R: Data Input

read.table {base}

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 = ".",
           row.names, col.names, as.is = FALSE, 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 = "#")

read.csv(file, header = TRUE, sep = ",", quote="\"", dec=".",
         fill = TRUE, ...)

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

read.delim(file, header = TRUE, sep = "\t", quote="\"", dec=".",
         fill = TRUE, ...)

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

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. Alternatively, `file` can be a `connection`, which will be opened if necessary, and if so closed at the end of the function call. `file` can also be a complete 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 `sep = ""` (the default for `read.table`) the separator is “white space”, that is one or more spaces, tabs or newlines.
`quote`	the set of quoting characters. To disable quoting altogether, use `quote=""`. See `scan` for the behaviour on quotes embedded in quotes.
`dec`	the character used in the file for decimal points.
`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.
`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 this conversion. Its value is either a vector of logicals (values are recycled if necessary), or a vector of numeric indices which specify which columns should not be converted to factors. Note: to suppress all conversions including those of numeric columns, set `colClasses = "character"`.
`na.strings`	a vector of strings which are to be interpreted as `NA` values. Blank fields are also considered to be missing values.
`colClasses`	character. A vector of classes to be assumed for the columns. Recycled as necessary. If this is not one of the atomic vector classes (logical, integer, numeric, complex and character), there needs to be an `as` method for conversion from `"character"` to the specified class, or `NA` when `type.convert` is used.
`nrows`	the maximum number of rows to read in. Negative values are ignored.
`skip`	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.
`fill`	logical. If `TRUE` then in case the rows have unequal length, blank fields are implicitly added.
`strip.white`	logical. Used only when `sep` has been specified, and allows the stripping of leading and trailing white space from `character` fields (`numeric` fields are always stripped). See `scan` for further details, 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.
`...`	Further arguments to `read.table`.

Details

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.

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 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.

Comment characters are allowed unless comment.char = "", and 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.

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.

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

Note

The columns referred to in as.is and colClasses include the column of row names (if any).

Less memory will be used if colClasses is specified as one of the five atomic vector classes.

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

Using comment.char = "" will be appreciably faster.

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.