Introduction to document

Andreas Dominik Cullmann

2018-02-06, 14:02:19

Teaser

Have you ever been tempted to create roxygen2-style documentation comments for one of your functions that was not part of one of your packages (yet)?

This is exactly what this package is about: running roxygen2 on (chunks of) a single code file.

Features

This package enables you to

It does this by creating a temporary package from (the chunks of) your single code file. It runs R CMD check to see if your code and documentation match. For the sake of cpu time on CRAN, I have disabled that check in all examples below by setting check_package = FALSE. You should always stick with the default. This is what this package is about!

Writing Documentation Files to Disk

A Minimal Example

Suppose you have a script

path <- system.file("files", "minimal.R", package = "document")
cat(readLines(path), sep = "\n")
#' Nothing Good For
#'
#' Just prints "foo!".
#' @author Your Name <you@@somewhe.re> 
#' @param x Not needed.
#' @return NULL
#' @export
#' @examples
#' foo(x = 2)
foo <- function(x) {
    print("foo!")
    return(invisible(NULL))
}

#' Uhh
#'
#' Just prints "bar!".
#' @author Your Name <you@@somewhe.re> 
#' @return NULL
#' @export
#' @examples
#' bar()
bar <- function() {
    print("bar!")
    return(invisible(NULL))
}

Then

d <- document::document(file_name = path, check_package = FALSE)

creates a Portable Document Format (pdf) file, an Hypertext Markup Language (html) file and a plain text file. The plain text reads

cat(readLines(d[["txt_path"]]), sep = "\n")
Uhh

Description:

     Just prints "bar!".

Usage:

     bar()
     
Author(s):

     Your Name <you@somewhe.re>

Examples:

     bar()
     

Nothing Good For

Description:

     Just prints "foo!".

Usage:

     foo(x)
     
Arguments:

       x: Not needed.

Author(s):

     Your Name <you@somewhe.re>

Examples:

     foo(x = 2)
     

You can view a copy of the html file here. The pdf file resembles a package’s documentation pdf file.

Checking the code with R CMD check

By default, document checks the temporary package it creates from your code file using R CMD check. The corresponding call would be:

res <- document(file_name = system.file("files", "minimal.R",
                                        package = "document"),
                check_package = TRUE)

After that you could display the check results with:

cat(res[["check_result"]][["output"]][["stdout"]], sep = "\n")
cat(res[["check_result"]][["output"]][["stderr"]], sep = "\n")

A Simple Example

Suppose you have a script

path <- system.file("files", "simple.R", package = "document")
cat(readLines(path), sep = "\n")
#!/usr/bin/Rscript --vanilla
#' \emph{File} simple.R
#'
#' Provide a simple example of a file using roxygen and standard R comments.
#'
#' @author Dominik Cullmann <adc-r@@arcor.de>
#' @note This header will show up in the documentation, but it's got nothing to
#' do with the R statements below. Usually this is not intended.
#' @section Warning: DO NOT CHANGE THE FOLLWOWING THREE LINES.
#' @docType data
#' @name A Header for
NULL
# ROXYGEN_STOP

#% Front Matter
##% load packages
library("methods") # load an example package from the standard library


##% load local code
# This would usually be functions defined and stored away in files.

##% define local functions
# ROXYGEN_START

#' a first function example XXX
#'
#' This really is just an example, the function prints \code{utils::head()} and
#' \code{utils::str()} of the given \code{data.frame}.
#' @author Dominik Cullmann <adc-r@@arcor.de> 
#' @param df Name of a data.frame to ... do whatever needs to be done. 
#' @return NULL. This is no good. 
#' @export
#' @examples
#' data(iris, package = "datasets")
#' a_first_function(iris)
a_first_function <- function(df) {
    message(paste("# Structure of", deparse(substitute(df)), ":"))
    utils::str(df)
    message(paste("# Head of", deparse(substitute(df)), ":"))
    print(utils::head(df))
    return(invisible(NULL))
}
# ROXYGEN_STOP

##% set "global" options
options(warn = 1)

#% Body Matter
##% Load data
data(iris, package = "datasets")

##% Analysize the data
a_first_function(iris)

#% Back Matter

Then you can write documentation using:

d <- document::document(file_name = path, check_package = FALSE)
cat(readLines(d[["txt_path"]]), sep = "\n")
_File_ simple.R

Description:

     Provide a simple example of a file using roxygen and standard R
     comments.

Warning:

     DO NOT CHANGE THE FOLLWOWING THREE LINES.

Note:

     This header will show up in the documentation, but it's got
     nothing to do with the R statements below. Usually this is not
     intended.

Author(s):

     Dominik Cullmann <adc-r@arcor.de>


a first function example XXX

Description:

     This really is just an example, the function prints
     ‘utils::head()’ and ‘utils::str()’ of the given ‘data.frame’.

Usage:

     a_first_function(df)
     
Arguments:

      df: Name of a data.frame to ... do whatever needs to be done.

Value:

     NULL. This is no good.

Author(s):

     Dominik Cullmann <adc-r@arcor.de>

Examples:

     data(iris, package = "datasets")
     a_first_function(iris)
     

Displaying Temporary Help Files

You can display the help page for one of the documented functions using

path <- system.file("files", "minimal.R", package = "document")
document::man(x = path, topic = "foo")
_N_o_t_h_i_n_g _G_o_o_d _F_o_r

_D_e_s_c_r_i_p_t_i_o_n:

     Just prints "foo!".

_U_s_a_g_e:

     foo(x)
     
_A_r_g_u_m_e_n_t_s:

       x: Not needed.

_A_u_t_h_o_r(_s):

     Your Name <you@somewhe.re>

_E_x_a_m_p_l_e_s:

     foo(x = 2)