scan.Read data into vector or list using function scan.
readReportTable(task, type, ext = "csv", subdir = NULL, dirCreate = FALSE, ...)the data read, or NULL if the file does not exist.
Object of class D4TAlinkTask, as created by initTask.
Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]
Filename extension.
(optional) Subdirectory.
Logical, if TRUE (by default) the directory is created.
Arguments passed on to utils::read.table
filethe 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.)
headera 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.
septhe 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.
quotethe 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.
decthe character used in the file for decimal points.
numeralsstring indicating how to convert numbers whose conversion
to double precision would lose accuracy, see type.convert.
Can be abbreviated. (Applies also to complex-number inputs.)
row.namesa 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.namesa vector of optional names for the variables.
The default is to use "V" followed by the column number.
as.iscontrols conversion of character variables (insofar as
they are not converted to logical, numeric or complex) to factors,
if 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.
tryLogicala logical determining if columns
consisting entirely of "F", "T", "FALSE", and
"TRUE" should be converted to logical; passed to
type.convert, true by default.
na.stringsa 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 na.strings
values may need their own white space stripped in advance.
colClassescharacter. 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.
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).
nrowsinteger: the maximum number of rows to read in. Negative and other invalid values are ignored.
skipinteger: the number of lines of the data file to skip before beginning to read data.
check.nameslogical. 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.
filllogical. If TRUE then in case the rows have unequal
length, blank fields are implicitly added. See ‘Details’.
strip.whitelogical. 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.skiplogical: if TRUE blank lines in the
input are ignored.
comment.charcharacter: a character vector of length one
containing a single character or an empty string. Use "" to
turn off the interpretation of comments altogether.
allowEscapeslogical. 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.
flushlogical: 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.
stringsAsFactorslogical: should character vectors be converted
to factors? Note that this is overridden by as.is and
colClasses, both of which allow finer control.
fileEncodingcharacter 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’.
encodingencoding 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’.
textcharacter 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.
skipNullogical: should nuls be skipped?