R: Options Settings

options {base} | R Documentation

## Options Settings

### Description

Allow the user to set and examine a variety of global options which affect the way in which R computes and displays its results.

### Usage

    options(...)

    getOption(x, default = NULL)

    .Options

### Arguments

`...` | any options can be defined, using `name = value`. However, only the ones below are used in base R. Options can also be passed by giving a single unnamed argument which is a named list.
`x` | a character string holding an option name.
`default` | if the specified option is not set in the options list, this value is returned. This facilitates retrieving an option and checking whether it is set and setting it separately if not.

### Details

Invoking `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, e.g., `getOption("width")` rather than `options("width")` which is a list of length one.

### Value

For `getOption`, the current value set for option `x`, or `NULL` if the option is unset.

For `options()`, a list of all set options sorted by name. For `options(name)`, a list of length one containing the set value, or `NULL` if it is unset. For uses setting one or more options, a list with the previous values of the options changed (returned invisibly).

### Options used in base R

`add.smooth`:

  typically logical, defaulting to `TRUE`. Could also be set to an integer for specifying how many (simulated) smooths should be added. This is currently only used by `plot.lm`.

`browserNLdisabled`:

  logical: whether newline is disabled as a synonym for `"n"` is the browser.

`checkPackageLicense`:

  logical, not set by default. If true, `library` asks a user to accept any non-standard license at first use.

`check.bounds`:

  logical, defaulting to `FALSE`. If true, a warning is produced whenever a vector (atomic or `list`) is extended, by something like `x <- 1:3; x[5] <- 6`.

`CBoundsCheck`:

  logical, controlling whether `.C` and `.Fortran` make copies to check for array over-runs on the atomic vector arguments.

  Initially set from value of the environment variable R_C_BOUNDS_CHECK (set to `yes` to enable).

`continue`:

  a non-empty string setting the prompt used for lines which continue over one line.

`defaultPackages`:

  the packages that are attached by default when R starts up. Initially set from value of the environment variable R_DEFAULT_PACKAGES, or if that is unset to `c("datasets", "utils", "grDevices", "graphics", "stats", "methods")`. (Set R_DEFAULT_PACKAGES to `NULL` or a comma-separated list of package names.) A call to `options` should be in your ‘.Rprofile’ file to ensure that the change takes effect before the base package is initialized (see `Startup`).

`deparse.cutoff`:

  integer value controlling the printing of language constructs which are `deparse`d. Default `60`.

`deparse.max.lines`:

  controls the number of lines used when deparsing in `traceback`, `browser`, and upon entry to a function whose debugging flag is set. Initially unset, and only used if set to a positive integer.

`digits`:

  controls the number of digits to print when printing numeric values. It is a suggestion only. Valid values are 1...22 with default 7. See the note in `print.default` about values greater than 15.

`digits.secs`:

  controls the maximum number of digits to print when formatting time values in seconds. Valid values are 0...6 with default 0. See `strftime`.

`download.file.extra`:

  Extra command-line argument(s) for non-default methods: see `download.file`.

`download.file.method`:

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

`echo`:

  logical. Only used in non-interactive mode, when it controls whether input is echoed. Command-line option --slave sets this to `FALSE`, but otherwise it starts the session as `TRUE`.

`encoding`:

  The name of an encoding, default `"native.enc"`. See `connections`.

`error`:

  either a function or an expression governing the handling of non-catastrophic errors such as those generated by `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 `NULL`: see `stop` for the behaviour in that case. The functions `dump.frames` and `recover` provide alternatives that allow post-mortem debugging. Note that these need to specified as e.g. `options(error = utils::recover)` in startup files such as ‘.Rprofile’.

`expressions`:

  sets a limit on the number of nested expressions that will be evaluated. Valid values are 25...500000 with default 5000. If you increase it, you may also want to start R with a larger protection stack; see --max-ppsize in `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. Once the limit is reached an error is thrown. The current number under evaluation can be found by calling `Cstack_info`.

`keep.source`:

  When `TRUE`, the source code for functions (newly defined or loaded) is stored internally allowing comments to be kept in the right places. Retrieve the source by printing or using `deparse(fn, control = "useSource")`.

  The default is `interactive()`, i.e., `TRUE` for interactive use.

`keep.source.pkgs`:

  As for `keep.source`, used only when packages are installed. Defaults to `FALSE` unless the environment variable R_KEEP_PKG_SOURCE is set to `yes`.

`max.print`:

  integer, defaulting to `99999`. `print` or `show` methods can make use of this option, to limit the amount of information that is printed, to something in the order of (and typically slightly less than) `max.print` entries.

`OutDec`:

  character string containing a single-byte character. The preferred character to be used as the decimal point in output conversions, that is in printing, plotting, `format` and `as.character` but not when deparsing nor by `sprintf` nor `formatC` (which are sometimes used prior to printing.

`pager`:

  the command used for displaying text files by `file.show`. Defaults to ‘R_HOME/bin/pager’, which is a shell script running the command-line specified by the environment variable PAGER whose default is set at configuration, usually to `less`. Can be a character string or an R function, in which case it needs to accept the arguments `(files, header, title, delete.file)` corresponding to the first four arguments of `file.show`.

`papersize`:

  the default paper format used by `postscript`; set by environment variable R_PAPERSIZE when R is started: if that is unset or invalid it defaults to a value derived from the locale category `LC_PAPER`, or if that is unavailable to a default set when R was built.

`pdfviewer`:

  default PDF viewer. The default is set from the environment variable R_PDFVIEWER, the default value of which is set when R is configured.

`printcmd`:

  the command used by `postscript` for printing; set by environment variable R_PRINTCMD when R is started. This should be a command that expects either input to be piped to ‘stdin’ or to be given a single filename argument. Usually set to `"lpr"` on a Unix-alike.

`prompt`:

  a non-empty string to be used for R's prompt; should usually end in a blank (`" "`).

`rl_word_breaks`:

  Used for the readline-based terminal interface. Default value `" \t\n\"\\'`><=%;,|&{()}"`.

  This is the set of characters use to break the input line into tokens for object- and file-name completion. Those who do not use spaces around operators may prefer
  `" \t\n\"\\'`><=+-*%;,|&{()}"`

`save.defaults`, `save.image.defaults`:

  see `save`.

`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 `scipen` digits wider.

`showWarnCalls`, `showErrorCalls`:

  a logical. Should warning and error messages show a summary of the call stack? By default error calls are shown in non-interactive sessions.

`showNCalls`:

  integer. Controls how long the sequence of calls must be (in bytes) before ellipses are used. Defaults to 40 and should be at least 30 and no more than 500.

`show.error.locations`:

  Should source locations of errors be printed? If set to `TRUE` or `"top"`, the source location that is highest on the stack (the most recent call) will be printed. `"bottom"` will print the location of the earliest call found on the stack.

  Integer values can select other entries. The value `0` corresponds to `"top"` and positive values count down the stack from there. The value `-1` corresponds to `"bottom"` and negative values count up from there.

`show.error.messages`:

  a logical. Should error messages be printed? Intended for use with `try` or a user-installed error handler.

`stringsAsFactors`:

  The default setting for arguments of `data.frame` and `read.table`.

`texi2dvi`:

  used by functions `texi2dvi` and `texi2pdf` in package tools. Set at startup from the environment variable R_TEXI2DVICMD.

`timeout`:

  integer. The timeout for some Internet operations, in seconds. Default 60 seconds. See `download.file` and `connections`.

`topLevelEnvironment`:

  see `topenv` and `sys.source`.

`useFancyQuotes`:

  controls the use of directional quotes in `sQuote`, `dQuote` and in rendering text help (see `Rd2txt` in package tools). Can be `TRUE`, `FALSE`, `"TeX"` or `"UTF-8"`.

`verbose`:

  logical. Should R report extra information on progress? Set to `TRUE` by the command-line option --verbose.

`warn`:

  sets the handling of warning messages. If `warn` is negative all warnings are ignored. If `warn` is zero (the default) warnings are stored until the top–level function returns. If 10 or fewer warnings were signalled they will be printed otherwise a message saying how many were signalled. An object called `last.warning` is created and can be printed through the function `warnings`. If `warn` is one, warnings are printed as they occur. If `warn` is two or larger all warnings are turned into errors.

`warnPartialMatchArgs`:

  logical. If true, warns if partial matching is used in argument matching.

`warnPartialMatchAttr`:

  logical. If true, warns if partial matching is used in extracting attributes via `attr`.

`warnPartialMatchDollar`:

  logical. If true, warns if partial matching is used for extraction by `$`.

`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 `warn`.

`warning.length`:

  sets the truncation limit for error and warning messages. A non-negative integer, with allowed values 100...8170, default 1000.

`nwarnings`:

  the limit for the number of warnings kept when `warn = 0`, default 50. This will discard messages if called whilst they are being collected.

`width`:

  controls the maximum number of columns on a line used in printing vectors, matrices and arrays, and when filling by `cat`.

  Columns are normally the same as characters except in CJK languages.

  You may want to change this if you re-size the window that R is running in. Valid values are 10...10000 with default normally 80. (The limits on valid values are in file ‘Print.h’ and can be changed by re-compiling R.) Some R consoles automatically change the value when they are resized.

  See the examples on Startup for one way to set this automatically from the terminal width when R is started.

The ‘factory-fresh’ default settings of some of these options are

`add.smooth` | `TRUE`
`check.bounds` | `FALSE`
`continue` | `"+ "`
`digits` | `7`
`echo` | `TRUE`
`encoding` | `"native.enc"`
`error` | `NULL`
`expressions` | `5000`
`keep.source` | `interactive()`
`keep.source.pkgs` | `FALSE`
`max.print` | `99999`
`OutDec` | `"."`
`prompt` | `"> "`
`scipen` | `0`
`show.error.messages` | `TRUE`
`timeout` | `60`
`verbose` | `FALSE`
`warn` | `0`
`warning.length` | `1000`
`width` | `80`

Others are set from environment variables or are platform-dependent.

### Options set in package grDevices

These will be set when package grDevices (or its namespace) is loaded if not already set.

`bitmapType`:

  (Unix-only) character. The default type for the bitmap devices such as `png`. Defaults to `"cairo"` on systems where that is available, or to `"quartz"` on OS X where that is available.

`device`:

  a character string giving the name of a function, or the function object itself, which when called creates a new graphics device of the default type for that session. The value of this option defaults to the normal screen device (e.g., `X11`, `windows` or `quartz`) for an interactive session, and `pdf` in batch use or if a screen is not available. If set to the name of a device, the device is looked for first from the global environment (that is down the usual search path) and then in the grDevices namespace.

  The default values in interactive and non-interactive sessions are configurable via environment variables R_INTERACTIVE_DEVICE and R_DEFAULT_DEVICE respectively.

`device.ask.default`:

  logical. The default for `devAskNewPage("ask")` when a device is opened.

`locatorBell`:

  logical. Should selection in `locator` and `identify` be confirmed by a bell? Default `TRUE`. Honoured at least on `X11` and `windows` devices.

### Other options used by package graphics

`max.contour.segments`:

  positive integer, defaulting to `25000` if not set. A limit on the number of segments in a single contour line in `contour` or `contourLines`.

### Options set in package stats

These will be set when package stats (or its namespace) is loaded if not already set.

`contrasts`:

  the default `contrasts` used in model fitting such as with `aov` or `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 `c("unordered", "ordered")`, but the names are unused.

`na.action`:

  the name of a function for treating missing values (`NA`'s) for certain situations.

`show.coef.Pvalues`:

  logical, affecting whether P values are printed in summary tables of coefficients. See `printCoefmat`.

`show.nls.convergence`:

  logical, should `nls` convergence messages be printed for successful fits?

`show.signif.stars`:

  logical, should stars be printed on summary tables of coefficients? See `printCoefmat`.

`ts.eps`:

  the relative tolerance for certain time series (`ts`) computations. Default `1e-05`.

`ts.S.compat`:

  logical. Used to select S compatibility for plotting time-series spectra. See the description of argument `log` in `plot.spec`.

### Options set in package utils

These will be set when package utils (or its namespace) is loaded if not already set.

`BioC_mirror`:

  The URL of a Bioconductor mirror for use by `setRepositories`, e.g. the default "http://www.bioconductor.org" or the European mirror "http://bioconductor.statistik.tu-dortmund.de". Can be set by `chooseBioCmirror`.

`browser`:

  default HTML browser used by `help.start()` and `browseURL` on UNIX, or a non-default browser on Windows. Alternatively, an R function that is called with a URL as its argument.

`ccaddress`:

  default Cc: address used by `create.post` (and hence`bug.report` and `help.request`). Can be `FALSE` or `""`.

`citation.bibtex.max`:

  default 1; the maximal number of bibentries (`bibentry`) in a `citation` for which the bibtex version is printed in addition to the text one.

`de.cellwidth`:

  integer: the cell widths (number of characters) to be used in the data editor `dataentry`. If this is unset (the default), 0, negative or `NA`, variable cell widths are used.

`demo.ask`:

  default for the `ask` argument of `demo`.

`editor`:

  a non-empty string or a function that sets the default text editor, e.g., for `edit`. Set from the environment variable EDITOR on UNIX, or if unset VISUAL or `vi`.

`example.ask`:

  default for the `ask` argument of `example`.

`help.ports`:

  optional integer vector for setting ports of the internal HTTP server, see `startDynamicHelp`.

`help.search.types`:

  default types of documentation to be searched by `help.search` and `??`.

`help.try.all.packages`:

  default for an argument of `help`.

`help_type`:

  default for an argument of `help`, used also as the help type by `?`.

`HTTPUserAgent`:

  string used as the user agent in HTTP requests. If `NULL`, HTTP requests will be made without a user agent header. The default is `R (<version> <platform> <arch> <os>)`

`install.lock`:

  logical: should per-directory package locking be used by `install.packages`? Most useful for binary installs on OS X and Windows, but can be used in a startup file for source installs via `R CMD INSTALL`. For binary installs, can also be the character string `"pkgloack"`.

`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.

`mailer`:

  default emailing method used by `create.post` and hence `bug.report` and `help.request`.

`menu.graphics`:

  Logical: should graphical menus be used if available?. Defaults to `TRUE`. Currently applies to `select.list`, `chooseCRANmirror`, `setRepositories` and to select from multiple (text) help files in `help`.

`pkgType`:

  The default type of packages to be downloaded and installed – see `install.packages`. Possible values are `"source"` (the default except under the CRAN OS X build), `"mac.binary."` and `"mac.binary.mavericks"`. Windows uses `"win.binary"`. (`"mac.binary.leopard"` and `"mac.binary.universal"` are no longer in use.)

`repos`:

  URLs of the repositories for use by `update.packages`. Defaults to `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 `local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cran"; options(repos = r)})`.

  Note that you can add more repositories (Bioconductor and Omegahat, R-Forge, Rforge.net ...) using `setRepositories`.

`SweaveHooks`, `SweaveSyntax`:

  see `Sweave`.

`unzip`:

  a character string, the path of the command used for unzipping help files, or `"internal"`. Defaults to the value of R_UNZIPCMD, which is set in ‘etc/Renviron’ if an `unzip` command was found during configuration.

### Options set in package parallel

These will be set when package parallel (or its namespace) is loaded if not already set.

`mc.cores`:

  a integer giving the maximum allowed number of additional R processes allowed to be run in parallel to the current R process. Defaults to the setting of the environment variable MC_CORES if set. Most applications which use this assume a limit of `2` if it is unset.

### Options used on Unix only

`dvipscmd`:

  character string giving a command to be used in the (deprecated) off-line printing of help pages via PostScript. Defaults to `"dvips"`.

### Options used on Windows only

`warn.FPU`:

  logical, by default undefined. If true, a warning is produced whenever dyn.load repairs the control word damaged by a buggy DLL.

### Note

For compatibility with S there is a visible object `.Options` whose value is a pairlist containing the current `options()` (in no particular order). Assigning to it will make a local copy and not change the original.

### References

Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole.

### Examples

    op <- options(); utils::str(op) # op is a named list

    getOption("width") == options()$width # the latter needs more memory
    options(digits = 15)
    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")

    ## Not run: ## set contrast handling to be like S
    options(contrasts = c("contr.helmert", "contr.poly"))

    ## End(Not run)

    ## Not run: ## on error, terminate the R session with error status 66
    options(error = quote(q("no", status = 66, runLast = FALSE)))
    stop("test it")

    ## End(Not run)

    ## Not run: ## 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()}))

    ## End(Not run)

      # Compare the two ways to get an option and use it
      # acconting for the possibility it might not be set.
    if(as.logical(getOption("performCleanp", TRUE)))
       cat("do cleanup\n")

    ## Not run:
      # a clumsier way of expressing the above w/o the default.
    tmp <- getOption("performCleanup")
    if(is.null(tmp))
      tmp <- TRUE
    if(tmp)
       cat("do cleanup\n")

    ## End(Not run)

[Package base version 3.1.2 Index]