%% LyX 2.3.6 created this file.  For more info, see http://www.lyx.org/.
%% Do not edit unless you really know what you are doing.
\documentclass[american,noae]{scrartcl}
\usepackage{lmodern}
\renewcommand{\sfdefault}{lmss}
\renewcommand{\ttdefault}{cmtt}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{geometry}
\geometry{verbose,tmargin=1in,bmargin=1in,lmargin=1in,rmargin=1in}
\setlength{\parskip}{\smallskipamount}
\setlength{\parindent}{0pt}
\usepackage{color}
\usepackage{babel}
\usepackage{url}
\usepackage{enumitem}
\usepackage[authoryear]{natbib}
\usepackage[unicode=true,pdfusetitle,
 bookmarks=true,bookmarksnumbered=false,bookmarksopen=false,
 breaklinks=true,pdfborder={0 0 0},pdfborderstyle={},backref=section,colorlinks=true]
 {hyperref}
\hypersetup{
 colorlinks=true, linkcolor=darkblue, urlcolor=darkblue, citecolor=darkblue}

\makeatletter
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Textclass specific LaTeX commands.
<<echo=F>>=
  if(exists(".orig.enc")) options(encoding = .orig.enc)
@
\newlength{\lyxlabelwidth}      % auxiliary length 
\newenvironment{lyxcode}
	{\par\begin{list}{}{
		\setlength{\rightmargin}{\leftmargin}
		\setlength{\listparindent}{0pt}% needed for AMS classes
		\raggedright
		\setlength{\itemsep}{0pt}
		\setlength{\parsep}{0pt}
		\normalfont\ttfamily}%
	 \item[]}
	{\end{list}}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands.
%\VignetteIndexEntry{Rstyle}

\usepackage{Sweavel}
\usepackage{graphicx}
\usepackage{color}

\usepackage{babel}
\usepackage[samesize]{cancel}



\usepackage{ifthen}

\makeatletter

\renewenvironment{figure}[1][]{%

 \ifthenelse{\equal{#1}{}}{%
   \@float{figure}
 }{%
   \@float{figure}[#1]%
 }%
 \centering
}{%
 \end@float
}
\renewenvironment{table}[1][]{%
 \ifthenelse{\equal{#1}{}}{%
   \@float{table}
 }{%
   \@float{table}[#1]%
 }%
 \centering
%  \setlength{\@tempdima}{\abovecaptionskip}%
%  \setlength{\abovecaptionskip}{\belowcaptionskip}%
% \setlength{\belowcaptionskip}{\@tempdima}%
}{%
 \end@float
}

% In document Latex options:
\fvset{listparameters={\setlength{\topsep}{0em}}}
\def\Sweavesize{\normalsize} 
\def\Rcolor{\color{black}} 
\def\Rbackground{\color[gray]{0.95}}
\def\Routbackground{\color{white}}
\def\Routcolor{\color{black}}


\usepackage{listings}% Make ordinary listings look as if they come from Sweave
\lstset{tabsize=2, breaklines=true, style=Rstyle}

\usepackage{xcolor}
\definecolor{darkblue}{HTML}{1e2277}

\makeatother

\usepackage{listings}
\renewcommand{\lstlistingname}{\inputencoding{latin9}Listing}

\begin{document}
\title{R Style. An Rchaeological Commentary. }
\author{Paul E. Johnson <pauljohn @ ku.edu>}
\maketitle

\section{Introduction: Ugly Code that Runs}

Because there is no comprehensive official R style manual, students
and package writers seem to think that there is no style whatsoever
to be followed. While it may be true that ``ugly code runs,'' it
is also 1) difficult to read and 2) frustrating to extend, and 3)
tiring to debug. Code is a language, a medium of communication, and
one should not feel free no ignore its customs. 

After students have finished a semester of statistics with R, they
may be ready to start preparing functions or packages. Those R users
are the ones I'm trying to address with this note. It is important
to realize that the readability of code makes a difference. It sometimes
difficult to know that there is a ``right way'' and a ``wrong way''
because there are so many examples to study on CRAN.

This note describes R style from an Rchaeological\footnote{Definitions:
\begin{description}
\item [{Rchaeology:}] The study of R programming by investigation of R
source code. It is the effort to discern the programming strategies,
idioms, and style of R programmers in order to better communicate
with them.
\item [{Rchaeologist:}] One who practices Rchaeology.
\end{description}
} perspective. By examining the work of the R Core Development Team
\citep{RCore} and other notable package writers, we are able to discern
an implicit style guide. However, this note is not ``official''
or endorsed from R Core.\footnote{Yet :)} With one exception at the
end of this note, none of the advice here is ``my'' advice. Instead,
it is my best description of the standards followed by the leading
R programmers. 

At one point, the only guide was the Google R style guide,\footnote{\url{https://google.github.io/styleguide/Rguide.xml}}
which was used as a policy for R-related ``Google Summer of Code''
projects. There are many excellent suggestions in Hadley Wickham's
Style Guide.\footnote{\url{http://adv-r.had.co.nz/Style.html}} In
what follows, I'll try to explain why there are some variations among
these projects and offer some advice about how we (the users) should
sort through their advice.

<<echo=F>>=
dir.create("plots", showWarnings=F)
@

% In document Latex options:
\fvset{listparameters={\setlength{\topsep}{0em}}}
\SweaveOpts{prefix.string=plots/plot,ae=F,height=4,width=6}

<<Roptions, echo=F>>=
options(width=100, continue="+ ")
options(useFancyQuotes = FALSE) 
set.seed(12345)
pdf.options(onefile=F,family="Times",pointsize=12)
@

\section{Rchaeological Methodology}

I am a student of R as a programming language. I am also student of
the R community as an international success that created a working
open source computer program. One of the most interesting differences
between R and other open source projects I have observed is that R
attracts non-programmers. There is an abundance of statistical novices
and untrained computer programmers in the R user community. Many students
begin with R as a way of learning about computer programming. In contrast,
the developers of R are world-class software engineers. They have
formal training in computer programming and years of experience in
a variety of computer languages. The diversity creates a healthy tension
that is easy to see in the r-help email list or on Web forums for
R users. 

\subsection{\textquotedblleft Use the Source, Luke,\textquotedblright{} said Obi-Wan}

What should R code look like? Stop guessing. The implicit style guide
for R is the R source code itself. If users want to communicate with
R Core developers, they ought to communicate using the style that
developers use.

I'm often surprised to find that R users--even experienced ones--have
never looked at the R source code. Before going any further,
\begin{quote}
Open the source code for R. I mean, literally, download R-3.5.2.tar.gz
(or whatever is current when you read this). Unpack that, navigate
to the directory src/library/stats/R. Open the file ``lm.R''. 
\end{quote}
That's what R code should look like. 

Browse other R files in the source code. Notice the files are suffixed
by R, not r! 

Then go read a lot of R packages. Begin with the recommended packages
(in the R source code under src/library/Recommended). Then draw some
samples from CRAN. Choose packages that are prepared by members of
R Core, and then sample a few packages that are widely installed,
such as John Fox's car package \citep{fox_r_2011}. 

After that, pick a random sample of packages on CRAN. Don't be surprised
by ugly code in a randomly chosen R package. 

\subsection{Notice How R Describes its Own Style}

Type the name of a function at the R command prompt. That is the same
as using the function called \inputencoding{latin9}\lstinline!print.function()!\inputencoding{utf8}
to review the contents of a function from an R package. For example,
try ``lm''. The first few lines are\inputencoding{latin9}
\begin{lstlisting}
> lm
function (formula, data, subset, weights, na.action, method = "qr",
    model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE,
    contrasts = NULL, offset, ...)
{
    ret.x <- x
    ret.y <- y
    cl <- match.call()
    mf <- match.call(expand.dots = FALSE)
    m <- match(c("formula", "data", "subset", "weights", "na.action",
        "offset"), names(mf), 0L)
    mf <- mf[c(1L, m)]
    mf$drop.unused.levels <- TRUE
    mf[[1L]] <- as.name("model.frame")
    mf <- eval(mf, parent.frame())
    if (method == "model.frame")
        return(mf)
    else if (method != "qr")
        warning(gettextf("method = '%s' is not supported. Using 'qr'",
            method), domain = NA)
\end{lstlisting}
\inputencoding{utf8}
That's quite a bit like the code in the file lm.R, but it is not exactly
the same. Even if the code in lm.R were an ugly, horrible mess, its
output in the terminal would be indented and spaced just right. That
is an important Rchaeological finding!

Why can there be a difference between the code for a function in a
file (like ``lm.R'') and the output of the command (like ``lm'')?
Admittedly, this is difficult to understand. The on-screen output
is not (by default, anyway) the source that went into R, but rather
it is R's rendition of the internal structure of the function. I recently
had an epiphany while reading a section in the \emph{Writing R Extensions}
manual called ``Tidying R code''. That title is a bit misleading.
It is not about tidying R source code; rather, it is about beautifying
the rendition of internal structures for the terminal. ``R treats
function code loaded from packages and code entered by users differently.
By default code entered by users has the source code stored internally,
and when the function is listed, the original source is reproduced.
Loading code from a package (by default) discards the source code,
and the function listing is re-created from the parse tree of the
function.'' That is to say, if ugly code is syntatically valid, R
can parse it and structure it according to the internal dictates of
the R runtime system, and when we ask to see the function, we get
a nice looking result.

\subsection{Formulate SEA estimates.}

As already noted, there is no mandatory style for R code. The \emph{R
Internals} manual has a section ``R coding standards,'' but it is
quite brief. The main point that most readers take away concerns indentation:
subsections in code should be preceded by 4 blank spaces, not a tab
character. 

But there is a larger point in \emph{R Internals}, but novices don't
recognize the importance of it. R is a GNU project, and there are
GNU coding standards.\footnote{\url{http://www.gnu.org/prep/standards/standards.html}}
The R project's C code follows the standard closely. In the entire
body of the R source code, we find the GNU thumb print. The importance
of that fact is missed by untrained readers, who mistake the lack
of a comprehensive discussion of style for an encouragement to ``do
anything you want.'' 

In the following, I will try to point out the areas of greatest agreement
by assigning an SEA score to each point. SEA stands for ``Subjective
and completely unscientific personal Estimate of Agreement.'' These
are my Bayesian priors. If I could survey my favorite R programmers,
I'd find some variety, and I am trying to make it clear where the
disagreements might lie. But, then again, I may have been fooling
myself. It has recently been suggested to me that these recommendations
are not descriptions of the Rchaeological community I'm studying,
they are rather my personal litmus test for admirable R programmers. 

\section{Nearly Universally accepted standards.}

\subsection{(SEA 1.0) Indentation of code sections is required. }

This is explicitly spelled out in the R documentation. No tabs! Insert
4 blank spaces. Personally, I prefer 2 spaces, which has been the
default in Emacs. But I'm changing my code to use 4 spaces. If you
find my code with 2 spaces, please accept this apology and believe
that it is an oversight. 

\subsection{(SEA .95). Use \textquotedblleft <-\textquotedblright , not \textquotedblleft =\textquotedblright ,
for assignments. }

One cannot find the equal sign used for assignments in any file in
the R source code. Nor can one find it in any of the Recommended packages
(so far as I can tell). 

Students who have learned R in introductory textbooks are sometimes
shocked to learn that they were taught wrong. I'm sympathetic to their
outrage. How can this be? 

The equal sign was used by mistake so frequently that the R system
was re-designed to tolerate that mistake. \emph{Most} usages of the
equal sign for assignments do not cause runtime errors. Not all possible
problems were eliminated, however. Thus the equal sign is not recommended,
it is tolerated. Nevertheless, A horrible profusion of textbooks and
packages ensued using the equal sign for assignment. 

\subsection{(SEA .98) Blank spaces around symbols are required. }

This is a general GNU coding standard. 
\begin{enumerate}
\item Insert spaces before and after 

\begin{enumerate}
\item mathematical symbols like: ``='', ''<-'', ``<'', ``{*}'',
''+''
\item R binary operations like: ``\%{*}\%'', ``\%o\%'', and ``\%in\%''.
\end{enumerate}
\item Put one space after commas. 
\item Insert one space before the opening squiggly braces ``\{''.
\item Put one space after the closing parenthesis ``)'' and the closing
squiggly brace ``\}''.
\end{enumerate}
This is purely a matter of convention and legibility, it does not
affect the ``rightness'' of code. 

Other observations about spaces,
\begin{enumerate}
\item Do not insert spaces between function names and their opening parentheses.
\item After reviewing the R source code, I was uncertain about whether one
ought to insert one space after ``if'' and ``for''. From an Rchaeological
perspective, this is a little bit perplexing. In the help page for
those terms (see help(``for'')), there is no space after ``if''
or ``for''. In the R-3.0.0 source code folder src/library/base/R,
I count 1741 instances of ``if(`` and 683 instances of ``if (``.
The former style seemed right to me, at least at first, because people
often say that R's ``if'' and ``for'' are functions. I asked for
clarification in the R-devel email list, and Peter Dalgaard explained
that the space should be used because those terms are

\begin{quote}
language constructs (and they \emph{are} keywords, not names, that's
why ?for won't work). The function calls are `if`(fee, \{foo\}, \{fie\})
and something rebarbative for `for`(....).

Besides, both constructs are harder to read without the spaces. (r-devel,
April 18, 2013)
\end{quote}
For me, that settles the question. For R code, as in C, ``if'' and
``for'' should be treated as keywords, and there would be a space
after them, as in ``\inputencoding{latin9}\lstinline!if (x < 7)!\inputencoding{utf8}''.
\item Do not insert ``extra spaces'' inside parentheses. 

Programmers who have written in the BASH scripting language may recall
that a space inside brackets is required. That training causes me
to think that R code is a little bit ``jammed together.'' This is
pleasant to my eye:

\inputencoding{latin9}\begin{lstlisting}
if ( (x == 1) & (y == 2) ) {
\end{lstlisting}
\inputencoding{utf8}
but, from an Rchaeological point of view, more the correct style is:

\inputencoding{latin9}\begin{lstlisting}
if((x == 1) & (y == 2)) {
\end{lstlisting}
\inputencoding{utf8}
The insertion of the interior parentheses for the smaller conditions
inside the if statement is consistent with the GNU standard for C.
\end{enumerate}

\subsubsection*{Is there an \textquotedblleft argument exception\textquotedblright{}
to the space rule for equal signs?}

Package writers are not entirely consistent, and Rchaeologically speaking,
we cannot be sure if these variations are accidental. We sometimes
find no spaces, as in

\inputencoding{latin9}\begin{lstlisting}
plot(x, y, lwd=4, col=green, main="My Title")
\end{lstlisting}
\inputencoding{utf8}
It would surely be more correct like so:

\inputencoding{latin9}\begin{lstlisting}
plot(x, y, lwd = 4, col = green, main = "My Title")
\end{lstlisting}
\inputencoding{utf8}
Spaces may sometimes be omitted in an effort to keep code on one line.
Especially where publishers are concerned about the use of scarce
paper, the omission of spaces around equal signs is not uncommon.
Please note, however, that it is NEVER acceptable to omit the spaces
after commas!

\subsubsection*{What about indentation of long function declarations?}

One of the interesting space related questions is the indentation
of function declarations when there are many arguments. Consider the
R source code for the function lm():

\inputencoding{latin9}\begin{lstlisting}
lm <- function (formula, data, subset, weights, na.action,
                method = "qr", model = TRUE, x = FALSE, y = FALSE,
                qr = TRUE, singular.ok = TRUE, contrasts = NULL,
                offset, ...)
\end{lstlisting}
\inputencoding{utf8}
Note that lines 2-4 are indented under the letter ``f'' in formula.
If the function's name were longer, it would push all of that indented
code to the right, probably causing line wraps. The solution is to
put the function's name and the assignment symbol on separate line.
This is the format of R's function plot.lm(). 

\inputencoding{latin9}\begin{lstlisting}
plot.lm <-
function (x, which = c(1L:3L,5L), ## was which = 1L:4L,
          caption = list("Residuals vs Fitted", "Normal Q-Q",
          "Scale-Location", "Cook's distance",
          "Residuals vs Leverage",
          expression("Cook's dist vs Leverage  " * h[ii] / (1 - h[ii]))),
          panel = if(add.smooth) panel.smooth else points,
          sub.caption = NULL, main = "",
          ask = prod(par("mfcol")) < length(which) && dev.interactive(), ...,
          id.n = 3, labels.id = names(residuals(x)), cex.id = 0.75,
          qqline = TRUE, cook.levels = c(0.5, 1.0),
          add.smooth = getOption("add.smooth"),
          label.pos = c(4,2), cex.caption = 1)
{
\end{lstlisting}
\inputencoding{utf8}
The continuation is indented to be below the first argument. The benefit
of this ``declaration by itself'' approach is that the additional
lines are always re-formatted with consistent indentation and we are
not creating a huge empty white space due to indentation.

\subsubsection*{Try formatR::tidy.source()}

The advice so far mostly concerns ``white space''. We would like
a programmer's text editor to handle automatically as much of that
as possible. 

The R package ``formatR'' \citep{formatr} has a function called
tidy.source() which can often (but not always) clean up code. Below
I've pasted in part of an Emacs session. I wrote a badly formatted
function, myfn(), and copied it to the clipboard, and then tidy.source()
reads the clipboard. It works like magic. 

\inputencoding{latin9}\begin{lstlisting}
> myfn <- function(x){ if (x < 7) {i = 77; print(paste("x is less than 7 but i is", i))} else {print("x is excessive") }} 
> library(formatR)
> tidy.source()
function(x) {
    if (x < 7) {
        i = 77
        print(paste("x is less than 7 but i is", i))
    } else {
        print("x is excessive")
    }
}
\end{lstlisting}
\inputencoding{utf8}
The tidy.source() function can get rid of equals sign assignments
if we ask it to. (In my opinion, it should do that by default.)

\inputencoding{latin9}\begin{lstlisting}
> tidy.source(source = "clipboard", replace.assign = TRUE)
function(x) {
    if (x < 7) {
        i <- 77
        print(paste("x is less than 7 but i is", i))
    } else {
        print("x is excessive")
    }
} 
\end{lstlisting}
\inputencoding{utf8}
The tidy.source() function can receive input as files or whole directories.

There are two reasons why tidy.source() is not a panacea. First, by
design, tidy.source() will fail if there are programming errors in
the original source code. That leads to a Catch-22. I want to clean
up the code to find out why it does not run, but tidy.source() cannot
clean it up because it does not run. Second, quite often it happens
that tidy.source() chokes on unexpected user code. Especially problematic
is code that has comments inserted in unexpected places. For example,
I recently ran tidy.source() on the file emb.r in the package Amelia
\citep{Amelia}.

\inputencoding{latin9}\begin{lstlisting}
> library(formatR)
> tidy.source("emb.r")
Error in base::parse(text = text, srcfile = NULL) :
  152:88: unexpected SPECIAL
151: }
152: if (ncol(as.matrix(startvals)) == AMp+1 && nrow(as.matrix(startvals)) == AMp+1)        %InLiNe_IdEnTiFiEr%
                                                                                           ^
\end{lstlisting}
\inputencoding{utf8}
I would estimate that tidy.source() fails on about one-third of the
R code I randomly select from CRAN.

\subsection{(SEA .70) The \textquotedblleft\} else \{\textquotedblright{} policy. }

Did you notice ``\inputencoding{latin9}\lstinline!} else {!\inputencoding{utf8}''
in the \inputencoding{latin9}\lstinline!tidy.source()!\inputencoding{utf8}
output for \inputencoding{latin9}\lstinline!myfn()!\inputencoding{utf8}?
That's the correct style. We should not have the left squiggly brace
``\inputencoding{latin9}\lstinline!}!\inputencoding{utf8}'' on
a separate line from the ``\inputencoding{latin9}\lstinline!else!\inputencoding{utf8},''
and the right squiggly brace ``\inputencoding{latin9}\lstinline!{!\inputencoding{utf8}''
should be on that same line. This is, well, obviously good (in my
opinion).

Why? Try this at the command line. 

\inputencoding{latin9}\begin{lstlisting}
> if (x < 10) print("hello") 
[1] "hello" 
> else print("goodbye") 
Error: unexpected 'else' in "else"
\end{lstlisting}
\inputencoding{utf8}
R does not realize that it is not yet finished with the if keyword's
work. The keyword else appears to begin a new thought, which is illegal.
The if's help page (run \inputencoding{latin9}\lstinline!help("if")!\inputencoding{utf8}
or \inputencoding{latin9}\lstinline!?"if"!\inputencoding{utf8}) is
referring to this problem when it says, 
\begin{quote}
In particular, you should not have a newline between ‘\}’ and ‘else’
to avoid a syntax error in entering a ‘if ... else’ construct at the
keyboard or via ‘source’. For that reason, one (somewhat extreme)
attitude of defensive programming is to always use braces, e.g., for
‘if’ clauses.
\end{quote}
I agree with the somewhat extreme attitude, but will compromise: If
one uses squiggly braces, always follow the ``\inputencoding{latin9}\lstinline!} else {!\inputencoding{utf8}''
policy. 

Some might follow a soft line on this, suggesting only that \textbf{users
should not} \textbf{begin a line with the word else}. That does not
go quite far enough for me. I'd add, \textbf{always use squiggles
after else.} This is simply a way of avoiding a very common coding
error. This code is OK:

\inputencoding{latin9}\begin{lstlisting}
if (x < 7) print("so far, so good") else
print("this is else")
\end{lstlisting}
\inputencoding{utf8}
But it invites a coding error like so:

\inputencoding{latin9}\begin{lstlisting}
if (x < 7) print("so far, so good") else
print("this is else")
print("and we want this also to be with else, but it is not")
\end{lstlisting}
\inputencoding{utf8}
To be perfectly clear, and to protect ourselves against editing errors
in the future, we could follow the ``somewhat extreme'' advice and
write this:

\inputencoding{latin9}\begin{lstlisting}
if (x < 7) {
	print("so far, so good") 
} else {
    print("this is else")
    print("and we want this also to be with else")
}
\end{lstlisting}
\inputencoding{utf8}

\subsubsection*{Counter-argument based on the R source code}

This would be a completely closed case if not for the fact that the
``\inputencoding{latin9}\lstinline!} else {!\inputencoding{utf8}''
policy is ignored in vast expanses of the R source code. In the R
source code, scan for the keyword else and in almost every file, one
finds:

\inputencoding{latin9}\begin{lstlisting}
}
  else
\end{lstlisting}
\inputencoding{utf8}
A naked else! This is frustrating for writers of style guides. It
ignores the advice in the ``if'' help page. We cannot run this code
line-by-line. 

On the other hand, the function that includes that apparently runs!
Why doesn't that code crash? When an if/else statement is enclosed
in a larger area that is demarcated by squiggly braces, then R will
understand the naked else when it finds it. Observe the fix at the
command line:

\inputencoding{latin9}\begin{lstlisting}
> x <- 1
> {
+ if (x < 10) print("hello")
+ else
+ print("My dangling else")
+ }
[1] "hello"
\end{lstlisting}
\inputencoding{utf8}
I don't think I'm going to have any luck persuading the R Core Development
Team that their naked elses need to be fixed. The best I can do is
to urge code writers to use ``\inputencoding{latin9}\lstinline!} else {!\inputencoding{utf8}''
and make them responsible for errors that result from ignoring that
rule. 

One will note another interesting anomaly while reviewing R source
code. Unlike programs written in C, where a consistent style for the
placement of squiggly braces will be followed, in R we observe files
that do not follow a particular rule. In src/library/src/logLik.R,
we find functions in both the K\&R (\citealp{kernighan_c_1988}) C
style

\inputencoding{latin9}\begin{lstlisting}
nobs.logLik <- function(object, ...) {
    res <- attr(object, "nobs")
    if (is.null(res)) stop("no \"nobs\" attribute is available")
    res
}
\end{lstlisting}
\inputencoding{utf8}
and we also find the vertically aligned squiggly braces approach:

\inputencoding{latin9}\begin{lstlisting}
print.logLik <- function(x, digits = getOption("digits"), ...)
{
    cat("'log Lik.' ", paste(format(c(x), digits=digits), collapse=", "),
        " (df=",format(attr(x,"df")),")\n",sep="")
    invisible(x)
}
\end{lstlisting}
\inputencoding{utf8}
I am at a loss to explain these stylistic variations, so I conclude
that R users can follow either style, while keeping in mind the ``\inputencoding{latin9}\lstinline!} else {!\inputencoding{utf8}''
policy, which strongly pushes us toward the K\&R style.

\section{How to name functions.}

Now we begin to consider some issues that are more subjective. Many
styles are legal, but some are more easily understood. R syntax has
changed over the years, and some things that were illegal are now
allowed. And some styles that were standard might now be discouraged. 

\subsection{(.98 SEA) Avoid using names that are already in use by R, especially
common ones.}

Don't write functions named ``\inputencoding{latin9}\lstinline!rep()!\inputencoding{utf8}'',
``\inputencoding{latin9}\lstinline!seq()!\inputencoding{utf8}'',
``\inputencoding{latin9}\lstinline!c()!\inputencoding{utf8}'',
and so forth. Notice that my new function \inputencoding{latin9}\lstinline!lm()!\inputencoding{utf8}
does not obliterate the one from the stats package, but it sure does
make it harder to use it.

\inputencoding{latin9}\begin{lstlisting}
> lm <- function(z) print("Hi, I'm z where lm was")
> x <- rnorm(100)
> y <- rnorm(100)
> lm (y ~ x)
[1] "Hi, I'm z where lm was"
> stats::lm(y ~ x)

Call:
stats::lm(formula = y ~ x)

Coefficients:
(Intercept)            x
    0.02688      0.01796
\end{lstlisting}
\inputencoding{utf8}
As long as we remember that \inputencoding{latin9}\lstinline!lm()!\inputencoding{utf8}
is in the namespace stats, we can find it. 

Similarly, packages can declare namespaces of their own. (Since R
version 2.14, all packages \emph{must} do so.) We are allowed to place
a new function like \inputencoding{latin9}\lstinline!seq()!\inputencoding{utf8}
or \inputencoding{latin9}\lstinline!lm()!\inputencoding{utf8} into
a package if we want to. Nevertheless, almost everybody will hate
to read code like that. 

The danger that user functions might interfere with core functionality
was at one time very serious. Now it is, for the most part, a historical
footnote. It is still possible to obliterate a function that is embedded
within a namespace, but doing so requires a bit of effort and mischief.\footnote{In case you wonder, here's how to cause the worst case scenario.
\begin{lyxcode}
nseq~<-~function(x)~print(\textquotedbl Hello,~good~to~see~you\textquotedbl )

assignInNamespace(\textquotedbl seq.default\textquotedbl ,~nseq,~\textquotedbl base\textquotedbl )
\end{lyxcode}
}

When we say that a namespace is imported, it means that all of the
functions in that namespace can be accessed by the function's name,
without the namespace name as a prefix. We might write \inputencoding{latin9}\lstinline!base::seq(1, 10, length.out = 40)!\inputencoding{utf8}
to be clear, but we need only write \inputencoding{latin9}\lstinline!seq(1, 10, length.out = 40)!\inputencoding{utf8}
because an R session imports the namespace base. I notice a trend
in R to suggest that one should not import whole namespaces unless
that is truly necessary, and even if a namespace is imported, we should
strive for clarity by using syntax that includes the namespace name.
In the source code for many R examples, one will find syntax like
\inputencoding{latin9}\lstinline!graphics::par()!\inputencoding{utf8}
where, until recently, that would have simply been \inputencoding{latin9}\lstinline!par()!\inputencoding{utf8}.

\subsection{(.65 SEA)Use periods to indicate classes, otherwise don't use periods
in function names. }

Instead, use camel case to name functions. This function name \inputencoding{latin9}\lstinline!mySuperThing()!\inputencoding{utf8}
is better than \inputencoding{latin9}\lstinline!my.super.thing()!\inputencoding{utf8}. 

The period in a function name has a special meaning in the S3 object-oriented
framework. A ``generic function'' (such as print() or summary())
is accompanied by methods that implement its work for particular kinds
of objects, such as \inputencoding{latin9}\lstinline!print.function()!\inputencoding{utf8}
or \inputencoding{latin9}\lstinline!print.lm()!\inputencoding{utf8}.
Before the period, we have a function's name, and after the period,
we have the class name of the object being managed. The function name
\inputencoding{latin9}\lstinline!my.super.thing()!\inputencoding{utf8}
suggests the user might have an object of class ``thing'' and that
\inputencoding{latin9}\lstinline!my.super(x)!\inputencoding{utf8}
would diagnose the class of x and send the work to \inputencoding{latin9}\lstinline!my.super.thing()!\inputencoding{utf8}.
A camel cased function name \inputencoding{latin9}\lstinline!mySuperThing()!\inputencoding{utf8}
will not convey the wrong meaning. 

If we were starting with a clean slate, I believe many R functions
would be re-named for the purposes of consistency. Since we do not
have a clean slate, we live with an accumulation of function names
from olde S and R. Changes in computer science--the growth of object-oriented
programming--cause new naming conventions. Consider some of the traditional
S function names that are still used in R, like \inputencoding{latin9}\lstinline!read.table!\inputencoding{utf8}
and \inputencoding{latin9}\lstinline!read.csv!\inputencoding{utf8}.
Those are not method implementations of a generic function read().
The period is simply part of a shorthand of the form ``action.qualifier''.
Otherwise, if one had an object of type table, then read(x) would
call read.table(x). But it does not:

\inputencoding{latin9}\begin{lstlisting}
> example(table)
> class(tab) 
[1] "xtabs" "table"
> read(tab) 
Error: could not find function "read" 
\end{lstlisting}
\inputencoding{utf8}
I believe that, if these functions were being created today, they
would be named \inputencoding{latin9}\lstinline!readTable()!\inputencoding{utf8}
and \inputencoding{latin9}\lstinline!readCSV()!\inputencoding{utf8}. 

In the R source code, there are some very confusing function names
and I have a hard time believing we would use them if we were re-designing
everything today. The file src/library/base/readhttp.R has a function
called \inputencoding{latin9}\lstinline!url.show()!\inputencoding{utf8},
which follows none of the styles that I recognize. There's no class
\inputencoding{latin9}\lstinline!show!\inputencoding{utf8} and \inputencoding{latin9}\lstinline!url()!\inputencoding{utf8}
is not a generic function. In the ``action.qualifier'' tradition,
it would be \inputencoding{latin9}\lstinline!show.url()!\inputencoding{utf8}.
And why not \inputencoding{latin9}\lstinline!showURL()!\inputencoding{utf8}?
I hasten to point out that the same file includes some camel cased
functions like \inputencoding{latin9}\lstinline!defaultUserAgent()!\inputencoding{utf8}.

I like camel cased function names. They are common in Objective-C
and Java. Some programmers vigorously disagree. Programmers trained
in C++ seem to hate camel case names, almost at a visceral level.
As a result, we find a division of opinion on function names. As a
spot check, consider two of my favorite packages, MASS \citep{venables_modern_2002}
and car \citep{fox_r_2011}. There are not many camel case function
names in the MASS, where we find brief names in lower case letters
(such as \inputencoding{latin9}\lstinline!boxcox()!\inputencoding{utf8}).
In contrast, car calls that \inputencoding{latin9}\lstinline!boxCox()!\inputencoding{utf8}.
When I started using R, Professor Fox used function names with periods,
but he has been systematically weeding them out and replacing them
with camel case names. If those two packages are counterbalancing
each other in my mind (for and against camel case functions), the
leading packages for mixed effects models, nlme \citep{pinheiro_nlme:_2012}
and lme4 \citep{lme4}, weigh in on the camel case side of the ledger. 

In conclusion, users should avoid gratuitous periods in function names
because, after S3, the period has special meaning in R. When a function
has been declared as a generic, then that function's name followed
by a period has an object-oriented meaning. A period is not merely
word separation. New functions introduced in R tend to use either
camel case names (\inputencoding{latin9}\lstinline!browseVignettes()!\inputencoding{utf8})
or underscores (\inputencoding{latin9}\lstinline!get_all_vars()!\inputencoding{utf8}).
Considering recent additions to R, I believe that the chance of finding
a decorative period in a new function name is almost zero. But we
are still living with an awful lot of older counter-examples.

\section{How to name variables (and objects).}

\subsection{(1.0 SEA) Follow the \textquotedblleft letters and numbers\textquotedblright{}
rule.}

R variable names must 
\begin{enumerate}
\item begin with an alphabetical character
\item include only letters, numbers and the symbols ``\_'' and ``.''. 
\end{enumerate}
They must not include ``{*}'',''?'',''!'',''\&'' or other
special symbols. They must not include spaces.

One peculiar side effect of this rule is that the ellipsis symbol,
three periods, ``...'', is actually a legal object name. That's
three periods, which is just as legal as aaa or bbb. Many R functions
allow the argument ``...'', most users don't realize it literally
is a word. When that is listed as a function argument, then any argument
that the user includes is gobbled up by ``...''. 

\subsection{(1.0 SEA) Never name a variable T or F. }

Almost everybody (99.999\%) will agree with this. These are too easily
mistaken for TRUE and FALSE values. Since R uses TRUE and FALSE as
vital elements of almost all commands and functions, and since users
are allowed to abbreviate those as T or F, a horrible confusion can
develop if variables are named T or F. 

Here's some good news. R will not allow users to name variables TRUE
or FALSE:

\inputencoding{latin9}\begin{lstlisting}
> TRUE <- 7
Error in TRUE <- 7 : invalid (do_set) left-hand side to assignment
\end{lstlisting}
\inputencoding{utf8}
But R will not prevent the usage of T and F for variable names.

\subsection{(.75 SEA) Avoid declaring variables that have the same names as widely
used functions.}

This is just a handy rule of thumb now, but it used to be a ``watch
out for that tree!'' warning. In 2001, I created a variable ``rep''
(for Republican party members) and nothing worked in my program. In
exasperation, I wrote to the r-help list, and learned that I had obliterated
R's own function \inputencoding{latin9}\lstinline!rep()!\inputencoding{utf8}
with my variable. \inputencoding{latin9}\lstinline!rep()!\inputencoding{utf8}
is used inside many R functions and thus obliterating it was a very
serious mistake. In 2002 or so, the R system was revised so that user-declared
variables cannot ``step on'' R system functions. Nevertheless, it
is disconcerting to me (probably others) when users create variables
with names like ``lm'', ``rep'', ``seq'', and so forth. 

\subsection{(0.50 SEA) Use long names for infrequently used variables. }

And use short names for variables that will be used very often.

If a variable is going to be used twice, we might as well be verbose
about it. ``xlog'' is better than ``xl'', if we are only writing
it a few times. If we are going to use a name 50 times in a 5 line
program, we should choose a short one. For abbreviations, include
a comment to remind the reader what the thing stands for.

\subsection{(0.10 SEA) Suggested naming scheme: keep related objects in an alphabetically
sorted scheme.}

This is my personal naming scheme. Nobody but me follows this policy
now, but I like it so much I'm tacking it onto the end of this essay.
I believe that R code is much more readable if objects that ``go
together'' begin with the common series of letters. As seen by ls(),
the related pieces should always be together. From now on, when I
work with a variable named ``x'', then all transformations will
begin with ``x''. I will use ``xlog'' rather than ``logx'' and
so forth. 

Example 1. Create a numeric variable, recode it as a factor, then
create the ``dummy'' variables that correspond. I include the output
in order to emphasize the clarity due to the alphabetical emphasis:

<<>>=
x <- runif(1000, min = 0, max = 100)
xf <- cut(x, breaks = c(-1, 20, 50, 80, 101), labels = c("cold", "luke", "warm", "hot"))
xfdummies <- contrasts(xf, contrasts = FALSE )[xf,]
colnames(xfdummies) <-  paste("xf", c("cold", "luke", "warm", "hot"), sep="")
rownames(xfdummies) <- names(x)
dat <- data.frame(x, xf, xfdummies)
head(dat)
@

I have not included the output of these code chunks, but the alphabetical
emphasis is demonstrated in them.

Example 2. Estimate a regression, calculate summary information.

<<echo=T, eval=F>>=
set.seed(12345)
x1 <- rnorm(200, m = 300, s = 140)
x2 <- rnorm(200, m = 80, s = 30)
y <- 3 + 0.2 * x1 + 0.4 * x2 + rnorm(200, s=400)
dat <- data.frame(x1, x2, y); rm(x1,x2,y)
m1 <- lm (y ~ x1 + x2, data = dat)
m1summary <- summary(m1)
m1se <- m1summary$sigma
m1rsq <- m1summary$r.squared
m1coef <- m1summary$coef
m1aic <- AIC(m1)
@

Example 3. Run a regression, collect mean-centered and residual centered
variants of it.

<<ps10, fig=T, eval=F, height=5, width=9>>=
library(rockchalk)
dat$y2 = with(dat, 3 + 0.02 * x1 + 0.05 * x2 + 2.65 * x1 *x2 + rnorm(200, s=4000))
par(mfcol=c(1,2))
m1 <- lm(y2 ~ x1 + x2, data = dat)
m1i <- lm(y2 ~ x1 * x2, data = dat)
m1ps <- plotSlopes(m1, plotx = "x1", modx = "x2")
m1ips <- plotSlopes(m1i, plotx = "x1", modx = "x2")
m1imc <- meanCenter(m1i)
m1irc <- residualCenter(m1i)	
@

\section{Conclusion}

R can be understood at several levels, varying in sophistication from
an elementary statistics course or to an advanced platform for the
development of computer programming concepts. In the future, I will
be more cautious to teach new R users about coding style. I intend
to prevent the accumulation of bad habits that result in code that
is difficult to read and hard to debug. 

Users who ask for help in the r-help email list \footnote{\url{http://www.r-project.org/mail.html}}
or on web forums \footnote{e.g., \url{http://stackoverflow.com/questions/tagged/r}}
are well advised to remember the importance of style. Most newcomers
believe that the experts will understand what they write, but that's
not true. Experts will find it much easier to spot errors in code
that has the correct indentation and uses a proper naming scheme for
variables and functions. In my experience, the most likely source
of trouble in R code is not actually the style, but rather poor compartmentalization
of separate calculations. The potential to compartmentalize, however,
is obscured by bad style. 

When users throw together 2000 lines of spaghetti code with no indentation
(I can point to examples on CRAN), there's almost no chance than anyone
except the author will be able to understand and extend that kind
of code. Ugly code writers will respond, ``my ugly code runs!''
That misses the point. Coding style is not about making things ``work,''
it is about making them work in a way that is understood by the widest
possible audience. And where possible, the code should be re-usable
and extended to other purposes. 

\bibliographystyle{chicago}
\bibliography{rockchalk}

\end{document}
