R: Check Code/Documentation Consistency

codoc {tools}

R Documentation

Check Code/Documentation Consistency

Description

Find inconsistencies between actual and documented usage of R function objects in a package, by comparing names and optionally also corresponding positions and default values of the arguments of the functions.

Usage

codoc(package, dir, lib.loc = NULL,
      use.values = FALSE, use.positions = TRUE,
      ignore.generic.functions = FALSE,
      verbose = getOption("verbose"))

Arguments

`package`	a character string naming an installed package.
`dir`	a character string specifying the path to a package's root source directory. This must contain the subdirectories ‘man’ with R documentation sources (in Rd format) and ‘R’ with R code. Only used if `package` is not given.
`lib.loc`	a character vector of directory names of R libraries, or `NULL`. The default value of `NULL` corresponds to all libraries currently known. The specified library trees are used to to search for `package`.
`use.positions`	a logical indicating whether to use the positions of function arguments when comparing.
`use.values`	a logical indicating whether to use function default values when comparing code and docs.
`ignore.generic.functions`	if `TRUE`, functions the body of which contains `"UseMethod"` are ignored.
`verbose`	a logical. If `TRUE`, additional diagnostics are printed.

Details

The purpose of this function 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 manipulated in order to give function stubs corresponding to the indicated usage, which are then sourced in another new environment. For interpreted functions in both the code and docs environment, the formals are compared according to the values of the arguments use.positions and use.values.

Currently, synopsis sections are used, but multiple usage examples (such as in abline) are not combined when building the stubs. Occurences of synopsis sections are reported if verbose is true.

Value

An object of class "codoc" which is a list the names of which are the names of the functions where an inconsistency was found. The elements of the list are lists of length 2 with elements code and docs, giving the corresponding arguments obtained from the function's code and documented usage.