Package R.filesets

Description

A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.

This package should be considered to be in an alpha or beta phase. You should expect the API to be changing over time.

Installation

To install this package, call install.packages("R.filesets").

To get started

To get started, see:

1. GenericDataFileSet

2. TabularTextFile

How to cite this package

Please cite references [1] when using this package.

License

The releases of this package is licensed under LGPL version 2.1 or newer.

The development code of the packages is under a private licence (where applicable) and patches sent to the author fall under the latter license, but will be, if incorporated, released under the "release" license above.

Author(s)

Henrik Bengtsson

References

[1] H. Bengtsson, The R.oo package - Object-Oriented Programming with References Using Standard R Code, In Kurt Hornik, Friedrich Leisch and Achim Zeileis, editors, Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), March 20-22, Vienna, Austria. https://www.r-project.org/conferences/DSC-2003/Proceedings/

Gets and validates tags

Description

Gets and validates tags.

Usage

## Static method (use this):
## Arguments$getTags(..., na.rm=TRUE, collapse=",")

## Don't use the below:
## S3 method for class 'Arguments'
getTags(static, ..., na.rm=TRUE, collapse=",")

Arguments

Value

Returns a character string or character vector (iff collapse is NULL).

Author(s)

Henrik Bengtsson

See Also

For more information see Arguments.

The ChecksumFile class

Description

Package: R.filesets
Class ChecksumFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ChecksumFile

Directly known subclasses:

public abstract static class ChecksumFile
extends GenericDataFile

A ChecksumFile is an object referring to a file that contains a checksum for a corresponding "main" file.

Usage

ChecksumFile(...)

Arguments

Fields and Methods

Methods:

Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Author(s)

Henrik Bengtsson

The ChecksumFileSet class

Description

Package: R.filesets
Class ChecksumFileSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ChecksumFileSet

Directly known subclasses:

public static class ChecksumFileSet
extends GenericDataFileSet

An ChecksumFileSet object represents a set of ChecksumFiles.

Usage

ChecksumFileSet(...)

Arguments

Fields and Methods

Methods:

Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Author(s)

Henrik Bengtsson

The ColumnNamesInterface class interface

Description

Package: R.filesets
Class ColumnNamesInterface

Interface
~~|
~~+--ColumnNamesInterface

Directly known subclasses:
GenericTabularFile, TabularTextFile

public abstract class ColumnNamesInterface
extends Interface

Usage

ColumnNamesInterface(...)

Arguments

Fields and Methods

Methods:

Methods inherited from Interface:
extend, print, uses

Author(s)

Henrik Bengtsson

Deprecated and defunct objects

Description

The following objects are defunct:

• None

The following objects are deprecated:

• None

The FullNameInterface class interface

Description

Package: R.filesets
Class FullNameInterface

Interface
~~|
~~+--FullNameInterface

Directly known subclasses:
ChecksumFile, ChecksumFileSet, GenericDataFile, GenericDataFileSet, GenericDataFileSetList, GenericTabularFile, GenericTabularFileSet, RDataFile, RDataFileSet, RdsFile, RdsFileSet, TabularTextFile, TabularTextFileSet

public abstract class FullNameInterface
extends Interface

Usage

FullNameInterface(...)

Arguments

Details

The full name consists of a name followed by optional comma-separated tags. For instance, the full name of foo,a.2,b has name foo with tags a.2 and b.

Fields and Methods

Methods:

Methods inherited from Interface:
extend, print, uses

Author(s)

Henrik Bengtsson

Examples

# Setup a file set
path <- system.file("R", package="R.filesets")
ds <- GenericDataFileSet$byPath(path)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cat("Path of data set:\n")
print(getPath(ds))

cat("Fullname of data set:\n")
print(getFullName(ds))


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Data files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cat("Pathnames:\n")
print(getPathnames(ds))

cat("Filenames:\n")
print(sapply(ds, getFilename))

cat("Default fullnames:\n")
print(getFullNames(ds))

cat("Extensions:\n")
print(sapply(ds, getExtension))


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Translation of data file names
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Translate fullnames to lower case
setFullNamesTranslator(ds, function(names, ...) tolower(names))
cat("Lower-case fullnames:\n")
print(getFullNames(ds))

# Append a translator that reverse the order of the letters
revStr <- function(names, ...) {
  names <- strsplit(names, split="", fixed=TRUE)
  names <- lapply(names, FUN=rev)
  names <- sapply(names, FUN=paste, collapse="")
  names
}
appendFullNamesTranslator(ds, revStr)
cat("Reversed lower-case fullnames:\n")
fn3 <- getFullNames(ds)
print(fn3)


# Alternative for setting up a sequence of translators
setFullNamesTranslator(ds, list(function(names, ...) tolower(names), revStr))
cat("Reversed lower-case fullnames:\n")
fn3b <- getFullNames(ds)
print(fn3b)
stopifnot(identical(fn3b, fn3))

# Reset
clearFullNamesTranslator(ds)
cat("Default fullnames (after resetting):\n")
print(getFullNames(ds))

The abstract GenericDataFile class

Description

Package: R.filesets
Class GenericDataFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile

Directly known subclasses:
ChecksumFile, GenericTabularFile, RDataFile, RdsFile, TabularTextFile

public abstract static class GenericDataFile
extends FullNameInterface

A GenericDataFile is an object referring to a data file on a file system. Note that this class is abstract and can not be instantiated, but instead you have to use one of the subclasses or the generic *fromFile() method.

Usage

GenericDataFile(filename=NULL, path=NULL, mustExist=!is.na(filename), ...,
  .onUnknownArgs=c("error", "warning", "ignore"))

Arguments

Fields and Methods

Methods:

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Filename convention

The filename of an GenericDataFile is structured as follows:

filename

: "sample001,a,b,c.CEL" (this follows the R convention, but not the Unix convention)

fullname

: "sample001,a,b,c"

name

: "sample001"

tags

: c("a", "b", "c")

extension

: "CEL"

Author(s)

Henrik Bengtsson

See Also

An object of this class is typically part of an GenericDataFileSet.

Defines a GenericDataFile from a pathname

Description

Defines a GenericDataFile from a pathname.

Usage

## Static method (use this):
## GenericDataFile$fromFile(filename, path=NULL, ..., recursive=TRUE, verbose=FALSE,
##   .checkArgs=TRUE)

## Don't use the below:
## S3 method for class 'GenericDataFile'
fromFile(static, filename, path=NULL, ..., recursive=TRUE, verbose=FALSE,
  .checkArgs=TRUE)

Arguments

Value

Returns a GenericDataFile (or a subclass thereof).

Author(s)

Henrik Bengtsson

See Also

file.info(). For more information see GenericDataFile.

The GenericDataFileSet class

Description

Package: R.filesets
Class GenericDataFileSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet

Directly known subclasses:
ChecksumFileSet, GenericTabularFileSet, RDataFileSet, RdsFileSet, TabularTextFileSet

public static class GenericDataFileSet
extends FullNameInterface

A GenericDataFileSet object represents a set of GenericDataFiles.

Usage

GenericDataFileSet(files=NULL, tags="*", depth=NULL, ...,
  .onUnknownArgs=c("error", "warning", "ignore"))

Arguments

Fields and Methods

Methods:

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Author(s)

Henrik Bengtsson

Examples

# Setup a file set
path <- system.file(package="R.filesets")
ds <- GenericDataFileSet$byPath(path)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cat("Path of data set:\n")
print(getPath(ds))

cat("Fullname of data set:\n")
print(getFullName(ds))


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Data files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cat("Pathnames:\n")
print(getPathnames(ds))

cat("Filenames:\n")
print(sapply(ds, getFilename))

cat("Extensions:\n")
print(sapply(ds, getExtension))


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Subsetting
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
n <- length(ds)
ds2 <- extract(ds, 1:n)
print(ds2)

ds3 <- extract(ds, n:1)
print(ds3)

stopifnot(identical(rev(getPathnames(ds3)), getPathnames(ds2)))

idxs <- c(1,2,NA,n,NA)
ds4 <- extract(ds, idxs, onMissing="NA")
print(ds4)
print(getFullNames(ds4))
print(getFiles(ds4))

stopifnot(identical(is.na(idxs), unname(is.na(getPathnames(ds4)))))

Locates and sets up a file set by its name

Description

Locates and sets up a file set by its name, tags, root and sub directories.

Usage

## Static method (use this):
## GenericDataFileSet$byName(name, tags=NULL, subdirs=NULL, paths=NULL, ...,
##   verbose=FALSE)

## Don't use the below:
## S3 method for class 'GenericDataFileSet'
byName(static, name, tags=NULL, subdirs=NULL, paths=NULL, ..., verbose=FALSE)

Arguments

Value

Returns a GenericDataFileSet. If not found, an exception is thrown.

Author(s)

Henrik Bengtsson

See Also

Internally, *findByName() is used to locate the data set, and *byPath() to then set it up. For more information see GenericDataFileSet.

Defines a GenericDataFileSet by searching for files in a directory

Description

Defines a GenericDataFileSet by searching for files in a directory.

Usage

## Static method (use this):
## GenericDataFileSet$byPath(path=NULL, pattern=NULL, private=FALSE, recursive=FALSE,
##   depth=0L, fileClass=getFileClass(static), ..., .validate=FALSE, verbose=FALSE)

## Don't use the below:
## S3 method for class 'GenericDataFileSet'
byPath(static, path=NULL, pattern=NULL, private=FALSE, recursive=FALSE, depth=0L,
  fileClass=getFileClass(static), ..., .validate=FALSE, verbose=FALSE)

Arguments

Value

Returns an GenericDataFileSet object.

Reserved filenames

Note that files with names starting with a period . are not searched for. Such files are considered "private" and have to be included explicitly, if wanted.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFileSet.

Locates all file sets that match the requested name

Description

Locates all file sets that match the requested name, tags, and sub directories, in any of the root paths.

Usage

## Static method (use this):
## GenericDataFileSet$findByName(name, tags=NULL, subdirs=NULL, paths=NULL,
##   firstOnly=TRUE, mustExist=FALSE, ..., verbose=FALSE)

## Don't use the below:
## S3 method for class 'GenericDataFileSet'
findByName(static, name, tags=NULL, subdirs=NULL, paths=NULL, firstOnly=TRUE,
  mustExist=FALSE, ..., verbose=FALSE)

Arguments

Value

Returns a character vector of paths. If no file sets were found, NULL is returned.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFileSet.

The GenericDataFileSetList class

Description

Package: R.filesets
Class GenericDataFileSetList

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSetList

Directly known subclasses:

public static class GenericDataFileSetList
extends FullNameInterface

A GenericDataFileSetList object represents a list of GenericDataFileSets.

Usage

GenericDataFileSetList(dsList=list(), tags="*", ..., allowDuplicates=TRUE,
  .setClass="GenericDataFileSet")

Arguments

Fields and Methods

Methods:

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Author(s)

Henrik Bengtsson

Examples

# Setup a file set
path1 <- system.file(package="R.filesets")
ds1 <- GenericDataFileSet$byPath(path1)

path2 <- system.file(package="R.utils")
ds2 <- GenericDataFileSet$byPath(path2)

dsl <- GenericDataFileSetList(list(ds1, ds2), tags=c("*", "CustomTag"))
print(dsl)

df <- as.data.frame(dsl)
print(df)

print(df["DESCRIPTION","R.filesets"])

The abstract GenericTabularFile class

Description

Package: R.filesets
Class GenericTabularFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GenericTabularFile

Directly known subclasses:
TabularTextFile

public abstract static class GenericTabularFile
extends ColumnNamesInterface

A TabularTextFile is an object referring to a tabular text file on a file system containing data in a tabular format. Methods for reading all or a subset of the tabular data exist.

Usage

GenericTabularFile(..., .verify=TRUE, verbose=FALSE)

Arguments

Fields and Methods

Methods:

Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames

Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Author(s)

Henrik Bengtsson

See Also

An object of this class is typically part of an GenericTabularFileSet.

The GenericTabularFileSet class

Description

Package: R.filesets
Class GenericTabularFileSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--GenericTabularFileSet

Directly known subclasses:
TabularTextFileSet

public static class GenericTabularFileSet
extends GenericDataFileSet

An GenericTabularFileSet object represents a set of GenericTabularFiles.

Usage

GenericTabularFileSet(...)

Arguments

Fields and Methods

Methods:

Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Author(s)

Henrik Bengtsson

Non-documented objects

Description

This page contains aliases for all "non-documented" objects that R CMD check detects in this package.

Almost all of them are generic functions that have specific document for the corresponding method coupled to a specific class. Other functions are re-defined by setMethodS3() to default methods. Neither of these two classes are non-documented in reality. The rest are deprecated methods.

Author(s)

Henrik Bengtsson

The RDataFile class

Description

Package: R.filesets
Class RDataFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--RDataFile

Directly known subclasses:

public abstract static class RDataFile
extends GenericDataFile

An RDataFile represents a binary file containing R objects saved using the save() function.

Usage

RDataFile(...)

Arguments

Fields and Methods

Methods:

Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Author(s)

Henrik Bengtsson

See Also

An object of this class is typically part of an RDataFileSet.

The RDataFileSet class

Description

Package: R.filesets
Class RDataFileSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--RDataFileSet

Directly known subclasses:

public static class RDataFileSet
extends GenericDataFileSet

An RDataFileSet object represents a set of RDataFile:s.

Usage

RDataFileSet(...)

Arguments

Fields and Methods

Methods:

Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Author(s)

Henrik Bengtsson

The RdsFile class

Description

Package: R.filesets
Class RdsFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--RdsFile

Directly known subclasses:

public abstract static class RdsFile
extends GenericDataFile

An RdsFile represents a binary file containing an R object saved using the saveRDS() function.

Usage

RdsFile(...)

Arguments

Fields and Methods

Methods:

Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Author(s)

Henrik Bengtsson

See Also

An object of this class is typically part of an RdsFileSet.

The RdsFileSet class

Description

Package: R.filesets
Class RdsFileSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--RdsFileSet

Directly known subclasses:

public static class RdsFileSet
extends GenericDataFileSet

An RdsFileSet object represents a set of RdsFile:s.

Usage

RdsFileSet(...)

Arguments

Fields and Methods

Methods:

Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Author(s)

Henrik Bengtsson

The TabularTextFile class

Description

Package: R.filesets
Class TabularTextFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--TabularTextFile

Directly known subclasses:

public abstract static class TabularTextFile
extends GenericTabularFile

A TabularTextFile is an object referring to a tabular text file on a file system containing data in a tabular format. Methods for reading all or a subset of the tabular data exist.

Usage

TabularTextFile(..., sep=c("\t", ","), quote="\"", fill=FALSE, skip=0L, columnNames=NA,
  commentChar="#", .verify=TRUE, verbose=FALSE)

Arguments

Fields and Methods

Methods:

Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles

Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames

Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Author(s)

Henrik Bengtsson

See Also

An object of this class is typically part of an TabularTextFileSet.

Examples

path <- system.file("exData/dataSetA,original", package="R.filesets")

db <- TabularTextFile("fileA,20100112.dat", path=path)
print(db)

# Read all data
data <- readDataFrame(db)
print(data)

# Read columns 'x', 'y', and 'char'
data <- readDataFrame(db, colClasses=c("(x|y)"="integer", "char"="character"))
print(data)

# Translate column names on the fly
db <- setColumnNamesTranslator(db, function(names, ...) toupper(names))
data <- readDataFrame(db, colClasses=c("(X|Y)"="integer", "CHAR"="character"))
print(data)

The TabularTextFileSet class

Description

Package: R.filesets
Class TabularTextFileSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--GenericTabularFileSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--TabularTextFileSet

Directly known subclasses:

public static class TabularTextFileSet
extends GenericTabularFileSet

An TabularTextFileSet object represents a set of TabularTextFiles.

Usage

TabularTextFileSet(...)

Arguments

Fields and Methods

Methods:

Methods inherited from GenericTabularFileSet:
extractMatrix

Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Author(s)

Henrik Bengtsson

Examples

# Setup a file set consisting of all *.dat tab-delimited files
# in a particular directory
path <- system.file("exData/dataSetA,original", package="R.filesets")
ds <- TabularTextFileSet$byPath(path, pattern="[.]dat$")
print(ds)


# Read column 'y' and a subset of the rows from each of the
# tab-delimited files and combine into a matrix
rows <- c(3:5, 8, 2)
data <- extractMatrix(ds, column="y", colClass="integer", rows=rows)
print(data)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# See also help("readDataFrame.TabularTextFileSet")
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# ADVANCED: Translation of fullnames
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
fnts <- TabularTextFileSet$byPath(getPath(ds), pattern=",fullnames[.]txt$")
appendFullNamesTranslator(ds, as.list(fnts))

cat("Default fullnames:\n")
print(head(getFullNames(ds, translate=FALSE)))
cat("Translated fullnames:\n")
print(head(getFullNames(ds)))

cat("Default fullnames:\n")
print(getFullNames(ds, translate=FALSE))
cat("Translated fullnames:\n")
print(getFullNames(ds))

Checks whether any of the pathnames are missing

Description

Checks whether any of the pathnames are missing. Note that this only tests the pathnames of files, but it does not test whether the files exists or not.

Usage

## S3 method for class 'GenericDataFileSet'
anyNA(x, ...)

Arguments

Value

Returns a character.

Author(s)

Henrik Bengtsson

See Also

na.omit for dropping missing items. For more information see GenericDataFileSet.

Appends one data set to an existing one

Description

Appends one data set to an existing one. The fullname of the merged data set is that of the first data set.

Usage

## S3 method for class 'GenericDataFileSet'
append(x, values, ...)

Arguments

Details

By default, in order to avoid downstream side effects on the data set being appended, each of its file is cloned before being appended.

Value

Returns a merged GenericDataFileSet of the same class as the first data set.

Author(s)

Henrik Bengtsson

See Also

To append one or more files, see appendFiles(). For more information see GenericDataFileSet.

Appends a list of files to a data set

Description

Appends a list of files to a data set.

Usage

## S3 method for class 'GenericDataFileSet'
appendFiles(this, files, clone=TRUE, ..., .fileClass=getFileClass(this),
  .assertSameClass=TRUE, verbose=FALSE)

Arguments

Details

The files appended must inherit the same class as the first file of the data set, otherwise an exception is thrown.

Value

Returns (invisible) the appended data set (itself).

Author(s)

Henrik Bengtsson

See Also

To append a data set, see append(). For more information see GenericDataFileSet.

Returns a short string describing the file

Description

Returns a short string describing the file.

Usage

## S3 method for class 'GenericDataFile'
as.character(x, ...)

Arguments

Value

Returns a character string.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFile.

Returns a short string describing the file set

Description

Returns a short string describing the file set.

Usage

## S3 method for class 'GenericDataFileSet'
as.character(x, ...)

Arguments

Value

Returns a character string.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFileSet.

Returns the files of the file set

Description

Returns the files of the file set.

Usage

## S3 method for class 'GenericDataFileSet'
as.list(x, useNames=TRUE, ...)

Arguments

Value

Returns a list of files, each of class getFileClass().

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFileSet.

Compares the file checksum with the value of the checksum file

Description

Compares the file checksum with the value of the checksum file.

Usage

## S3 method for class 'GenericDataFile'
compareChecksum(this, ...)

Arguments

Value

Returns TRUE if the file checksum is identical to the stored value in the corresponding checksum file, otherwise FALSE. FALSE is also returned if the checksum file does not exist. An exception is thrown if the file does not exist.

Author(s)

Henrik Bengtsson

See Also

*validateChecksum(). *readChecksum(). *writeChecksum(). *getChecksum(). For more information see GenericDataFile.

Safely copies a file to a new pathname

Description

Safely copies a file to a new pathname.

Usage

## S3 method for class 'GenericDataFile'
copyTo(this, filename=getFilename(this), path=NULL, ...)

Arguments

Details

In order to minimize the risk for corrupt copies, the copyFile method of R.utils is used, which provides several protection against user, system and file errors.

Value

Returns a GenericDataFile (of the same class as the source file) referring to the new file copy.

Author(s)

Henrik Bengtsson

See Also

To link to a GenericDataFile, see *linkTo(). To rename a GenericDataFile, see *renameTo(). Internally copyFile is used. For more information see GenericDataFile.

Copies a data set to another directory

Description

Copies a data set to another directory.

Usage

## S3 method for class 'GenericDataFileSet'
copyTo(this, path=NULL, ..., verbose=FALSE)

Arguments

Details

Each file is copied safely, but if this method is interrupted, it may results in a data set consisting of fewer than the original data set.

Value

Returns a GenericDataFileSet consisting the new file copies.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFileSet.

Gets the dimension of data table

Description

Gets the dimension of data table, which is the number of rows and the number of columns.

Usage

## S3 method for class 'GenericTabularFile'
dim(x)

Value

Returns an integer vector of length two.

Author(s)

Henrik Bengtsson

See Also

*nbrOfRows(). For more information see GenericTabularFile.

Applies a function to each pair of file in two file sets

Description

Applies a function to each pair of file in two file sets.

Usage

## S3 method for class 'GenericDataFileSet'
dsApplyInPairs(ds1, ds2, FUN, ..., args=list(), skip=FALSE, verbose=FALSE,
  .parallel=NULL, .control=NULL)

Arguments

Details

WARNING: dsApplyInPairs() is defunct; instead use future.apply::future_mapply().

Value

Returns a list.

Author(s)

Henrik Bengtsson

Examples

## Not run: 

# - - - - - - - - - - - - - - - - - - - - - - - -
# Setting up a file set
# - - - - - - - - - - - - - - - - - - - - - - - -
path <- system.file(package="R.filesets")
ds <- GenericDataFileSet$byPath(path)


# - - - - - - - - - - - - - - - - - - - - - - - -
# Get the size of each file
# - - - - - - - - - - - - - - - - - - - - - - - -
sizes <- lapply(ds, FUN=getFileSize)
str(sizes)


## End(Not run)

Checks if a file equals another

Description

Checks if a file equals another.

Usage

## S3 method for class 'GenericDataFile'
equals(this, other, ...)

Arguments

Details

The two files compared are equal if they have the same pathname.

The two files compared are not equal if:

• Argument other is not a GenericDataFile, or

• their file sizes differ, or

• their file checksums differ.

If none of the above occurs, the two files are considered equal.

Note that subclasses use refined rules.

Value

Returns TRUE if the file equals the other, otherwise FALSE. If FALSE, attributes are added specifying the pathnames of the two files compared, and the reason for them being different.

Author(s)

Henrik Bengtsson

See Also

*getFileSize(). *getChecksum(). For more information see GenericDataFile.

Extract a subset of the file set

Description

Extract a subset of the file set.

Usage

## S3 method for class 'GenericDataFileSet'
extract(this, files, ..., onMissing=c("NA", "error", "drop", "dropall"),
  onDuplicates=c("ignore", "drop", "error"))

Arguments

Value

Returns a GenericDataFileSet with zero of more GenericDataFile:s.

Author(s)

Henrik Bengtsson

See Also

na.omit for dropping missing files from a fileset. For more information see GenericDataFileSet.

Reads one of the columns

Description

Reads one of the columns.

Usage

## S3 method for class 'GenericTabularFile'
extractMatrix(this, column=1L, drop=FALSE, ..., verbose=FALSE)

Arguments

Value

Returns a Jx1 matrix, or if drop=TRUE a vector of length J.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericTabularFile.

Gets the checksum of a file

Description

Gets the checksum of a file.

Usage

## S3 method for class 'GenericDataFile'
getChecksum(this, write=NA, force=FALSE, verbose=FALSE, ...)

Arguments

Value

Returns a character string, which can be NA if file is missing.

Author(s)

Henrik Bengtsson

See Also

Internally digest is used. *readChecksum(). *writeChecksum(). *compareChecksum(). For more information see GenericDataFile.

Generates a deterministic checksum for an R object

Description

Generates a deterministic checksum for an R object that can be used to identify the data set.

Usage

## S3 method for class 'GenericDataFileSet'
getChecksum(this, ...)

Arguments

Value

Returns the checksum as a character string.

Author(s)

Henrik Bengtsson

See Also

Internally, the checksum is calculated on the objects returned by *getChecksumObjects().

For more information see GenericDataFileSet.

Retrieves objects that uniquely identifying the data set

Description

Retrieves objects that uniquely identifying the data set.

Usage

## S3 method for class 'GenericDataFileSet'
getChecksumObjects(this, ..., verbose=FALSE)

Arguments

Details

By default, a GenericDataFileSet is assumed to be uniquely identifiable by its files and their fullnames (possibly translated).

Value

Returns a named list of objects that can be used to uniquely identifying the GenericDataFileSet.

Author(s)

Henrik Bengtsson

See Also

*getChecksum()

For more information see GenericDataFileSet.

Gets the column names

Description

Gets the column names.

Usage

## S3 method for class 'ColumnNamesInterface'
getColumnNames(this, ..., translate=TRUE)

Arguments

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

See Also

*getDefaultColumnNames(). For more information see ColumnNamesInterface.

Gets when the file was created

Description

Gets when the file was created.

Usage

## S3 method for class 'GenericDataFile'
getCreatedOn(this, ...)

Arguments

Value

Returns a POSIXct time stamp.

Author(s)

Henrik Bengtsson

See Also

file.info(). For more information see GenericDataFile.

Gets the default column names

Description

Gets the default column names, that is, the column names without translations.

Usage

## S3 method for class 'ColumnNamesInterface'
getDefaultColumnNames(...)

Arguments

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

See Also

*getColumnNames(). For more information see ColumnNamesInterface.

Gets the default column names

Description

Gets the default column names by inferring it from the file header.

Usage

## S3 method for class 'TabularTextFile'
getDefaultColumnNames(this, ...)

Arguments

Value

Returns character vector, or NULL if there are no column names in the file header.

Author(s)

Henrik Bengtsson

See Also

For more information see TabularTextFile.

Gets the default full name

Description

Gets the default full name, that is, the fullname without translations.

Usage

## S3 method for class 'FullNameInterface'
getDefaultFullName(...)

Arguments

Details

The full name of a file is the filename excluding any extension (and period). For instance, the full name of path/to/foo,a.2,b.ext is foo,a.2,b.

Value

Returns a character.

Author(s)

Henrik Bengtsson

See Also

*getName(). *getTags(). For more information see FullNameInterface.

Gets the full name of the file

Description

Gets the full name of the file, that is the filename without the filename extension.

Usage

## S3 method for class 'GenericDataFile'
getDefaultFullName(this, ...)

Arguments

Details

The full name of a file is the filename excluding any extension (and period). For instance, the full name of path/to/foo,a.2,b.ext is foo,a.2,b.

Value

Returns a character string (NA if "empty" file).

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFile.

Gets the default full name of the file set

Description

Gets the default full name of the file set, that is the name of the directory without parent directories.

Usage

## S3 method for class 'GenericDataFileSet'
getDefaultFullName(this, parent=getDepth(this, default = NULL), ...)

Arguments

Details

By default, the full name of a file set is the name of the directory containing all the files, e.g. the name of file set path/foo,c/to,a,b/* is to,a,b. Argument parent=1 specifies that the parent directory should be used, e.g. foo,c.

Value

Returns a character.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFileSet.

Gets the filename extension

Description

Gets the filename extension.

Usage

## S3 method for class 'GenericDataFile'
getExtension(this, ...)

Arguments

Value

Returns a character string (which is of length zero if "empty" file).

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFile.

Get a particular file of the file set

Description

Get a particular file of the file set.

Usage

## S3 method for class 'GenericDataFileSet'
getFile(this, idx, ...)

Arguments

Value

Returns a @GenericDataFile.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFileSet. If argument idx is a character, then internally *indexOf() is used to identify what to return.

Gets the size of a file

Description

Gets the size of a file.

Usage

## S3 method for class 'GenericDataFile'
getFileSize(this, what=c("numeric", "units"), sep="", ...)

Arguments

Value

Returns a numeric or a character string. A missing value (NA) is returned if the file does not exist.

Author(s)

Henrik Bengtsson

See Also

file.info(). For more information see GenericDataFile.

Gets the file type of a file

Description

Gets the file type of a file.

Usage

## S3 method for class 'GenericDataFile'
getFileType(this, ...)

Arguments

Details

By default, this methods returns the filename extension, but subclasses may override this.

Value

Returns a character in lower case letters (which is of length zero if "empty" file).

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFile.

Gets the filename of the file

Description

Gets the filename of the file.

Usage

## S3 method for class 'GenericDataFile'
getFilename(this, ...)

Arguments

Details

The filename of a file is the pathname excluding any path. For instance, the filename of path/to/foo,a.2,b.ext is foo,a.2,b.ext.

Value

Returns a character string (NA if an "empty" file).

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFile.

Gets the full name

Description

Gets the full name consisting of a name and tags.

Usage

## S3 method for class 'FullNameInterface'
getFullName(this, ..., translate=TRUE)

Arguments

Value

Returns a character.

Author(s)

Henrik Bengtsson

See Also

*getName(). *getTags(). For more information see FullNameInterface.

Gets the file header

Description

Gets the file header.

Usage

## S3 method for class 'TabularTextFile'
getHeader(this, ..., header=TRUE, force=FALSE)

Arguments

Value

Returns a named list.

Author(s)

Henrik Bengtsson

See Also

For more information see TabularTextFile.

Gets when the file was last accessed

Description

Gets when the file was last accessed.

Usage

## S3 method for class 'GenericDataFile'
getLastAccessedOn(this, ...)

Arguments

Value

Returns a POSIXct time stamp.

Author(s)

Henrik Bengtsson

See Also

file.info(). For more information see GenericDataFile.

Gets when the file was last modified

Description

Gets when the file was last modified.

Usage

## S3 method for class 'GenericDataFile'
getLastModifiedOn(this, ...)

Arguments

Value

Returns a POSIXct time stamp.

Author(s)

Henrik Bengtsson

See Also

file.info(). For more information see GenericDataFile.

Gets the name

Description

Gets the name.

Usage

## S3 method for class 'FullNameInterface'
getName(this, ...)

Arguments

Details

The name is the part of the fullname that precedes any comma. For instance, the name of foo,a.2,b is foo.

Value

Returns a character.

Author(s)

Henrik Bengtsson

See Also

*getFullName(). *getTags(). For more information see FullNameInterface.

Gets the names (or fullnames) of the files in the file set

Description

Gets the names (or fullnames) of the files in the file set.

Usage

 ## S3 method for class 'GenericDataFileSet'
getNames(this, ...)
 ## S3 method for class 'GenericDataFileSet'
getFullNames(this, ..., onRemapping=getOption("R.filesets::onRemapping", "ignore"))

Arguments

Value

Returns a character vector of length equal to the number of files in the set.

Author(s)

Henrik Bengtsson

See Also

*indexOf() For more information see GenericDataFileSet.

Gets the path (directory) of the file

Description

Gets the path (directory) of the file.

Usage

## S3 method for class 'GenericDataFile'
getPath(this, ...)

Arguments

Value

Returns a character string (NA if an "empty" file).

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFile.

Gets the path (directory) of the file set

Description

Gets the path (directory) of the file set.

Usage

## S3 method for class 'GenericDataFileSet'
getPath(this, ...)

Arguments

Value

Returns a character.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFileSet.

Gets the pathname of the file

Description

Gets the pathname of the file.

Usage

## S3 method for class 'GenericDataFile'
getPathname(this, absolute=FALSE, ...)

Arguments

Value

Returns the pathname as character string (or NULL if an "empty" file).

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFile.

Gets the pathnames of the files in the file set

Description

Gets the pathnames of the files in the file set.

Usage

## S3 method for class 'GenericDataFileSet'
getPathnames(this, ...)

Arguments

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFileSet.

Gets the tags

Description

Gets the tags.

Usage

## S3 method for class 'FullNameInterface'
getTags(this, pattern=NULL, collapse=NULL, ..., named=FALSE, na.rm=TRUE,
  useCustomTags=TRUE)

Arguments

Details

The tags of a fullname are the comma separated parts of the fullname that follows the the first comma, if any. For instance, the tags of foo,a.2,b are a.2 and b.

Any custom tag that equals "*" is replaced by the comma separated tags from the fullname.

Value

Returns a character vector (possibly NA) or NULL.

Author(s)

Henrik Bengtsson

See Also

*getFullName(). *getName(). For more information see FullNameInterface.

Compresses/uncompresses a file

Description

Compresses/uncompresses a file using gzip compression. When compressing (uncompressing), the new filename has suffix .gz appended (removed), which is also used to test if a file is gzip'ed or not.

Usage

 ## S3 method for class 'GenericDataFile'
gzip(this, ...)
 ## S3 method for class 'GenericDataFile'
gunzip(this, ...)
 ## S3 method for class 'GenericDataFile'
isGzipped(this, ...)

Arguments

Value

Returns (invisibly) the updated pathname. When compressing (uncompressing), an exception is thrown if the file is already compressed (not compressed). An exception is thrown if the file does not exist.

Author(s)

Henrik Bengtsson

See Also

Internally gzip is used. For more information see GenericDataFile.

Compresses/uncompresses a set of files

Description

Compresses/uncompresses a set of files using gzip compression. When compressing (uncompressing), each of the GenericDataFile of the file set are compressed (uncompressed).

Usage

 ## S3 method for class 'GenericDataFileSet'
gzip(this, ...)
 ## S3 method for class 'GenericDataFileSet'
gunzip(this, ...)

Arguments

Value

Returns (invisibly) itself.

Author(s)

Henrik Bengtsson

See Also

Internally gzip and gunzip are used. For more information see GenericDataFileSet.

Checks whether the file has been modified

Description

Checks whether the file has been modified since last time checked.

Usage

## S3 method for class 'GenericDataFile'
hasBeenModified(this, update=TRUE, unknown=TRUE, ...)

Arguments

Value

Returns TRUE, FALSE, or the value of argument unknown.

Author(s)

Henrik Bengtsson

See Also

file.info(). For more information see GenericDataFile.

Checks if there are column names in the header

Description

Checks if there are column names in the header.

Usage

## S3 method for class 'TabularTextFile'
hasColumnHeader(this, ...)

Arguments

Value

Returns a logical.

Author(s)

Henrik Bengtsson

See Also

For more information see TabularTextFile.

Checks whether the fullname contains a given set of tag(s)

Description

Checks whether the fullname contains a given set of tag(s).

Usage

 ## S3 method for class 'FullNameInterface'
hasTags(this, tags, ...)
 ## S3 method for class 'FullNameInterface'
hasTag(this, tag, ...)

Arguments

Value

Returns TRUE if all tags are part of the fullname, otherwise FALSE.

Author(s)

Henrik Bengtsson

See Also

*getTags(). *getName(). For more information see FullNameInterface.

Finds indices of a subset of files

Description

Finds indices of a subset of files whose names match a given set of names or name patterns.

Usage

## S3 method for class 'GenericDataFileSet'
indexOf(this, patterns=NULL, by=c("exact", "regexp", "fixed"), ...,
  onMissing=c("NA", "error"))

Arguments

Details

If an element of patterns contains a comma, then that element is matched against the *getFullNames(), otherwise it is matched against *getNames(). First each pattern is matched by regular expression rules, and if there is not match, then by fixed strings.

Value

Returns an integer vector of length K with elements in [1,*length()] or (integer) NA (for non-matched names).

Author(s)

Henrik Bengtsson

See Also

*getNames() For more information see GenericDataFileSet.

Checks if this is an existing file

Description

Checks if this is an existing file and not a directory.

Usage

## S3 method for class 'GenericDataFile'
isFile(this, ...)

Arguments

Value

Returns a TRUE if an existing file (and not a directory), otherwise FALSE.

Author(s)

Henrik Bengtsson

See Also

isFile. For more information see GenericDataFile.

Gets the number of files in the set

Description

Gets the number of files in the set.

Usage

 ## S3 method for class 'GenericDataFileSet'
length(x)
 ## S3 method for class 'GenericDataFileSet'
nbrOfFiles(this, ...)

Value

Returns an non-negative integer.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFileSet.

Creates a symbolic file link

Description

Creates a symbolic file link to a GenericDataFile at/from a given destination pathname.

Usage

## S3 method for class 'GenericDataFile'
linkTo(this, filename=getFilename(this), path=NULL, skip=!overwrite, overwrite=FALSE,
  ...)

Arguments

Value

Returns a GenericDataFile (of the same class as the source file) referring to the file via the link.

Required privileges on Windows

In order for this method to succeed on Windows, the client/R session must run with sufficient privileges. See createLink for more details.

Author(s)

Henrik Bengtsson

See Also

To copy a GenericDataFile, see *copyTo(). Internally createLink is used. For more information see GenericDataFile.

Reads data from a RDS file

Description

Reads data from a RDS file.

Usage

 ## Default S3 method:
loadRDS(file, ...)
 ## S3 method for class 'RdsFile'
loadRDS(file, ...)

Arguments

Value

Returns an R object.

Author(s)

Henrik Bengtsson

See Also

readRDS().

Reads data from a RDS file

Description

Reads data from a RDS file.

Usage

 ## S3 method for class 'RDataFile'
loadToEnv(file, ...)

Arguments

Value

Returns an environment.

Author(s)

Henrik Bengtsson

See Also

loadToEnv.

Gets the number of columns

Description

Gets the number of columns.

Usage

## S3 method for class 'ColumnNamesInterface'
nbrOfColumns(this, ...)

Arguments

Value

Returns an integer. If the number of columns cannot be inferred, NA is returned.

Author(s)

Henrik Bengtsson

See Also

*getColumnNames(). For more information see ColumnNamesInterface.

Counts the number of lines in the data file

Description

Counts the number of lines in the data file. The count include header rows, comments and more.

Usage

## S3 method for class 'TabularTextFile'
nbrOfLines(this, fast=FALSE, ...)

Arguments

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

See Also

To count the number of data rows is the data table, use *nbrOfRows(). Internally, countLines is used. For more information see TabularTextFile.

Gets the number of data rows

Description

Gets the number of data rows.

Usage

## S3 method for class 'GenericTabularFile'
nbrOfRows(...)

Arguments

Value

Returns an integer.

Author(s)

Henrik Bengtsson

See Also

*dim(). For more information see GenericTabularFile.

Counts the number of data rows

Description

Counts the number of data rows. The count does not include the header rows or comments.

Usage

## S3 method for class 'TabularTextFile'
nbrOfRows(this, fast=FALSE, ...)

Arguments

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

See Also

The number of data rows is always less or equal to the number of lines as returned by *nbrOfLines(). Internally, countLines is used. For more information see TabularTextFile.

Reads the checksum value

Description

Reads the checksum value.

Usage

## S3 method for class 'ChecksumFile'
readChecksum(this, ...)

Arguments

Details

The content of the checksum file is trimmed from comment lines, whitespaces and then validated that the remaining part contains a hexadecimal value.

Value

Returns a lower-case character string.

Author(s)

Henrik Bengtsson

See Also

For more information see ChecksumFile.

Reads the value of the corresponding checksum file

Description

Reads the value of the corresponding checksum file, if existing.

Usage

## S3 method for class 'GenericDataFile'
readChecksum(this, ...)

Arguments

Details

The content of the checksum file is trimmed from comment lines, whitespaces and then validated that the remaining part contains a hexadecimal value.

Value

Returns a character string, which can be NA if file is missing. An exception is thrown if the file does not exist, and hence not the checksum file.

Author(s)

Henrik Bengtsson

See Also

*validateChecksum(). *compareChecksum(). *writeChecksum(). *getChecksum(). For more information see GenericDataFile.

Reads a subset of the columns as a data frame

Description

Reads a subset of the columns as a data frame.

Usage

## S3 method for class 'GenericTabularFile'
readColumns(...)

Arguments

Value

Returns a data.frame.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericTabularFile.

Reads data from a tabular file

Description

Reads data from a tabular file or a set of such files.

Usage

## Default S3 method:
readDataFrame(filename, path=NULL, ...)

Arguments

Details

When reading multiple files at once, first each file is read into a data.frame, and then these data.frames are (by default) merged into one data.frame using rbind(). This requires that the same set of columns are read for each file. Which columns to read can be controlled by specifying their names in argument colClasses. To change how the data.frames are merged, use argument combineBy. For more information, follow the help on the above to readDataFrame() help links.

Value

Returns a data.frame.

Author(s)

Henrik Bengtsson

See Also

read.table. For further details, see classes TabularTextFile and TabularTextFileSet.

Examples

path <- system.file("exData/dataSetA,original", package="R.filesets")

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Example: Standard tab-delimited file with header comments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
pathname <- file.path(path, "fileA,20100112.dat")

# Read all data
df <- readDataFrame(pathname)
print(df)

# Read columns 'x', 'y', and 'char'
df <- readDataFrame(pathname, colClasses=c("(x|y)"="integer", "char"="character"))
print(df)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Example: Tab-delimited file with header comments but
#          also two garbage at the very beginning
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
pathname <- file.path(path, "fileA,20130116.datx")

# Explicitly skip the two rows
df <- readDataFrame(pathname, skip=2)
print(df)


# Skip until the first data row
df <- readDataFrame(pathname, skip="^x")
print(df)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Example: Tab-delimited file without column header
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
path <- system.file("exData/dataSetB", package="R.filesets")
pathname <- file.path(path, "fileF,noHeader.dat")

# Incorrectly assuming column header
df <- readDataFrame(pathname)
print(df)

# No column header
df <- readDataFrame(pathname, header=FALSE)
print(df)

Reads the tabular data as a data frame

Description

Reads the tabular data as a data frame.

Usage

## S3 method for class 'GenericTabularFile'
readDataFrame(...)

Arguments

Value

Returns a data.frame.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericTabularFile.

Reads the tabular data as a data frame

Description

Reads the tabular data as a data frame.

Usage

## S3 method for class 'TabularTextFile'
readDataFrame(this, con=NULL, rows=NULL, nrow=NULL, trimQuotes=FALSE, ..., debug=FALSE,
  verbose=FALSE)

Arguments

Value

Returns a data.frame.

Reading quoted numerics

If a specific data column is specified as being numeric in argument colClasses and that column contains quoted values it is necessary to use argument trimQuotes=TRUE, otherwise scan() throws an exception similar to: scan() expected 'a real', got '"1.0"'.

Author(s)

Henrik Bengtsson

See Also

For more information see TabularTextFile.

Reads the tabular data from all files as data frames

Description

Reads the tabular data from all files as data frames and combines them into one data frame (by default).

Usage

## S3 method for class 'TabularTextFileSet'
readDataFrame(this, ..., combineBy=function(x) Reduce(rbind, x), verbose=FALSE)

Arguments

Value

Returns what combineBy returns, which defaults to a data.frame. If combineBy=NULL, then a named list of data.frame:s is returned.

Author(s)

Henrik Bengtsson

See Also

For more information see TabularTextFileSet.

Examples

# Setup a file set consisting of all *.dat tab-delimited files
# in a particular directory
path <- system.file("exData/dataSetA,original", package="R.filesets")
ds <- TabularTextFileSet$byPath(path, pattern="[.]dat$")
print(ds)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Read data frames from each of the files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dataList <- lapply(ds, readDataFrame)
print(dataList)

rows <- c(3:5, 8, 2)
dataList <- lapply(ds, readDataFrame, rows=rows)
print(dataList)



# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Read common columns and stack into one data frame
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
colNames <- Reduce(intersect, lapply(ds, getColumnNames))
cat("Common column names:\n")
print(colNames)

# Read the *common* columns "as is" (hence 'NA')
colClasses <- rep(NA, times=length(colNames))
names(colClasses) <- colNames
cat("Column class patterns:\n")
print(colClasses)

data <- readDataFrame(ds, colClasses=colClasses)
print(data)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Translate column names on the fly
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
lapply(ds, FUN=setColumnNamesTranslator, function(names, ...) toupper(names))
data <- readDataFrame(ds, colClasses=c("(X|Y)"="integer", "CHAR"="character"))
print(data)

Reads the lines of the data file as strings

Description

Reads the lines of the data file as strings.

Usage

## S3 method for class 'TabularTextFile'
readLines(con, ...)

Arguments

Value

Returns a character vector.

Author(s)

Henrik Bengtsson

See Also

*readDataFrame(). For more information see TabularTextFile.

Renames/moves a file

Description

Renames/moves a file.

Usage

## S3 method for class 'GenericDataFile'
renameTo(this, filename=getFilename(this), path=NULL, ..., verbose=FALSE)

Arguments

Value

Returns the source GenericDataFile.

Author(s)

Henrik Bengtsson

See Also

Internally renameFile. *copyTo(). For more information see GenericDataFile.

Sets the column names

Description

Sets the column names. This is done using a names translator function that returns the specified names.

Usage

## S3 method for class 'ColumnNamesInterface'
setColumnNames(this, ...)

Arguments

Value

Returns (invisibly) itself.

Author(s)

Henrik Bengtsson

See Also

*getColumnNames(). For more information see ColumnNamesInterface.

Sets the full name

Description

Sets the full name. This is done using a fullname translator function that returns the specified fullname.

Usage

## S3 method for class 'FullNameInterface'
setFullName(this, ...)

Arguments

Value

Returns (invisibly) itself.

Author(s)

Henrik Bengtsson

See Also

*getFullName(). *setName(). For more information see FullNameInterface.

Sets the name part of the fullname

Description

Sets the name part of the fullname, leaving the tags untouched.

Usage

## S3 method for class 'FullNameInterface'
setName(this, name=NULL, ...)

Arguments

Value

Returns (invisibly) itself.

Author(s)

Henrik Bengtsson

See Also

*setFullName(). *getName(). For more information see FullNameInterface.

Sets the tags

Description

Sets the tags.

Usage

## S3 method for class 'FullNameInterface'
setTags(this, tags="*", ...)

Arguments

Details

See *getTags() for so called special tags.

Value

Returns (invisibly) itself.

Author(s)

Henrik Bengtsson

See Also

*getTags(). For more information see FullNameInterface.

Sorts the set

Description

Sorts the set by one of several ordering schema.

Usage

## S3 method for class 'GenericDataFileSet'
sortBy(this, by=c("lexicographic", "mixedsort", "mixeddecimal", "mixedroman",
  "filesize"), decreasing=FALSE, caseSensitive=FALSE, ...)

Arguments

Details

The set is ordering by the fullnames. If by="lexicographic", lexicographic ordering is used, sometimes also referred to as alphabetic ordering. If by="mixeddecimal", mixedsort ordering acknowledging decimal numbers is used, cf. mixedsort. If by="mixedroman", mixedsort ordering acknowledging roman numerals is used, cf. mixedsort.

Value

Returns returns itself with the set ordered accordingly.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFileSet.

Asserts that the checksum matches the checksum of file

Description

Asserts that the checksum matches the checksum of file.

Usage

## S3 method for class 'ChecksumFile'
validate(this, ..., verbose=FALSE)

Arguments

Value

Returns TRUE. If checksum on record does not match the file, an exception is thrown.

Author(s)

Henrik Bengtsson

See Also

For more information see ChecksumFile.

Validates the content of a file

Description

Validates the content of a file.

Usage

## S3 method for class 'GenericDataFile'
validate(this, ...)

Arguments

Value

If the file is invalid, then an error is thrown. If the files is valid, then TRUE is returned. Otherwise, NA is returned, which happens if the file was not validated.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFile.

Validates all files in the data set

Description

Validates all files in the data set.

Usage

## S3 method for class 'GenericDataFileSet'
validate(this, ...)

Arguments

Value

If one of the files is invalid, then an error is thrown. If all of the files are valid, then TRUE is returned. Otherwise, NA is returned.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericDataFileSet.

Asserts that the file checksum matches the one of the checksum file

Description

Asserts that the file checksum matches the one of the checksum file.

Usage

## S3 method for class 'GenericDataFile'
validateChecksum(this, ...)

Arguments

Value

An exception is thrown if not, that is, if *compareChecksum() returns FALSE.

Author(s)

Henrik Bengtsson

See Also

*validateChecksum(). *readChecksum(). *writeChecksum(). *getChecksum(). For more information see GenericDataFile.

Write the file checksum to a checksum file

Description

Write the file checksum to a checksum file having the same filename with suffix .md5 added.

Usage

## S3 method for class 'GenericDataFile'
writeChecksum(this, ..., skip=FALSE)

Arguments

Value

Returns (invisibly) the pathname to the checksum file. An exception is thrown if the file does not exist.

Author(s)

Henrik Bengtsson

See Also

*validateChecksum(). *compareChecksum(). *readChecksum(). *getChecksum(). For more information see GenericDataFile.

Read each column from a data file and exports it to a separate file

Description

Read each column from a data file and exports it to a separate file. Since each column is processed independently of the others, this method is memory efficient and can handle very large data files.

Usage

## S3 method for class 'GenericTabularFile'
writeColumnsToFiles(this, destPath, filenameFmt="%s.txt", tags=NULL, columnName=NULL,
  header=NULL, ..., verbose=FALSE)

Arguments

Details

Each file generated is written atomically by first writing to a temporary file which is then renamed if successfully written. This minimizes the risk for creating incomplete files, which otherwise may occur if for instance an interrupt occurred.

Value

Returns (invisibly) a character vector of all output files.

Author(s)

Henrik Bengtsson

See Also

For more information see GenericTabularFile.