The R Project SVN R

Rev

Rev 35847 | Rev 37455 | Go to most recent revision | Blame | Compare with Previous | Last modification | View Log | Download | RSS feed 

\name{options}
\alias{options}
\alias{.Options}
\alias{getOption}
\title{Options Settings}
\description{
  Allow the user to set and examine a variety of global \dQuote{options}
  which affect the way in which \R computes and displays its results.
}
\usage{
options(\dots)

getOption(x)

.Options
}
%%-- NOTE : Keep the list up-to-date,
%%-- ====   Consider also the leading comments in ../../../main/options.c
\arguments{
  \item{\dots}{any options can be defined, using \code{name = value} or
    by passing a list of such tagged values.  However, only the ones
    below are used in \dQuote{base \R}.
    Further, \code{options('name') == options()['name']}, see the example.
  }
  \item{x}{a character string holding an option name.}
}
\details{
  Invoking \code{options()} with no arguments returns a list with the
  current values of the options.  Note that not all options listed below
  are set initially.  To access the value of a single option, one should
  use \code{getOption("width")}, e.g., rather than
  \code{options("width")} which is a \emph{list} of length one.

  \code{.Options} also always contains the \code{options()} list (as a
  pairlist, unsorted), for S compatibility.  Assigning to it will make a
  local copy and not change the original.
}
\value{
  For \code{getOption}, the current value set for option \code{x}, or
  \code{NULL} if the option is unset.

  For \code{options()}, a list of all set options sorted by name.  For
  \code{options(name)}, a list of length one containing the set value,
  or \code{NULL} if it is unset.  For uses setting one or more options,
  a list with the previous values of the options changed (returned
  invisibly).
}
\section{Options used in base \R}{
  \describe{
    \item{\code{add.smooth}:}{typically logical, defaulting to
      \code{TRUE}.  Could also be set to an integer for specifying how
      many (simulated) smooths should be added.  This is currently only
      used by \code{\link[stats]{plot.lm}}.}

    \item{\code{check.bounds}:}{logical, defaulting to \code{FALSE}.  If
      true, a \link{warning} is produced whenever a \dQuote{generalized
      vector} (atomic or \code{\link{list}}) is extended, by something
      like \code{x <- 1:3; x[5] <- 6}.}

    \item{\code{continue}:}{a string setting the prompt used for lines
      which continue over one line.}

    \item{\code{defaultPackages}:}{the packages that are attached by
      default when \R starts up.  Initially set from value of the
      environment variable \env{R\_DEFAULT\_PACKAGES}, or if that is unset
      %%  default is set in ../../profile/Common.R :
      to \code{c("datasets", "utils", "grDevices", "graphics", "stats",
    "methods")}.  (Set \env{R\_DEFAULT\_PACKAGES} to \code{NULL} or
      a comma-separated list of package names.)   A call to
      \code{options} should be in your \file{.Rprofile} file to ensure
      that the change takes effect before the base package is
      initialized (see \code{\link{Startup}}).}

    \item{\code{digits}:}{controls the number of digits to print when
      printing numeric values.  It is a suggestion only.  Valid values
      are 1\dots22 with default 7.  See \code{\link{print.default}}.}

    \item{\code{download.file.method}:}{Method to be used for
      \code{download.file}.  Currently download methods
      \code{"internal"}, \code{"wget"} and \code{"lynx"} are available.
      There is no default for this option, when \code{method = "auto"}
      is chosen: see \code{\link{download.file}}.}

    % note use of \code as otherwise -- is an en-dash.
    \item{\code{echo}:}{logical.  Only used in non-interactive mode,
      when it controls whether input is echoed.  Command-line option
      \code{--slave} sets this initially to \code{FALSE}.}

    \item{\code{encoding}:}{The name of an encoding, default
      \code{"native.enc"}).  See \code{\link{connections}}.}

    \item{\code{error}:}{either a function or an expression governing
      the handling of non-catastrophic errors such as those generated by
      \code{\link{stop}} as well as by signals and internally detected
      errors.  If the option is a function, a call to that function,
      with no arguments, is generated as the expression.  The default
      value is \code{NULL}: see \code{\link{stop}} for the behaviour in
      that case.  The functions \code{\link{dump.frames}} and
      \code{\link{recover}} provide alternatives that allow post-mortem
      debugging.}

    \item{\code{expressions}:}{sets a limit on the number of nested
      expressions that will be evaluated.  Valid values are
      25\dots500000 with default 5000.  If you increase it, you may
      also want to start \R with a larger protection stack;
      see \code{--max-ppsize} in \code{\link{Memory}}.  Note too that
      you may cause a segfault from overflow of the C stack, and on OSes
      where it is possible you may want to increase that.}

    \item{\code{keep.source}:}{When \code{TRUE}, the source code for
      functions (newly defined or loaded) is stored in their
      \code{"source"} attribute (see \code{\link{attr}}) allowing
      comments to be kept in the right places.

      The default is \code{\link{interactive}()}, i.e., \code{TRUE} for
      interactive use.}

    \item{\code{keep.source.pkgs}:}{As for \code{keep.source}, for
      functions in packages loaded by \code{\link{library}} or
      \code{\link{require}}.  Defaults to \code{FALSE} unless the
      environment variable \env{R\_KEEP\_PKG\_SOURCE} is set to
      \code{yes}.

      Note this does not apply to packages using lazy-loading or saved
      images.  Whether they have kept source is determined when they are
      installed (and is almost certainly false).}

    \item{\code{mailer}:}{default mailer used by
      \code{\link{bug.report}()}.  Can be \code{"none"}.}

    \item{\code{max.print}:}{integer, defaulting to \code{10000}.
      \code{\link{print}} or \code{\link{show}} methods can make use of
      this option, to limit the amount of information that is printed,
      typically to something in the order \code{max.print} lines.

      This is not yet used in base \R.}

    \item{\code{OutDec}:}{one-character string.  The character to be
      used as the decimal point in output conversions, that is in
      printing, plotting and \code{as.character} but not deparsing.}

    \item{\code{pager}:}{the (stand-alone) program used for displaying
      text files on \R's console, also used by \code{\link{file.show}} and
      sometimes \code{\link{help}}.
#ifdef unix
      Defaults to \file{\$R\_HOME/bin/pager}.}
#endif
#ifdef windows
      Defaults to \code{"internal"}, which uses a pager similar to the
      GUI console.  Another possibility is \code{"console"} to use the
      console itself.}
#endif

    \item{\code{papersize}:}{the default paper format used by
      \code{\link{postscript}};  set by environment variable
      \env{R\_PAPERSIZE} when \R is started: if that is unset or invalid
      it defaults to
#ifdef unix
      \code{"a4"}.}
#endif
#ifdef windows
    \code{"a4"}, or \code{"letter"} in US and Canadian locales.}
#endif

    \item{\code{printcmd}:}{the command used by \code{\link{postscript}}
      for printing; set by environment variable \env{R\_PRINTCMD} when
      \R is started.  This should be a command that expects either input
      to be piped to \file{stdin} or to be given a single filename
      argument.}

    \item{\code{prompt}:}{a string, used for \R's prompt; should usually
      end in a blank (\code{" "}).}

    \item{\code{save.defaults}, \code{save.image.defaults}:}{
      see \code{\link{save}}.}

    \item{\code{scipen}:}{integer.  A penalty to be applied
      when deciding to print numeric values in fixed or exponential
      notation.  Positive values bias towards fixed and negative towards
      scientific notation: fixed notation will be preferred unless it is
      more than \code{scipen} digits wider.}

    \item{\code{show.error.messages}:}{a logical.  Should error messages
      be printed?  Intended for use with \code{\link{try}} or a
      user-installed error handler.}

    \item{\code{texi2dvi}:}{used by the unexported function
      \code{texi2dvi} in namespace \pkg{tools}.}

    \item{\code{timeout}:}{integer.  The timeout for some Internet
      operations, in seconds.  Default 60 seconds.  See
      \code{\link{download.file}} and \code{\link{connections}}.}

    \item{\code{topLevelEnvironment}:}{see \code{\link{topenv}} and
      \code{\link{sys.source}}.}

    \item{\code{verbose}:}{logical.  Should \R report extra information
      on progress?  Set to \code{TRUE} by the command-line option
      \option{--verbose}.}

    \item{\code{warn}:}{sets the handling of warning messages.  If
      \code{warn} is negative all warnings are ignored.  If \code{warn}
      is zero (the default) warnings are stored until the top--level
      function returns.  If fewer than 10 warnings were signalled they
      will be printed otherwise a message saying how many (max 50) were
      signalled.  A top--level variable called \code{last.warning} is
      created and can be viewed through the function
      \code{\link{warnings}}.  If \code{warn} is one, warnings are
      printed as they occur.  If \code{warn} is two or larger all
      warnings are turned into errors.}

    \item{\code{warning.expression}:}{an \R code expression to be called
      if a warning is generated, replacing the standard message.  If
      non-null it is called irrespective of the value of option
      \code{warn}.}

    \item{\code{warnings.length}:}{sets the truncation limit for error
      and warning messages.  A non-negative integer, with allowed values
      100\dots8192, default 1000.}

    \item{\code{width}:}{controls the number of characters on a line.
      You may want to change this if you re-size the window that \R is
      running in.  Valid values are 10\dots10000 with default normally
      80.  (The limits on valid values are in file \file{Print.h} and can be
      changed by re-compiling \R.)}
 }

  The \sQuote{factory-fresh} default settings of some of these options are
  \tabular{ll}{
    \code{add.smooth} \tab \code{TRUE}\cr
    \code{check.bounds} \tab \code{FALSE}\cr
    \code{continue} \tab \code{"+ "}\cr
    \code{digits} \tab \code{7}\cr
    \code{echo} \tab \code{TRUE}\cr
    \code{encoding} \tab \code{"native.enc"}\cr
    \code{error} \tab \code{NULL}\cr
    \code{expressions} \tab \code{5000}\cr
    \code{keep.source} \tab \code{interactive()}\cr
    \code{keep.source.pkgs} \tab \code{FALSE}\cr
    \code{max.print} \tab \code{1000}\cr
    \code{OutDec} \tab \code{"."}\cr
    \code{prompt} \tab \code{"> "}\cr
    \code{scipen} \tab \code{0} \cr
    \code{show.error.messages} \tab \code{TRUE}\cr
    \code{timeout} \tab \code{60}\cr
    \code{verbose} \tab \code{FALSE}\cr
    \code{warn} \tab \code{0}\cr
    \code{warnings.length} \tab \code{1000}\cr
    \code{width}  \tab \code{80}\cr
  }
  Others are set from environment variables or are platform-dependent.
}
\section{Options set in package grDevices}{
  These will be set when package \pkg{grDevices} (or its name space)
  is loaded if not already set.
  \describe{
    \item{\code{device}:}{a character string giving the default device
      for that session.  This defaults to the normal screen device
      (e.g., \code{x11}, \code{windows} or \code{quartz}) for an
      interactive session, and \code{postscript} in batch use or if a
      screen is not available.}

    \item{\code{locatorBell}:}{logical.  Should selection in \code{locator}
      and \code{identify} be confirmed by a bell.  Default \code{TRUE}.
      Honoured at least on \code{X11} and \code{windows} devices.}

#ifdef unix
    \item{\code{X11colortype}:}{The default colour type for
      \code{\link{X11}} devices.  Default \code{"true"}.}

    \item{\code{X11fonts}:}{character vector of length 2.
      See \code{\link{X11}}.}

    \item{\code{gamma}:}{double.  The default value of
      \code{gamma} for \code{\link{X11}} devices, defaulting to 1
      if unset (the default).}
#endif
#ifdef windows
    \item{\code{gamma}:}{double. The default value of
      \code{gamma} for \code{\link{windows}} devices, defaulting to 1
      if unset (the default).}

    \item{\code{graphics.record}:}{logical.  The default value of
      \code{record} for \code{\link{windows}} devices.  Default
      \code{FALSE}.}

    \item{\code{windowsBuffered}:}{logical.  Should
      \code{\link{windows}} devices be double-buffered?.  Default
      \code{TRUE}.}

    \item{\code{windowsTimeout}:}{integer vector of length 2
      representing two times in milliseconds.  These control the
      double-buffering of \code{\link{windows}} devices when that is
      enabled: the first is the delay after plotting finishes
      (default 100) and the second is the update interval during
      continuous plotting (default 500).}

    \item{\code{xpinch, ypinch}:}{double.  Pixels per inch, horizontally and
      vertically.  If unset (the default), taken from Windows.}
#endif
  }
}
\section{Options set in package stats}{
  These will be set when package \pkg{stats} (or its name space)
  is loaded if not already set.
  \describe{
    \item{\code{contrasts}:}{the default \code{\link{contrasts}} used in
      model fitting such as with \code{\link{aov}} or \code{\link{lm}}.
      A character vector of length two, the first giving the function to
      be used with unordered factors and the second the function to be
      used with ordered factors.  By default the elements are named
      \code{c("unordered", "ordered")}, but the names are unused.}

    \item{\code{na.action}:}{the name of a function for treating missing
      values (\code{\link{NA}}'s) for certain situations.}

    \item{\code{show.coef.Pvalues}:}{logical, affecting whether P
      values are printed in summary tables of coefficients.  See
      \code{\link{printCoefmat}}.}

    \item{\code{show.signif.stars}:}{logical, should stars be printed on
      summary tables of coefficients?  See \code{\link{printCoefmat}}.}

    \item{\code{ts.eps}:}{the relative tolerance for certain time series
      (\code{\link{ts}}) computations.  Default \code{1e-05}.}

    \item{\code{ts.S.compat}:}{logical.  Used to select S compatibility
      for plotting time-series spectra.  See the description of argument
      \code{log} in \code{\link{plot.spec}}.}
  }
}
\section{Options set in package utils}{
  These will be set when package \pkg{utils} (or its name space)
  is loaded if not already set.
  \describe{
    \item{\code{browser}:}{default HTML browser used by
      \code{\link{help.start}()} on UNIX, or a non-default browser on
      Windows.}

    \item{\code{de.cellwidth}:}{integer: the cell widths (number of
      characters) to be used in the data editor \code{\link{dataentry}}.
      If this is unset (the default), 0, negative or \code{NA}, variable
      cell widths are used.}

    \item{\code{editor}:}{sets the default text editor, e.g., for
      \code{\link{edit}}.  Set from the environment variable
      \code{VISUAL} on UNIX.}

    \item{\code{help.try.all.packages}:}{default for an argument of
      \code{\link{help}}.}

    \item{\code{internet.info}:}{The minimum level of information to be
      printed on URL downloads etc.  Default is 2, for failure causes.
      Set to 1 or 0 to get more information.}

    \item{\code{pkgType}:}{The default type of packages to be downloaded
      and installed -- see \code{\link{install.packages}}.
#ifdef windows
      Possible values are \code{"win.binary"} (the default) and
      \code{"source"}.}
#endif
#ifdef unix
      Possible values are \code{"source"} (the default except under the
      CRAN Mac OS X build) and \code{"mac.binary"}.}
#endif

    \item{\code{repos}:}{URLs of the repositories for use by
      \code{\link{update.packages}}.  Defaults to
      \code{c(CRAN="@CRAN@")}, a value that causes some utilities to
      prompt for a CRAN mirror.  To avoid this do set the CRAN mirror,
      by something like
      \code{local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cran";
                   options(repos=r)})}.

      Note that you can add more repositories (Bioconductor and
      Omegahat, notably) using \code{\link{setRepositories}()}.
    }
    \item{\code{SweaveHooks}, \code{SweaveSyntax}:}{see \code{\link{Sweave}}.}

    \item{\code{unzip}:}{the command used for unzipping help files.
#ifdef unix
      Defaults to the value of \env{R\_UNZIPCMD}, which is set in
      \file{etc/Renviron} if an \code{unzip} command was found during
      configuration.}
#endif
#ifdef windows
      Defaults to \code{"internal"} when the internal unzip code is
      used.}
#endif
  }
}

#ifdef unix
\section{Options used on Unix only}{
  \describe{
    \item{\code{latexcmd, dvipscmd}:}{character strings giving commands
      to be used in off-line printing of help pages.}

    \item{\code{pdfviewer}:}{default PDF viewer.  Set from the
      environment variable \env{R\_PDFVIEWER}.}
  }
}
#endif
#ifdef windows
\section{Options used on Windows only}{
  \describe{
    \item{\code{warn.FPU}:}{logical, by default undefined.  If true,
      a \link{warning} is produced whenever \link{dyn.load} repairs the
      control word damaged by a buggy DLL.}
  }
}
#endif

\references{
  Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988)
  \emph{The New S Language}.
  Wadsworth \& Brooks/Cole.
}
\examples{
options() # printing all current options
op <- options(); str(op) # nicer printing

options('width')[[1]] == options()$width # the latter needs more memory
options(digits = 20)
pi

# set the editor, and save previous value
old.o <- options(editor = "nedit")
old.o

options(check.bounds = TRUE, warn = 1)
x <- NULL; x[4] <- "yes" # gives a warning

options(digits=5)
print(1e5)
options(scipen=3); print(1e5)

options(op)     # reset (all) initial options
options('digits')

\dontrun{## set contrast handling to be like S
options(contrasts = c("contr.helmert", "contr.poly"))
}
\dontrun{## on error, terminate the R session with error status 66
options(error = quote(q("no", status=66, runLast=FALSE)))
stop("test it")
}
\dontrun{## Set error actions for debugging:
## enter browser on error, see ?recover:
options(error = recover)
## allows to call debugger() afterwards, see ?debugger:
options(error = dump.frames)
## A possible setting for non-interactive sessions
options(error = quote({dump.frames(to.file=TRUE); q()}))
}}
\keyword{environment}
\keyword{error}
\keyword{print}