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# Writing R Extensions

This is a guide to extending R, describing the process of creating R add-on packages, writing R documentation, R's system and foreign language interfaces, and the R API.

The current version of this document is 1.5.0 (2002-04-29). ISBN 3-901167-54-4

Node:Acknowledgements, Next:, Previous:Top, Up:Top

# Acknowledgements

The contributions of Saikat DebRoy (who wrote the first draft of a guide to using .Call and .External) and of Adrian Trapletti (who provided information on the C++ interface) are gratefully acknowledged.

Node:Creating R packages, Next:, Previous:Acknowledgements, Up:Top

# Creating R packages

Packages provide a mechanism for loading optional code and attached documentation as needed. The R distribution provides several packages, such as eda, mva, and stepfun.

In the following, we assume that you know the library() command, including its lib.loc argument, and we also assume basic knowledge of R CMD INSTALL. Otherwise, please look at R's help pages

?library
?INSTALL


Node:Package structure, Next:, Previous:Creating R packages, Up:Creating R packages

## Package structure

A package consists of a subdirectory containing the files DESCRIPTION and INDEX, and the subdirectories R, data, demo, exec, inst, man, src, and tests (some of which can be missing).

Optionally the package can also contain (Bourne shell) script files configure and cleanup which are executed before and (provided that option --clean was given) after installation on Unix, See Configure and cleanup.

Node:The DESCRIPTION file, Next:, Previous:Package structure, Up:Package structure

### The DESCRIPTION file

The DESCRIPTION file contains basic information about the package in the following format:

Package: pkgname
Version: 0.5-1
Date: 2000-01-04
Title: My first collection of functions
Author: Friedrich Leisch <F.Leisch@ci.tuwien.ac.at>, with
contributions from A. User <A.User@whereever.net>.
Maintainer: Friedrich Leisch <F.Leisch@ci.tuwien.ac.at>
Depends: R (>= 0.99), nlme
Description: A short (one paragraph) description of what
the package does and why it may be useful.
URL: http://www.r-project.org, http://www.another.url


Continuation lines (for example, for descriptions longer than one line) start with a space or tab. The Package, Version, License, Description, Title, Author, and Maintainer fields are mandatory, the remaining fields (Date, Depends, URL, ...) are optional.

The License field should contain an explicit statement or a well-known abbreviation (such as GPL, LGPL, BSD, or Artistic), perhaps followed by a reference to the actual license file. It is very important that you include this information! Otherwise, it may not even be legally correct for others to distribute copies of the package.

The Title field should give a short description of the package and not have any continuation lines. Older versions of R used a separate file TITLE for giving this information; this is now deprecated in favor of using the Title field in file DESCRIPTION file.

The Maintainer field should give a single name with email address in angle brackets (for sending bug reports etc.). It should not end in a period or comma.

The optional URL field may give a list of URLs separated by commas or whitespace, for example the homepage of the author or a page where additional material describing the software can be found. These URLs are converted to active hyperlinks on CRAN.

The optional Depends field gives a comma-separated list of package names which this package depends on. The package name may be optionally followed by a comparison operator (currently only >= and <= are supported) and a version number in parentheses. You can also use the special package name R if your package depends on a certain version of R. E.g., if the package works only with R version 0.90 or newer, include R (>= 0.90) in the Depends field. Future versions of R will use this field to autoload required packages, hence it is an error to use improper syntax or misuse the Depends field for comments on other software that might be needed. Other dependencies (external to the R system) should be listed in the Description field or a separate README file. The R INSTALL facilities already check if the version of R used is recent enough for the package being installed.

Node:The INDEX file, Next:, Previous:The DESCRIPTION file, Up:Package structure

### The INDEX file

The file INDEX contains a line for each sufficiently interesting object in the package, giving its name and a description (functions such as print methods not usually called explicitly might not be included). Note that you can automatically create this file using something like R CMD Rdindex man > INDEX, provided that Perl (5.005 or later) is available on your system, or use the package builder (see Checking and building packages) to do so.

Node:Package subdirectories, Next:, Previous:The INDEX file, Up:Package structure

### Package subdirectories

The R subdirectory contains R code files. The code files to be installed must start with a (lower or upper case) letter and have one of the extensions .R, .S, .q, .r, or .s. We recommend using .R, as this extension seems to be not used by any other software. It should be possible to read in the files using source(), so R objects must be created by assignments. Note that there need be no connection between the name of the file and the R objects created by it. If necessary, one of these files (historically zzz.R) should use library.dynam() inside .First.lib() to load compiled code.

The man subdirectory should contain documentation files for the objects in the package in R documentation (Rd) format. The documentation files to be installed must also start with a (lower or upper case) letter and have the extension .Rd (the default) or .rd. See Writing R help files, for more information. Note that all user-level objects in a package should be documented; if a package pkg contains user-level objects which are for "internal" use only, it should provide a file pkg-internal.Rd which documents all such objects, and clearly states that these are not meant to be called by the user. See e.g. the sources for package modreg in the R distribution for an example.

The R and man subdirectories may contain OS-specific subdirectories named unix, windows or mac.

The C, C++, or FORTRAN1 source files for the compiled code are in src, plus optionally file Makevars or Makefile. When a package is installed using R CMD INSTALL, Make is used to control compilation and linking into a shared library for loading into R. There are default variables and rules for this (determined when R is configured and recorded in R_HOME/etc/Makeconf). These rules can be tweaked by setting macros in a file src/Makevars (see Using Makevars). Note that this mechanism should be general enough to eliminate the need for a package-specific Makefile. If such a file is to be distributed, considerable care is needed to make it general enough to work on all R platforms. In addition, it should have a target clean which removes all files generated by Make. If necessary, platform-specific files can be used, for example Makevars.win or Makefile.win on Windows take precedence over Makevars or Makefile.

The data subdirectory is for additional data files the package makes available for loading using data(). Currently, data files can have one of three types as indicated by their extension: plain R code (.R or .r), tables (.tab, .txt, or .csv), or save() images (.RData or .rda). (As from R 1.5.0 one can assume that all ports of R have the same binary (XDR) format and can read compressed images. For portability to earlier versions use images saved with save(, ascii = TRUE, version = 1).) Note that R code should be "self-sufficient" and not make use of extra functionality provided by the package, so that the data file can also be used without having to load the package. The data subdirectory should also contain a 00Index file that describes the datasets available. Ideally this should have a one-line description of each dataset, with full documentation in the man directory. Note that you can automatically create this file using something like R CMD Rdindex --data man > data/00Index, provided that Perl (5.005 or later) is available on your system, or use the package builder (see Checking and building packages) to do so.

The demo subdirectory is for R scripts (for running via demo()) which demonstrate some of the functionality of the package. The script files must start with a (lower or upper case) letter and have one of the extensions .R or .r. If present, the demo subdirectory should also have a 00Index file, see above. (Note that it is currently not possible to generate this index file automatically.)

The contents of the inst subdirectory will be copied recursively to the installation directory.

Subdirectory tests is for additional package-specific test code, similar to the specific tests that come with the R distribution. Test code can either be provided directly in a .R file, or via a .Rin file containing code which in turn creates the corresponding .R file (e.g., by collecting all function objects in the package and then calling them with the strangest arguments). The results of running a .R file are written to a .Rout file. If there is a corresponding .Rout.save file, these two are compared, with differences being reported but not causing an error.

Finally, exec could contain additional executables the package needs, typically scripts for interpreters such as the shell, Perl, or Tcl. This mechanism is currently used only by a very few packages, and still experimental.

Node:Package bundles, Previous:Package subdirectories, Up:Package structure

### Package bundles

Sometimes it is convenient to distribute several packages as a bundle. (The main current example is VR which contains four packages.) The installation procedures on both Unix and Windows can handle package bundles.

The DESCRIPTION file of a bundle has an extra Bundle field, as in

Bundle: VR
Contains: MASS class nnet spatial
Version: 6.1-6
Date: 1999/11/26
Author: S original by Venables & Ripley.
R port by Brian Ripley <ripley@stats.ox.ac.uk>, following
earlier work by Kurt Hornik and Albrecht Gebhardt.
BundleDescription: Various functions from the libraries of
Venables and Ripley, Modern Applied Statistics with S-PLUS'
(3rd edition).
License: GPL (version 2 or later)


The Contains field lists the packages, which should be contained in separate subdirectories with the names given. These are standard packages in all respects except that the DESCRIPTION file is replaced by a DESCRIPTION.in file which just contains fields additional to the DESCRIPTION file of the bundle, for example

Package: spatial
Description: Functions for kriging and point pattern analysis.


Node:Configure and cleanup, Next:, Previous:Package structure, Up:Creating R packages

## Configure and cleanup

Note that most of this section is Unix-specific: see the comments later on about the Windows and classic MacOS ports of R.

If your package needs some system-dependent configuration before installation you can include a (Bourne shell) script configure in your package which (if present) is executed by R CMD INSTALL before any other action is performed. This can be a script created by the autoconf mechanism, but may also be a script written by yourself. Use this to detect if any nonstandard libraries are present such that corresponding code in the package can be disabled at install time rather than giving error messages when the package is compiled or used. To summarize, the full power of Autoconf is available for your extension package (including variable substitution, searching for libraries, etc.).

The (Bourne shell) script cleanup is executed as last thing by R CMD INSTALL if present and option --clean was given, and by R CMD build when preparing the package for building from its source. It can be used to clean up the package source tree. In particular, it should remove all files created by configure.

As an example consider we want to use functionality provided by a (C or FORTRAN) library foo. Using autoconf, we can write a configure script which checks for the library, sets variable HAVE_FOO to TRUE if it was found and with FALSE otherwise, and then substitutes this value into output files (by replacing instances of @HAVE_FOO@ in input files with the value of HAVE_FOO). For example, if a function named bar is to be made available by linking against library foo (i.e., using -lfoo), one could use

AC_CHECK_LIB(foo, fun, [HAVE_FOO=TRUE], [HAVE_FOO=FALSE])
AC_SUBST(HAVE_FOO)
......
AC_CONFIG_FILES([foo.R])
AC_OUTPUT


in configure.ac (assuming Autoconf 2.50 or better).

The definition of the respective R function in foo.R.in could be

foo <- function(x) {
if(!@HAVE_FOO@) stop("Sorry, library foo' is not available")
...


From this file configure creates the actual R source file foo.R looking like

foo <- function(x) {
if(!FALSE) stop("Sorry, library foo' is not available")
...


if library foo was not found (with the desired functionality). In this case, the above R code effectively disables the function.

One could also use different file fragments for available and missing functionality, respectively.

You will very likely need to ensure that the same C compiler and compiler flags are used in the configure tests as when compiling R or your package. Under Unix, you can achieve this by including the following fragment early in configure.ac

: ${R_HOME=R RHOME} if test -z "${R_HOME}"; then
echo "could not determine R_HOME"
exit 1
fi
CC=${R_HOME}/bin/R CMD config CC CFLAGS=${R_HOME}/bin/R CMD config CFLAGS


(using ${R_HOME}/bin/R rather than just R is necessary in order to use the right' version of R when running the script as part of R CMD INSTALL. Note that earlier versions of this document recommended obtaining the configure information by direct extraction (using grep and sed) from R_HOME/etc/Makeconf, which only works for variables recorded there as literals. R 1.5.0 has added R CMD config for getting the value of the basic configuration variables, or the header and library flags necessary for linking against R, see R CMD config --help for more information. If R was configured to use the FORTRAN-to-C converter, configure variable F77 is set to a shell script wrapper to compile/link FORTRAN 77 code based on f2c which for the purpose of Autoconf qualifies as a FORTRAN 77 compiler. E.g., to check for an exteral BLAS library using the ACX_BLAS macro from the Official Autoconf Macro Archive, one can simply do F77=${R_HOME}/bin/R CMD config F77
AC_PROG_F77
ACX_BLAS([], AC_MSG_ERROR([could not find your BLAS library], 1))


You should bear in mind that the configure script may well not work on Windows systems (this seems normally to be the case for those generated by autoconf, although simple shell scripts do work). If your package is to be made publicly available, please give enough information for a user on a non-Unix platform to configure it manually, or provide a configure.win script to be used on that platform.

It is essential to provide manual configuration information if the package is to be usable on classic MacOS.

In some rare circumstances, the configuration and cleanup scripts need to know the location into which the package is being installed. An example of this is a package that uses C code and creates two shared libraries/DLLs. Usually, the library that is dynamically loaded by R is linked against the second, dependent, library. On some systems, we can add the location of this dependent library to the library that is dynamically loaded by R. This means that each user does not have to set the value of the LD_LIBRARY_PATH (or equivalent) environment variable, but that the secondary library is automatically resolved. Another example is when a package installs support files that are required at run time, and their location is substituted into an R data structure at installation time. (This happens with the Java Archive files in the Java package.)

The names of the top-level library directory (i.e., specifiable via the -l argument) and the directory of the package itself are made available to the installation scripts via the two shell/environment variables R_LIBRARY_DIR and R_PACKAGE_DIR. Additionally, the name of the package (e.g., survival or MASS) being installed is available from the shell variable R_PACKAGE_NAME.

Node:Using Makevars, Previous:Configure and cleanup, Up:Configure and cleanup

### Using Makevars

Sometimes writing your own configure script can be avoided by supplying a file Makevars: also one of the commonest uses of a configure script is to make Makevars from Makevars.in.

The most common use of a Makevars file is to set additional compiler flags (for example include paths) by setting PKG_CFLAGS, PKG_CXXFLAGS and PKG_FFLAGS, for C, C++, or FORTRAN respectively (see Creating shared libraries).

Also, Makevars can be used to set flags for the linker, for example -L and -l options.

There are some macros which are built whilst configuring the building of R itself, are stored in R_HOME/etc/Makeconf and can be used in Makevars. These include

FLIBS
A macro containing the set of libraries need to link FORTRAN code. This may need to be included in PKG_LIBS.
BLAS_LIBS
A macro containing the BLAS libraries used when building R. This may need to be included in PKG_LIBS. Beware that if it is empty then the R executable will contain all the double-precision BLAS routines, but no single-precision, complex nor double-complex routines.

Node:Checking and building packages, Next:, Previous:Configure and cleanup, Up:Creating R packages

## Checking and building packages

Using R CMD check, the R package checker, one can test whether source R packages work correctly. (Under Windows the equivalent command is Rcmd check.) This runs a series of checks.

1. The package is installed. This will warn about missing cross-references and duplicate aliases in help files.
2. The files and directories are checked for sufficient permissions (Unix only).
3. The DESCRIPTION file is checked for completeness, and some of its entries for correctness.
4. The R files are checked for syntax errors.
5. The R files are checked for correct calls to library.dynam (with no extension). In addition, it is checked whether methods have all arguments of the corresponding generic, and whether the final argument of assignment functions is called value.
6. The Rd files are checked for the mandatory (\name, \alias, \title, \description and \keyword) fields, and for unbalanced braces (which indicate Rd syntax errors). The keywords found are compared to the standard ones.
7. A check is made for undocumented user-level objects in the package.
8. The functions and their documentation are compared, and any differences in the call sequences reported.
9. It is checked whether all function arguments given in \usage sections of Rd files are documented in the corresponding \arguments section.
10. C source and header files are tested for correct (CR-only) line endings.
11. The examples provided by the package's documentation are run. (see Writing R help files, for information on using \examples to create executable example code.)

Of course, released packages should be able to run at least their own examples.

12. If the package sources contain a tests directory then the tests specified in that directory are run. (Typically they will consist of a set of .R source files and target output files .Rout.save.)
13. The code in package vignettes (see Writing package vignettes) is executed.
14. If a working latex program is available, the .dvi version of the package's manual is created (to check that the Rd files can be converted successfully).

Use R CMD check --help (Rcmd check --help on Windows) to obtain more information about the usage of the R package checker. A subset of the checking steps can be selected by adding flags.

Using R CMD build, the R package builder, one can build R packages from their sources (for example, for subsequent release). The Windows equivalent is Rcmd build.

Prior to actually building the package in the common gzipped tar file format, a variety of diagnostic checks and cleanups are performed. In particular, it is tested whether the DESCRIPTION file contains the required entries, whether object and data indices exist (it will build them if they do not) and can be assumed to be up-to-date.

Run-time checks whether the package works correctly should be performed using R CMD check prior to invoking the build procedure.

To exclude files from being put into the package, one can specify a list of exclude patterns in file .Rbuildignore in the top-level source directory. These patterns should be Perl regexps, one per line, to be matched against the file names relative to the top-level source directory. In addition, files called CVS or GNUMakefile, or with base names starting with .#, or starting and ending with #, or ending in ~ or .swp, are excluded by default.

Note: file exclusion does not work correctly with GNU tar 1.13 but does work with later versions (e.g., version 1.13.17).

Use R CMD build --help (Rcmd build --help on Windows) to obtain more information about the usage of the R package builder.

R CMD build can also build pre-compiled version of packages for binary distributions.

Note to Windows users: Rcmd check and Rcmd build work well under Windows NT4/2000 but may not work correctly on Windows 95/98/ME because of problems with some versions of Perl on those limited OSes. Experiences vary.

Node:Writing package vignettes, Next:, Previous:Checking and building packages, Up:Creating R packages

## Writing package vignettes

In addition to the help files in Rd format, R packages allow the inclusion of documents in arbitrary other formats. The standard location for these is subdirectory inst/doc of a source package, the contents will be copied to subdirectory doc when the package is installed. Pointers from package help indices to the installed documents are automatically created. Documents in inst/doc can be in arbitrary format, however we strongly recommend to provide them in PDF format, such that users on all platforms can easily read them.

A special case are documents in Sweave format, which we call package vignettes. Sweave allows to integrate LaTeX documents and R code and is contained in package tools which is part of the base R distribution, see the Sweave help page for details on the document format. Package vignettes found in directory inst/doc are tested by R CMD check by executing all R code they contain to ensure consistency between code and documentation.

R CMD build will automatically create PDF versions of the vignettes for distribution with the package sources. By including the PDF version in the package sources it is not necessary that the vignettes can be compiled at install time, i.e., the package author can use private LaTeX extensions which are only available on his machine. Only the R code inside the vignettes is part of the checking procedure, typesetting manuals is not part of the package QA.

By default R CMD build will run Sweave on all files in Sweave format. If no Makefile is found in directory inst/doc, then texi2dvi --pdf is run on all vignettes. Whenever a Makefile is found, then R CMD build will try to run make after the Sweave step, such that PDF manuals can be created from arbitrary source formats (plain LaTeX files, ...). The Makefile should take care of both creation of PDF files and cleaning up afterwards, i.e., delete all files that shall not appear in the final package archive. Note that the make step is executed independently from the presence of any files in Sweave format.

The directory inst/doc should contain an index named 00Index.dcf of all documentation files, the format is similar to the format of the DESCRIPTION file:

foo-summary.pdf:    A short introduction to package foo.
foo-manual.pdf:     A comprehensive manual for package foo.
someTips.pdf:       Tips that might be useful.


If no index file is present, then R CMD build looks for \VignetteIndexEntry statements in all Sweave files and auto-generates the index. The \VignetteIndexEntry statement is best placed in LaTeX comment, such that no definition of the command is necessary.

Node:Submitting a package to CRAN, Previous:Writing package vignettes, Up:Creating R packages

## Submitting a package to CRAN

CRAN is a network of WWW sites holding the R distributions and contributed code, especially R packages. Users of R are encouraged to join in the collaborative project and to submit their own packages to CRAN.

Before submitting a package mypkg, do run the following steps to test it is complete and will install properly. (Unix procedures only, run from the directory containing mypkg as a subdirectory.)

1. Run R CMD check to check that the package will install and will runs its examples, and that the documentation is complete and can be processed.
2. Run R CMD build to run a few further checks and to make the release .tar.gz file.

Please ensure that you can run through the complete procedure with only warnings that you understand and have reasons not to eliminate.

When all the testing is done, upload the .tar.gz file to

<ftp://ftp.ci.tuwien.ac.at/incoming>


and send a message to <cran@r-project.org> about it. The CRAN maintainers will run these tests before putting a submission in the main archive.

Note that the fully qualified name of the .tar.gz file must be of the form

package_version[_engine[_type]],

where the [ ] indicates that the enclosed component is optional, package and version are the corresponding entries in file DESCRIPTION, engine gives the S engine the package is targeted for and defaults to R, and type indicated whether the file contains source or binaries for a certain platform, and defaults to source. I.e.,

OOP_0.1-3.tar.gz
OOP_0.1-3_R.tar.gz
OOP_0.1-3_R_source.tar.gz


are all equivalent and indicate an R source package, whereas

OOP_0.1-3_Splus6_sparc-sun-solaris.tar.gz


is a binary package for installation under Splus6 on the given platform.

This naming scheme has been adopted to ensure usability of code across S engines. R code and utilities operating on package .tar.gz files can only be assumed to work provided that this naming scheme is respected. E.g., R CMD INSTALL will not work on package.tgz files. Of course, R CMD build automatically creates valid file names.

Node:Writing R help files, Next:, Previous:Creating R packages, Up:Top

# Writing R help files

Node:Rd format, Next:, Previous:Writing R help files, Up:Writing R help files

## Rd format

R objects are documented in files written in "R documentation" (Rd) format, a simple markup language closely resembling (La)TeX, which can be processed into a variety of formats, including LaTeX, HTML and plain text. The translation is carried out by the Perl script Rdconv in R_HOME/bin and by the installation scripts for packages.

The R distribution contains more than 900 such files which can be found in the src/library/pkg/man directories of the R source tree, where pkg stands for package base where all the standard objects are, and for the standard packages such as eda and mva which are included in the R distribution.

As an example, let us look at the file src/library/base/man/load.Rd which documents the R function load.

\name{load}
\description{
Reload the datasets written to a file with the function
\code{save}.
}
\usage{
}
\arguments{
\item{file}{a connection or a character string giving the
name of the file to load.}
\item{envir}{the environment where the data should be
}
\seealso{
}
\examples{
## save all data
save(list = ls(), file= "all.Rdata")

## restore the saved values to the current environment

## restore the saved values to the workspace
}
\keyword{file}


An Rd file consists of three parts. The header gives basic information about the name of the file, the topics documented, a title, a short textual description and R usage information for the objects documented. The body gives further information (for example, on the function's arguments and return value, as in the above example). Finally, there is a footer with keyword information. The header and footer are mandatory.

See the "Guidelines for Rd files" for guidelines for writing documentation in Rd format which should be useful for package writers.

### Documenting functions

The basic markup commands used for documenting R objects (in particular, functions) are given in this subsection.

\name{name}
name typically is the basename of the Rd file containing the documentation. (It is the "name" of the Rd object represented by the file, and has to be unique in a package.)
\alias{topic}
The \alias entries specify all "topics" the file documents. This information is collected into index data bases for lookup by the on-line (plain text and HTML) help systems.

There may be several \alias entries. Quite often it is convenient to document several R objects in one file. For example, file Normal.Rd documents the density, distribution function, quantile function and generation of random variates for the normal distribution, and hence starts with

\name{Normal}
\alias{dnorm}
\alias{pnorm}
\alias{qnorm}
\alias{rnorm}


Note that the \name is not necessarily a topic documented.

\title{Title}
Title information for the Rd file. This should be capitalized, not end in a period, and not use any markup (which would cause problems for hypertext search).
\description{...}
A short description of what the function(s) do(es) (one paragraph, a few lines only). (If a description is "too long" and cannot easily be shortened, the file probably tries to document too much at once.)
\usage{fun(arg1, arg2, ...)}
One or more lines showing the synopsis of the function(s) and variables documented in the file. These are set verbatim in typewriter font.

The usage information specified should in general match the function definition exactly (such that automatic checking for consistency between code and documentation is possible). Otherwise, include a \synopsis section with the actual definition.

For example, abline is a function for adding a straight line to a plot which can be used in several different ways, depending on the named arguments specified. Hence, abline.Rd contains

\synopsis{
abline(a = NULL, b = NULL, h = NULL, v = NULL, reg = NULL,
coef = NULL, untf = FALSE, col = par("col"),
lty = par("lty"), lwd = NULL, ...)
}
\usage{
abline(a, b, \dots)
abline(h=, \dots)
abline(v=, \dots)
...
}


Use \method{generic}{class} to indicate the name of an S3 method for the generic function generic for objects inheriting from class "class". In the printed versions, this will come out as generic (reflecting the understanding that methods should not be invoked directly but via method dispatch), but codoc() and other tools always have access to the full name.

For example, print.ts.Rd contains

\usage{
\method{print}{ts}(x, calendar, \dots)
}


\arguments{...}
Description of the function's arguments, using an entry of the form
\item{arg_i}{Description of arg_i.}


for each element of the argument list. There may be optional text before and after these entries.

\details{...}
A detailed if possible precise description of the functionality provided, extending the basic information in the \description slot.
\value{...}
Description of the function's return value.

If a list with multiple values is returned, you can use entries of the form

\item{comp_i}{Description of comp_i.}


for each component of the list returned. Optional text may precede this list (see the introductory example for rle).

\references{...}
A section with references to the literature. Use \url{} for web pointers.
\note{...}
Use this for a special note you want to have pointed out.

For example, piechart.Rd contains

\note{
Pie charts are a very bad way of displaying information.
The eye is good at judging linear measures and bad at
judging relative areas.
...
}


\author{...}
Information about the author(s) of the Rd file. Use \email{} without extra delimiters (( ) or < >) to specify email addresses, or \url{} for web pointers.
\seealso{...}
Pointers to related R objects, using \code{\link{...}} to refer to them (\code is the correct markup for R object names, and \link produces hyperlinks in output formats which support this. See Marking text, and Cross-references).
\examples{...}
Examples of how to use the function. These are set verbatim in typewriter font.

Examples are not only useful for documentation purposes, but also provide test code used for diagnostic checking of R. By default, text inside \examples{} will be displayed in the output of the help page and run by R CMD check. You can use \dontrun{} for commands that should only be shown, but not run, and \testonly{} for extra commands for testing that should not be shown to users.

For example,

x <- runif(10)       # Shown and run.
\dontrun{plot(x)}    # Only shown.
\testonly{log(x)}    # Only run.


Thus, example code not included in \dontrun must be executable! In addition, it should not use any system-specific features or require special facilities (such as Internet access or write permission to specific directories).

Data needed for making the examples executable can be obtained by random number generation (for example, x <- rnorm(100)), or by using standard data sets loadable via data() (see ?data for more info).

\keyword{key}
Each \keyword entry should specify one of the standard keywords (as listed in the file R_HOME/doc/KEYWORDS.db). There must be at least one \keyword entry, but can be more that one if the R object being documented falls into more than one category.

The special keyword internal marks a page of internal objects that are not part of the packages' API. If the help page for object foo has keyword internal, then help(foo) gives this help page, but foo is excluded from several object indices, like the alphabetical list of objects in the HTML help system.

The R function prompt facilitates the construction of files documenting R objects. If foo is an R function, then prompt(foo) produces file foo.Rd which already contains the proper function and argument names of foo, and a structure which can be filled in with information.

### Documenting datasets

The structure of Rd files which document R data sets is slightly different. Whereas sections such as \arguments and \value are not needed, the format and source of the data should be explained.

As an example, let us look at src/library/base/man/rivers.Rd which documents the standard R data set rivers.

\name{rivers}
\alias{rivers}
\title{Lengths of Major North American Rivers}
\description{
This data set gives the lengths (in miles) of 141 major''
rivers in North America, as compiled by the US Geological
Survey.
}
\usage{data(rivers)}
\format{A vector containing 141 observations.}
\source{World Almanac and Book of Facts, 1975, page 406.}
\references{
McNeil, D. R. (1977) \emph{Interactive Data Analysis}.
New York: Wiley.
}
\keyword{datasets}


This uses the following additional markup commands.

\format{...}
A description of the format of the dataset (as a vector, matrix, data frame, time series, ...). For matrices and data frames this should give a description of each column, preferably as a list or table. See Lists and tables, for more information.
\source{...}
Details of the original source (a reference or URL). In addition, section \references could give secondary sources and usages.

Note also that when documenting data set bar,

• The \usage entry is always data(bar).
• The \keyword entry is always datasets.

If bar is a data frame, documenting it as a data set can again be initiated via prompt(bar).

Node:Sectioning, Next:, Previous:Rd format, Up:Writing R help files

## Sectioning

To begin a new paragraph or leave a blank line in an example, just insert an empty line (as in (La)TeX). To break a line, use \cr.

In addition to the predefined sections (such as \description{}, \value{}, etc.), you can "define" arbitrary ones by \section{section_title}{...}. For example

\section{Warning}{You must not call this function unless ...}


For consistency with the pre-assigned sections, the section name (the first argument to \section) should be capitalized (but not all upper case).

Note that the additional named sections are always inserted at fixed positions in the output (before \note, \seealso and the examples), no matter where they appear in the input.

Node:Marking text, Next:, Previous:Sectioning, Up:Writing R help files

## Marking text

The following logical markup commands are available for indicating specific kinds of text.

 \bold{word} set word in bold font if possible \emph{word} emphasize word using italic font if possible \code{word} for pieces of code, using typewriter font if possible \file{word} for file names \email{word} for email addresses \url{word} for URLs

The first two, \bold and \emph, should be used in plain text for emphasis.

Fragments of R code, including the names of R objects, should be marked using \code. Only backslashes and percent signs need to be escaped (by a backslash) inside \code.

Node:Lists and tables, Next:, Previous:Marking text, Up:Writing R help files

## Lists and tables

The \itemize and \enumerate commands take a single argument, within which there may be one or more \item commands. The text following each \item is formatted as one or more paragraphs, suitably indented and with the first paragraph marked with a bullet point (\itemize) or a number (\enumerate).

\itemize and \enumerate commands may be nested.

The \describe command is similar to \itemize but allows initial labels to be specified. The \items take two arguments, the label and the body of the item, in exactly the same way as argument and value \items. \describe commands are mapped to <DL> lists in HTML and \description lists in LaTeX.

The \tabular command takes two arguments. The first gives for each of the columns the required alignment (l for left-justification, r for right-justification or c for centering.) The second argument consists of an arbitrary number of lines separated by \cr, and with fields separated by \tab. For example:

  \tabular{rlll}{
[,1] \tab Ozone   \tab numeric \tab Ozone (ppb)\cr
[,2] \tab Solar.R \tab numeric \tab Solar R (lang)\cr
[,3] \tab Wind    \tab numeric \tab Wind (mph)\cr
[,4] \tab Temp    \tab numeric \tab Temperature (degrees F)\cr
[,5] \tab Month   \tab numeric \tab Month (1--12)\cr
[,6] \tab Day     \tab numeric \tab Day of month (1--31)
}


There must be the same number of fields on each line as there are alignments in the first argument, and they must be non-empty (but can contain only spaces).

Node:Cross-references, Next:, Previous:Lists and tables, Up:Writing R help files

## Cross-references

The markup \link{foo} (usually in the combination \code{\link{foo}}) produces a hyperlink to the help page for object foo. One main usage of \link is in the \seealso section of the help page, see Rd format. (This only affects the creation of hyperlinks, for example in the HTML pages used by help.start() and the PDF version of the reference manual.)

There are optional arguments specified as \link[pkg]{foo} and \link[pkg:bar]{foo} to link to the package pkg with topic (file?) foo and bar respectively.

Node:Mathematics, Next:, Previous:Cross-references, Up:Writing R help files

## Mathematics

Mathematical formulae should be set beautifully for printed documentation yet we still want something useful for text and HTML online help. To this end, the two commands \eqn{latex}{ascii} and \deqn{latex}{ascii} are used. Where \eqn is used for "inline" formula (corresponding to TeX's $...$, \deqn gives "displayed equations" (as in LaTeX's displaymath environment, or TeX's $$...$$).

Both commands can also be used as \eqn{latexascii} (only one argument) which then is used for both latex and ascii.

The following example is from Poisson.Rd:

  \deqn{p(x) = \frac{\lambda^x e^{-\lambda}}{x!}}{%
p(x) = lambda^x exp(-lambda)/x!}
for \eqn{x = 0, 1, 2, \ldots}.


For HTML and text on-line help we get

    p(x) = lambda^x exp(-lambda)/x!

for x = 0, 1, 2, ....


Node:Insertions, Next:, Previous:Mathematics, Up:Writing R help files

## Insertions

Use \R for the R system itself (you don't need extra {} or \). Use \dots for the dots in function argument lists ..., and \ldots for ellipsis dots in ordinary text.

After a %, you can put your own comments regarding the help text. The rest of the line will be completely disregarded, normally. Therefore, you can also use it to make part of the "help" invisible.

You can produce a backslash (\) by escaping it by another backslash. (Note that \cr is used for generating line breaks.)

The "comment" and "control" characters % and \ always need to be escaped. Inside the verbatim-like commands (\code and \examples), no other2 characters are special. Note that \file is not a verbatim-like command.

In "regular" text (no verbatim, no \eqn, ...), you currently must escape most LaTeX special characters, i.e., besides %, {, and }, the four specials $, #, and _ are produced by preceding each with a \. (& can also be escaped, but need not be.) Further, enter ^ as \eqn{\mbox{\textasciicircum}}{^}, and ~ by \eqn{\mbox{\textasciitilde}}{~} or \eqn{\sim}{~} (for a short and long tilde respectively). Also, <, >, and | must only be used in math mode, i.e., within \eqn or \deqn. Node:Platform-specific sections, Next:, Previous:Insertions, Up:Writing R help files ## Platform-specific documentation Sometimes the documentation needs to differ by platform. Currently three OS-specific options are available, unix, windows and mac, and lines in the help source file can be enclosed in #ifdef OS ... #endif  or #ifndef OS ... #endif  for OS-specific inclusion or exclusion. If the differences between platforms are extensive or the R objects documented are only relevant to one platform, platform-specific Rd files can be put in a unix, windows or mac subdirectory. Node:Processing Rd format, Previous:Platform-specific sections, Up:Writing R help files ## Processing Rd format Under UNIX versions of R there are several commands to process Rd files. Windows equivalents are described at the end of the section. All of these need Perl to be installed. Using R CMD Rdconv one can convert R documentation format to other formats, or extract the executable examples for run-time testing. Currently, conversions to plain text, HTML, LaTeX, and S version 3 or 4 documentation formats are supported. In addition to this low-level conversion tool, the R distribution provides two user-level programs for processing Rd format. R CMD Rd2txt produces "pretty" plain text output from an Rd file, and is particularly useful as a previewer when writing Rd format documentation within Emacs. R CMD Rd2dvi generates DVI (or, if option --pdf is given, PDF) output from documentation in Rd files, which can be specified either explicitly or by the path to a directory with the sources of a package (or bundle). In the latter case, a reference manual for all documented objects in the package is created, including the information in the DESCRIPTION files. Using R CMD Rdindex one can produce nicely formatted index files displaying names and titles of the Rd files specified as arguments. This can be used to create the INDEX of an add-on package and, if it also contains data, the 00Index data index in the data directory. Note that the R package builder R CMD build can be used to automatically create these indices when building a package. Finally, R CMD Sd2Rd converts S version 3 documentation files (which use an extended Nroff format) and S version 4 documentation (which uses SGML markup) to Rd format. This is useful when porting a package originally written for the S system to R. S version 3 files usually have extension .d, whereas version 4 ones have extension .sgml or .sgm. The exact usage and a detailed list of available options for each of the above commands can be obtained by running R CMD command --help, e.g., R CMD Rdconv --help. All available commands can be listed using R --help. All of these have Windows equivalents. For most just replace R CMD by Rcmd, with the exception that it is Rcmd Rd2dvi.sh (and that needs the tools to build packages from source to be installed). (You will need the files in the R binary Windows distribution for installing source packages to be installed.) Node:Tidying and profiling R code, Next:, Previous:Writing R help files, Up:Top # Tidying and profiling R code R code which is worth preserving in a package and perhaps making available for others to use is worth documenting, tidying up and perhaps optimizing. The last two of these activities are the subject of this chapter. Node:Tidying R code, Next:, Previous:Tidying and profiling R code, Up:Tidying and profiling R code ## Tidying R code R treats function code loaded from packages and code entered by users differently. Code entered by users has the source code stored in an attribute, 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. Normally keeping the source code is a good idea, and in particular it avoids comments being moved around in the source. However, we can make use of the ability to re-create a function listing from its parse tree to produce a tidy version of the function, with consistent indentation, spaces around operators and consistent use of the preferred assignment operator <-. This tidied version is much easier to read, not least by other users who are used to the standard format. We can subvert the keeping of source in two ways. 1. The option keep.source can be set to FALSE before the code is loaded into R. 2. The stored source code can be removed by removing the source attribute, for example by attr(myfun, "source") <- NULL  In each case if we then list the function we will get the standard layout. Suppose we have a file of functions myfuns.R that we want to tidy up. Create a file tidy.R containing options(keep.source = FALSE) source("myfuns.R") dump(ls(all = TRUE), file = "new.myfuns.R")  and run R with this as the source file, for example by R --vanilla < tidy.R (Unix) or Rterm --vanilla < tidy.R (Windows) or by pasting into an R session. Then the file new.myfuns.R will contain the functions in alphabetical order in the standard layout. You may need to move comments to more appropriate places. The standard format provides a good starting point for further tidying. Most package authors use a version of Emacs (on Unix or Windows) to edit R code, using the ESS[S] mode of the ESS Emacs package. See R coding standards for style options within the ESS[S] mode recommended for the source code of R itself. Node:Profiling R code, Previous:Tidying R code, Up:Tidying and profiling R code ## Profiling R code It is possible to profile R code on most Unix-like versions of R, R has to be built to enable this, by supplying the option --enable-R-profiling, profiling being enabled in a default build. Profiling is also available on Windows, but not on the Macintosh. The command Rprof is used to control profiling, and its help page can be consulted for full details. Profiling works by recording at fixed intervals (by default every 20 msecs) which R function is being used, and recording the results in a file (default Rprof.out in the working directory). Then the utility R CMD Rprof Rprof.out can be used to summarize the activity. (Use Rcmd Rprof Rprof.out on Windows.) As an example, consider the following code (from Venables & Ripley, 1999). library(MASS); library(boot); library(nls) data(stormer) storm.fm <- nls(Time ~ b*Viscosity/(Wt - c), stormer, start = c(b=29.401, c=2.2183)) st <- cbind(stormer, fit=fitted(storm.fm)) storm.bf <- function(rs, i) { st$Time <-  st$fit + rs[i] tmp <- nls(Time ~ (b * Viscosity)/(Wt - c), st, start = coef(storm.fm)) tmp$m$getAllPars() } rs <- scale(resid(storm.fm), scale = FALSE) # remove the mean Rprof("boot.out") storm.boot <- boot(rs, storm.bf, R = 4999) # pretty slow Rprof(NULL)  Having run this we can summarize the results by R CMD Rprof boot.out Each sample represents 0.02 seconds. Total run time: 80.74 seconds. Total seconds: time spent in function and callees. Self seconds: time spent in function alone. % total % self total seconds self seconds name 100.00 80.74 0.22 0.18 "boot" 99.65 80.46 1.19 0.96 "statistic" 96.33 77.78 2.68 2.16 "nls" 50.21 40.54 1.54 1.24 "<Anonymous>" 47.11 38.04 1.83 1.48 ".Call" 23.06 18.62 2.43 1.96 "eval" 19.87 16.04 0.67 0.54 "as.list" 18.97 15.32 0.64 0.52 "switch" 17.88 14.44 0.47 0.38 "model.frame" 17.41 14.06 1.73 1.40 "model.frame.default" 17.41 14.06 2.80 2.26 "nlsModel" 15.43 12.46 1.88 1.52 "qr.qty" 13.40 10.82 3.07 2.48 "assign" 12.73 10.28 2.33 1.88 "storage.mode<-" 12.34 9.96 1.81 1.46 "qr.coef" 10.13 8.18 5.42 4.38 "paste" ... % self % total self seconds total seconds name 5.42 4.38 10.13 8.18 "paste" 3.37 2.72 6.71 5.42 "as.integer" 3.29 2.66 5.00 4.04 "as.double" 3.20 2.58 4.29 3.46 "seq.default" 3.07 2.48 13.40 10.82 "assign" 2.92 2.36 5.95 4.80 "names" 2.80 2.26 17.41 14.06 "nlsModel" 2.68 2.16 96.33 77.78 "nls" 2.53 2.04 2.53 2.04 ".Fortran" 2.43 1.96 23.06 18.62 "eval" 2.33 1.88 12.73 10.28 "storage.mode<-" ...  This often produces surprising results and can be used to identify bottlenecks or pieces of R code that could benefit from being replaced by compiled code. Two warnings: profiling does impose a small performance penalty, and the output files can be very large if long runs are profiled. Node:System and foreign language interfaces, Next:, Previous:Tidying and profiling R code, Up:Top # System and foreign language interfaces Node:Operating system access, Next:, Previous:System and foreign language interfaces, Up:System and foreign language interfaces ## Operating system access Access to operating system functions is via the R function system. The details will differ by platform (see the on-line help), and about all that can safely be assumed is that the first argument will be a string command that will be passed for execution (not necessarily by a shell) and the second argument will be internal which if true will collect the output of the command into an R character vector. The function system.time is available for timing (although the information available may be limited on non-Unix-like platforms). Node:Interface functions .C and .Fortran, Next:, Previous:Operating system access, Up:System and foreign language interfaces ## Interface functions .C and .Fortran These two functions provide a standard interface to compiled code that has been linked into R, either at build time or via dyn.load (see dyn.load and dyn.unload). They are primarily intended for compiled C and FORTRAN code respectively, but the .C function can be used with other languages which can generate C interfaces, for example C++ (see Interfacing C++ code). The first argument to each function is a character string given the symbol name as known to C or FORTRAN, that is the function or subroutine name. (The mapping to the symbol name in the load table is given by the functions symbol.C and symbol.For; that the symbol is loaded can be tested by, for example, is.loaded(symbol.C("loglin")).) There can be up to 65 further arguments giving R objects to be passed to compiled code. Normally these are copied before being passed in, and copied again to an R list object when the compiled code returns. If the arguments are given names, these are used as names for the components in the returned list object (but not passed to the compiled code). The following table gives the mapping between the modes of R vectors and the types of arguments to a C function or FORTRAN subroutine.  R storage mode C type FORTRAN type logical int * INTEGER integer int * INTEGER double double * DOUBLE PRECISION complex Rcomplex * DOUBLE COMPLEX character char ** CHARACTER*255 C type Rcomplex is a structure with double members r and i defined in the header file Complex.h included by R.h. Only a single character string can be passed to or from FORTRAN, and the success of this is compiler-dependent. Other R objects can be passed to .C, but it is better to use one of the other interfaces. An exception is passing an R function for use with call_R, when the object can be handled as void * en route to call_R, but even there .Call is to be preferred. It is possible to pass numeric vectors of storage mode double to C as float * or FORTRAN as REAL by setting the attribute Csingle, most conveniently by using the R functions as.single, single or storage.mode. This is intended only to be used to aid interfacing to existing C or FORTRAN code. Unless formal argument NAOK is true, all the other arguments are checked for missing values NA and for the IEEE special values NaN, Inf and -Inf, and the presence of any of these generates an error. If it is true, these values are passed unchecked. Argument DUP can be used to suppress copying. It is dangerous: see the on-line help for arguments against its use. It is not possible to pass numeric vectors as float * or REAL if DUP=FALSE. Finally, argument PACKAGE confines the search for the symbol name to a specific shared library (or use "base" for code compiled into R). Its use is highly desirable, as there is no way to avoid two package writers using the same symbol name, and such name clashes are normally sufficient to cause R to crash. Note that the compiled code should not return anything except through its arguments: C functions should be of type void and FORTRAN subprograms should be subroutines. To fix ideas, let us consider a very simple example which convolves two finite sequences. (This is hard to do fast in interpreted R code, but easy in C code.) We could do this using .C by void convolve(double *a, int *na, double *b, int *nb, double *ab) { int i, j, nab = *na + *nb - 1; for(i = 0; i < nab; i++) ab[i] = 0.0; for(i = 0; i < *na; i++) for(j = 0; j < *nb; j++) ab[i + j] += a[i] * b[j]; }  called from R by conv <- function(a, b) .C("convolve", as.double(a), as.integer(length(a)), as.double(b), as.integer(length(b)), ab = double(length(a) + length(b) - 1))$ab


Note that we take care to coerce all the arguments to the correct R storage mode before calling .C; mistakes in matching the types can lead to wrong results or hard-to-catch errors.

Node:dyn.load and dyn.unload, Next:, Previous:Interface functions .C and .Fortran, Up:System and foreign language interfaces

## dyn.load and dyn.unload

Compiled code to be used with R is loaded as a shared library (Unix, see Creating shared libraries for more information) or DLL (Windows).

The library/DLL is loaded by dyn.load and unloaded by dyn.unload. Unloading is not normally necessary, but it is needed to allow the DLL to be re-built on some platforms, including Windows.

The first argument to both functions is a character string giving the path to the library. Programmers should not assume a specific file extension for the library (such as .so) but use a construction like

file.path(path1, path2, paste("mylib", .Platform$dynlib.ext, sep=""))  for platform independence. On Unix systems the path supplied to dyn.load can be an absolute path, one relative to the current directory or, if it starts with ~, relative to the user's home directory. Loading is most often done via a call to library.dynam in the .First.lib function of a package. This has the form library.dynam("libname", package, lib.loc)  where libname is the library/DLL name with the extension omitted. Under some Unix systems there is a choice of how the symbols are resolved when the library is loaded, governed by the arguments local and now. Only use these if really necessary: in particular using now=FALSE and then calling an unresolved symbol will terminate R unceremoniously. If a library/DLL is loaded more than once the most recent version is used. More generally, if the same symbol name appears in several libraries, the most recently loaded occurrence is used. The PACKAGE argument provides a good way to avoid any ambiguity in which occurrence is meant. Node:Creating shared libraries, Next:, Previous:dyn.load and dyn.unload, Up:System and foreign language interfaces ## Creating shared libraries Under Unix, shared libraries for loading into R can be created using R CMD SHLIB. This accepts as arguments a list of files which must be object files (with extension .o) or C, C++, or FORTRAN sources (with extensions .c, .cc or .cpp or .C, and .f, respectively). See R CMD SHLIB --help, or the on-line help for SHLIB, for usage information. If compiling the source files does not work "out of the box", you can specify additional flags by setting some of the variables PKG_CPPFLAGS (for the C preprocessor, typically -I flags), PKG_CFLAGS, PKG_CXXFLAGS, and PKG_FFLAGS (for the C, C++, and FORTRAN compilers, respectively) in the file Makevars in the compilation directory, or write a Makefile in the compilation directory containing the rules required (or, of course, create the object files directly from the command line). Similarly, variable PKG_LIBS in Makevars can be used for additional -l and -L flags to be passed to the linker when building the shared library. If an add-on package pkg contains C, C++, or FORTRAN code in its src subdirectory, R CMD INSTALL creates a shared library (for loading into R in the .First.lib function of the package) either automatically using the above R CMD SHLIB mechanism, or using make if directory src contains a Makefile. In both cases, if file Makevars exists it is read first when invoking make. If a Makefile is really needed or provided, it needs to ensure that the shared library created is linked against all FORTRAN 77 intrinsic and run-time libraries that R was linked against; Make variable FLIBS contains this information. The Windows equivalent is the command Rcmd SHLIB; files Makevars.win or Makefile.win are used in preference to Makevars or Makefile if they exist. (This does need the files in the R binary Windows distribution for installing source packages to be installed.) Node:Interfacing C++ code, Next:, Previous:Creating shared libraries, Up:System and foreign language interfaces ## Interfacing C++ code Suppose we have the following hypothetical C++ library, consisting of the two files X.hh and X.cc, and implementing the two classes X and Y which we want to use in R. // X.hh class X { public: X (); ~X (); }; class Y { public: Y (); ~Y (); };  // X.cc #include <iostream.h> #include "X.hh" static Y y; X::X() { cout << "constructor X" << endl; } X::~X() { cout << "destructor X" << endl; } Y::Y() { cout << "constructor Y" << endl; } Y::~Y() { cout << "destructor Y" << endl; }  To use with R, the only thing we have to do is writing a wrapper function and ensuring that the function is enclosed in extern "C" { }  For example, // X_main.cc: #include "X.hh" extern "C" { void X_main () { X x; } } // extern "C"  Compiling and linking should be done with the C++ compiler-linker (rather than the C compiler-linker or the linker itself); otherwise, the C++ initialization code (and hence the constructor of the static variable Y) are not called. On a properly configured Unix system (support for C++ was added in R version 1.1), one can simply use R CMD SHLIB X.cc X_main.cc  to create the shared library, typically X.so (the file name extension may be different on your platform). Now starting R yields R : Copyright 2000, The R Development Core Team Version 1.1.0 Under development (unstable) (April 14, 2000) ... Type "q()" to quit R. R> dyn.load(paste("X", .Platform$dynlib.ext, sep = ""))
constructor Y
R> .C("X_main")
constructor X
destructor X
list()
R> q()
Save workspace image? [y/n/c]: y
destructor Y


The R for Windows FAQ (rw-FAQ) contains details of how to compile this example under various Windows compilers.

Using C++ iostreams, as in this example, is best avoided. There is no guarantee that the output will appear in the R console, and indeed it will not on the R for Windows console. Use R code or the C entry points (see Printing) for all I/O if at all possible.

Node:Handling R objects in C, Next:, Previous:Interfacing C++ code, Up:System and foreign language interfaces

## Handling R objects in C

Using C code to speed up the execution of an R function is often very fruitful. Traditionally this has been done via the .C function in R. One restriction of this interface is that the R objects can not be handled directly in C. This becomes more troublesome when one wishes to call R functions from within the C code. There is a C function provided called call_R (also known as call_S for compatibility with S) that can do that, but it is cumbersome to use, and the mechanisms documented here are usually simpler to use, as well as more powerful.

If a user really wants to write C code using internal R data structures, then that can be done using the .Call and .External function. The syntax for the calling function in R in each case is similar to that of .C, but the two functions have rather different C interfaces. Generally the .Call interface (which is modelled on the interface of the same name in S version 4) is a little simpler to use, but .External is a little more general.

A call to .Call is very similar to .C, for example

.Call("convolve2", a, b)


The first argument should be a character string giving a C symbol name of code that has already been loaded into R. Up to 65 R objects can passed as arguments. The C side of the interface is

#include <R.h>
#include <Rinternals.h>

SEXP convolve2(SEXP a, SEXP b)
...


A call to .External is almost identical

.External("convolveE", a, b)


but the C side of the interface is different, having only one argument

#include <R.h>
#include <Rinternals.h>

SEXP convolveE(SEXP args)
...


Here args is a LISTSXP, a Lisp-style list from which the arguments can be extracted.

In each case the R objects are available for manipulation via a set of functions and macros defined in the header file Rinternals.h or some higher-level macros defined in Rdefines.h. See Interface functions .Call and .External for details on .Call and .External.

Before you decide to use .Call or .External, you should look at other alternatives. First, consider working in interpreted R code; if this is fast enough, this is normally the best option. You should also see if using .C is enough. If the task to be performed in C is simple enough requiring no call to R, .C suffices. The new interfaces are recent additions to S and R, and a great deal of useful code has been written using just .C before they were available. The .Call and .External interfaces allow much more control, but they also impose much greater responsibilities so need to be used with care. Neither .Call nor .External copy their arguments. You should treat arguments you receive through these interfaces as read-only.

There are two approaches that can be taken to handling R objects from within C code. The first (historically) is to use the macros and functions that have been used to implement the core parts of R through .Internal calls. A public subset of these is defined in the header file Rinternals.h in the directory R_HOME/include that should be available on any R installation.

A more recent approach is to use R versions of the macros and functions defined for the S version 4 interface .Call, which are defined in the header file Rdefines.h. This is a somewhat simpler approach, and is certainly to be preferred if the code might be shared with S at any stage.

A substantial amount of R is implemented using the functions and macros described here, so the R source code provides a rich source of examples and "how to do it": indeed many of the examples here were developed by examining closely R system functions for similar tasks. Do make use of the source code for inspirational examples.

It is necessary to know something about how R objects are handled in C code. All the R objects you will deal with will be handled with the type SEXP3, which is a pointer to a structure with typedef SEXPREC. Think of this structure as a variant type that can handle all the usual types of R objects, that is vectors of various modes, functions, environments, language objects and so on. The details are given later in this section, but for most purposes the programmer does not need to know them. Think rather of a model such as that used by Visual Basic, in which R objects are handed around in C code (as they are in interpreted R code) as the variant type, and the appropriate part is extracted for, for example, numerical calculations, only when it is needed. As in interpreted R code, much use is made of coercion to force the variant object to the right type.

Node:Garbage Collection, Next:, Previous:Handling R objects in C, Up:Handling R objects in C

### Handling the effects of garbage collection

We need to know a little about the way R handles memory allocation. The memory allocated for R objects is not freed by the user; instead, the memory is from time to time garbage collected. That is, some or all of the allocated memory not being used is freed. (Prior to R 1.2, objects could be moved, too.)

The R object types are represented by a C structure defined by a typedef SEXPREC in Rinternals.h. It contains several things among which are pointers to data blocks and to other SEXPRECs. A SEXP is simply a pointer to a SEXPREC.

If you create an R object in your C code, you must tell R that you are using the object by using the PROTECT macro on a pointer to the object. This tells R that the object is in use so it is not destroyed. Notice that it is the object which is protected, not the pointer variable. It is a common mistake to believe that if you invoked PROTECT(p) at some point then p is protected from then on, but that is not true once a new object is assigned to p.

Protecting an R object automatically protects all the R objects pointed to in the corresponding SEXPREC.

The programmer is solely responsible for housekeeping the calls to PROTECT. There is a corresponding macro UNPROTECT that takes as argument an int giving the number of objects to unprotect when they are no longer needed. The protection mechanism is stack-based, so UNPROTECT(n) unprotects the last n objects which were protected. The calls to PROTECT and UNPROTECT must balance when the user's code returns. R will warn about "stack imbalance in .Call" (or .External) if the housekeeping is wrong.

Here is a small example of creating an R numeric vector in C code. First we use the macros in Rdefines.h:

#include <R.h>
#include <Rdefines.h>

SEXP ab;
....
PROTECT(ab = NEW_NUMERIC(2));
NUMERIC_POINTER(ab)[0] = 123.45;
NUMERIC_POINTER(ab)[1] = 67.89;
UNPROTECT(1);


and then those in Rinternals.h:

#include <R.h>
#include <Rinternals.h>

SEXP ab;
....
PROTECT(ab = allocVector(REALSXP, 2));
REAL(ab)[0] = 123.45;
REAL(ab)[1] = 67.89;
UNPROTECT(1);


Now, the reader may ask how the R object could possibly get removed during those manipulations, as it is just our C code that is running. As it happens, we can do without the protection in this example, but in general we do not know (nor want to know) what is hiding behind the R macros and functions we use, and any of them might cause memory to be allocated, hence garbage collection and hence our object ab to be removed. It is usually wise to err on the side of caution and assume that any of the R macros and functions might remove the object.

In some cases it is necessary to keep better track of whether protection is really needed. Be particularly aware of situations where a large number of objects are generated. The pointer protection stack has a fixed size (default 10,000) and can become full. It is not a good idea then to just PROTECT everything in sight and UNPROTECT several thousand objects at the end. It will almost invariably be possible to either assign the objects as part of another object (which automatically protects them) or unprotect them immediately after use.

Protection is not needed for objects which R already knows are in use. In particular, this applies to function arguments.

There is a less-used macro UNPROTECT_PTR(s) that unprotects the object pointed to by the SEXP s, even if it is not the top item on the pointer protection stack. This is rarely needed outside the parser (the R sources have one example, in src/main/plot3d.c).

Node:Allocating storage, Next:, Previous:Garbage Collection, Up:Handling R objects in C

### Allocating storage

For many purposes it is sufficient to allocate R objects and manipulate those. There are quite a few allocXxx functions defined in Rinternals.h--you may want to explore them. These allocate R objects of various types, and for the standard vector types there are NEW_XXX macros defined in Rdefines.h.

If storage is required for C objects during the calculations this is best allocating by calling R_alloc; see Memory allocation. All of these memory allocation routines do their own error-checking, so the programmer may assume that they will raise an error and not return if the memory cannot be allocated.

Node:Details of R types, Next:, Previous:Allocating storage, Up:Handling R objects in C

### Details of R types

Users of the Rinternals.h macros will need to know how the R types are known internally: this is more or less completely hidden if the Rdefines.h macros are used.

The different R data types are represented in C by SEXPTYPE. Some of these are familiar from R and some are internal data types. The usual R object modes are given in the table.

 SEXPTYPE R equivalent REALSXP numeric with storage mode double INTSXP integer CPLXSXP complex LGLSXP logical STRSXP character VECSXP list (generic vector) LISTSXP "dotted-pair" list DOTSXP a ... object NILSXP NULL SYMSXP name/symbol CLOSXP function or function closure ENVSXP environment

Among the important internal SEXPTYPEs are LANGSXP, CHARSXP etc.

Unless you are very sure about the type of the arguments, the code should check the data types. Sometimes it may also be necessary to check data types of objects created by evaluating an R expression in the C code. You can use functions like isReal, isInteger and isString to do type checking. See the header file Rinternals.h for definitions of other such functions. All of these take a SEXP as argument and return 1 or 0 to indicate TRUE or FALSE. Once again there are two ways to do this, and Rdefines.h has macros such as IS_NUMERIC.

What happens if the SEXP is not of the correct type? Sometimes you have no other option except to generate an error. You can use the function error for this. It is usually better to coerce the object to the correct type. For example, if you find that an SEXP is of the type INTEGER, but you need a REAL object, you can change the type by using, equivalently,

PROTECT(newSexp = coerceVector(oldSexp, REALSXP));


or

PROTECT(newSexp = AS_NUMERIC(oldSexp));


Protection is needed as a new object is created; the object formerly pointed to by the SEXP is re-used is still protected but now unused.

All the coercion functions do their own error-checking, and generate NAs with a warning or stop with an error as appropriate.

So far we have only seen how to create and coerce R objects from C code, and how to extract the numeric data from numeric R vectors. These can suffice to take us a long way in interfacing R objects to numerical algorithms, but we may need to know a little more to create useful return objects.

Node:Attributes, Next:, Previous:Details of R types, Up:Handling R objects in C

### Attributes

Many R objects have attributes: some of the most useful are classes and the dim and dimnames that mark objects as matrices or arrays. It can also be helpful to work with the names attribute of vectors.

To illustrate this, let us write code to take the outer product of two vectors (which outer and %o% already do). As usual the R code is simple

out <- function(x, y) .Call("out", as.double(x), as.double(y))


where we expect x and y to be numeric vectors, possibly with names. This time we do the coercion in the calling R code.

C code to do the computations is

#include <R.h>
#include <Rinternals.h>

SEXP out(SEXP x, SEXP y)
{
int i, j, nx, ny;
double tmp;
SEXP ans;

nx = length(x); ny = length(y);
PROTECT(ans = allocMatrix(REALSXP, nx, ny));
for(i = 0; i < nx; i++) {
tmp = REAL(x)[i];
for(j = 0; j < ny; j++)
REAL(ans)[i + nx*j] = tmp * REAL(y)[j];
}
UNPROTECT(1);
return(ans);
}


but we would like to set the dimnames of the result. Although allocMatrix provides a short cut, we will show how to set the dim attribute directly.

#include <R.h>
#include <Rinternals.h>

SEXP out(SEXP x, SEXP y)
{
int i, j, nx, ny;
double tmp;
SEXP ans, dim, dimnames;

nx = length(x); ny = length(y);
PROTECT(ans = allocVector(REALSXP, nx*ny));
for(i = 0; i < nx; i++) {
tmp = REAL(x)[i];
for(j = 0; j < ny; j++)
REAL(ans)[i + nx*j] = tmp * REAL(y)[j];
}

PROTECT(dim = allocVector(INTSXP, 2));
INTEGER(dim)[0] = nx; INTEGER(dim)[1] = ny;
setAttrib(ans, R_DimSymbol, dim);

PROTECT(dimnames = allocVector(VECSXP, 2));
SET_VECTOR_ELT(dimnames, 0, getAttrib(x, R_NamesSymbol));
SET_VECTOR_ELT(dimnames, 1, getAttrib(y, R_NamesSymbol));
setAttrib(ans, R_DimNamesSymbol, dimnames);

UNPROTECT(3);
return(ans);
}


This example introduces several new features. The getAttrib and setAttrib functions get and set individual attributes. Their second argument is a SEXP defining the name in the symbol table of the attribute we want; these and many such symbols are defined in the header file Rinternals.h.

There are shortcuts here too: the functions namesgets, dimgets and dimnamesgets are the internal versions of names<-, dim<- and dimnames<-, and there are functions such as GetMatrixDimnames and GetArrayDimnames.

What happens if we want to add an attribute that is not pre-defined? We need to add a symbol for it via a call to install. Suppose for illustration we wanted to add an attribute "version" with value 3.0. We could use

  SEXP version;
PROTECT(version = allocVector(REALSXP, 1));
REAL(version) = 3.0;
setAttrib(ans, install("version"), version);
UNPROTECT(1);


Using install when it is not needed is harmless and provides a simple way to retrieve the symbol from the symbol table if it is already installed.

Node:Classes, Next:, Previous:Attributes, Up:Handling R objects in C

### Classes

In R the class is just the attribute named "class" so it can be handled as such, but there is a shortcut classgets. Suppose we want to give the return value in our example the class "mat". We can use

#include <R.h>
#include <Rdefines.h>
....
SEXP ans, dim, dimnames, class;
....
PROTECT(class = allocVector(STRSXP, 1));
SET_STRING_ELT(class, 0, mkChar("mat"));
classgets(ans, class);
UNPROTECT(4);
return(ans);
}


As the value is a character vector, we have to know how to create that from a C character array, which we do using the function mkChar.

Node:Handling lists, Next:, Previous:Classes, Up:Handling R objects in C

### Handling lists

Some care is needed with lists, as R has moved from using LISP-like lists (now called "pairlists") to S-like generic vectors. As a result, the appropriate test for an object of mode list is isNewList, and we need allocVector(VECSXP, n) and not allocList(n).

List elements can be retrieved or set by direct access to the elements of the generic vector. Suppose we have a list object

a <- list(f=1, g=2, h=3)


Then we can access a$g as a[[2]] by  double g; .... g = REAL(VECTOR_ELT(a, 1))[0];  This can rapidly become tedious, and the following function (based on one in package nls) is very useful: /* get the list element named str, or return NULL */ SEXP getListElement(SEXP list, char *str) { SEXP elmt = R_NilValue, names = getAttrib(list, R_NamesSymbol); int i; for (i = 0; i < length(list); i++) if(strcmp(CHAR(STRING_ELT(names, i)), str) == 0) { elmt = VECTOR_ELT(list, i); break; } return elmt; }  and enables us to say  double g; g = REAL(getListElement(a, "g"))[0];  Node:Finding and setting variables, Previous:Handling lists, Up:Handling R objects in C ### Finding and setting variables It will be usual that all the R objects needed in our C computations are passed as arguments to .Call or .External, but it is possible to find the values of R objects from within the C given their names. The following code is the equivalent of get(name, envir = rho). SEXP getvar(SEXP name, SEXP rho) { SEXP ans; if(!isString(name) || length(name) != 1) error("name is not a single string"); if(!isEnvironment(rho)) error("rho should be an environment"); ans = findVar(install(CHAR(STRING_ELT(name, 0))), rho); printf("first value is %f\n", REAL(ans)[0]); return(R_NilValue); }  The main work is done by findVar, but to use it we need to install name as a name in the symbol table. As we wanted the value for internal use, we return NULL. Similar functions with syntax void defineVar(SEXP symbol, SEXP value, SEXP rho) void setVar(SEXP symbol, SEXP value, SEXP rho)  can be used to assign values to R variables. defineVar creates a new binding or changes the value of an existing binding in the specified environment frame; it is the analogue of assign(symbol, value, envir = rho, inherits = FALSE), but unlike assign, defineVar does not make a copy of the object value.4 setVar searches for an existing binding for symbol in rho or its enclosing environments. If a binding is found, its value is changed to value. Otherwise, a new binding with the specified value is created in the global environment. This corresponds to assign(symbol, value, envir = rho, inherits = TRUE). Node:Interface functions .Call and .External, Next:, Previous:Handling R objects in C, Up:System and foreign language interfaces ## Interface functions .Call and .External In this section we consider the details of the R/C interfaces. These two interfaces have almost the same functionality. .Call is based on the interface of the same name in S version 4, and .External is based on .Internal. .External is more complex but allows a variable number of arguments. Node:Calling .Call, Next:, Previous:Interface functions .Call and .External, Up:Interface functions .Call and .External ### Calling .Call Let us convert our finite convolution example to use .Call, first using the Rdefines.h macros. The calling function in R is conv <- function(a, b) .Call("convolve2", a, b)  which could hardly be simpler, but as we shall see all the type checking must be transferred to the C code, which is #include <R.h> #include <Rdefines.h> SEXP convolve2(SEXP a, SEXP b) { int i, j, na, nb, nab; double *xa, *xb, *xab; SEXP ab; PROTECT(a = AS_NUMERIC(a)); PROTECT(b = AS_NUMERIC(b)); na = LENGTH(a); nb = LENGTH(b); nab = na + nb - 1; PROTECT(ab = NEW_NUMERIC(nab)); xa = NUMERIC_POINTER(a); xb = NUMERIC_POINTER(b); xab = NUMERIC_POINTER(ab); for(i = 0; i < nab; i++) xab[i] = 0.0; for(i = 0; i < na; i++) for(j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j]; UNPROTECT(3); return(ab); }  Note that unlike the macros in S version 4, the R versions of these macros do check that coercion can be done and raise an error if it fails. They will raise warnings if missing values are introduced by coercion. Although we illustrate doing the coercion in the C code here, it often is simpler to do the necessary coercions in the R code. Now for the version in R-internal style. Only the C code changes. #include <R.h> #include <Rinternals.h> SEXP convolve2(SEXP a, SEXP b) { int i, j, na, nb, nab; double *xa, *xb, *xab; SEXP ab; PROTECT(a = coerceVector(a, REALSXP)); PROTECT(b = coerceVector(b, REALSXP)); na = length(a); nb = length(b); nab = na + nb - 1; PROTECT(ab = allocVector(REALSXP, nab)); xa = REAL(a); xb = REAL(b); xab = REAL(ab); for(i = 0; i < nab; i++) xab[i] = 0.0; for(i = 0; i < na; i++) for(j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j]; UNPROTECT(3); return(ab); }  This is called in exactly the same way. Node:Calling .External, Next:, Previous:Calling .Call, Up:Interface functions .Call and .External ### Calling .External We can use the same example to illustrate .External. The R code changes only by replacing .Call by .External conv <- function(a, b) .External("convolveE", a, b)  but the main change is how the arguments are passed to the C code, this time as a single SEXP. The only change to the C code is how we handle the arguments. #include <R.h> #include <Rinternals.h> SEXP convolveE(SEXP args) { int i, j, na, nb, nab; double *xa, *xb, *xab; SEXP a, b, ab; PROTECT(a = coerceVector(CADR(args), REALSXP)); PROTECT(b = coerceVector(CADDR(args), REALSXP)); ... }  Once again we do not need to protect the arguments, as in the R side of the interface they are objects that are already in use. The macros  first = CADR(args); second = CADDR(args); third = CADDDR(args); fourth = CAD4R(args);  provide convenient ways to access the first four arguments. More generally we can use the CDR and CAR macros as in  args = CDR(args); a = CAR(args); args = CDR(args); b = CAR(args);  which clearly allows us to extract an unlimited number of arguments (whereas .Call has a limit, albeit at 65 not a small one). More usefully, the .External interface provides an easy way to handle calls with a variable number of arguments, as length(args) will give the number of arguments supplied (of which the first is ignored). We may need to know the names (tags') given to the actual arguments, which we can by using the TAG macro and using something like the following example, that prints the names and the first value of its arguments if they are vector types. #include <R_ext/PrtUtil.h> SEXP showArgs(SEXP args) { int i, nargs; Rcomplex cpl; char *name; if((nargs = length(args) - 1) > 0) { for(i = 0; i < nargs; i++) { args = CDR(args); name = CHAR(PRINTNAME(TAG(args))); switch(TYPEOF(CAR(args))) { case REALSXP: Rprintf("[%d] '%s' %f\n", i+1, name, REAL(CAR(args))[0]); break; case LGLSXP: case INTSXP: Rprintf("[%d] '%s' %d\n", i+1, name, INTEGER(CAR(args))[0]); break; case CPLXSXP: cpl = COMPLEX(CAR(args))[0]; Rprintf("[%d] '%s' %f + %fi\n", i+1, name, cpl.r, cpl.i); break; case STRSXP: Rprintf("[%d] '%s' %s\n", i+1, name, CHAR(STRING_ELT(CAR(args), 0))); break; default: Rprintf("[%d] '%s' R type\n", i+1, name); } } } return(R_NilValue); }  This can be called by the wrapper function showArgs <- function(...) .External("showArgs", ...)  Note that this style of programming is convenient but not necessary, as an alternative style is showArgs <- function(...) .Call("showArgs1", list(...))  Node:Missing and special values, Previous:Calling .External, Up:Interface functions .Call and .External ### Missing and special values One piece of error-checking the .C call does (unless NAOK is true) is to check for missing (NA) and IEEE special values (Inf, -Inf and NaN) and give an error if any are found. With the .Call interface these will be passed to our code. In this example the special values are no problem, as IEEE arithmetic will handle them correctly. In the current implementation this is also true of NA as it is a type of NaN, but it is unwise to rely on such details. Thus we will re-write the code to handle NAs using macros defined in Arith.h included by R.h. The code changes are the same in any of the versions of convolve2 or convolveE:  ... for(i = 0; i < na; i++) for(j = 0; j < nb; j++) if(ISNA(xa[i]) || ISNA(xb[j]) || ISNA(xab[i + j])) xab[i + j] = NA_REAL; else xab[i + j] += xa[i] * xb[j]; ...  Note that the ISNA macro, and the similar macros ISNAN (which checks for NaN or NA) and R_FINITE (which is false for NA and all the special values), only apply to numeric values of type double. Missingness of integers, logicals and character strings can be tested by equality to the constants NA_INTEGER, NA_LOGICAL and NA_STRING. These and NA_REAL can be used to set elements of R vectors to NA. The constants R_NaN, R_PosInf, R_NegInf and R_NaReal can be used to set doubles to the special values. Node:Evaluating R expressions from C, Next:, Previous:Interface functions .Call and .External, Up:System and foreign language interfaces ## Evaluating R expressions from C We noted that the call_R interface could be used to evaluate R expressions from C code, but the current interfaces are much more convenient to use. The main function we will use is SEXP eval(SEXP expr, SEXP rho);  the equivalent of the interpreted R code eval(expr, envir = rho), although we can also make use of findVar, defineVar and findFun (which restricts the search to functions). To see how this might be applied, here is a simplified internal version of lapply for expressions, used as a <- list(a = 1:5, b = rnorm(10), test = runif(100)) .Call("lapply", a, quote(sum(x)), new.env())  with C code SEXP lapply(SEXP list, SEXP expr, SEXP rho) { int i, n = length(list); SEXP ans; if(!isNewList(list)) error("list' must be a list"); if(!isEnvironment(rho)) error("rho' should be an environment"); PROTECT(ans = allocVector(VECSXP, n)); for(i = 0; i < n; i++) { defineVar(install("x"), VECTOR_ELT(list, i), rho); SET_VECTOR_ELT(ans, i, eval(expr, rho)); } setAttrib(ans, R_NamesSymbol, getAttrib(list, R_NamesSymbol)); UNPROTECT(1); return(ans); }  It would be closer to lapply if we could pass in a function rather than an expression. One way to do this is via interpreted R code as in the next example, but it is possible (if somewhat obscure) to do this in C code. The following is based on the code in src/main/optimize.c. SEXP lapply2(SEXP list, SEXP fn, SEXP rho) { int i, n = length(list); SEXP R_fcall, ans; if(!isNewList(list)) error("list' must be a list"); if(!isFunction(fn)) error("fn' must be a function"); if(!isEnvironment(rho)) error("rho' should be an environment"); PROTECT(R_fcall = lang2(fn, R_NilValue)); PROTECT(ans = allocVector(VECSXP, n)); for(i = 0; i < n; i++) { SETCADR(R_fcall, VECTOR_ELT(list, i)); SET_VECTOR_ELT(ans, i, eval(R_fcall, rho)); } setAttrib(ans, R_NamesSymbol, getAttrib(list, R_NamesSymbol)); UNPROTECT(2); return(ans); }  used by .Call("lapply2", a, sum, new.env())  Function lang2 creates an executable list' of two elements, but this will only be clear to those with a knowledge of a LISP-like language. ### Zero-finding In this section we re-work the example of call_S in Becker, Chambers & Wilks (1988) on finding a zero of a univariate function, which used to be used as an example for call_R in the now defunct demo(dynload). The R code and an example are zero <- function(f, guesses, tol = 1e-7) { f.check <- function(x) { x <- f(x) if(!is.numeric(x)) stop("Need a numeric result") as.double(x) } .Call("zero", body(f.check), as.double(guesses), as.double(tol), new.env()) } cube1 <- function(x) (x^2 + 1) * (x - 1.5) zero(cube1, c(0, 5))  where this time we do the coercion and error-checking in the R code. The C code is SEXP mkans(double x) { SEXP ans; PROTECT(ans = allocVector(REALSXP, 1)); REAL(ans)[0] = x; UNPROTECT(1); return ans; } double feval(double x, SEXP f, SEXP rho) { defineVar(install("x"), mkans(x), rho); return(REAL(eval(f, rho))[0]); } SEXP zero(SEXP f, SEXP guesses, SEXP stol, SEXP rho) { double x0 = REAL(guesses)[0], x1 = REAL(guesses)[1], tol = REAL(stol)[0]; double f0, f1, fc, xc; if(tol <= 0.0) error("non-positive tol value"); f0 = feval(x0, f, rho); f1 = feval(x1, f, rho); if(f0 == 0.0) return mkans(x0); if(f1 == 0.0) return mkans(x1); if(f0*f1 > 0.0) error("x[0] and x[1] have the same sign"); for(;;) { xc = 0.5*(x0+x1); if(fabs(x0-x1) < tol) return mkans(xc); fc = feval(xc, f, rho); if(fc == 0) return mkans(xc); if(f0*fc > 0.0) { x0 = xc; f0 = fc; } else { x1 = xc; f1 = fc; } } }  The C code is essentially unchanged from the call_R version, just using a couple of functions to convert from double to SEXP and to evaluate f.check. ### Calculating numerical derivatives We will use a longer example (by Saikat DebRoy) to illustrate the use of evaluation and .External. This calculates numerical derivatives, something that could be done as effectively in interpreted R code but may be needed as part of a larger C calculation. An interpreted R version and an example are numeric.deriv <- function(expr, theta, rho=sys.frame(sys.parent())) { eps <- sqrt(.Machine$double.eps)
ans <- eval(substitute(expr), rho)
dimnames=list(NULL, theta))
for (i in seq(along=theta)) {
old <- get(theta[i], envir=rho)
delta <- eps * min(1, abs(old))
assign(theta[i], old+delta, envir=rho)
ans1 <- eval(substitute(expr), rho)
assign(theta[i], old, envir=rho)
grad[, i] <- (ans1 - ans)/delta
}
ans
}
omega <- 1:5; x <- 1; y <- 2
numeric.deriv(sin(omega*x*y), c("x", "y"))


where expr is an expression, theta a character vector of variable names and rho the environment to be used.

For the compiled version the call from R will be

.External("numeric_deriv", expr, theta, rho)


with example usage

.External("numeric_deriv", quote(sin(omega*x*y)),
c("x", "y"), .GlobalEnv)


Note the need to quote the expression to stop it being evaluated.

Here is the complete C code which we will explain section by section.

#include <R.h> /* for DOUBLE_EPS */
#include <Rinternals.h>

SEXP numeric_deriv(SEXP args)
{
SEXP theta, expr, rho, ans, ans1, gradient, par, dimnames;
double tt, xx, delta, eps = sqrt(DOUBLE_EPS);
int start, i, j;

error("theta should be of type character");
error("rho should be an environment");

PROTECT(ans = coerceVector(eval(expr, rho), REALSXP));

for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(ans)) {
PROTECT(par = findVar(install(CHAR(STRING_ELT(theta, i))), rho));
tt = REAL(par)[0];
xx = fabs(tt);
delta = (xx < 1) ? eps : xx*eps;
REAL(par)[0] += delta;
PROTECT(ans1 = coerceVector(eval(expr, rho), REALSXP));
for(j = 0; j < LENGTH(ans); j++)
(REAL(ans1)[j] - REAL(ans)[j])/delta;
REAL(par)[0] = tt;
UNPROTECT(2); /* par, ans1 */
}

PROTECT(dimnames = allocVector(VECSXP, 2));
SET_VECTOR_ELT(dimnames, 1,  theta);
UNPROTECT(3); /* ans  gradient  dimnames */
return ans;
}


The code to handle the arguments is

  expr = CADR(args);
error("theta should be of type character");
error("rho should be an environment");


Note that we check for correct types of theta and rho but do not check the type of expr. That is because eval can handle many types of R objects other than EXPRSXP. There is no useful coercion we can do, so we stop with an error message if the arguments are not of the correct mode.

The first step in the code is to evaluate the expression in the environment rho, by

  PROTECT(ans = coerceVector(eval(expr, rho), REALSXP));


We then allocate space for the calculated derivative by

  PROTECT(gradient = allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta)));


The first argument to allocMatrix gives the SEXPTYPE of the matrix: here we want it to be REALSXP. The other two arguments are the numbers of rows and columns.

  for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(ans)) {
PROTECT(par = findVar(install(CHAR(STRING_ELT(theta, i))), rho));


Here, we are entering a for loop. We loop through each of the variables. In the for loop, we first create a symbol corresponding to the i'th element of the STRSXP theta. Here, STRING_ELT(theta, i) accesses the i'th element of the STRSXP theta. Macro CHAR() extracts the actual character representation of it: it returns a pointer. We then install the name and use findVar to find its value.

    tt = REAL(par)[0];
xx = fabs(tt);
delta = (xx < 1) ? eps : xx*eps;
REAL(par)[0] += delta;
PROTECT(ans1 = coerceVector(eval(expr, rho), REALSXP));


We first extract the real value of the parameter, then calculate delta, the increment to be used for approximating the numerical derivative. Then we change the value stored in par (in environment rho) by delta and evaluate expr in environment rho again. Because we are directly dealing with original R memory locations here, R does the evaluation for the changed parameter value.

    for(j = 0; j < LENGTH(ans); j++)
(REAL(ans1)[j] - REAL(ans)[j])/delta;
REAL(par)[0] = tt;
UNPROTECT(2);
}


Now, we compute the i'th column of the gradient matrix. Note how it is accessed: R stores matrices by column (like FORTRAN).

  PROTECT(dimnames = allocVector(VECSXP, 2));
SET_VECTOR_ELT(dimnames, 1, theta);
UNPROTECT(3);
return ans;
}


First we add column names to the gradient matrix. This is done by allocating a list (a VECSXP) whose first element, the row names, is NULL (the default) and the second element, the column names, is set as theta. This list is then assigned as the attribute having the symbol R_DimNamesSymbol. Finally we set the gradient matrix as the gradient attribute of ans, unprotect the remaining protected locations and return the answer ans.

Node:Debugging, Previous:Evaluating R expressions from C, Up:System and foreign language interfaces

## Debugging compiled code

Sooner or later programmers will be faced with the need to debug compiled code loaded into R. Some "tricks" are worth knowing.

Node:Finding entry points, Next:, Previous:Debugging, Up:Debugging

### Finding entry points in dynamically loaded code

Under most compilation environments, compiled code dynamically loaded into R cannot have breakpoints set within it until it is loaded. To use a symbolic debugger on such dynamically loaded code under UNIX use

• Call the debugger on the R executable, for example by R -d gdb.
• Start R.
• At the R prompt, use dyn.load or library to load your library.
• Send an interrupt signal. This will put you back to the debugger prompt.
• Set the breakpoints in your code.
• Continue execution of R by typing signal 0<RET>.

Under Windows the R engine is itself in a DLL, and the procedure is

• Start R under the debugger after setting a breakpoint for WinMain.
gdb .../bin/Rgui.exe
(gdb) break WinMain
(gdb) run
[ stops with R.dll loaded ]
(gdb) continue
[ stops with console running ]
(gdb) continue

• At the R prompt, use dyn.load or library to load your library.
• Set the breakpoints in your code.
• Use
(gdb) clear R_ReadConsole
(gdb) continue


to continue running with the breakpoints set.

Windows has little support for signals, so the usual idea of running a program under a debugger and sending it a signal to interrupt it and drop control back to the debugger only works with some debuggers.

Node:Inspecting R objects, Previous:Finding entry points, Up:Debugging

### Inspecting R objects when debugging

The key to inspecting R objects from compiled code is the function PrintValue(SEXP s) which uses the normal R printing mechanisms to print the R object pointed to by s, or the safer version R_PV(SEXP s) which will only print objects'.

One way to make use to PrintValue is to insert suitable calls into the code to be debugged.

Another way is to call R_PV from the symbolic debugger. (PrintValue is hidden as Rf_PrintValue.) For example, from gdb we can use

(gdb) p R_PV(ab)


using the object ab from the convolution example, if we have placed a suitable breakpoint in the convolution C code.

To examine an arbitrary R object we need to work a little harder. For example, let

R> DF <- data.frame(a = 1:3, b = 4:6)


By setting a breakpoint at do_get and typing get("DF") at the R prompt, one can find out the address in memory of DF, for example

Value returned is $1 = (SEXPREC *) 0x40583e1c (gdb) p *$1
$2 = { sxpinfo = {type = 19, obj = 1, named = 1, gp = 0, mark = 0, debug = 0, trace = 0, = 0}, attrib = 0x40583e80, u = { vecsxp = { length = 2, type = {c = 0x40634700 "0>X@D>X@0>X@", i = 0x40634700, f = 0x40634700, z = 0x40634700, s = 0x40634700}, truelength = 1075851272, }, primsxp = {offset = 2}, symsxp = {pname = 0x2, value = 0x40634700, internal = 0x40203008}, listsxp = {carval = 0x2, cdrval = 0x40634700, tagval = 0x40203008}, envsxp = {frame = 0x2, enclos = 0x40634700}, closxp = {formals = 0x2, body = 0x40634700, env = 0x40203008}, promsxp = {value = 0x2, expr = 0x40634700, env = 0x40203008} } }  (Debugger output reformatted for better legibility). Using R_PV() one can "inspect" the values of the various elements of the SEXP, for example, (gdb) p R_PV($1->attrib)
$names [1] "a" "b"$row.names
[1] "1" "2" "3"

$class [1] "data.frame"$3 = void


To find out where exactly the corresponding information is stored, one needs to go "deeper":

(gdb) set $a =$1->attrib
(gdb) p $a->u.listsxp.tagval->u.symsxp.pname->u.vecsxp.type.c$4 = 0x405d40e8 "names"
(gdb) p $a->u.listsxp.carval->u.vecsxp.type.s[1]->u.vecsxp.type.c$5 = 0x40634378 "b"
(gdb) p $1->u.vecsxp.type.s[0]->u.vecsxp.type.i[0]$6 = 1
(gdb) p $1->u.vecsxp.type.s[1]->u.vecsxp.type.i[1]$7 = 5


Node:The R API, Next:, Previous:System and foreign language interfaces, Up:Top

# The R API: entry points for C code

There are a large number of entry points in the R executable/DLL that can be called from C code (and some that can be called from FORTRAN code). Only those documented here are stable enough that they will only be changed with considerable notice.

The recommended procedure to use these is to include the header file R.h in your C code by

#include <R.h>


This will include several other header files from the directory R_HOME/include/R_ext, and there are other header files there that can be included too, but many of the features they contain should be regarded as undocumented and unstable.

An alternative is to include the header file S.h, which may be useful when porting code from S. This includes rather less than R.h, and has some compatibility definitions (for example the S_complex type from S).

Most of these header files, including all those included by R.h, can be used from C++ code.

Note: Because R re-maps many of its external names to avoid clashes with user code, it is essential to include the appropriate header files when using these entry points.

Node:Memory allocation, Next:, Previous:The R API, Up:The R API

## Memory allocation

There are two types of memory allocation available to the C programmer, one in which R manages the clean-up and the other in which user has full control (and responsibility).

Node:Transient, Next:, Previous:Memory allocation, Up:Memory allocation

### Transient storage allocation

Here R will reclaim the memory at the end of the call to .C. Use

char* R_alloc(long n, int size)


which allocates n units of size bytes each. A typical usage (from package mva) is

x = (int *) R_alloc(nrows(merge)+2, sizeof(int));


There is a similar call, S_alloc, for compatibility with S, which differs only in zeroing the memory allocated, and

S_realloc(char *p, long new, long old, int size)


which changes the allocation size from old to new units, and zeroes the additional units.

This memory is taken from the heap, and released at the end of the .C, .Call or .External call. Users can also manage it, by noting the current position with a call to vmaxget and clearing memory allocated subsequently by a call to vmaxset. This is only recommended for experts.

Node:User-controlled, Previous:Transient, Up:Memory allocation

### User-controlled memory

The other form of memory allocation is an interface to malloc, the interface providing R error handling. This memory lasts until freed by the user and is additional to the memory allocated for the R workspace.

The interface functions are

type* Calloc(size_t n, type)
type* Realloc(any *p, size_t n, type)
void Free(any *p)


providing analogues of calloc, realloc and free. If there is an error it is handled by R, so if these routines return the memory has been successfully allocated or freed. Free will set the pointer p to NULL. (Some but not all versions of S do so.)

Node:Error handling, Next:, Previous:Memory allocation, Up:The R API

## Error handling

The basic error handling routines are the equivalents of stop and warning in R code, and use the same interface.

void error(const char * format, ...);
void warning(const char * format, ...);


These have the same call sequences as calls to printf, but in the simplest case can be called with a single character string argument giving the error message. (Don't do this if the string contains % or might otherwise be interpreted as a format.)

There is also an S-compatibility interface which uses calls of the form

PROBLEM ...... ERROR
MESSAGE ...... WARN
PROBLEM ...... RECOVER(NULL_ENTRY)
MESSAGE ...... WARNING(NULL_ENTRY)


the last two being the forms available in all S versions. Here ...... is a set of arguments to printf, so can be a string or a format string followed by arguments separated by commas.

### Error handling from FORTRAN

There are two interface function provided to call error and warning from FORTRAN code, in each case with a simple character string argument. They are defined as

subroutine rexit(message)
subroutine rwarn(message)


Messages of more than 255 characters are truncated, with a warning.

Node:Random numbers, Next:, Previous:Error handling, Up:The R API

## Random number generation

The interface to R's internal random number generation routines is

double unif_rand();
double norm_rand();
double exp_rand();


giving one uniform, normal or exponential pseudo-random variate. However, before these are used, the user must call

GetRNGstate();


and after all the required variates have been generated, call

PutRNGstate();


These essentially read in (or create) .Random.seed and write it out after use.

File S.h defines seed_in and seed_out for S-compatibility rather than GetRNGstate and PutRNGstate. These take a long * argument which is ignored.

The random number generator is private to R; there is no way to select the kind of RNG or set the seed except by evaluating calls to the R functions.

The C code behind R's rxxx functions can be accessed by including the header file Rmath.h; See Distribution functions. Those calls generate a single variate and should also be enclosed in calls to GetRNGstate and PutRNGstate.

Node:Missing and IEEE values, Next:, Previous:Random numbers, Up:The R API

## Missing and IEEE special values

It is possible to compile R on a platform without IEC 559 (more commonly known as IEEE 754)-compatible arithmetic, so users should not assume that it is available. Rather a set of functions is provided to test for NA, Inf, -Inf (which exists on all platforms) and NaN. These functions are accessed via macros:

ISNA(x)        True for R's NA only
ISNAN(x)       True for R's NA and IEEE NaN
R_FINITE(x)    False for Inf, -Inf, NA, NaN


and function R_IsNaN is true for NaN but not NA. Do use these rather than isnan or finite; the latter in particular is often mendacious.

You can check for Inf or -Inf by testing equality to R_PosInf or R_NegInf, and set (but not test) an NA as NA_REAL.

All of the above apply to double variables only. For integer variables there is a variable accessed by the macro NA_INTEGER which can used to set or test for missingness.

Beware that these special values may be represented by extreme values which could occur in ordinary computations which run out of control, so you may need to test that they have not been generated inadvertently.

Node:Printing, Next:, Previous:Missing and IEEE values, Up:The R API

## Printing

The most useful function for printing from a C routine compiled into R is Rprintf. This is used in exactly the same way as printf, but is guaranteed to write to R's output (which might be a GUI console rather than a file). It is wise to write complete lines (including the "\n") before returning to R.

The function REprintf is similar but writes on the error stream (stderr) which may or may not be different from the standard output stream. Functions Rvprintf and REvprintf are the analogues using the vprintf interface.

### Printing from FORTRAN

In theory FORTRAN write and print statements can be used, but the output may not interleave well with that of C, and will be invisible on GUI interfaces. They are best avoided.

Three subroutines are provided to ease the output of information from FORTRAN code.

subroutine dblepr(label, nchar, data, ndata)
subroutine realpr(label, nchar, data, ndata)
subroutine intpr (label, nchar, data, ndata)


Here label is a character label of up to 255 characters, nchar is its length (which can be -1 if the whole label is to be used), and data is an array of length at least ndata of the appropriate type (double precision, real and integer respectively). These routines print the label on one line and then print data as if it were an R vector on subsequent line(s). They work with zero ndata, and so can be used to print a label alone.

Node:Calling C from FORTRAN and vice versa, Next:, Previous:Printing, Up:The R API

## Calling C from FORTRAN and vice versa

Naming conventions for symbols generated by FORTRAN differ by platform: it is not safe to assume that FORTRAN names appear to C with a trailing underscore. To help cover up the platform-specific differences there is a set of macros that should be used.

F77_SUB(name)
to define a function in C to be called from FORTRAN
F77_NAME(name)
to declare a FORTRAN routine in C before use
F77_CALL(name)
to call a FORTRAN routine from C
F77_COMDECL(name)
to declare a FORTRAN common block in C
F77_COM(name)
to access a FORTRAN common block from C

On most current platforms these are all the same, but it is unwise to rely on this.

For example, suppose we want to call R's normal random numbers from FORTRAN. We need a C wrapper along the lines of

#include <R.h>

void F77_SUB(rndstart)(void) { GetRNGstate(); }
void F77_SUB(rndend)(void) { PutRNGstate(); }
double F77_SUB(normrnd)(void) { return norm_rand(); }


to be called from FORTRAN as in

      subroutine testit()
double precision normrnd, x
call rndstart()
x = normrnd()
call dblepr("X was", 5, x, 1)
call rndend()
end


Note that this is not guaranteed to be portable, for the return conventions might not be compatible between the C and FORTRAN compilers used. (Passing values via arguments is safer.)

The standard packages, for example modreg, are a rich source of further examples.

Node:Numerical analysis subroutines, Next:, Previous:Calling C from FORTRAN and vice versa, Up:The R API

## Numerical analysis subroutines

R contains a large number of mathematical functions for its own use, for example numerical linear algebra computations and special functions.

The header file R_ext/Linpack.h contains details of the BLAS, LINPACK and EISPACK linear algebra functions included in R. These are expressed as calls to FORTRAN subroutines, and they will also be usable from users' FORTRAN code. Although not part of the official API, this set of subroutines is unlikely to change (but might be supplemented).

The header file Rmath.h lists many other functions that are available and documented in the following subsections. Many of these are C interfaces to the code behind R functions, so the R function documentation may give further details.

Node:Distribution functions, Next:, Previous:Numerical analysis subroutines, Up:Numerical analysis subroutines

### Distribution functions

The routines used to calculate densities, cumulative distribution functions and quantile functions for the standard statistical distributions are available as entry points.

The arguments for the entry points follow the pattern of those for the normal distribution:

double dnorm(double x, double mu, double sigma, int give_log);
double pnorm(double x, double mu, double sigma, int lower_tail,
int give_log);
double qnorm(double p, double mu, double sigma, int lower_tail,
int log_p);
double rnorm(double mu, double sigma);


That is, the first argument gives the position for the density and CDF and probability for the quantile function, followed by the distribution's parameters. Argument lower_tail should be TRUE (or 1) for normal use, but can be FALSE (or 0) if the probability of the upper tail is desired or specified.

Finally, give_log should be non-zero if the result is required on log scale, and log_p should be non-zero if p has been specified on log scale.

Note that you directly get the cumulative (or "integrated") hazard function, H(t) = - log(1 - F(t)), by using

- pdist(t, ..., /*lower_tail = */ FALSE, /* give_log = */ TRUE)


or shorter (and more cryptic) - pdist(t, ..., 0, 1).

The random-variate generation routine rnorm returns one normal variate. See Random numbers, for the protocol in using the random-variate routines.

Note that these argument sequences are (apart from the names and that rnorm has no n) exactly the same as the corresponding R functions of the same name, so the documentation of the R functions can be used.

For reference, the following table gives the basic name (to be prefixed by d, p, q or r apart from the exceptions noted) and distribution-specific arguments for the complete set of distributions.

 beta beta a, b non-central beta nbeta a, b, lambda binomial binom n, p Cauchy cauchy location, scale chi-squared chisq df non-central chi-squared nchisq df, lambda exponential exp scale F f n1, n2 non-central F nf (*) n1, n2, ncp gamma gamma shape, scale geometric geom p hypergeometric hyper NR, NB, n logistic logis location, scale lognormal lnorm logmean, logsd negative binomial nbinom n, p normal norm mu, sigma Poisson pois lambda Student's t t n non-central t nt (*) df, delta Studentized range tukey (*) rr, cc, df uniform unif a, b Weibull weibull shape, scale Wilcoxon rank sum wilcox m, n Wilcoxon signed rank signrank n

Entries marked only have p and q functions available.

The argument names are not all quite the same as the R ones.

Node:Mathematical functions, Next:, Previous:Distribution functions, Up:Numerical analysis subroutines

### Mathematical functions

 double gammafn (double x) Function double lgammafn (double x) Function double digamma (double x) Function double trigamma (double x) Function double tetragamma (double x) Function double pentagamma (double x) Function
 The Gamma function, its natural logarithm and first four derivatives.

 double beta (double a, double b) Function double lbeta (double a, double b) Function
 The (complete) Beta function and its natural logarithm.

 double choose (double n, double k) Function double lchoose (double n, double k) Function
 The number of combinations of k items chosen from from n and its natural logarithm. n and k are rounded to the nearest integer.

 double bessel_i (double x, double nu, double expo) Function double bessel_j (double x, double nu) Function double bessel_k (double x, double nu, double expo) Function double bessel_y (double x, double nu) Function
 Bessel functions of types I, J, K and Y with index nu. For bessel_i and bessel_k there is the option to return exp(-x) I(x; nu) or exp(x) K(x; nu) if expo is 2. (Use expo == 1 for unscaled values.)

Node:Utilities, Next:, Previous:Mathematical functions, Up:Numerical analysis subroutines

### Utilities

There are a few other numerical utility functions available as entry points.

 double R_pow (double x, double y) Function double R_pow_di (double x, int i) Function
 R_pow(x, y) and R_pow_di(x, i) compute x^y and x^i, respectively using R_FINITE checks and returning the proper result (the same as R) for the cases where x, y or i are 0 or missing or infinite or NaN.

 double pythag (double a, double b) Function
 pythag(a, b) computes sqrt(a^2 + b^2) without overflow or destructive underflow: for example it still works when both a and b are between 1e200 and 1e300 (in IEEE double precision).

 double log1p (x) Function
 Computes log(1 + x) (log 1 plus x), accurately even for small x, i.e. |x| << 1. This may be provided by your platform, in which case it is not included in Rmath.h, but is (probably) in math.h. For backwards compatibility with R versions prior to 1.5.0, the entry point Rf_log1p is still provided.

 double expm1 (x) Function
 Computes exp(x) - 1 (exp x minus 1), accurately even for small x, i.e. |x| << 1. This may be provided by your platform, in which case it is not included in Rmath.h, but is (probably) in math.h.

 int imax2 (int x, int y) Function int imin2 (int x, int y) Function double fmax2 (double x, double y) Function double fmin2 (double x, double y) Function
 Return the larger (max) or smaller (min) of two integer or double numbers, respectively.

 double sign (double x) Function
 Compute the signum function, where sign(x) is 1, 0, or -1, when x is positive, 0, or negative, respectively.

 double fsign (double x, double y) Function
 Performs "transfer of sign" and is defined as |x| * sign(x).

 double fprec (double x, double digits) Function
 Returns the value of x rounded to digits decimal digits (after the decimal point). This is the function used by R's round().

 double fround (double x, double digits) Function
 Returns the value of x rounded to digits significant decimal digits. This is the function used by R's signif().

 double ftrunc (double x) Function
 Returns the value of x truncated (to an integer value) towards zero.

Node:Mathematical constants, Previous:Utilities, Up:Numerical analysis subroutines

### Mathematical constants

R has a set of commonly used mathematical constants encompassing constants usually found math.h and contains further ones that are used in statistical computations. All these are defined to (at least) 30 digits accuracy in Rmath.h. The following definitions use ln(x) for the natural logarithm (log(x) in R).

 Name Definition (ln = log) round(value, 7) M_E e 2.7182818 M_LOG2E log2(e) 1.4426950 M_LOG10E log10(e) 0.4342945 M_LN2 ln(2) 0.6931472 M_LN10 ln(10) 2.3025851 M_PI pi 3.1415927 M_PI_2 pi/2 1.5707963 M_PI_4 pi/4 0.7853982 M_1_PI 1/pi 0.3183099 M_2_PI 2/pi 0.6366198 M_2_SQRTPI 2/sqrt(pi) 1.1283792 M_SQRT2 sqrt(2) 1.4142136 M_SQRT1_2 1/sqrt(2) 0.7071068 M_SQRT_3 sqrt(3) 1.7320508 M_SQRT_32 sqrt(32) 5.6568542 M_LOG10_2 log10(2) 0.3010300 M_2PI 2*pi 6.2831853 M_SQRT_PI sqrt(pi) 1.7724539 M_1_SQRT_2PI 1/sqrt(2*pi) 0.3989423 M_SQRT_2dPI sqrt(2/pi) 0.7978846 M_LN_SQRT_PI ln(sqrt(pi)) 0.5723649 M_LN_SQRT_2PI ln(sqrt(2*pi)) 0.9189385 M_LN_SQRT_PId2 ln(sqrt(pi/2)) 0.2257914

There are a set of constants (PI, DOUBLE_EPS) defined in the included header R_ext/Constants.h, the latter two mainly for compatibility with S.

Further, the included header R_ext/Boolean.h has constants TRUE and FALSE = 0 of type Rboolean in order to provide a way of using "logical" variables in C consistently.

Node:Optimization, Next:, Previous:Numerical analysis subroutines, Up:The R API

## Optimization

The C code underlying optim can be accessed directly. The user needs to supply a function to compute the function to be minimized, of the type

typedef double optimfn(int n, double *par, void *ex);


where the first argument is the number of parameters in the second argument. The third argument is a pointer passed down from the calling routine, normally used to carry auxiliary information.

Some of the methods also require a gradient function

typedef double optimgr(int n, double *par, double *gr, void *ex);


which passes back the gradient in the gr argument. No function is provided for finite-differencing, nor for approximating the Hessian at the result.

The interfaces are

void nmmin(int n, double *xin, double *x, double *Fmin, optimfn fn,
int *fail, double abstol, double intol, void *ex,
double alpha, double beta, double gamma, int trace,
int *fncount, int maxit);

• BFGS:
void vmmin(int n, double *x, double *Fmin,
optimfn fn, optimgr gr, int maxit, int trace,
int *mask, double abstol, double reltol, int nREPORT,
void *ex, int *fncount, int *grcount, int *fail);

void cgmin(int n, double *xin, double *x, double *Fmin,
optimfn fn, optimgr gr, int *fail, double abstol,
double intol, void *ex, int type, int trace,
int *fncount, int *grcount, int maxit);

• Limited-memory BFGS with bounds:
void lbfgsb(int n, int lmm, double *x, double *lower,
double *upper, int *nbd, double *Fmin, optimfn fn,
optimgr gr, int *fail, void *ex, double factr,
double pgtol, int *fncount, int *grcount,
int maxit, char *msg, int trace, int nREPORT);

• Simulated annealing:
void samin(int n, double *x, double *Fmin, optimfn fn, int maxit,
int tmax, double temp, int trace, void *ex);


Many of the arguments are common to the various methods. n is the number of parameters, x or xin is the starting parameters on entry and x the final parameters on exit, with final value returned in Fmin. Most of the other parameters can be found from the help page for optim: see the source code src/appl/lbfgsb.c for the values of nbd, which specifies which bounds are to be used.

Node:Integration, Next:, Previous:Optimization, Up:The R API

## Integration

The C code underlying integrate can be accessed directly. The user needs to supply a vectorizing C function to compute the function to be integrated, of the type

typedef void integr_fn(double *x, int n, void *ex);


where x[] is both input and output and has length n, i.e., a C function, say fn, of type integr_fn must basically do for(i in 1:n) x[i] := f(x[i], ex). The vectorization requirement can be used to speed up the integrand instead of calling it n times. Note that in the current implementation built on QUADPACK, n will be either 15 or 21. The ex argument is a pointer passed down from the calling routine, normally used to carry auxiliary information.

There are interfaces for definite and for indefinite integrals. Indefinite' means that at least one of the integration boundaries is not finite.

• Finite:
void Rdqags(integr_fn f, void *ex, double *a, double *b,
double *epsabs, double *epsrel,
double *result, double *abserr, int *neval, int *ier,
int *limit, int *lenw, int *last,
int *iwork, double *work);

• Indefinite:
void Rdqagi(integr_fn f, void *ex, double *bound, int *inf,
double *epsabs, double *epsrel,
double *result, double *abserr, int *neval, int *ier,
int *limit, int *lenw, int *last,
int *iwork, double *work);


Only the 3rd and 4th argument differ for the two integrators; for the definite integral, using Rdqags, a and b are the integration interval bounds, whereas for an indefinite integral, using Rdqagi, bound is the finite bound of the integration (if the integral is not doubly-infinite) and inf is a code indicating the kind of integration range,

inf = 1
corresponds to (bound, +Inf),
inf = -1
corresponds to (-Inf, bound),
inf = 2
corresponds to (-Inf, +Inf),

<-   <<-  [<-  [[<-  $<- + - * / ^ %% %*% %/% < <= == != >= > | || & && !  3. "Low level" 0- and 1-argument functions which belong to one of the following groups of functions: 1. Basic mathematical functions with a single argument, i.e., sign abs floor ceiling trunc sqrt exp cos sin tan acos asin atan cosh sinh tanh acosh asinh atanh cumsum cumprod cummax cummin Im Re Arg Conj Mod  Note however that the R function log has an optional named argument base, and therefore is defined as log <- function(x, base = exp(1)) { if(missing(base)) .Internal(log(x)) else .Internal(log(x, base)) }  in order to ensure that log(x = pi, base = 2) is identical to log(base = 2, x = pi). 2. Functions rarely used outside of "programming" (i.e., mostly used inside other functions), such as nargs missing interactive is.xxx .Primitive .Internal .External symbol.C symbol.For globalenv pos.to.env unclass  (where xxx stands for almost 30 different notions, such as function, vector, numeric, and so forth). 3. The programming and session management utilities debug undebug trace untrace browser proc.time  4. The following basic assignment and extractor functions length length<- class class<- attr attr<- attributes attributes<- dim dim<- dimnames dimnames<- environment<-  5. The following few N-argument functions are "primitive" for efficiency reasons. Care is taken in order to treat named arguments properly: : ~ c list unlist call as.call expression substitute UseMethod invisible .C .Fortran .Call  Node:Testing R code, Previous:.Internal and .Primitive, Up:R (internal) programming miscellanea ## Testing R code When you (as R developer) add new functions to the R base (all the packages distributed with R), be careful to check if make test-Specific or particularly, cd tests; make no-segfault.Rout still works (without interactive user intervention, and on a standalone computer). If the new function, for example, accesses the Internet, or requires GUI interaction, please add its name to the "stop list" in tests/no-segfault.Rin. Node:R coding standards, Next:, Previous:R (internal) programming miscellanea, Up:Top # R coding standards R is meant to run on a wide variety of platforms, including Linux and most variants of Unix as well as 32-bit Windows versions and on the Power Mac. Therefore, when extending R by either adding to the R base distribution or by providing an add-on package, one should not rely on features specific to only a few supported platforms, if this can be avoided. In particular, although most R developers use GNU tools, they should not employ the GNU extensions to standard tools. Whereas some other software packages explicitly rely on e.g. GNU make or the GNU C++ compiler, R does not. Nevertheless, R is a GNU project, and the spirit of the GNU Coding Standards should be followed if possible. The following tools can "safely be assumed" for R extensions. • An ISO 9899, also known as ISO C89 or ANSI C compiler. If you do not have access to this C standard, refer to the 2nd edition of Brian W. Kernighan & Dennis M. Ritchie, The C Programming Language. Any extensions, such as POSIX or ISO C99, must be tested for, typically using Autoconf (see Configure and cleanup). • A FORTRAN 77 compiler or f2c, the FORTRAN-to-C converter. • A simple make, considering the features of make in 4.2 BSD systems as a baseline. GNU or other extensions, including pattern rules using %, the automatic variable $^, the += syntax to append to the value of a variable, the ("safe") inclusion of makefiles with no error, conditional execution, and many more, must not be used (see Chapter "Features" in the GNU Make Manual for more information). On the other hand, building R in a separate directory (not containing the sources) should work provided that make supports the VPATH mechanism.

Windows-specific makefiles can assume GNU make 3.75 or later, as no other make is viable on that platform.

• A Bourne shell and the "traditional" Unix programming tools, including grep, sed, and awk.

There are POSIX standards for these tools, but these may not fully be supported, and the precise standards are typically hard to access. Baseline features could be determined from a book such as The UNIX Programming Environment by Brian W. Kernighan & Rob Pike. Note in particular that | in a regexp is an extended regexp, and is not supported by all versions of grep or sed.

Under Windows, these tools can be assumed because versions (specifically, of basename, cat, comm, cp, cut, diff, echo, egrep, expr, find, gawk, grep, ls, mkdir, mv, rm, sed, sort, tar, touch, unzip, wc and zip) are provided at <http://www.stats.ox.ac.uk/pub/Rtools/tools.zip>. However, redirection cannot be assumed to be available via system as this does not use a standard shell (let alone a Bourne shell).

• Perl version 5 is needed for converting documentation written in Rd format to plain text, HTML, LaTeX, and to extract the examples. In addition, several other tools, in particular check and build (see Checking and building packages), require Perl.

The R Core Team has decided that Perl (version 5) can safely be assumed for building R from source, building and checking add-on packages, and for installing add-on packages from source. On the other hand, Perl cannot be assumed at all for installing binary (pre-built) versions of add-on packages, or at run time.

• Makeinfo version 4 is needed to build the Info files for the R manuals written in the GNU Texinfo system. (Future distributions of R will contain the Info files.)

It is also important that code is written in a way that allows others to understand it. This is particularly helpful for fixing problems, and includes using self-descriptive variable names, commenting the code, and also formatting it properly. The R Core Team recommends to use a basic indentation of 4 for R and C (and most likely also Perl) code, and 2 for documentation in Rd format. Emacs users can implement this indentation style by putting the following in one of their startup files. (For GNU Emacs 20: for GNU Emacs 21 use customization to set the c-default-style to "bsd" and c-basic-offset to 4.)

;;; C
(lambda () (c-set-style "bsd")))
;;; ESS
(lambda ()
(ess-set-style 'C++)
;; Because
;;                                 DEF GNU BSD K&R C++
;; ess-indent-level                  2   2   8   5   4
;; ess-continued-statement-offset    2   2   8   5   4
;; ess-brace-offset                  0   0  -8  -5  -4
;; ess-arg-function-offset           2   4   0   0   0
;; ess-expression-offset             4   2   8   5   4
;; ess-else-offset                   0   0   0   0   0
;; ess-close-brace-offset            0   0   0   0   0
(lambda ()
(nuke-trailing-whitespace)))))
;;; Perl
(lambda () (setq perl-indent-level 4)))


(The GNU' styles for Emacs' C and R modes use a basic indentation of 2, which has been determined not to display the structure clearly enough when using narrow fonts.)

Node:Function and variable index, Next:, Previous:R coding standards, Up:Top

# Function and variable index

Node:Concept index, Previous:Function and variable index, Up:Top

# Concept index

#### Footnotes

1. Note that Ratfor is not supported. If you have Ratfor source code, you need to convert it to FORTRAN. On many Solaris systems mixing Ratfor and FORTRAN code will work.

2. This is not quite true. Unpaired braces will give problems and should be escaped. See the examples section in the file Paren.Rd for an example.

3. SEXP is an acronym for Simple EXPression, common in LISP-like language syntaxes.

4. You can assign a copy of the object in the environment frame rho using defineVar(symbol, duplicate(value), rho)).