Allow the user to set and examine a variety of global options which affect the way in which R computes and displays its results.
options(…)getOption(x, default = NULL)
.Options
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.
a character string holding an option name.
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.
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).
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" in the browser.
checkPackageLicense:logical, not set by default. If
true, loadNamespace asks a user to accept any
non-standard license at first load of the package.
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.
%% default is set in ../../profile/Common.R :
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.) It will not work to set
this in a .Rprofile file, as its value is consulted before
that file is read.
deparse.cutoff:integer value controlling the
printing of language constructs which are deparsed.
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 significant 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", "wininet" (Windows only),
"libcurl", "wget" and "curl" are available.
If not set, 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.
interrupt:a function taking no arguments to be called on a user interrupt if the interrupt condition is not otherwise handled.
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.
%% used by tools::makeLazyLoading
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.
matprod:a string selecting the implementation of
the matrix products %*%, crossprod, and
tcrossprod for double and complex vectors:
"internal"uses an unoptimized 3-loop algorithm
which correctly propagates NaN and
Inf values and is consistent in precision with
other summation algorithms inside R like sum or
colSums (which now means that it uses a long
double accumulator for summation if available and enabled,
see capabilities).
"default"uses BLAS to speed up computation, but
to ensure correct propagation of NaN and Inf
values it uses an unoptimized 3-loop algorithm for inputs that may
contain NaN or Inf values. When deemed
beneficial for performance, "default" may call the
3-loop algorithm unconditionally, i.e., without checking the
input for NaN/Inf values. The 3-loop algorithm uses (only) a
double accumulator for summation, which is consistent
with the reference BLAS implementation.
"blas"uses BLAS unconditionally without any
checks and should be used with extreme caution. BLAS
libraries do not propagate NaN or
Inf values correctly and for inputs with
NaN/Inf values the results may be undefined.
"default.simd"is experimental and will likely be
removed in future versions of R. It provides the same behavior
as "default", but the check whether the input contains
NaN/Inf values is faster on some SIMD hardware. On older
systems it will run correctly, but may be much slower than
"default".
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
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.
Defaults to "internal", which uses a pager similar to the
GUI console. Another possibility is "console" to use the
console itself.
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.
"a4", or "letter" in US and Canadian locales.
PCRE_limit_recursion:Logical: should
grep(perl = TRUE) and similar limit the maximal
recursion allowed when matching? PCRE can be built not to use a
recursion stack (see pcre_config, but it is by
default with a recursion limit of 10000000 which potentially needs
a very large C stack: see the discussion at
http://www.pcre.org/original/doc/html/pcrestack.html. If
true, the limit is reduced using R's estimate of the C stack size
available (if known), otherwise 10000. If NA, the limit is
imposed only if any input string has 1000 or more bytes.
PCRE_study:Logical or integer: should
grep(perl = TRUE) and similar ‘study’ the
patterns? Either logical or a numerical threshold for the minimum
number of strings to be matched for the pattern to be studied (the
default is 10)). Missing values and negative numbers are
treated as false.
PCRE_use_JIT:Logical: should grep(perl =
TRUE), strsplit(perl = TRUE) and similar make use
of PCRE's Just-In-Time compiler for studied patterns, if
available? Missing values are treated as false.
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.
which defaults to the full path to open.exe, a utility
supplied with R.
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 (" ").
% verbatim, for checking " \t\n\"\\'`><=%;,|&{()}"
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,
which defaults first to the value of environment variable
TEXI2DVI, and then to a value set when R was installed (the
full path to a texi2dvi script if one was found). If
necessary, that environment variable can be set to "emulation".
timeout:integer. The timeout for some Internet
operations, in seconds. Default 60 seconds. See
download.file and connections.
topLevelEnvironment:see topenv and
sys.source.
url.method:character string: the default method for
url. Normally unset, which is equivalent to
"default", which is "internal" except on Windows.
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. If you increase this
limit, be aware that the current implementation pre-allocates
the equivalent of a named list for them, i.e., do not increase it to
more than say a million.
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 East Asian 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.
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 macOS 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.
The search logic for ‘the normal screen device’ is that
this is windows on Windows, and quartz if available
on macOS (running at the console, and compiled into the build).
Otherwise X11 is used if environment variable DISPLAY
is set.
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.
windowsTimeout:(Windows-only) integer vector of length 2
representing two times in milliseconds. These control the
double-buffering of 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). The values at the time the
device is opened are used.
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.
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, see
na.action and na.pass.
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.
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 "https://bioconductor.org"
or the European mirror
"https://bioconductor.statistik.tu-dortmund.de". Can be set
by chooseBioCmirror.
browser:The HTML browser to be used by
browseURL. This sets the default browser on UNIX or
a non-default browser on Windows. Alternatively, an R function
that is called with a URL as its argument. See
browseURL for further details.
ccaddress:default Cc: address used by
create.post (and hencebug.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(S)
requests. If NULL, 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 macOS 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, using the "internal" and
"libcurl" methods.
Default is 2, for failure causes. Set to 1 or 0 to get more
detailed information (for the "internal" method 0 provides
more information than 1).
install.packages.check.source:Used by
install.packages (and indirectly
update.packages) on platforms which support binary
packages. Possible values "yes" and "no", with
unset being equivalent to "yes".
install.packages.compile.from.source:Used by
install.packages(type = "both") (and indirectly
update.packages) on platforms which
support binary packages. Possible values are "never",
"interactive" (which means ask in interactive use and
"never" in batch use) and "always". The default is
taken from environment variable
R_COMPILE_AND_INSTALL_PACKAGES, with default
"interactive" if unset. However, install.packages
uses "never" unless a make program is found,
consulting the environment variable MAKE.
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 "win.binary", "source" and
"both" (the default). Some macOS builds use
"mac.binary.el-capitan".
Possible values are "source" (the default except under a
CRAN macOS build), "mac.binary.el-capitan" and
"both" (the default for CRAN macOS builds). Windows uses
"win.binary". ("mac.binary.mavericks",
"mac.binary.leopard", "mac.binary.universal" are no
longer in use.)
Value "binary" is a synonym for the native binary type (if
there is one); "both" is used by
install.packages to choose between source and binary
installs.
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,
R-Forge, Rforge.net …)
using setRepositories.
SweaveHooks, SweaveSyntax:see Sweave.
unzip:a character string used by unzip:
the path of the external program unzip or "internal".
Defaults to the value of R_UNZIPCMD, which is set in
etc/Renviron if an unzip command was found during
configuration.
Defaults to "internal" when the internal unzip code is
used.
useHTTPS:logical. Used by chooseCRANmirror:
are secure mirrors preferred? If not set, TRUE is assumed.
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.
dvipscmd:character string giving a command to be used in
the (deprecated) off-line printing of help pages via
PostScript. Defaults to "dvips".
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.
Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole.
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")
## set contrast handling to be like S
options(contrasts = c("contr.helmert", "contr.poly"))
## on error, terminate the R session with error status 66
options(error = quote(q("no", status = 66, runLast = FALSE)))
stop("test it")
## 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()}))
# 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")
# 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")
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