10/29/2018 R: Data Input

[Link] {utils} R Documentation

Data Input

Description

Reads a file in table format and creates a data frame from it, with cases corresponding to lines and variables to
fields in the file.

Usage
[Link](file, header = FALSE, sep = "", quote = "\"'",
dec = ".", numerals = c("[Link]", "[Link]", "[Link]"),
[Link], [Link], [Link] = !stringsAsFactors,
[Link] = "NA", colClasses = NA, nrows = -1,
skip = 0, [Link] = TRUE, fill = ![Link],
[Link] = FALSE, [Link] = TRUE,
[Link] = "#",
allowEscapes = FALSE, flush = FALSE,
stringsAsFactors = [Link](),
fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)

[Link](file, header = TRUE, sep = ",", quote = "\"",

dec = ".", fill = TRUE, [Link] = "", ...)

read.csv2(file, header = TRUE, sep = ";", quote = "\"",

dec = ",", fill = TRUE, [Link] = "", ...)

[Link](file, header = TRUE, sep = "\t", quote = "\"",

dec = ".", fill = TRUE, [Link] = "", ...)

read.delim2(file, header = TRUE, sep = "\t", quote = "\"",

dec = ",", fill = TRUE, [Link] = "", ...)

Arguments

file
the name of the file which the data are to be read from. Each row of the table appears as one
line of the file. If it does not contain an absolute path, the file name is relative to the current
working directory, getwd(). Tilde-expansion is performed where supported. This can be a
compressed file (see file).

Alternatively, file can be a readable text-mode connection (which will be opened for reading
if necessary, and if so closed (and hence destroyed) at the end of the function call). (If
stdin() is used, the prompts for lines may be somewhat confusing. Terminate input with a
blank line or an EOF signal, Ctrl-D on Unix and Ctrl-Z on Windows. Any pushback on
stdin() will be cleared before return.)

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

header
a logical value indicating whether the file contains the names of the variables as its first line.
If missing, the value is determined from the file format: header is set to TRUE if and only if
the first row contains one fewer field than the number of columns.

sep
the field separator character. Values on each line of the file are separated by this character. If
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sep = "" (the default for [Link]) the separator is ‘white space’, that is one or more
spaces, tabs, newlines or carriage returns.

quote
the set of quoting characters. To disable quoting altogether, use quote = "". See scan for the
behaviour on quotes embedded in quotes. Quoting is only considered for columns read as
character, which is all of them unless colClasses is specified.

dec
the character used in the file for decimal points.

numerals
string indicating how to convert numbers whose conversion to double precision would lose
accuracy, see [Link]. Can be abbreviated. (Applies also to complex-number inputs.)

[Link]
a vector of row names. This can be a vector giving the actual row names, or a single number
giving the column of the table which contains the row names, or character string giving the
name of the table column containing the row names.

If there is a header and the first row contains one fewer field than the number of columns, the
first column in the input is used for the row names. Otherwise if [Link] is missing, the
rows are numbered.

Using [Link] = NULL forces row numbering. Missing or NULL [Link] generate row
names that are considered to be ‘automatic’ (and not preserved by [Link]).

[Link]
a vector of optional names for the variables. The default is to use "V" followed by the column
number.

[Link]
the default behavior of [Link] is to convert character variables (which are not converted
to logical, numeric or complex) to factors. The variable [Link] controls the conversion of
columns not otherwise specified by colClasses. Its value is either a vector of logicals (values
are recycled if necessary), or a vector of numeric or character indices which specify which
columns should not be converted to factors.

Note: to suppress all conversions including those of numeric columns, set colClasses =
"character".

Note that [Link] is specified per column (not per variable) and so includes the column of row
names (if any) and any columns to be skipped.

[Link]
a character vector of strings which are to be interpreted as 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, so [Link] values may need
their own white space stripped in advance.

colClasses
character. A vector of classes to be assumed for the columns. If unnamed, recycled as
necessary. If named, names are matched with unspecified values being taken to be NA.

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Possible values are NA (the default, when [Link] is used), "NULL" (when the column is
skipped), one of the atomic vector classes (logical, integer, numeric, complex, character,
raw), or "factor", "Date" or "POSIXct". Otherwise there needs to be an as method (from
package methods) for conversion from "character" to the specified formal class.

Note that colClasses is specified per column (not per variable) and so includes the column of
row names (if any).

nrows
integer: the maximum number of rows to read in. Negative and other invalid values are
ignored.

skip
integer: the number of lines of the data file to skip before beginning to read data.

[Link]
logical. If TRUE then the names of the variables in the data frame are checked to ensure that
they are syntactically valid variable names. If necessary they are adjusted (by [Link]) so
that they are, and also to ensure that there are no duplicates.

fill
logical. If TRUE then in case the rows have unequal length, blank fields are implicitly added.
See ‘Details’.

[Link]
logical. Used only when sep has been specified, and allows the stripping of leading and
trailing white space from unquoted character fields (numeric fields are always stripped). See
scan for further details (including the exact meaning of ‘white space’), remembering that the
columns may include the row names.

[Link]
logical: if TRUE blank lines in the input are ignored.

[Link]
character: a character vector of length one containing a single character or an empty string.
Use "" to turn off the interpretation of comments altogether.

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

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.

stringsAsFactors
logical: should character vectors be converted to factors? Note that this is overridden by
[Link] and colClasses, both of which allow finer control.

fileEncoding
character string: if non-empty declares the encoding used on a file (not a connection) so the
character data can be re-encoded. See the ‘Encoding’ section of the help for file, the ‘R Data
Import/Export Manual’ and ‘Note’.
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encoding
encoding to be assumed for input strings. It is used to mark character strings as known to be
in Latin-1 or UTF-8 (see Encoding): it is not used to re-encode the input, but allows R to
handle encoded strings in their native encoding (if one of those two). See ‘Value’ and ‘Note’.

text
character string: if file is not supplied and this is, then data are read from the value of text
via a text connection. Notice that a literal string can be used to include (small) data sets
within R code.

skipNul
logical: should nuls be skipped?

...
Further arguments to be passed to [Link].

Details

This function is the principal means of reading tabular data into R.

Unless colClasses is specified, all columns are read as character columns and then converted using
[Link] to logical, integer, numeric, complex or (depending on [Link]) factor as appropriate. Quotes are (by
default) interpreted in all fields, so a column of values like "42" will result in an integer column.

A field or line is ‘blank’ if it contains nothing (except whitespace if no separator is specified) before a comment
character or the end of the field or line.

If [Link] is not specified and the header line has one less entry than the number of columns, the first column
is taken to be the row names. This allows data frames to be read in from the format in which they are printed. If
[Link] is specified and does not refer to the first column, that column is discarded from such files.

The number of data columns is determined by looking at the first five lines of input (or the whole input if it has
less than five lines), or from the length of [Link] if it is specified and is longer. This could conceivably be
wrong if fill or [Link] are true, so specify [Link] if necessary (as in the ‘Examples’).

[Link] and read.csv2 are identical to [Link] except for the defaults. They are intended for reading
‘comma separated value’ files (‘.csv’) or (read.csv2) the variant used in countries that use a comma as decimal
point and a semicolon as field separator. Similarly, [Link] and read.delim2 are for reading delimited files,
defaulting to the TAB character for the delimiter. Notice that header = TRUE and fill = TRUE in these variants,
and that the comment character is disabled.

The rest of the line after a comment character is skipped; quotes are not processed in comments. Complete
comment lines are allowed provided [Link] = TRUE; however, comment lines prior to the header must
have the comment character in the first non-blank column.

Quoted fields with embedded newlines are supported except after a comment character. Embedded nuls are
unsupported: skipping them (with skipNul = TRUE) may work.

Value

A data frame ([Link]) containing a representation of the data in the file.

Empty input is an error unless [Link] is specified, when a 0-row data frame is returned: similarly giving just
a header line if header = TRUE results in a 0-row data frame. Note that in either case the columns will be logical
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unless colClasses was supplied.

Character strings in the result (including factor levels) will have a declared encoding if encoding is "latin1" or
"UTF-8".

Memory usage

These functions can use a surprising amount of memory when reading large files. There is extensive discussion
in the ‘R Data Import/Export’ manual, supplementing the notes here.

Less memory will be used if colClasses is specified as one of the six atomic vector classes. This can be
particularly so when reading a column that takes many distinct numeric values, as storing each distinct value as a
character string can take up to 14 times as much memory as storing it as an integer.

Using nrows, even as a mild over-estimate, will help memory usage.

Using [Link] = "" will be appreciably faster than the [Link] default.

[Link] is not the right tool for reading large matrices, especially those with many columns: it is designed to
read data frames which may have columns of very different classes. Use scan instead for matrices.

Note

The columns referred to in [Link] and colClasses include the column of row names (if any).

There are two approaches for reading input that is not in the local encoding. If the input is known to be UTF-8 or
Latin1, use the encoding argument to declare that. If the input is in some other encoding, then it may be
translated on input. The fileEncoding argument achieves this by setting up a connection to do the re-encoding
into the current locale. Note that on Windows or other systems not running in a UTF-8 locale, this may not be
possible.

References

Chambers, J. M. (1992) Data for models. Chapter 3 of Statistical Models in S eds J. M. Chambers and T. J.
Hastie, Wadsworth & Brooks/Cole.

See Also

The ‘R Data Import/Export’ manual.

scan, [Link], [Link] for reading fixed width formatted input; [Link]; [Link].

[Link] can be useful to determine problems with reading files which result in reports of incorrect record
lengths (see the ‘Examples’ below).

[Link] for the IANA definition of CSV files (which requires comma as separator and
CRLF line endings).

Examples

## using [Link] to handle unknown maximum number of fields

## when fill = TRUE
test1 <- c(1:5, "6,7", "8,9,10")
tf <- tempfile()
writeLines(test1, tf)

[Link](tf, fill = TRUE) # 1 column

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ncol <- max([Link](tf, sep = ","))
[Link](tf, fill = TRUE, header = FALSE,
[Link] = paste0("V", seq_len(ncol)))
unlink(tf)

## "Inline" data set, using text=

## Notice that leading and trailing empty lines are auto-trimmed

[Link](header = TRUE, text = "

a b
1 2
3 4
")

[Package utils version 3.6.0 Index]

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