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

Share:

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.

Author
Henrik Bengtsson [aut, cre, cph]
Date of publication
2016-01-05 07:03:05
Maintainer
Henrik Bengtsson <henrikb@braju.com>
License
LGPL (>= 2.1)
Version
2.10.0
URLs

View on CRAN

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