data types

Description Usage Arguments Details Value Author(s)

read.table admits that it's not so good at reading large tables with many columns. read.table recommends using scan, but scan is tricky unless you know the number of columns. NCOL is easy & VERY fast to determine on systems with awk. This function essentially mashes the results from scan into a data.frame On a 15MB file with 16x88742 elements, I got a 19x speed improvement using this (25.5s) vs read.table (484.5s).

read.table.wide(file, header = FALSE, sep = "", quote = if (identical(sep,
  "\n")) "" else "\"", dec = ".", 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")

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

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

`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. As from R 2.10.0 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 `file`d (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 ‘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.
`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.
`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 `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`.
`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 ‘as.is’ 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’.
`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’.
`...`	Further arguments to be passed to `read.table`.