\HeaderA{codoc}{Check Code/Documentation Consistency}{codoc}
\aliasA{codocClasses}{codoc}{codocClasses}
\aliasA{codocData}{codoc}{codocData}
\aliasA{print.codoc}{codoc}{print.codoc}
\aliasA{print.codocClasses}{codoc}{print.codocClasses}
\aliasA{print.codocData}{codoc}{print.codocData}
\keyword{documentation}{codoc}
\begin{Description}\relax
Find inconsistencies between actual and documented \dQuote{structure}
of \R{} objects in a package.  \code{codoc} compares names and
optionally also corresponding positions and default values of the
arguments of functions.  \code{codocClasses} and \code{codocData}
compare slot names of S4 classes and variable names of data sets,
respectively.
\end{Description}
\begin{Usage}
\begin{verbatim}
codoc(package, dir, lib.loc = NULL,
      use.values = NULL, verbose = getOption("verbose"))
codocClasses(package, lib.loc = NULL)
codocData(package, lib.loc = NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{package}] a character string naming an installed package.
\item[\code{dir}] a character string specifying the path to a package's root
source directory.  This must contain the subdirectories \file{man}
with \R{} documentation sources (in Rd format) and \file{R} with \R{}
code.  Only used if \code{package} is not given.
\item[\code{lib.loc}] a character vector of directory names of \R{} libraries,
or \code{NULL}.  The default value of \code{NULL} corresponds to all
libraries currently known.  The specified library trees are used to
to search for \code{package}.
\item[\code{use.values}] if \code{FALSE}, do not use function default values
when comparing code and docs.  Otherwise, compare \emph{all} default
values if \code{TRUE}, and only the ones documented in the usage
otherwise (default).
\item[\code{verbose}] a logical.  If \code{TRUE}, additional diagnostics are
printed.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The purpose of \code{codoc} is to check whether the documented usage
of function objects agrees with their formal arguments as defined in
the \R{} code.  This is not always straightforward, in particular as the
usage information for methods to generic functions often employs the
name of the generic rather than the method.

The following algorithm is used.  If an installed package is used, it
is loaded (unless it is the base package), after possibly detaching an
already loaded version of the package.  Otherwise, if the sources are
used, the \R{} code files of the package are collected and sourced in a
new environment.  Then, the usage sections of the Rd files are
extracted and parsed \dQuote{as much as possible} to give the formals
documented.  For interpreted functions in the code environment, the
formals are compared between code and documentation according to the
values of the argument \code{use.values}.  Synopsis sections are used
if present; their occurrence is reported if \code{verbose} is true.

If a package has a namespace both exported and unexported objects are
checked, as well as registered S3 methods.  (In the unlikely event of
differences the order is exported objects in the package, registered
S3 methods and finally objects in the namespace and only the first
found is checked.)

Currently, the R documentation format has no high-level markup for the
basic \dQuote{structure} of classes and data sets (similar to the usage
sections for function synopses).  Variable names for data frames in
documentation objects obtained by suitably editing \dQuote{shells}
created by \code{\LinkA{prompt}{prompt}} are recognized by \code{codocData}
and used provided that the documentation object is for a single data
frame (i.e., only has one alias).  \code{codocClasses} analogously
handles slot names for classes in documentation objects obtained by
editing shells created by \code{\LinkA{promptClass}{promptClass}}.

Help files named \code{pkg\_name-defunct.Rd} for the appropriate
\code{pkg\_name} are checked more loosely, as they may have
undocumented arguments.
\end{Details}
\begin{Value}
\code{codoc} returns an object of class \code{"codoc"}.  Currently,
this is a list which, for each Rd object in the package where an
inconsistency was found, contains an element with a list of the
mismatches (which in turn are lists with elements \code{code} and
\code{docs}, giving the corresponding arguments obtained from the
function's code and documented usage).

\code{codocClasses} and \code{codocData} return objects of class
\code{"codocClasses"} and \code{"codocData"}, respectively, with a
structure similar to class \code{"codoc"}.

There are \code{print} methods for nicely displaying the information
contained in such objects.
\end{Value}
\begin{Section}{Warning}
Both \code{codocClasses} and \code{codocData} are still experimental.
Names, interfaces and values might change in future versions.
\end{Section}
\begin{Note}\relax
The default for \code{use.values} has been changed from
\code{FALSE} to \code{NULL}, for \R{} versions 1.9.0 and later.
\end{Note}
\begin{SeeAlso}\relax
\code{\LinkA{undoc}{undoc}}, \code{\LinkA{QC}{QC}}
\end{SeeAlso}

