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R.utils (version 2.0.0)

Various Programming Utilities

Description

Utility functions useful when programming and developing R packages.

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Install

install.packages('R.utils')

Monthly Downloads

163,892

Version

2.0.0

License

LGPL (>= 2.1)

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Repository

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

Maintainer

Henrik Bengtsson

Last Published

March 1st, 2015

Functions in R.utils (2.0.0)

as.character.binmode

Converts a binary/octal/hexadecimal number into a string

Java$asShort

Converts a numeric to a Java short

copyDirectory

Copies a directory

getLoadedPathname.Settings

Gets the pathname of the settings file loaded

Arguments$getLogicals

Coerces to a logical vector and validates

FileProgressBar

A progress bar that sets the size of a file accordingly

as.list.MultiVerbose

Gets a list of Verbose objects

convertComment.VComments

Converts a verbose comment to R code

createFileAtomically

Creates a file atomically

dataFrame

Allocates a data frame with given column classes

resample

Sample values from a set of elements

withTimeout

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

Options

The Options class

Java$asInt

Converts an numeric to a Java integer

filePath

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

env

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

countLines

Counts the number of lines in a text file

getAbsolutePath

Gets the absolute pathname string

gcat

Parses, evaluates and outputs a GString

isDone.ProgressBar

Checks if progress bar is completed

createWindowsShortcut

Creates a Microsoft Windows Shortcut (.lnk file)

System$findGraphicsDevice

Searches for a working PNG device

isZero

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

cat.Verbose

Concatenates and prints objects if above threshold

addFinalizerToLast

Modifies .Last() to call 'finalizeSession()

callHooks

Call hook functions by hook name

commandArgs

Extract command-line arguments

Arguments$getIndices

Coerces to a integer vector and validates

R.utils-package

Package R.utils

equals.Options

Checks if this object is equal to another Options object

setTicks.ProgressBar

Sets values for which ticks should be visible

Arguments$getInstanceOf

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

Java

Static class for Java related methods

use

Attaches or loads packages

colClasses

Creates a vector of column classes used for tabular reading

as.character.GString

Gets the processed character string

as.character.ProgressBar

Gets a string description of the progress bar

getMessage.TimeoutException

Gets the message of the exception

System$currentTimeMillis

Get the current time in milliseconds

Settings

Class for applicational settings

Arguments$getNumerics

Coerces to a numeric vector and validates

evaluate.GString

Parses and evaluates a GString

as.character.Verbose

Returns a character string version of this object

finalizeSession

Function to call for finalizing the R session

detachPackage

Detaches packages by name

createLink

Creates a link to a file or a directory

Java$writeInt

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

GString$getBuiltinDate

Gets the current date

update.TextStatusBar

Updates the status bar (visually)

GString$getBuiltinHostname

Gets the hostname of the system running R

attachLocally.list

Assigns an objects elements locally

TextStatusBar

A status bar at the R prompt that can be updated

Sys.readlink2

Read File Symbolic Links (also on Windows)

GString$getBuiltinRversion

Gets the current R version

Assert

The Assert class

cleanup.FileProgressBar

Removes the progress file for a file progress bar

Arguments$getDoubles

Coerces to a double vector and validates

MultiVerbose

A Verbose class ignoring everything

captureOutput

Evaluate an R expression and captures the output

getRelativePath

Gets the relative pathname relative to a directory

doCall

Executes a function call with option to ignore unused arguments

Java$asByte

Converts a numeric to a Java byte

copyFile

Copies a file atomically

mapToIntervals.numeric

Maps values to intervals

cmdArgs

Simple access to parsed command-line arguments

capture.Verbose

Captures output of a function

getTimestampFormat.Verbose

Gets the default timestamp format

lastModified

Gets the time when the file was last modified

callHooks.function

Call hook functions

Arguments$getRegularExpression

Gets a valid regular expression pattern

mout

Miscellaneous functions for outputting via message()

draw.density

Draws a density curve

capitalize

Capitalizes/decapitalizes each character string in a vector

exit.Verbose

Writes a message and unindents the following output

readWindowsShellLink

Reads a Microsoft Windows Shortcut (.lnk file)

System$getHostname

Retrieves the computer name of the current host

GString$getVariableValue

Gets a variable value given a name and attributes

saveAnywhere.Settings

Saves settings to file

downloadFile.character

Downloads a file

System$findGhostscript

Searches for a Ghostview executable on the current system

LComments

The LComments class

GString$getBuiltinRhome

Gets the path where R is installed

Arguments$getReadablePathnames

Gets a readable pathname

Arguments$getIntegers

Coerces to a integer vector and validates

isAbsolutePath

Checks if this pathname is absolute

Arguments$getVector

Validates a vector

setDefaultLevel.Verbose

Sets the current default verbose level

Arguments$getReadablePathname

Gets a readable pathname

displayCode

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

popMessage.TextStatusBar

Adds a message above the status bar

as.character.Options

Returns a character string version of this object

GString$getBuiltinDatetime

Gets the current date and time

NullVerbose

A Verbose class ignoring everything

mpager

A "pager" function that outputs to standard error

setLabels.TextStatusBar

Sets new values of given labels

Arguments

Static class to validate and process arguments

SmartComments

Abstract class SmartComments

Assert$isMatrix

Static method asserting thatan object is a matrix

GString

Character string with advanced substitutions

getParent

Gets the string of the parent specified by this pathname

Arguments$getVerbose

Coerces to Verbose object

arrayIndex

Converts vector indices to array indices

sourceTo

Parses and evaluates code from a file or a connection

Verbose

Class to writing verbose messages to a connection or file

inAnyInterval.numeric

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

as.logical.Verbose

Gets a logical value of this object

setProgress.ProgressBar

Sets current progress

parse.SmartComments

Parses one single smart comment

Non-documented objects

on.Verbose

Turn on the output

as.double.Verbose

Gets a numeric value of this object

sourceDirectory

Sources files recursively to either local or global environment

isPackageInstalled

Checks if a package is installed or not

findFiles

Finds one or several files in multiple directories

enter.Verbose

Writes a message and indents the following output

Assert$check

Static method asserting that a generic condition is true

getThreshold.Verbose

Gets current verbose threshold

readWindowsShortcut

Reads a Microsoft Windows Shortcut (.lnk file)

parse.GString

Parses a GString

splitByPattern

Splits a single character string by pattern

insert

Insert values to a vector at certain positions

Static method asserting thatan object is a single value

Java$writeUTF

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

newline.Verbose

Writes one or several empty lines

reset.VComments

Resets a VComments compiler

GString$getBuiltinPid

Gets the process id of the current R session

Java$readInt

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

isVisible.NullVerbose

Checks if a certain verbose level will be shown or not

promptAndSave.Settings

Prompt user to save modified settings

readTable

Reads a file in table format

hasOption.Options

Checks if an option exists

setLabel.TextStatusBar

Sets the value of a label

setOption

Sets a option in R

extract.array

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

validate.VComments

Validates the compiled lines

isSingle

Identifies all entries that exists exactly ones

ruler.Verbose

Writes a ruler

file.info2

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

fileAccess

Checks the permission of a file or a directory

evaluate.Verbose

Evaluates a function and prints its results if above threshold

GString$getBuiltinUsername

Gets the username of the user running R

isFile

Checks if the file specification is a file

loadAnywhere.Settings

Loads settings from file

GString$getBuiltinOs

Gets the operating system of the running machine

header.Verbose

Writes a header

convertComment.SmartComments

Converts a single smart comment to R code

isPackageLoaded

Checks if a package is loaded or not

unwrap.array

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

moveInSearchPath

Moves a environment in the search path to another position

setStepLength.ProgressBar

Sets default step length

systemR

Launches another R process from within R

listDirectory

Gets the file names in the directory

eget

Gets a variable by name

onSessionExit

Registers a function to be called when the R session finishes

withLocale

Evaluate an R expression with locale set temporarily

withCapture

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

flush.TextStatusBar

Flushes the output

newline.TextStatusBar

Writes a newline

isVisible.Verbose

Checks if a certain verbose level will be shown or not

isDirectory

Checks if the file specification is a directory

withSink

Evaluate an R expression while temporarily diverting output

Arguments$getEnvironment

Gets an existing environment

System$parseDebian

Parses a string, file or connection for Debian formatted parameters

isEof.connection

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

timestampOn.Verbose

Turns automatic timestamping on and off

readRdHelp

Reads one or more Rd help files in a certain format

Arguments$getCharacters

Coerces to a character vector and validates

loadObject

Method to load object from a file or a connection

off.Verbose

Turn off the output

getLeaves.Options

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

increase.ProgressBar

Increases (steps) progress bar

GString$getBuiltinTime

Gets the current time

Settings$findSettings

Searches for the settings file in one or several directories

timestamp.Verbose

Writes a timestamp

hpaste

Concatenating vectors into human-readable strings

System$openBrowser

Opens an HTML document using the OS default HTML browser

str.Verbose

Prints the structure of an object if above threshold

warnings.Verbose

Outputs any warnings recorded

intervalsToSeq.matrix

Generates a vector of indices from a matrix of intervals

Assert$inherits

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

TimeoutException

TimeoutException represents timeout errors

ProgressBar

Provides text based counting progress bar

reassignInPackage

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

popBackupFile

Drops a backup suffix from the backup pathname

update.FileProgressBar

Updates file progress bar

isOn.Verbose

Checks if the output is on

isReplicated

Identifies all entries with replicated values

withSeed

Evaluate an R expression with a temporarily set random set

useRepos

Sets package repositories

wrap.array

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

isOpen.character

Checks if there is an open connection to a file

writeBinFragments

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

Arguments$getFilename

Gets and validates a filename

onGarbageCollect

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

compile.SmartComments

Preprocess a vector of code lines

writeDataFrame.data.frame

Writes a data.frame to tabular text file

System$getUsername

Retrieves the name of the user running R

Java$readByte

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

dimNA< -

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

readTableIndex

Reads a single column from file in table format

print.Verbose

Prints objects if above threshold

pushState.Verbose

Pushes the current indentation state of the Verbose object

reset.SmartComments

Resets a SmartComments compiler

hasUrlProtocol

Checks if one or several pathnames has a URL protocol

isUrl

Checks if one or several pathnames is URLs

shell.exec2

Open a file or URL using Windows File Associations

mergeIntervals.numeric

Merges intervals

toUrl

Converts a pathname into a URL

printf.Verbose

Formats and prints object if above threshold

whichVector.logical

Identifies TRUE elements in a logical vector

names.Options

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

updateLabels.TextStatusBar

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

str.Options

Prints the structure of the options

nbrOfOptions.Options

Gets the number of options set

patchCode

Patches installed and loaded packages and more

removeDirectory

Removes a directory

Arguments$getWritablePathname

Gets a writable pathname

pushBackupFile

Appends a backup suffix to the pathname

installPackages

Install R packages by name or URL

seqToHumanReadable

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

isModified.Settings

Checks if settings has been modified compared to whats on file

less.Verbose

Creates a cloned instance with a higher threshold

readBinFragments

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

update.ProgressBar

Updates progress bar

pushTemporaryFile

Appends a temporary suffix to the pathname

more.Verbose

Creates a cloned instance with a lower threshold

saveObject

Saves an object to a file or a connection

validate.SmartComments

Validates the compiled lines

Assert$isVector

Static method asserting thatan object is a vector

queryRCmdCheck

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

reset.ProgressBar

Reset progress bar

System

Static class to query information about the system

print.GString

Prints the processed GString

summary.Verbose

Generates a summary of an object if above threshold

setTimestampFormat.Verbose

Sets the default timestamp format

writeRaw.Verbose

Writes objects if above threshold

renameFile

Renames a file (or a directory) atomically/safely

toCamelCase

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

Java$readUTF

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

Java$asLong

Converts a numeric to a Java long

as.list.Options

Gets a list representation of the options

Java$writeShort

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

withOptions

Evaluate an R expression with options set temporarily

tempvar

Gets a unique non-existing temporary variable name

findSourceTraceback

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

cmdArgsCall

Calls an R function passing command-line arguments

equals.Verbose

Checks if this object is equal to another

compressFile

Compressing and decompressing files

isOn.NullVerbose

Checks if the output is on

getBarString.ProgressBar

Gets the progress bar string to be displayed

getLabel.TextStatusBar

Gets the current value of a label

getRaw.GString

Gets the unprocessed GString

PERCENT< -PERCENT

Assignment operator for delayed assignments

intToBin

Converts an integer to a binary/octal/hexadecimal number

popTemporaryFile

Drops a temporary suffix from the temporary pathname

printf

C-style formatted output

resetWarnings

Resets recorded warnings

Global substitute of expression using regular expressions

seqToIntervals

Gets all contigous intervals of a vector of indices

setThreshold.Verbose

Sets verbose threshold

stext

Writes text in the margin along the sides of a plot

withRepos

Evaluate an R expression with repositories set temporarily

writeRaw.NullVerbose

All output methods

Java$readShort

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

writeRaw.MultiVerbose

Writes to each of the Verbose objects

loadToEnv

Method to load objects to a new environment

mkdirs

Creates a directory including any necessary but nonexistent parent directories

subplots

Creates a grid of subplots

setMaxValue.ProgressBar

Sets maximum value

swapXY.density

Swaps x and y coordinates of a density object

touchFile

Updates the timestamp of a file

Java$writeByte

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