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R: Data Input

read.table {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

read.table(file, header = FALSE, sep = “”, quote = “\”‘”,
dec = “.”, numerals = c(“allow.loss”, “warn.loss”, “no.loss”),
row.names, col.names, as.is = !stringsAsFactors,
na.strings = “NA”, colClasses = NA, nrows = -1,
skip = 0, check.names = TRUE, fill = !blank.lines.skip,
strip.white = FALSE, blank.lines.skip = TRUE,
comment.char = “#”,
allowEscapes = FALSE, flush = FALSE,
stringsAsFactors = default.stringsAsFactors(),
fileEncoding = “”, encoding = “unknown”, text, skipNul = FALSE)

read.csv(file, header = TRUE, sep = “,”, quote = “\””,
dec = “.”, fill = TRUE, comment.char = “”, …)

read.csv2(file, header = TRUE, sep = “;”, quote = “\””,
dec = “,”, fill = TRUE, comment.char = “”, …)

read.delim(file, header = TRUE, sep = “\t”, quote = “\””,
dec = “.”, fill = TRUE, comment.char = “”, …)

read.delim2(file, header = TRUE, sep = “\t”, quote = “\””,
dec = “,”, fill = TRUE, comment.char = “”, …)

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

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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 sep = “” (the default for read.table) 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 type.convert. Can be abbreviated.

row.names
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 row.names
is missing, the rows are numbered.

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

col.names
a vector of optional names for the variables. The default is to use “V” followed by the
column number.

as.is
the default behavior of read.table is to convert character variables (which are not
converted to logical, numeric or complex) to factors. The variable as.is 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 as.is is specified per column (not per variable) and so includes the column of
row names (if any) and any columns to be skipped.

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na.strings
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.

colClasses
character. A vector of classes to be assumed for the columns. Recycled as necessary, or if
the character vector is named, unspecified values are taken to be NA.

Possible values are NA (the default, when type.convert 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.

check.names
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
make.names) 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’.

strip.white
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.

blank.lines.skip
logical: if TRUE blank lines in the input are ignored.

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.

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.

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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
type.convert to logical, integer, numeric, complex or (depending on as.is) 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 row.names 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 row.names 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 file if it has
less than five lines), or from the length of col.names if it is specified and is longer. This could conceivably be
wrong if fill or blank.lines.skip are true, so specify col.names if necessary (as in the ‘Examples’).

read.csv and read.csv2 are identical to read.table 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, read.delim 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 blank.lines.skip = 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 (data.frame) containing a representation of the data in the file.

Empty input is an error unless col.names 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 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

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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 comment.char = “” will be appreciably faster than the read.table default.

read.table 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 as.is 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.

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