R.filesets: Easy Handling of and Access to Files Organized in Structured Directories

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.

AuthorHenrik Bengtsson [aut, cre, cph]
Date of publication2016-01-05 07:03:05
MaintainerHenrik Bengtsson <henrikb@braju.com>
LicenseLGPL (>= 2.1)
Version2.10.0
https://github.com/HenrikBengtsson/R.filesets, http://www.aroma-project.org/

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Man pages

anyNA.GenericDataFileSet: Checks whether any of the pathnames are missing

appendFiles.GenericDataFileSet: Appends a list of files to a data set

append.GenericDataFileSet: Appends one data set to an existing one

as.character.GenericDataFile: Returns a short string describing the file

as.character.GenericDataFileSet: Returns a short string describing the file set

as.list.GenericDataFileSet: Returns the files of the file set

byName.GenericDataFileSet: Locates and sets up a file set by its name

byPath.GenericDataFileSet: Defines a GenericDataFileSet by searching for files in a...

ChecksumFile: The ChecksumFile class

ChecksumFileSet: The ChecksumFileSet class

ColumnNamesInterface: The ColumnNamesInterface class interface

compareChecksum.GenericDataFile: Compares the file checksum with the value of the checksum...

copyTo.GenericDataFile: Safely copies a file to a new pathname

copyTo.GenericDataFileSet: Copies a data set to another directory

Deprecated_and_defunct_objects: Deprecated and defunct objects

dim.GenericTabularFile: Gets the dimension of data table

dsApply.GenericDataFileSet: Applies a function to each file in the file set

equals.GenericDataFile: Checks if a file equals another

extract.GenericDataFileSet: Extract a subset of the file set

extractMatrix.GenericTabularFile: Reads one of the columns

findByName.GenericDataFileSet: Locates all file sets that match the requested name

fromFile.GenericDataFile: Defines a GenericDataFile from a pathname

FullNameInterface: The FullNameInterface class interface

GenericDataFile: The abstract GenericDataFile class

GenericDataFileSet: The GenericDataFileSet class

GenericDataFileSetList: The GenericDataFileSetList class

GenericTabularFile: The abstract GenericTabularFile class

GenericTabularFileSet: The GenericTabularFileSet class

getChecksum.GenericDataFile: Gets the checksum of a file

getChecksum.GenericDataFileSet: Generates a deterministic checksum for an R object

getChecksumObjects.GenericDataFileSet: Retrieves objects that uniquely identifying the data set

getColumnNames.ColumnNamesInterface: Gets the column names

getCreatedOn.GenericDataFile: Gets when the file was created

getDefaultColumnNames.ColumnNamesInterface: Gets the default column names

getDefaultColumnNames.TabularTextFile: Gets the default column names

getDefaultFullName.FullNameInterface: Gets the default full name

getDefaultFullName.GenericDataFile: Gets the full name of the file

getDefaultFullName.GenericDataFileSet: Gets the default full name of the file set

getExtension.GenericDataFile: Gets the filename extension

getFile.GenericDataFileSet: Get a particular file of the file set

getFilename.GenericDataFile: Gets the filename of the file

getFileSize.GenericDataFile: Gets the size of a file

getFileType.GenericDataFile: Gets the file type of a file

getFullName.FullNameInterface: Gets the full name

getHeader.TabularTextFile: Gets the file header

getLastAccessedOn.GenericDataFile: Gets when the file was last accessed

getLastModifiedOn.GenericDataFile: Gets when the file was last modified

getName.FullNameInterface: Gets the name

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

getPath.GenericDataFile: Gets the path (directory) of the file

getPath.GenericDataFileSet: Gets the path (directory) of the file set

getPathname.GenericDataFile: Gets the pathname of the file

getPathnames.GenericDataFileSet: Gets the pathnames of the files in the file set

getTags.Arguments: Gets and validates tags

getTags.FullNameInterface: Gets the tags

gzip.GenericDataFile: Compresses/uncompresses a file

gzip.GenericDataFileSet: Compresses/uncompresses a set of files

hasBeenModified.GenericDataFile: Checks whether the file has been modified

hasColumnHeader.TabularTextFile: Checks if there are column names in the header

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

indexOf.GenericDataFileSet: Finds indices of a subset of files

isFile.GenericDataFile: Checks if this is an existing file

length.GenericDataFileSet: Gets the number of files in the set

linkTo.GenericDataFile: Creates a symbolic file link

loadRDS: Reads data from a RDS file

loadToEnv: Reads data from a RDS file

nbrOfColumns.ColumnNamesInterface: Gets the number of columns

nbrOfLines.TabularTextFile: Counts the number of lines in the data file

nbrOfRows.GenericTabularFile: Gets the number of data rows

nbrOfRows.TabularTextFile: Counts the number of data rows

Non-documented_objects: Non-documented objects

RDataFile: The RDataFile class

RDataFileSet: The RDataFileSet class

RdsFile: The RdsFile class

RdsFileSet: The RdsFileSet class

readChecksum.ChecksumFile: Reads the checksum value

readChecksum.GenericDataFile: Reads the value of the corresponding checksum file

readColumns.GenericTabularFile: Reads a subset of the columns as a data frame

readDataFrame: Reads data from a tabular file

readDataFrame.GenericTabularFile: Reads the tabular data as a data frame

readDataFrame.TabularTextFile: Reads the tabular data as a data frame

readDataFrame.TabularTextFileSet: Reads the tabular data from all files as data frames

readLines.TabularTextFile: Reads the lines of the data file as strings

renameTo.GenericDataFile: Renames/moves a file

R.filesets-package: Package R.filesets

setColumnNames.ColumnNamesInterface: Sets the column names

setFullName.FullNameInterface: Sets the full name

setName.FullNameInterface: Sets the name part of the fullname

setTags.FullNameInterface: Sets the tags

sortBy.GenericDataFileSet: Sorts the set

TabularTextFile: The TabularTextFile class

TabularTextFileSet: The TabularTextFileSet class

validate.ChecksumFile: Asserts that the checksum matches the checksum of file

validateChecksum.GenericDataFile: Asserts that the file checksum matches the one of the...

validate.GenericDataFile: Validates the content of a file

validate.GenericDataFileSet: Validates all files in the data set

writeChecksum.GenericDataFile: Write the file checksum to a checksum file

writeColumnsToFiles.GenericTabularFile: Read each column from a data file and exports it to a...

Files in this package

R.filesets
R.filesets/inst
R.filesets/inst/exData
R.filesets/inst/exData/dataSetB
R.filesets/inst/exData/dataSetB/fileG,EOL.txt
R.filesets/inst/exData/dataSetB/fileF,noHeader.dat
R.filesets/inst/exData/dataSetB/fileG,noEOL.txt
R.filesets/inst/exData/dataSetA,original
R.filesets/inst/exData/dataSetA,original/fileFF.txt
R.filesets/inst/exData/dataSetA,original/fileA,20100112.dat
R.filesets/inst/exData/dataSetA,original/fileF.txt
R.filesets/inst/exData/dataSetA,original/fileD,3cols.dat
R.filesets/inst/exData/dataSetA,original/11.2(a).txt
R.filesets/inst/exData/dataSetA,original/fileA,20130116.datx
R.filesets/inst/exData/dataSetA,original/fileC,inverted.dat
R.filesets/inst/exData/dataSetA,original/all,fullnames.txt
R.filesets/inst/exData/dataSetA,original/1.2(a).txt
R.filesets/inst/exData/dataSetA,original/fileE,headerArgs.dat
R.filesets/inst/exData/dataSetA,original/fileB,other,tags.dat
R.filesets/tests
R.filesets/tests/GenericDataFileSet,sortBy.R
R.filesets/tests/readDataFrame.R
R.filesets/tests/ChecksumFile.R
R.filesets/tests/GenericDataFileSet.R
R.filesets/tests/VectorAndListAPI.R
R.filesets/tests/RdsFileSet.R
R.filesets/tests/fullname.R
R.filesets/tests/TabularTextFile,huge.R
R.filesets/tests/RDataFileSet.R
R.filesets/tests/TabularTextFile.R
R.filesets/tests/TabularTextFileSet.R
R.filesets/tests/GenericDataFile.R
R.filesets/tests/TabularTextFile,extend.R
R.filesets/tests/GenericDataFileSet,dsApply.R
R.filesets/NAMESPACE
R.filesets/NEWS
R.filesets/R
R.filesets/R/GenericDataFileSetList.R R.filesets/R/FullNameInterface.appendFullNameTranslatorByNnn.R R.filesets/R/dropRootPathTags.R R.filesets/R/readTableHeader.R R.filesets/R/utils.R R.filesets/R/000.R R.filesets/R/ColumnNamesInterface.R R.filesets/R/readDataFrame.R R.filesets/R/ChecksumFile.R R.filesets/R/RDataFile.R R.filesets/R/GenericDataFileSet.R R.filesets/R/GenericDataFile.ATTRS.R R.filesets/R/999.DEPRECATED.R R.filesets/R/GenericTabularFileSet.R R.filesets/R/RdsFileSet.R R.filesets/R/fullname.R R.filesets/R/RdsFile.R R.filesets/R/FullNameInterface.R R.filesets/R/GenericTabularFile.writeColumnsToFiles.R R.filesets/R/ChecksumFileSet.R R.filesets/R/RDataFileSet.R R.filesets/R/006.fixVarArgs.R R.filesets/R/TabularTextFile.R R.filesets/R/TabularTextFileSet.R R.filesets/R/GenericDataFileSet.getChecksum.R R.filesets/R/Arguments.EXTRAS.R R.filesets/R/GenericDataFile.R R.filesets/R/GenericDataFileList.R R.filesets/R/999.NonDocumentedObjects.R R.filesets/R/999.package.R R.filesets/R/GenericTabularFile.R R.filesets/R/GenericDataFileSet.PARALLEL.R R.filesets/R/zzz.R
R.filesets/MD5
R.filesets/DESCRIPTION
R.filesets/man
R.filesets/man/readDataFrame.Rd R.filesets/man/getChecksum.GenericDataFileSet.Rd R.filesets/man/GenericDataFileSetList.Rd R.filesets/man/compareChecksum.GenericDataFile.Rd R.filesets/man/validate.ChecksumFile.Rd R.filesets/man/as.character.GenericDataFileSet.Rd R.filesets/man/getFullName.FullNameInterface.Rd R.filesets/man/appendFiles.GenericDataFileSet.Rd R.filesets/man/copyTo.GenericDataFileSet.Rd R.filesets/man/setName.FullNameInterface.Rd R.filesets/man/getNames.GenericDataFileSet.Rd R.filesets/man/getLastModifiedOn.GenericDataFile.Rd R.filesets/man/gzip.GenericDataFile.Rd R.filesets/man/fromFile.GenericDataFile.Rd R.filesets/man/loadRDS.Rd R.filesets/man/getFileSize.GenericDataFile.Rd R.filesets/man/readDataFrame.TabularTextFile.Rd R.filesets/man/RdsFile.Rd R.filesets/man/setFullName.FullNameInterface.Rd R.filesets/man/indexOf.GenericDataFileSet.Rd R.filesets/man/getDefaultFullName.FullNameInterface.Rd R.filesets/man/getPathname.GenericDataFile.Rd R.filesets/man/getPath.GenericDataFileSet.Rd R.filesets/man/loadToEnv.Rd R.filesets/man/setColumnNames.ColumnNamesInterface.Rd R.filesets/man/dsApply.GenericDataFileSet.Rd R.filesets/man/GenericTabularFile.Rd R.filesets/man/nbrOfRows.GenericTabularFile.Rd R.filesets/man/RdsFileSet.Rd R.filesets/man/getHeader.TabularTextFile.Rd R.filesets/man/ColumnNamesInterface.Rd R.filesets/man/GenericTabularFileSet.Rd R.filesets/man/getTags.FullNameInterface.Rd R.filesets/man/ChecksumFileSet.Rd R.filesets/man/getChecksumObjects.GenericDataFileSet.Rd R.filesets/man/getDefaultFullName.GenericDataFileSet.Rd R.filesets/man/FullNameInterface.Rd R.filesets/man/getFile.GenericDataFileSet.Rd R.filesets/man/readDataFrame.GenericTabularFile.Rd R.filesets/man/getDefaultFullName.GenericDataFile.Rd R.filesets/man/getCreatedOn.GenericDataFile.Rd R.filesets/man/as.character.GenericDataFile.Rd R.filesets/man/byPath.GenericDataFileSet.Rd R.filesets/man/nbrOfLines.TabularTextFile.Rd R.filesets/man/hasColumnHeader.TabularTextFile.Rd R.filesets/man/extractMatrix.GenericTabularFile.Rd R.filesets/man/readChecksum.ChecksumFile.Rd R.filesets/man/readChecksum.GenericDataFile.Rd R.filesets/man/renameTo.GenericDataFile.Rd R.filesets/man/getPath.GenericDataFile.Rd R.filesets/man/readDataFrame.TabularTextFileSet.Rd R.filesets/man/getChecksum.GenericDataFile.Rd R.filesets/man/getExtension.GenericDataFile.Rd R.filesets/man/R.filesets-package.Rd R.filesets/man/getName.FullNameInterface.Rd R.filesets/man/linkTo.GenericDataFile.Rd R.filesets/man/RDataFileSet.Rd R.filesets/man/getLastAccessedOn.GenericDataFile.Rd R.filesets/man/nbrOfRows.TabularTextFile.Rd R.filesets/man/writeChecksum.GenericDataFile.Rd R.filesets/man/byName.GenericDataFileSet.Rd R.filesets/man/getFilename.GenericDataFile.Rd R.filesets/man/gzip.GenericDataFileSet.Rd R.filesets/man/readLines.TabularTextFile.Rd R.filesets/man/nbrOfColumns.ColumnNamesInterface.Rd R.filesets/man/findByName.GenericDataFileSet.Rd R.filesets/man/setTags.FullNameInterface.Rd R.filesets/man/readColumns.GenericTabularFile.Rd R.filesets/man/validate.GenericDataFileSet.Rd R.filesets/man/TabularTextFile.Rd R.filesets/man/as.list.GenericDataFileSet.Rd R.filesets/man/getTags.Arguments.Rd R.filesets/man/extract.GenericDataFileSet.Rd R.filesets/man/hasBeenModified.GenericDataFile.Rd R.filesets/man/getDefaultColumnNames.ColumnNamesInterface.Rd R.filesets/man/getPathnames.GenericDataFileSet.Rd R.filesets/man/getColumnNames.ColumnNamesInterface.Rd R.filesets/man/append.GenericDataFileSet.Rd R.filesets/man/length.GenericDataFileSet.Rd R.filesets/man/TabularTextFileSet.Rd R.filesets/man/GenericDataFile.Rd R.filesets/man/anyNA.GenericDataFileSet.Rd R.filesets/man/validateChecksum.GenericDataFile.Rd R.filesets/man/Deprecated_and_defunct_objects.Rd R.filesets/man/isFile.GenericDataFile.Rd R.filesets/man/hasTags.FullNameInterface.Rd R.filesets/man/sortBy.GenericDataFileSet.Rd R.filesets/man/ChecksumFile.Rd R.filesets/man/RDataFile.Rd R.filesets/man/GenericDataFileSet.Rd R.filesets/man/writeColumnsToFiles.GenericTabularFile.Rd R.filesets/man/getDefaultColumnNames.TabularTextFile.Rd R.filesets/man/equals.GenericDataFile.Rd R.filesets/man/copyTo.GenericDataFile.Rd R.filesets/man/validate.GenericDataFile.Rd R.filesets/man/dim.GenericTabularFile.Rd R.filesets/man/getFileType.GenericDataFile.Rd R.filesets/man/Non-documented_objects.Rd

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