scan {base}

Read Data Values

Description

Read data into a vector or list from the console or file.

Usage

scan(file = "", what = double(), nmax = -1, n = -1, sep = "",
     quote = if(identical(sep, "\n")) "" else "'\"", dec = ".",
     skip = 0, nlines = 0, na.strings = "NA",
     flush = FALSE, fill = FALSE, strip.white = FALSE,
     quiet = FALSE, blank.lines.skip = TRUE, multi.line = TRUE,
     comment.char = "", allowEscapes = FALSE,
     fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)

Arguments

file

the name of a file to read data values from. If the specified file is "", then input is taken from the keyboard (or whatever stdin() reads if input is redirected or R is embedded). (In this case input can be terminated by a blank line or an EOF signal, ‘⁠Ctrl-D⁠’ on Unix and ‘⁠Ctrl-Z⁠’ on Windows.)

Otherwise, the file name is interpreted relative to the current working directory (given by getwd()), unless it specifies an absolute path. Tilde-expansion is performed where supported. When running R from a script, file = "stdin" can be used to refer to the process's stdin file stream.

This can be a compressed file (see file).

Alternatively, file can be a connection, which will be opened if necessary, and if so closed at the end of the function call. Whatever mode the connection is opened in, any of LF, CRLF or CR will be accepted as the EOL marker for a line and so will match sep = "\n".

file can also be a complete URL. (For the supported URL schemes, see the ‘URLs’ section of the help for url.)

To read a data file not in the current encoding (for example a Latin-1 file in a UTF-8 locale or conversely) use a file connection setting its encoding argument (or scan's fileEncoding argument).

what

the type of what gives the type of data to be read. (Here ‘type’ is used in the sense of typeof.) The supported types are logical, integer, numeric, complex, character, raw and list. If what is a list, it is assumed that the lines of the data file are records each containing length(what) items (‘fields’) and the list components should have elements which are one of the first six (atomic) types listed or NULL, see section ‘Details’ below.

nmax

the maximum number of data values to be read, or if what is a list, the maximum number of records to be read. If omitted or not positive or an invalid value for an integer (and nlines is not set to a positive value), scan will read to the end of file.

n

integer: the maximum number of data values to be read, defaulting to no limit. Invalid values will be ignored.

sep

by default, scan expects to read ‘white-space’ delimited input fields. Alternatively, sep can be used to specify a character which delimits fields. A field is always delimited by an end-of-line marker unless it is quoted.

If specified this should be the empty character string (the default) or NULL or a character string containing just one single-byte character.

quote

the set of quoting characters as a single character string or NULL. In a multibyte locale the quoting characters must be ASCII (single-byte).

dec

decimal point character. This should be a character string containing just one single-byte character. (NULL and a zero-length character vector are also accepted, and taken as the default.)

skip

the number of lines of the input file to skip before beginning to read data values.

nlines

if positive, the maximum number of lines of data to be read.

na.strings

character vector. Elements of this vector are to be interpreted as missing (NA) values. Blank fields are also considered to be missing values in logical, integer, numeric and complex fields. Note that the test happens after white space is stripped from the input (if enabled), so na.strings values may need their own white space stripped in advance.

flush

logical: if TRUE, scan will flush to the end of the line after reading the last of the fields requested. This allows putting comments after the last field, but precludes putting more than one record on a line.

fill

logical: if TRUE, scan will implicitly add empty fields to any lines with fewer fields than implied by what.

strip.white

vector of logical value(s) corresponding to items in the what argument. It is used only when sep has been specified, and allows the stripping of leading and trailing ‘white space’ from character fields (other fields are always stripped). Note: white space inside quoted strings is not stripped.

If strip.white is of length 1, it applies to all fields; otherwise, if strip.white[i] is TRUE and the i-th field is of mode character (because what[i] is) then the leading and trailing unquoted white space from field i is stripped.

quiet

logical: if FALSE (default), scan() will print a line, saying how many items have been read.

blank.lines.skip

logical: if TRUE blank lines in the input are ignored, except when counting skip and nlines.

multi.line

logical. Only used if what is a list. If FALSE, all of a record must appear on one line (but more than one record can appear on a single line). Note that using fill = TRUE implies that a record will be terminated at the end of a line.

comment.char

character: a character vector of length one containing a single character or an empty string. Use "" to turn off the interpretation of comments altogether (the default).

allowEscapes

logical. Should C-style escapes such as ‘⁠\n⁠’ be processed (the default) or read verbatim? Note that if not within quotes these could be interpreted as a delimiter (but not as a comment character).

The escapes which are interpreted are the control characters ‘⁠\a, \b, \f, \n, \r, \t, \v⁠’ and octal and hexadecimal representations like ‘⁠\040⁠’ and ‘⁠\0x2A⁠’. Any other escaped character is treated as itself, including backslash. Note that Unicode escapes (starting ‘⁠\u⁠’ or ‘⁠\U⁠’: see Quotes) are never processed.

fileEncoding

character string: if non-empty declares the encoding used on a file (not a connection nor the keyboard) so the character data can be re-encoded. See the ‘Encoding’ section of the help for file, and the ‘R Data Import/Export Manual’.

encoding

encoding to be assumed for input strings. If the value is "latin1" or "UTF-8" it is used to mark character strings as known to be in Latin-1 or UTF-8: it is not used to re-encode the input (see fileEncoding). See also ‘Details’.

text

character string: if file is not supplied and this is, then data are read from the value of text via a text connection.

skipNul

logical: should NULs be skipped when reading character fields?

Details

The value of what can be a list of types, in which case scan returns a list of vectors with the types given by the types of the elements in what. This provides a way of reading columnar data. If any of the types is NULL, the corresponding field is skipped (but a NULL component appears in the result).

The type of what or its components can be one of the six atomic vector types or NULL (see is.atomic).

‘White space’ is defined for the purposes of this function as one or more contiguous characters from the set space, horizontal tab, carriage return and line feed (aka “newline”, "\n"). It does not include form feed nor vertical tab, but in Latin-1 and Windows 8-bit locales (but not UTF-8) 'space' includes the non-breaking space ‘⁠"\xa0"⁠’.

Empty numeric fields are always regarded as missing values. Empty character fields are scanned as empty character vectors, unless na.strings contains "" when they are regarded as missing values.

The allowed input for a numeric field is optional whitespace, followed by either NA or an optional sign followed by a decimal or hexadecimal constant (see NumericConstants), or NaN, Inf or infinity (ignoring case). Out-of-range values are recorded as Inf, -Inf or 0.

For an integer field the allowed input is optional whitespace, followed by either NA or an optional sign and one or more digits (‘⁠0-9⁠’): all out-of-range values are converted to NA_integer_.

If sep is the default (""), the character ‘⁠\⁠’ in a quoted string escapes the following character, so quotes may be included in the string by escaping them.

If sep is non-default, the fields may be quoted in the style of ‘.csv’ files where separators inside quotes ('' or "") are ignored and quotes may be put inside strings by doubling them. However, if sep = "\n" it is assumed by default that one wants to read entire lines verbatim.

Quoting is only interpreted in character fields and in NULL fields (which might be skipping character fields).

Note that since sep is a separator and not a terminator, reading a file by scan("foo", sep = "\n", blank.lines.skip = FALSE) will give an empty final line if the file ends in a line feed ("\n") and not if it does not. This might not be what you expected; see also readLines.

If comment.char occurs (except inside a quoted character field), it signals that the rest of the line should be regarded as a comment and be discarded. Lines beginning with a comment character (possibly after white space with the default separator) are treated as blank lines.

There is a line-length limit of 4095 bytes when reading from the console (which may impose a lower limit: see ‘An Introduction to R’).

There is a check for a user interrupt every 1000 lines if what is a list, otherwise every 10000 items.

If file is a character string and fileEncoding is non-default, or if it is a not-already-open connection with a non-default encoding argument, the text is converted to UTF-8 and declared as such (and the encoding argument to scan is ignored). See the examples of readLines.

Embedded NULs in the input stream will terminate the field currently being read, with a warning once per call to scan. Setting skipNul = TRUE causes them to be ignored.

Value

if what is a list, a list of the same length and same names (as any) as what.

Otherwise, a vector of the type of what.

Character strings in the result will have a declared encoding if encoding is "latin1" or "UTF-8".

Note

The default for multi.line differs from S. To read one record per line, use flush = TRUE and multi.line = FALSE. (Note that quoted character strings can still include embedded newlines.)

If number of items is not specified, the internal mechanism re-allocates memory in powers of two and so could use up to three times as much memory as needed. (It needs both old and new copies.) If you can, specify either n or nmax whenever inputting a large vector, and nmax or nlines when inputting a large list.

Using scan on an open connection to read partial lines can lose chars: use an explicit separator to avoid this.

Having nul bytes in fields (including ‘⁠\0⁠’ if allowEscapes = TRUE) may lead to interpretation of the field being terminated at the nul. They not normally present in text files – see readBin.

References

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

See Also

read.table for more user-friendly reading of data matrices; readLines to read a file a line at a time. write.

Quotes for the details of C-style escape sequences.

readChar and readBin to read fixed or variable length character strings or binary representations of numbers a few at a time from a connection.

Examples

cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data", sep = "\n")
pp <- scan("ex.data", skip = 1, quiet = TRUE)
scan("ex.data", skip = 1)
scan("ex.data", skip = 1, nlines = 1) # only 1 line after the skipped one
scan("ex.data", what = list("","","")) # flush is F -> read "7"
scan("ex.data", what = list("","",""), flush = TRUE)
unlink("ex.data") # tidy up

## "inline" usage
scan(text = "1 2 3")