reduce the computation time; Chapter \ref{chap:reference}
shows how to reuse source code by chunk references and organize child
documents; Chapter \ref{chap:hooks} consists of an advanced topic
--- chunk hooks, which make a literate programming document really
programmable and extensible; and Chapter \ref{chap:engines} illustrates
how to integrate other languages, such as Python and awk, etc. into
one report in the \textbf{knitr} framework.

Chapter \ref{chap:tricks} introduces some useful tricks that make
it easier to write documents with \textbf{knitr}; Chapter \ref{chap:publish}
shows how to publish reports in a variety of formats including PDF,
HTML, and HTML5 slides; Chapter \ref{chap:applications} covers a
few significant applications; and Chapter \ref{chap:other} introduces
other tools for dynamic report generation, such as Sweave, other R
packages, and software in other languages. Appendix \ref{chap:internals}
is a guide to some internal structures of \textbf{knitr}, which may
be helpful to other package developers.

The topics from Chapter \ref{chap:text} to \ref{chap:engines} are
parallel to each other. For example, if you want to know more about
graphics output, you can skip Chapter \ref{chap:text} and jump to
Chapter \ref{chap:graphics} directly.

In all, we will show how to improve our efficiency in writing reports,
fine tune every aspect of a report, and go from program output to
publication quality reports.


\section*{Acknowledgments}

First, I want to thank my wireless router, which was broken when I
started writing the core chapters of this book (in the boring winter
of Ames). Besides, I also thank my wife for not giving me the Ethernet
cable during that period.

This book would certainly not have been possible without the powerful
R language, for which I thank the R core team and its contributors.
The seminal work of Sweave (by Friedrich Leisch and R-core) is the
most important source of inspiration of \textbf{knitr}. Some additional
features were inspired by other R packages including \textbf{cacheSweave}
(Roger Peng), \textbf{pgfSweave} (Cameron Bracken and Charlie Sharpsteen),
\textbf{weaver} (Seth Falcon), \textbf{SweaveListingUtils} (Peter
Ruckdeschel), \textbf{highlight} (Romain Francois), and \textbf{brew}
(Jeffrey Horner). The initial design was based on Hadley Wickham's
\textbf{decumar} package, and the evaluator is based on his \textbf{evaluate}
package. Both \LyX{} and RStudio quickly included support to \textbf{knitr}
after it came out, which made it a lot easier to write source documents,
and I'd like to thank their developers (especially Jean-Marc Lasgouttes,
JJ Allaire, and Joe Cheng); similarly I thank the developers of other
editors such as Emacs/ESS.

The R/\textbf{knitr} user community is truly amazing. There has been
a lot of feedback since the beginning of its development in late 2011.
I still remember some users shouted it from the rooftops when I released
the first beta version. I appreciate this kind of excitement. Hundreds
of questions and comments in the mailing list (\url{https://groups.google.com/group/knitr})
and on StackOverflow (\url{http://stackoverflow.com/questions/tagged/knitr})
made this package far more powerful than I imagined. The development
repository is on Github, where I have received nearly 500 issues and
more than 50 pull requests (patches) from several contributors (\url{https://github.com/yihui/knitr/pulls}),
including Ramnath Vaidyanathan, Taiyun Wei, and J.J. Allaire.

<<knitr-contributors, eval=FALSE>>=
# to see a full list of contributors
packageDescription('knitr', fields='Authors@R')
@

I thank my PhD advisors at Iowa State University, Di Cook and Heike
Hofmann, for their open-mindedness and consistent support for my research
in this ``non-classical'' area of statistics.

Lastly I thank the reviewers Frank Harrell, Douglas Bates, Carl Boettiger,
Joshua Wiley, and Scott Kostyshak for their valuable advice on improving
the quality of this book (which is the first book of my career), and
I'm grateful to the editor John Kimmel, without whom I would not have
been able to publish my first book quickly.

\begin{flushright}
Yihui Xie\\
Ames, IA
\par\end{flushright}


\chapter*{Author}

\addcontentsline{toc}{chapter}{Author}Yihui Xie (\url{http://yihui.name})
is a PhD student in the Department of Statistics, Iowa State University.
His research interests include interactive statistical graphics and
statistical computing. He is an active R user and the author of several
R packages, such as \textbf{animation}, \textbf{formatR}, \textbf{Rd2roxygen},
and \textbf{knitr}, among which the \textbf{animation} package won
the 2009 John M. Chambers Statistical Software Award (ASA), and the
\textbf{knitr} package was awarded the ``Honorable Mention'' prize
in the ``Applications of R in Business Contest 2012'' thanks to
Revolution Analytics.

In 2006 he founded the ``Capital of Statistics'' (\url{http://cos.name}),
which has grown into a large online community on statistics in China.
He initiated the first Chinese R conference in 2008 and has been organizing
R conferences in China since then. During his PhD training at the
Iowa State University, he won the Vince Sposito Statistical Computing
Award (2011) and the Snedecor Award (2012) in the Department of Statistics.

\cleardoublepage{}

\phantomsection\addcontentsline{toc}{chapter}{List of Figures}\listoffigures


\cleardoublepage{}

\phantomsection\addcontentsline{toc}{chapter}{List of Tables}\listoftables



\chapter{Introduction\label{chap:intro}}

\pagenumbering{arabic}

The basic idea behind dynamic documents stems from \emph{literate
programming}\index{literate programming}, a programming paradigm
conceived by Donald Knuth \citep{knuth1984}. The original idea was
mainly for writing software: mix the source code and documentation
together; we can either extract the source code out (called \emph{tangle}\index{tangle})
or execute the code to get the compiled results (called \emph{weave}\index{weave}).
A dynamic document is not entirely different from a computer program:
for a dynamic document, we need to run software packages to compile
our ideas (often implemented as source code) into numeric or graphical
output, and insert the output into our literal writings (like documentation).

We explain the idea with a trivial example: suppose we need to write
the value of $2\pi$ into a report; of course, we can directly write
the number $\Sexpr{2*pi}$. Now, if I change my mind and I want $6\pi$
instead, I may have to find a calculator, erase the previous value,
and write the new answer. Since it is extremely easy for the computer
to calculate $6\pi$, why not leave this job to the computer completely
and free oneself from this kind of manual work? What we need to do
is to leave the source code in the document instead of a hard-coded
value, and tell the computer how to find and execute the source code.
Usually we use special markers for computer code in the source report,
e.g., we can write
\begin{verse}
\texttt{The correct answer is \{\{ 6 {*} pi \}\}.}
\end{verse}
in which \texttt{\{\{} and \texttt{\}\}} is a pair of markers that
tell the computer \texttt{6 {*} pi} is the source code and should
be executed. Note here \texttt{pi} ($\pi$) is a constant in R.

If you know a web scripting language such as PHP (which can embed
program code into HTML documents), this idea should look familiar.
The above example shows the \emph{inline} code output, which means
source code is mixed inline with a sentence. The other type of output
is the \emph{chunk} output, which gives the results from a whole block
of code. The chunk output has much more flexibility; for example,
we can produce graphics and tables from a code chunk.

Figure \ref{fig:intro-plot} was dynamically created with a chunk
of R code, which is printed below:

\begin{figure}
<<intro-plot, fig.height=2, par=TRUE>>=
set.seed(1213)  # for reproducibility of random numbers
x = cumsum(rnorm(100))
plot(x, type = 'l', ylab = '$x_{i+1}=x_i + \\epsilon_{i+1}$', xlab = 'step')
@

\caption[A simulation of the Brownian motion]{A simulation of the Brownian motion for 100 steps: $x_{1}=\epsilon_{1},\, x_{i+1}=x_{i}+\epsilon_{i+1},\,\epsilon_{i}\protect\overset{iid}{\sim}N(0,1),\, i=1,2,\cdots,100$
\label{fig:intro-plot}}
\end{figure}


If we were to do this by hand, we would have to open R, paste the
code into the R console to draw the plot, save it as a PDF file, and
insert it into a \LaTeX{} document with \texttt{\textbackslash{}includegraphics\{\}}.
This is both tedious for the author and difficult to maintain ---
supposing we want to change the random seed in \emph{set.seed()},
increase the number of steps, or use a scatterplot instead of a line
graph, we will have to update both the source code and the output.
In practice, the computing and analysis can be far more complicated
than the toy example in Figure \ref{fig:intro-plot}, and more manual
work will be required accordingly.

The spirit of dynamic documents may best be described by the philosophy
of the ESS\index{ESS} project \citep{rossini2004} for the S language:

\begin{VF}
The source code is real.

\VA{Philosophy for using ESS[S]}{}

\end{VF}

Since the output can be produced by the source code, we can maintain
the source code only. However, in most cases, the direct output from
the source code alone does not constitute a report that is readable
for a human. That is why we need the literate programming paradigm.
In this paradigm, an author has two tasks:
\begin{enumerate}
\item write program code to do computing, and
\item write narratives to explain what is being done by the program code
\end{enumerate}
The traditional approach to doing the second task is to write comments
for the code, but comments are often limited in terms of expressing
the full thoughts of the authors. Normally we write our ideas in a
paper or a report instead of hundreds of lines of code comments.

\begin{VF}
Let us change our traditional attitude to the construction of programs:
Instead of imagining that our main task is to instruct a computer what to do,
let us concentrate rather on explaining to humans what we want the computer to do.

\VA{Donald E. Knuth}{Literate Programming, 1984}

\end{VF}

Technically, literate programming involves three steps:
\begin{enumerate}
\item parse the source document and separate code from narratives
\item execute source code and return results
\item mix results from the source code with the original narratives
\end{enumerate}
These steps can be implemented in software packages, so the authors
do not need to take care of these technical details. Instead, we only
control what the output should look like. There are many details that
we can tune for a report (especially for reports related to data analysis),
although the idea of literate programming seems to be simple. For
example, data reports often include tables, and Table \ref{tab:intro-table}
is a table generated from the R code below using the \emph{kable()}
function in \textbf{knitr}:

<<intro-table, results='hide', echo=-3>>=
library(knitr)
kable(head(mtcars[,1:6]))
mtcars.tab=kable(head(mtcars[, 1:6]), vline='', toprule=NULL, bottomrule=NULL, output=FALSE)
@

\begin{table}
\caption[A subset of the \texttt{mtcars} dataset]{A subset of the \texttt{mtcars} dataset: the first 6 rows and 6 columns.\label{tab:intro-table}}


\Sexpr{mtcars.tab}
\end{table}


Think how easy it is to maintain two lines of R code compared to maintaining
many lines of messy \LaTeX{} code!

Generating reports dynamically by integrating computer code with narratives
is not only easier, but also closely related to reproducible research,
which we will discuss in the next chapter.


\chapter{Reproducible Research\label{chap:rr}}

Results from scientific research have to be reproducible to be trustworthy.
We do not want a finding to be merely due to an isolated occurrence,
e.g., only one specific laboratory researcher can produce the results
on one specific day, and nobody else can produce the same results
under the same conditions.

\index{reproducible research}Reproducible research (RR) is one possible
by-product of dynamic documents, but dynamic documents do not absolutely
guarantee RR. Because there is usually no human intervention when
we generate a report dynamically, it is likely to be reproducible
since it is relatively easy to prepare the same software and hardware
environment, which is everything we need to reproduce the results.
However, the meaning of reproducibility can be beyond reproducing
one result or one report. As a trivial example, one might have done
a Monte Carlo simulation with a certain random seed and got a good
estimate of a parameter, but the result was actually due to a ``lucky''
random seed\index{random seed}. Although we can strictly reproduce
the estimate, it is not actually reproducible in the general sense.
Similar problems exist in optimization algorithms, e.g., different
starting values can lead to different roots of the same equation.

Anyway, dynamic report generation is still an important step towards
RR. In this chapter, we discuss a selection of the RR literature and
practices of RR.


\section{Literature}

The term reproducible research was first proposed by Jon Claerbout
at Stanford University \citep{fomel2009}. The idea is that the final
product of research is not only the paper itself, but also the full
computational environment used to produce the results in the paper
such as the code and data necessary for reproduction of the results
and building upon the research.

Similarly, \citet{buckheit1995} pointed out the essence of the scholarship
of an article as follows:

\begin{VF}
An article about computational science in a scientific publication
is not the scholarship itself, it is merely advertising of the scholarship.
The actual scholarship is the complete software development environment and
the complete set of instructions which generated the figures.

\VA{D. Donoho}{WaveLab and Reproducible Research}

\end{VF}

That was well said! Fortunately, journals have been moving in that
direction as well. For example, \citet{peng2009} provided detailed
instructions to authors on the criteria of reproducibility and how
to submit materials for reproducing the paper in the \emph{Biostatistics}
journal.

At the technical level, RR is often related to literate programming
\citep{knuth1984}, a paradigm conceived by Donald Knuth to integrate
computer code with software documentation in one document. However,
early implementations like WEB\index{WEB} \citep{knuth1983} and
Noweb\index{Noweb} \citep{ramsey1994} were not directly suitable
for data analysis and report generation. There are other tools on
this path of documentation generation, such as \textbf{roxygen2} \citep{R-roxygen2},
which is an R implementation of Doxygen \citep{heesch2008}. Sweave\index{Sweave}
\citep{leisch2002} was among the first implementations for dealing
with dynamic documents in R \citep{ihaka1996,R-base}. There are still
a number of challenges that were not solved by the existing tools;
for example, Sweave is closely tied to \LaTeX{} and hard to extend.
The \textbf{knitr} package \citep{R-knitr} was built upon the ideas
of previous tools with a framework redesign, enabling easy and fine
control of many aspects of a report. We will introduce other tools
in Chapter \ref{chap:other}.

An overview of literate programming applied to statistical analysis
can be found in \citet{rossini2002}. \citet{gentleman2004} introduced
general concepts of literate programming documents for statistical
analysis, with a discussion of the software architecture. \citet{gentleman2005}
is a practical example based on \citet{gentleman2004}, using an R
package \textbf{GolubRR} to distribute reproducible analysis. \citet{baggerly2004}
revealed several problems that may arise with the standard practice
of publishing data analysis results, which can lead to false discoveries
due to lack of details for reproducibility (even with datasets supplied).
Instead of separating results from computing, we can put everything
in one document (called a \emph{compendium} in \citet{gentleman2004}),
including the computer code and narratives. When we compile this document,
the computer code will be executed, giving us the results directly.


\section{Good and Bad Practices}

The key to keep in mind for RR is that other people should be able
to reproduce our results, therefore we should try our best to make
our computation \emph{portable}. We discuss some good practices for
RR below and explain why it can be bad not to follow them.
\begin{itemize}
\item Manage all source files under the same directory and use relative
paths whenever possible: absolute paths can break reproducibility,
e.g., a data file like \textsf{C:/Users/someone/foo.csv} or \textsf{/home/someone/foo.csv}
may only exist in one computer, and other people may not be able to
read it since the absolute path is likely to be different in their
hard disk. If we keep everything under the same directory, we can
read a data file with \texttt{read.csv('foo.csv')} (if it is under
the current working directory) or \texttt{read.csv('../data/foo.csv')}
(go one level up and find the file under the \textsf{data/} directory);
when we disseminate the results, we can make an archive of the whole
directory (e.g., as a zip package).
\item Do not change the working directory after the computing has started:
\emph{setwd()} is the function in R to set the working directory,
and it is not uncommon to see \texttt{setwd('path/to/some/dir')} in
user's code, which is bad because it is not only an absolute path,
but also has a global effect on the rest of the source document. In
that case, we have to keep in mind that all relative paths may need
adjustments since the root directory has changed, and the software
may write the output in an unexpected place (e.g., the figures are
expected to be generated in the \textsf{./figures/} directory, but
are actually written to \textsf{./data/figures/} instead if we \texttt{setwd('./data/')}).
If we have to set the working directory at all, do it in the very
beginning of an R session; most of the editors to be introduced in
Chapter \ref{chap:editors} follow this rule, and the working directory
is set to the directory of the source document before \textbf{knitr}
is called to compile documents.
\item Compile the documents in a clean R session: existing R objects in
the current R session may ``contaminate'' the results in the output.
It is fine if we write a report by accumulating code chunks one by
one and running them interactively to check the results, but in the
end we should compile a report in the batch mode with a new R session
so all the results are freshly generated from the code.
\item Avoid the commands that require human interaction: human input can
be highly unpredictable, e.g., we do not know for sure which file
the user will choose if we pop up a dialog box asking the user to
choose a data file. Instead of using functions like \emph{file.choose()}
to input a file to \emph{read.table()}, we should write the filename
explicitly, e.g., \texttt{read.table('a-specific-file.txt')}.
\item Avoid environment variables for data analysis: while environment variables
are often heavily used in programming for configuration purposes,
it is ill-advised to use them in data analysis because they require
additional instructions for users to set up, and humans can simply
forget to do this. If there are any options to set up, do it inside
the source document.
\item Attach \emph{sessionInfo()} and instructions on how to compile this
document: the session information makes a reader aware of the software
environment, such as the version of R, the operating system and add-on
packages used. Sometimes it is not as simple as calling one single
function to compile a document, and we have to make it clear how to
compile it if additional steps are required; but it is better to provide
the instructions in the form of a computer script, e.g., a shell script,
a Makefile, or a batch file.
\end{itemize}
These practices are not necessarily restricted to the R language,
although we used R for examples. The same rules also apply to other
computing environments.

Note that literate programming tools often require users to compile
the documents in batch mode, and it is good for reproducible research,
but the batch mode can be cumbersome for exploratory data analysis.
When we have not decided what to put in the final document, we may
need to interact with the data and code frequently, and it is not
worth compiling the whole document each time we update the code. This
problem can be solved by a capable editor such as RStudio and Emacs/ESS,
which are introduced in Chapter \ref{chap:editors}. In these editors,
we can interact with the code and explore the data freely (e.g., send
or write R code in an associated R session), and once we finish the
coding work, we can compile the whole document in the batch mode to
make sure all the code works in a clean R session.


\section{Barriers}

Despite all the advantages of RR, there are some practical barriers,
and here is a non-exhaustive list:
\begin{itemize}
\item the data can be huge: for example, it is common that high energy physics
and next-generation sequencing data in biology can produce tens of
terabytes of data, and it is not trivial to archive the data with
the reports and distribute them
\item confidentiality of data: it may be prohibited to release the raw data
with the report, especially when it is involved with human subjects
due to the confidentiality issues
\item software version and configuration: a report may be generated with
an old version of a software package that is no longer available,
or with a software package that compiles differently on different
operating systems
\item competition: one may choose not release the code or data with the
report due to the fact that potential competitors can easily get everything
for free, whereas the original authors have invested a large amount
of money and effort
\end{itemize}
We certainly should not expect all reports in the world to be publicly
available and strictly reproducible, but it is better to share even
mediocre or flawed code or problematic datasets than not to share
anything at all. Instead of persuading people into RR by policies,
we may try to create tools that make RR easier than cut-and-paste,
and \textbf{knitr} is such an attempt. The success of RPubs\index{RPubs}
(\url{http://rpubs.com}) is evidence that an easy tool can quickly
promote RR, because users enjoy using it. Readers can find hundreds
of reports contributed by users in the above Web site. It is fairly
common to see student homework and exercises there, and once the students
are trained in this manner, we may expect more reproducible scientific
research in the future.


\chapter{A First Look\label{chap:first}}

The \textbf{knitr} package is a general-purpose literate programming
engine --- it supports document formats including \LaTeX{}, HTML,
and Markdown (see Chapter \ref{chap:formats}), and programming languages
such as R, Python, awk, C++, and shell scripts (Chapter \ref{chap:engines}).
Before we get started, we need to install \textbf{knitr} in R. Then
we will introduce the basic concepts with minimal examples. Finally,
we will show how to generate reports quickly from pure R scripts,
which can be useful for beginners who do not know anything about dynamic
documents.


\section{Setup}

Since \textbf{knitr} is an R package, it can be installed from CRAN
in the usual way in R:

<<install-knitr, eval=FALSE>>=
install.packages('knitr', dependencies=TRUE)
@

Note here that \texttt{dependencies = TRUE} is optional, and will
install all packages that are not absolutely necessary but can enhance
this package with some useful features. The development version is
hosted on Github\index{Github}: \url{https://github.com/yihui/knitr},
and you can always check out the latest development version, which
may not be stable but contains the latest bug fixes and new features.
If you have any problems with \textbf{knitr}, the first thing to check
is its version:

<<knitr-version, eval=FALSE>>=
packageVersion('knitr')
# if not the latest version, run
update.packages()
@

If you choose \LaTeX{} as the typesetting tool, you may need to install
MiK\TeX{} (Windows, \url{http://miktex.org/}), Mac\TeX{} (Mac OS,
\url{http://tug.org/mactex/}) or \TeX{}Live (Linux, \url{http://tug.org/texlive/}).
If you are going to work with HTML or Markdown, nothing else needs
to be installed, since the output will be Web pages, which you can
view with a Web browser.

Once we have \textbf{knitr} installed, we can compile source documents
using the function \emph{knit()\index{knit()}}, e.g.,

<<knitr-usage, eval=FALSE>>=
library(knitr)
knit('your-file.Rnw')
@

A \textsf{{*}.Rnw} file is usually a \LaTeX{} document with R code
embedded in it, as we will see in the following section and Chapter
\ref{chap:formats}, in which more types of documents will be introduced.


\section{Minimal Examples}

We use two minimal examples written in \LaTeX{} and Markdown, respectively,
to illustrate the structure of dynamic documents. We do not discuss
the syntax of \LaTeX{} or Markdown for the time being (see Chapter
\ref{chap:formats} instead). For the sake of simplicity, the \texttt{cars}
dataset in base R is used to build a simple linear regression model.
Type \texttt{?cars} in R to see detailed documentation. Basically
it has two variables, speed and distance:

<<str-cars>>=
str(cars)
@


\subsection{An Example in \protect\LaTeX{}}

Figure \ref{fig:minimal-rnw} is a full example of R code embedded
in \LaTeX{}\index{LaTeX@\LaTeX{}}; we call this kind of documents
\emph{Rnw documents\index{Rnw document}} hereafter because their
filename extension is Rnw by convention. If we save it as a file \textsf{minimal.Rnw}
and run \texttt{knit('minimal.Rnw')} in R as described before, \textbf{knitr}
will generate a \LaTeX{} output document named \textsf{minimal.tex}.
For those who are familiar with \LaTeX{}, you can compile this document
to PDF via \texttt{pdflatex}. Figure \ref{fig:minimal-latex} is the
PDF document compiled from the Rnw document.

\begin{figure}
\framebox{\parbox[t]{1\columnwidth}{%
\verbatiminput{knitr-examples/048-cars-demo.Rnw}%
}}

\caption[The source of a minimal Rnw document]{The source of a minimal Rnw document: see output in Figure \ref{fig:minimal-latex}.\label{fig:minimal-rnw}}
\end{figure}


\begin{figure}
\begin{centering}
\framebox{\parbox[t]{1\columnwidth}{%
\begin{center}
\includegraphics[bb=1.7in 2.8500000000000001in 6.7000000000000002in 8.75in,clip,width=1\linewidth]{knitr-examples/048-cars-demo}
\par\end{center}%
}}
\par\end{centering}

\caption[A minimal example in \protect\LaTeX{}]{A minimal example in \protect\LaTeX{} with an R code chunk, a plot, and numeric
output (regression coefficient).\label{fig:minimal-latex}}
\end{figure}


What is essential here is how we embedded R code in \LaTeX{}. In an
Rnw document, \texttt{<\textcompwordmark{}<>\textcompwordmark{}>=}
marks the beginning of code chunks\index{code chunks}, and \texttt{@}
terminates a code chunk (this description is not rigorous but is often
easier to understand); we have four lines of R code between the two
markers in this example to draw a scatterplot, fit a linear model,
and add a regression line to the scatterplot. The command \texttt{\textbackslash{}Sexpr\{\}}
is used to embed inline R code\index{inline R code}, e.g., \texttt{coef(fit){[}2{]}}
in this example. We can write chunk options\index{chunk options}
for a code chunk between \texttt{<\textcompwordmark{}<} and \texttt{>\textcompwordmark{}>=};
the chunk options in this example specified the plot size to be 4
by 3 inches (\texttt{fig.width} and \texttt{fig.height}), and plots
should be aligned in the center (\texttt{fig.align}).

In this minimal example, we have most basic elements of a report:
\begin{enumerate}
\item title, author, and date
\item model description
\item data and computation
\item graphics
\item numeric results
\end{enumerate}
All the output is generated dynamically from R. Even if the data has
changed, we do not need to redo the report from the ground up, and
the output will be updated accordingly if we update the data and recompile
the report.


\subsection{An Example in Markdown\label{sub:minimal-markdown}}

\LaTeX{} may look overwhelming to beginners due to the large number
of commands. By comparison, Markdown\index{Markdown} \citep{markdown}
is a much simpler format. Figure \ref{fig:minimal-rmd} is a Markdown
example doing the same analysis with the previous example:

\begin{figure}
\framebox{\parbox[t]{1\columnwidth}{%
\verbatiminput{knitr-examples/049-cars-demo.Rmd}%
}}

\caption[The source of a minimal Rmd document]{The source of a minimal Rmd document: see output in Figure \ref{fig:minimal-markdown}.\label{fig:minimal-rmd}}
\end{figure}


The ideal output from Markdown is an HTML\index{HTML} Web page, as
shown in Figure \ref{fig:minimal-markdown} (in Mozilla Firefox).
Similarly, we can see the syntax for R code in a Markdown document:
\verb|```{r}| opens a code chunk, \verb|```| terminates a chunk,
and inline R code can be put inside \verb|`r `|, where \verb|`|
is a backtick.

\begin{figure}
\begin{centering}
\includegraphics[interpolate,width=\maxwidth]{figure-shot/minimal-browser}
\par\end{centering}

\caption[A minimal example in Markdown]{A minimal example in Markdown with the same analysis as in Figure
\ref{fig:minimal-latex}, but the output is HTML instead of PDF now.\label{fig:minimal-markdown}}
\end{figure}


A slightly longer example in \textbf{knitr} is a demo named \texttt{notebook}\index{notebook},
which is based on Markdown. It shows not only the potential power
of Markdown, but also the possibility of building Web applications
with \textbf{knitr}. To watch the demo, run the code below:

<<demo-notebook, eval=FALSE>>=
if (!require('shiny')) install.packages('shiny')
demo('notebook', package = 'knitr')
@

Your default Web browser will be launched to show a Web notebook.
The source code is in the left panel, and the live results are in
the right panel. You are free to experiment with the source code and
re-compile the notebook.


\section{Quick Reporting\label{sec:stitch}}

If a user only has basic knowledge of R but knows nothing about \textbf{knitr},
or one does not want to write anything other than an R script, it
is also possible to generate a quick report from this R script using
the \emph{stitch()\index{stitch()}} function.

The basic idea of \emph{stitch()} is that \textbf{knitr} provides
a template of the source document with some default settings, so that
the user only needs to feed this template with an R script (as one
code chunk); then \textbf{knitr} will compile the template to a report.
Currently it has built-in templates for \LaTeX{}, HTML, and Markdown.
The usage is like this:

<<stitch-usage, eval=FALSE>>=
library(knitr)
stitch('your-script.R')
@


\section{Extracting R Code\label{sec:purl-brief}}

For a literate programming document, we can either compile it to a
report (run the code), or extract the program code in it. They are
called ``weaving''\index{weave} and ``tangling\index{tangle},''
respectively. Apparently the function \emph{knit()} is for weaving,
and the corresponding tangling function is \emph{purl()\index{purl()}}
in \textbf{knitr}. For example,

<<purl-usage, eval=FALSE>>=
library(knitr)
purl('your-file.Rnw')
purl('your-file.Rmd')
@

The result of tangling is an R script; in the above examples, the
default output will be \textsf{your-file.R}, which consists of all
code chunks in the source document.

So far we have been introducing the command line usage of \textbf{knitr},
and it is often tedious to type the commands repeatedly. In the next
chapter, we show how a decent editor can help edit and compile the
source document with one single mouse click or a keyboard shortcut.


\chapter{Editors\label{chap:editors}}


\section{RStudio\label{sec:rstudio}}


\section{\protect\LyX{}\label{sec:lyx}}


\section{Emacs/ESS}


\section{Other Editors}


\chapter{Document Formats\label{chap:formats}}


\section{Input Syntax\label{sec:input-syntax}}


\subsection{Chunk Options\label{sub:chunk-options}}


\subsection{Chunk Label}


\subsection{Global Options}


\subsection{Chunk Syntax}


\section{Document Formats}


\subsection{Markdown\label{sub:syntax-markdown}}


\subsection{\protect\LaTeX{}}


\subsection{HTML}


\subsection{reStructuredText\label{sub:reStructuredText}}


\subsection{Customization}


\section{Output Renderers\label{sec:output-renderers}}


\section{R Scripts\label{sec:r-scripts}}


\chapter{Text Output\label{chap:text}}


\section{Inline Output\label{sec:inline-output}}


\section{Chunk Output}


\subsection{Chunk Evaluation}


\subsection{Code Formatting\label{sub:code-formatting}}


\subsection{Code Decoration\label{sub:code-decoration}}


\subsection{Show/Hide Output\label{sub:hide-output}}


\section{Tables}


\section{Themes}


\chapter{Graphics\label{chap:graphics}}


\section{Graphical Devices}


\subsection{Custom Device}


\subsection{Choose a Device}


\subsection{Device Size}


\subsection{More Device Options}


\subsection{Encoding}


\subsection{The Dingbats Font}


\section{Plot Recording\label{sec:plot-recording}}


\section{Plot Rearrangement}


\subsection{Animation\label{sub:animation}}


\subsection{Alignment}


\section{Plot Size in Output\label{sec:plot-size}}


\section{Extra Output Options}


\section{The tikz Device\label{sec:tikz-device}}


\section{Figure Environment}




\section{Figure Path}


\chapter{Cache\label{chap:cache}}


\section{Implementation}


\section{Write Cache}


\section{When to Update Cache\label{sec:cache-update}}


\section{Side Effects\label{sec:side-effects}}


\section{Chunk Dependencies}


\subsection{Manual Dependency}


\subsection{Automatic Dependency}


\chapter{Cross Reference\label{chap:reference}}


\section{Chunk Reference}


\subsection{Embed Code Chunks}


\subsection{Reuse Whole Chunks\label{sub:reuse-whole-chunks}}


\section{Code Externalization\label{sec:code-externalization}}


\subsection{Labeled Chunks}


\subsection{Line-based Chunks\label{sub:read-chunk}}


\section{Child Documents\label{sec:child-documents}}


\subsection{Input Child Documents}


\subsection{Child Documents as Templates}


\subsection{Standalone Mode}


\chapter{Hooks\label{chap:hooks}}


\section{Chunk Hooks}


\subsection{Create Chunk Hooks}


\subsection{Trigger Chunk Hooks}


\subsection{Hook Arguments}


\subsection{Hooks and Chunk Options}


\subsection{Write Output}


\section{Examples}


\subsection{Crop Plots}


\subsection{rgl Plots\label{sub:rgl-plots}}


\subsection{Manually Save Plots}


\subsection{Optimize PNG Plots}


\subsection{Close an rgl Device}


\subsection{WebGL}


\chapter{Language Engines\label{chap:engines}}


\section{Design}


\subsection{The Engine Function}


\subsection{Engine Options}


\section{Languages and Tools}


\subsection{C++\label{sub:C++}}


\subsection{Interpreted Languages}


\subsection{TikZ}


\subsection{Graphviz}


\subsection{Highlight}


\chapter{Tricks and Solutions\label{chap:tricks}}


\section{Chunk Options}


\subsection{Option Aliases\label{sub:option-aliases}}


\subsection{Option Templates\label{sub:option-templates}}


\subsection{Program Chunk Options\label{sub:program-chunk-opts}}


\subsection{Code in Appendix}


\section{Package Options\label{sec:package-options}}


\section{Typesetting}


\subsection{Output Width}


\subsection{Message Colors}


\subsection{Box Padding}


\subsection{Beamer\label{sub:beamer}}


\subsection{Suppress Long Output}


\subsection{Escape Special Characters\label{sub:escape-chars}}


\subsection{The Example Environment}


\section{Utilities}


\subsection{R Package Citation\label{sub:write-bib}}


\subsection{Image URI\label{sub:image-uri}}


\subsection{Upload Images\label{sub:imgur-upload}}


\subsection{Compile Documents}


\subsection{Construct Code Chunks\label{sub:construct-chunks}}


\subsection{Extract Source Code}


\subsection{Reproducible Simulation\label{sub:rand-seed}}


\subsection{R Documentation\label{sub:r-documentation}}


\subsection{Rst2pdf}


\subsection{Package Demos}


\subsection{Pretty Printing}


\subsection{A Macro Preprocessor}


\section{Debugging}


\section{Multilingual Support}


\chapter{Publishing Reports\label{chap:publish}}


\section{RStudio}


\section{Pandoc}


\section{HTML5 Slides}


\section{Jekyll\label{sec:jekyll}}


\section{WordPress}


\chapter{Applications\label{chap:applications}}


\section{Homework}


\section{Web Site and Blogging}


\subsection{Vistat and Rcpp Gallery}


\subsection{UCLA R Tutorial}


\subsection{The cda and RHadoop Wiki}


\subsection{The ggbio Package}


\subsection{Geospatial Data in R and Beyond}


\section{Package Vignettes}


\subsection{PDF Vignette}


\subsection{HTML Vignette}


\section{Books}


\subsection{This Book}


\subsection{The Analysis of Data}


\subsection{The Statistical Sleuth in R}


\chapter{Other Tools\label{chap:other}}


\section{Sweave\label{sec:sweave}}


\subsection{Syntax}


\subsection{Options}


\subsection{Problems}


\section{Other R Packages}


\section{Python Packages}


\subsection{Dexy}


\subsection{Python\protect\TeX{}}


\subsection{IPython}


\section{More Tools}


\subsection{Org-mode}


\subsection{SASweave}


\subsection{Office}

\appendix

\chapter{Internals\label{chap:internals}}


\section{Documentation\label{sec:knitr-documentation}}


\section{Closures}


\section{Implementation}


\subsection{Parser}


\subsection{Chunk Hooks}


\subsection{Option Aliases}


\subsection{Cache}


\subsection{Compatibility with Sweave}


\subsection{Concordance}


\section{Syntax}

<<write-bib, include=FALSE, bib=file.info('cache-book/__packages')[,'size']>>=
write_bib(c(readLines('cache-book/__packages'), 'tikzDevice', 'xtable', 'rgl', 'markdown', 'evaluate', 'formatR', 'R2SWF', 'rggobi', 'Rcpp', 'slidify', 'brew', 'R2HTML', 'corrplot', 'roxygen2', 'Hmisc', 'highr'),
'DDR-packages.bib')
@



\cleardoublepage{}

\bibliographystyle{apalike}
\phantomsection\addcontentsline{toc}{chapter}{\bibname}\bibliography{DDR-Yihui-Xie,DDR-packages}


\printindex{}

\end{document}