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R.utils (version 2.0.1)

Various Programming Utilities

Description

Utility functions useful when programming and developing R packages.

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install.packages('R.utils')

Monthly Downloads

163,892

Version

2.0.1

License

LGPL (>= 2.1)

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Repository

https://github.com/HenrikBengtsson/R.utils

Maintainer

Henrik Bengtsson

Last Published

April 26th, 2015

Functions in R.utils (2.0.1)

NullVerbose

A Verbose class ignoring everything

MultiVerbose

A Verbose class ignoring everything

doCall

Executes a function call with option to ignore unused arguments

egsub

Global substitute of expression using regular expressions

findFiles

Finds one or several files in multiple directories

Verbose

Class to writing verbose messages to a connection or file

Sys.readlink2

Read File Symbolic Links (also on Windows)

Java$asByte

Converts a numeric to a Java byte

System$currentTimeMillis

Get the current time in milliseconds

countLines

Counts the number of lines in a text file

as.character.Verbose

Returns a character string version of this object

Arguments$getWritablePathname

Gets a writable pathname

findSourceTraceback

Finds all 'srcfile' objects generated by source() in all call frames

Options

The Options class

GString$getBuiltinRversion

Gets the current R version

System$getHostname

Retrieves the computer name of the current host

getLoadedPathname.Settings

Gets the pathname of the settings file loaded

GString

Character string with advanced substitutions

cleanup.FileProgressBar

Removes the progress file for a file progress bar

equals.Options

Checks if this object is equal to another Options object

colClasses

Creates a vector of column classes used for tabular reading

intToBin

Converts an integer to a binary/octal/hexadecimal number

Settings$findSettings

Searches for the settings file in one or several directories

isDirectory

Checks if the file specification is a directory

Arguments$getInstanceOf

Gets an instance of the object that is of a particular class

Assert$check

Static method asserting that a generic condition is true

commandArgs

Extract command-line arguments

convertComment.SmartComments

Converts a single smart comment to R code

fileAccess

Checks the permission of a file or a directory

capitalize

Capitalizes/decapitalizes each character string in a vector

as.character.Options

Returns a character string version of this object

as.double.Verbose

Gets a numeric value of this object

GString$getBuiltinPid

Gets the process id of the current R session

LComments

The LComments class

mpager

A "pager" function that outputs to standard error

getAbsolutePath

Gets the absolute pathname string

eget

Gets a variable by name

as.character.GString

Gets the processed character string

captureOutput

Evaluate an R expression and captures the output

TimeoutException

TimeoutException represents timeout errors

R.utils-package

Package R.utils

Arguments$getNumerics

Coerces to a numeric vector and validates

Arguments

Static class to validate and process arguments

cmdArgs

Simple access to parsed command-line arguments

createWindowsShortcut

Creates a Microsoft Windows Shortcut (.lnk file)

draw.density

Draws a density curve

gcat

Parses, evaluates and outputs a GString

extract.array

Extract a subset of an array, matrix or a vector with unknown dimensions

GString$getBuiltinRhome

Gets the path where R is installed

as.character.binmode

Converts a binary/octal/hexadecimal number into a string

Assert

The Assert class

TextStatusBar

A status bar at the R prompt that can be updated

displayCode

Displays the contents of a text file with line numbers and more

enter.Verbose

Writes a message and indents the following output

evaluate.GString

Parses and evaluates a GString

filePath

Construct the path to a file from components and expands Windows Shortcuts along the pathname from root to leaf

GString$getVariableValue

Gets a variable value given a name and attributes

Arguments$getIndices

Coerces to a integer vector and validates

System

Static class to query information about the system

compressFile

Compressing and decompressing files

GString$getBuiltinDatetime

Gets the current date and time

Java$asLong

Converts a numeric to a Java long

isFile

Checks if the file specification is a file

downloadFile.character

Downloads a file

cat.Verbose

Concatenates and prints objects if above threshold

evaluate.Verbose

Evaluates a function and prints its results if above threshold

isUrl

Checks if one or several pathnames is URLs

createLink

Creates a link to a file or a directory

GString$getBuiltinDate

Gets the current date

listDirectory

Gets the file names in the directory

Arguments$getVerbose

Coerces to Verbose object

isOn.Verbose

Checks if the output is on

Arguments$getRegularExpression

Gets a valid regular expression pattern

setOption.Options

Sets an option

Settings

Class for applicational settings

names.Options

Gets the full pathname of all (non-list) options

file.info2

Extract File Information (acknowledging symbolic file links also on Windows)

Arguments$getLogicals

Coerces to a logical vector and validates

Arguments$getVector

Validates a vector

PERCENT< -PERCENT

Assignment operator for delayed assignments

ProgressBar

Provides text based counting progress bar

Arguments$getEnvironment

Gets an existing environment

setStepLength.ProgressBar

Sets default step length

promptAndSave.Settings

Prompt user to save modified settings

isSingle

Identifies all entries that exists exactly ones

isOpen.character

Checks if there is an open connection to a file

getTimestampFormat.Verbose

Gets the default timestamp format

mkdirs

Creates a directory including any necessary but nonexistent parent directories

dataFrame

Allocates a data frame with given column classes

hasOption.Options

Checks if an option exists

getMessage.TimeoutException

Gets the message of the exception

finalizeSession

Function to call for finalizing the R session

Arguments$getReadablePathname

Gets a readable pathname

Java$asInt

Converts an numeric to a Java integer

lastModified

Gets the time when the file was last modified

Checks if progress bar is completed

GString$getBuiltinHostname

Gets the hostname of the system running R

reset.SmartComments

Resets a SmartComments compiler

createFileAtomically

Creates a file atomically

isAbsolutePath

Checks if this pathname is absolute

getBarString.ProgressBar

Gets the progress bar string to be displayed

hasUrlProtocol

Checks if one or several pathnames has a URL protocol

getRaw.GString

Gets the unprocessed GString

setTicks.ProgressBar

Sets values for which ticks should be visible

Java$readInt

Reads a Java formatted int (32 bits) from a connection

onSessionExit

Registers a function to be called when the R session finishes

GString$getBuiltinOs

Gets the operating system of the running machine

on.Verbose

Turn on the output

Assert$isMatrix

Static method asserting thatan object is a matrix

exit.Verbose

Writes a message and unindents the following output

installPackages

Install R packages by name or URL

sourceTo

Parses and evaluates code from a file or a connection

getParent

Gets the string of the parent specified by this pathname

System$openBrowser

Opens an HTML document using the OS default HTML browser

Java$readShort

Reads a Java formatted short (16 bits) from a connection

header.Verbose

Writes a header

useRepos

Sets package repositories

Arguments$getIntegers

Coerces to a integer vector and validates

GString$getBuiltinUsername

Gets the username of the user running R

isPackageInstalled

Checks if a package is installed or not

Arguments$getCharacters

Coerces to a character vector and validates

as.character.ProgressBar

Gets a string description of the progress bar

readTableIndex

Reads a single column from file in table format

str.Verbose

Prints the structure of an object if above threshold

cmdArgsCall

Calls an R function passing command-line arguments

summary.Verbose

Generates a summary of an object if above threshold

inAnyInterval.numeric

Checks if a set of values are inside one or more intervals

addFinalizerToLast

Modifies .Last() to call 'finalizeSession()

mapToIntervals.numeric

Maps values to intervals

loadAnywhere.Settings

Loads settings from file

touchFile

Updates the timestamp of a file

update.FileProgressBar

Updates file progress bar

as.logical.Verbose

Gets a logical value of this object

tempvar

Gets a unique non-existing temporary variable name

isOn.NullVerbose

Checks if the output is on

less.Verbose

Creates a cloned instance with a higher threshold

popMessage.TextStatusBar

Adds a message above the status bar

shell.exec2

Open a file or URL using Windows File Associations

popTemporaryFile

Drops a temporary suffix from the temporary pathname

withSink

Evaluate an R expression while temporarily diverting output

writeRaw.Verbose

Writes objects if above threshold

isZero

Checks if a value is (close to) zero or not

newline.Verbose

Writes one or several empty lines

removeDirectory

Removes a directory

withOptions

Evaluate an R expression with options set temporarily

systemR

Launches another R process from within R

writeDataFrame.data.frame

Writes a data.frame to tabular text file

update.ProgressBar

Updates progress bar

GString$getBuiltinTime

Gets the current time

copyFile

Copies a file atomically

moveInSearchPath

Moves a environment in the search path to another position

print.GString

Prints the processed GString

Java$asShort

Converts a numeric to a Java short

timestampOn.Verbose

Turns automatic timestamping on and off

getLeaves.Options

Gets all (non-list) options in a flat list

withSeed

Evaluate an R expression with a temporarily set random set

mergeIntervals.numeric

Merges intervals

resample

Sample values from a set of elements

isVisible.NullVerbose

Checks if a certain verbose level will be shown or not

FileProgressBar

A progress bar that sets the size of a file accordingly

env

Creates a new environment, evaluates an expression therein, and returns the environment

readWindowsShellLink

Reads a Microsoft Windows Shortcut (.lnk file)

Arguments$getDoubles

Coerces to a double vector and validates

validate.SmartComments

Validates the compiled lines

printf.Verbose

Formats and prints object if above threshold

Non-documented objects

loadObject

Method to load object from a file or a connection

pushState.Verbose

Pushes the current indentation state of the Verbose object

dimNA< -

Sets the dimension of an object with the option to infer one dimension autmatically

equals.Verbose

Checks if this object is equal to another

print.Verbose

Prints objects if above threshold

SmartComments

Abstract class SmartComments

writeRaw.MultiVerbose

Writes to each of the Verbose objects

pushTemporaryFile

Appends a temporary suffix to the pathname

reset.VComments

Resets a VComments compiler

setThreshold.Verbose

Sets verbose threshold

Java$readByte

Reads a Java formatted byte (8 bits) from a connection

update.TextStatusBar

Updates the status bar (visually)

withCapture

Evaluates an expression and captures the code and/or the output

loadToEnv

Method to load objects to a new environment

readBinFragments

Reads binary data from disjoint sections of a connection or a file

toCamelCase

Converts a string of words into a merged camel-cased word

setTimestampFormat.Verbose

Sets the default timestamp format

newline.TextStatusBar

Writes a newline

mout

Miscellaneous functions for outputting via message()

parse.GString

Parses a GString

onGarbageCollect

Registers a function to be called when the R garbage collector is (detected to be) running

nbrOfOptions.Options

Gets the number of options set

setMaxValue.ProgressBar

Sets maximum value

Assert$isScalar

Static method asserting thatan object is a single value

hpaste

Concatenating vectors into human-readable strings

more.Verbose

Creates a cloned instance with a lower threshold

setDefaultLevel.Verbose

Sets the current default verbose level

withRepos

Evaluate an R expression with repositories set temporarily

swapXY.density

Swaps x and y coordinates of a density object

renameFile

Renames a file (or a directory) atomically/safely

withTimeout

Evaluate an R expression and interrupts it if it takes too long

isEof.connection

Checks if the current file position for a connection is at the 'End of File'

queryRCmdCheck

Gets the on R CMD check if the current R session was launched by it

Java

Static class for Java related methods

sourceDirectory

Sources files recursively to either local or global environment

Java$writeInt

Writes a integer (32 bits) to a connection in Java format

Java$writeUTF

Writes a string to a connection in Java format (UTF-8)

Gets a short human readable string representation of an vector of indices

unwrap.array

Unwrap an array, matrix or a vector to an array of more dimensions

pushBackupFile

Appends a backup suffix to the pathname

use

Attaches or loads packages

reassignInPackage

Re-assigns a new value to an existing object in a loaded package

capture.Verbose

Captures output of a function

patchCode

Patches installed and loaded packages and more

whichVector.logical

Identifies TRUE elements in a logical vector

toUrl

Converts a pathname into a URL

increase.ProgressBar

Increases (steps) progress bar

warnings.Verbose

Outputs any warnings recorded

intervalsToSeq.matrix

Generates a vector of indices from a matrix of intervals

compile.SmartComments

Preprocess a vector of code lines

off.Verbose

Turn off the output

Assert$isVector

Static method asserting thatan object is a vector

isPackageLoaded

Checks if a package is loaded or not

writeRaw.NullVerbose

All output methods

popBackupFile

Drops a backup suffix from the backup pathname

subplots

Creates a grid of subplots

copyDirectory

Copies a directory

isModified.Settings

Checks if settings has been modified compared to whats on file

writeBinFragments

Writes binary data to disjoint sections of a connection or a file

detachPackage

Detaches packages by name

withLocale

Evaluate an R expression with locale set temporarily

readRdHelp

Reads one or more Rd help files in a certain format

System$parseDebian

Parses a string, file or connection for Debian formatted parameters

isReplicated

Identifies all entries with replicated values

Java$readUTF

Reads a Java (UTF-8) formatted string from a connection

setOption

Sets a option in R

updateLabels.TextStatusBar

Sets the new values of given labels and updates the status bar

stext

Writes text in the margin along the sides of a plot

System$findGhostscript

Searches for a Ghostview executable on the current system

saveAnywhere.Settings

Saves settings to file

str.Options

Prints the structure of the options

getOption.Options

Gets an option

validate.VComments

Validates the compiled lines

getRelativePath

Gets the relative pathname relative to a directory

wrap.array

Reshape an array or a matrix by permuting and/or joining dimensions

Arguments$getReadablePathnames

Gets a readable pathname

resetWarnings

Resets recorded warnings

printf

C-style formatted output

isVisible.Verbose

Checks if a certain verbose level will be shown or not

splitByPattern

Splits a single character string by pattern

setProgress.ProgressBar

Sets current progress

getThreshold.Verbose

Gets current verbose threshold

readWindowsShortcut

Reads a Microsoft Windows Shortcut (.lnk file)

seqToIntervals

Gets all contigous intervals of a vector of indices

timestamp.Verbose

Writes a timestamp

as.list.MultiVerbose

Gets a list of Verbose objects

arrayIndex

Converts vector indices to array indices

callHooks

Call hook functions by hook name

as.list.Options

Gets a list representation of the options

insert

Insert values to a vector at certain positions

attachLocally.list

Assigns an objects elements locally

convertComment.VComments

Converts a verbose comment to R code

System$findGraphicsDevice

Searches for a working PNG device

ruler.Verbose

Writes a ruler

setLabel.TextStatusBar

Sets the value of a label

Arguments$getFilename

Gets and validates a filename

getLabel.TextStatusBar

Gets the current value of a label

Assert$inherits

Static method asserting that an object inherits from of a certain class

System$getUsername

Retrieves the name of the user running R

parse.SmartComments

Parses one single smart comment

reset.ProgressBar

Reset progress bar

saveObject

Saves an object to a file or a connection

setLabels.TextStatusBar

Sets new values of given labels

readTable

Reads a file in table format

Java$writeByte

Writes a byte (8 bits) to a connection in Java format

Java$writeShort

Writes a short (16 bits) to a connection in Java format