Reads a file in table format

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.

WARNING: This method is very much in an alpha stage. Expect it to change.

This method is an extension to the default read.table function in R. It is possible to specify a column name to column class map such that the column classes are automatically assigned from the column header in the file.

In addition, it is possible to read any subset of rows. The method is optimized such that only columns and rows that are of interest are parsed and read into R's memory. This minimizes memory usage at the same time as it speeds up the reading.

# S3 method for default
readTable(file, colClasses=NULL, isPatterns=FALSE, defColClass=NA, header=FALSE, skip=0,
  nrows=-1, rows=NULL, col.names=NULL, check.names=FALSE, path=NULL, ...,
  stripQuotes=TRUE, method=c("readLines", "intervals"), verbose=FALSE)

Arguments

file

A connection or a filename. If a filename, the path specified by path is added to the front of the filename. Unopened files are opened and closed at the end.

colClasses

Either a named or an unnamed character vector. If unnamed, it specified the column classes just as used by read.table. If it is a named vector, names(colClasses) are used to match the column names read (this requires that header=TRUE) and the column classes are set to the corresponding values.

isPatterns

If TRUE, the matching of names(colClasses) to the read column names is done by regular expressions matching.

defColClass

If the column class map specified by a named colClasses argument does not match some of the read column names, the column class is by default set to this class. The default is to read the columns in an "as is" way.

header

If TRUE, column names are read from the file.

skip

The number of lines (commented or non-commented) to skip before trying to read the header or alternatively the data table.

nrows

The number of rows to read of the data table. Ignored if rows is specified.

rows

An row index vector specifying which rows of the table to read, e.g. row one is the row following the header. Non-existing rows are ignored. Note that rows are returned in the same order they are requested and duplicated rows are also returned.

col.names

Same as in read.table().

check.names

Same as in read.table(), but default value is FALSE here.

path

If file is a filename, this path is added to it, otherwise ignored.

...

Arguments passed to read.table used internally.

stripQuotes

If TRUE, quotes are stripped from values before being parse. This argument is only effective when method=="readLines".

method

If "readLines", (readLines()) is used internally to first only read rows of interest, which is then passed to read.table(). If "intervals", contiguous intervals are first identified in the rows of interest. These intervals are the read one by one using read.table(). The latter methods is faster and especially more memory efficient if the intervals are not too many, where as the former is preferred if many "scattered" rows are to be read.

verbose

A logical or a Verbose object.

Value

Returns a data.frame.

Author

Henrik Bengtsson