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R.utils (version 2.3.0)

Various Programming Utilities

Description

Utility functions useful when programming and developing R packages.

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Install

install.packages('R.utils')

Monthly Downloads

191,979

Version

2.3.0

License

LGPL (>= 2.1)

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Repository

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

Maintainer

Henrik Bengtsson

Last Published

April 14th, 2016

Functions in R.utils (2.3.0)

getBarString.ProgressBar

Gets the progress bar string to be displayed

createFileAtomically

Creates a file atomically

as.list.MultiVerbose

Gets a list of Verbose objects

filePath

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

Arguments$getRegularExpression

Gets a valid regular expression pattern

setDefaultLevel.Verbose

Sets the current default verbose level

GString$getBuiltinPid

Gets the process id of the current R session

readWindowsShellLink

Reads a Microsoft Windows Shortcut (.lnk file)

GString$getBuiltinOs

Gets the operating system of the running machine

LComments

The LComments class

str.Options

Prints the structure of the options

Arguments$getInstanceOf

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

hasUrlProtocol

Checks if one or several pathnames has a URL protocol

as.character.ProgressBar

Gets a string description of the progress bar

downloadFile.character

Prints objects if above threshold

isSingle

Identifies all entries that exists exactly ones

System$getUsername

Retrieves the name of the user running R

getLabel.TextStatusBar

Gets the current value of a label

NullVerbose

A Verbose class ignoring everything

writeRaw.NullVerbose

All output methods

Java$asShort

Converts a numeric to a Java short

Assert

The Assert class

callHooks

Call hook functions by hook name

exit.Verbose

Writes a message and unindents the following output

hasOption.Options

Checks if an option exists

Non-documented objects

Java$asLong

Converts a numeric to a Java long

attachLocally.list

Assigns an objects elements locally

TextStatusBar

A status bar at the R prompt that can be updated

as.character.GString

Gets the processed character string

ProgressBar

Provides text based counting progress bar

compile.SmartComments

Preprocess a vector of code lines

Java

Static class for Java related methods

enter.Verbose

Writes a message and indents the following output

Assert$isScalar

Static method asserting thatan object is a single value

as.logical.Verbose

Gets a logical value of this object

MultiVerbose

A Verbose class ignoring everything

System$currentTimeMillis

Get the current time in milliseconds

as.list.Options

Gets a list representation of the options

cat.Verbose

Concatenates and prints objects if above threshold

addFinalizerToLast

Modifies .Last() to call 'finalizeSession()

cmdArgsCall

Calls an R function passing command-line arguments

getRaw.GString

Gets the unprocessed GString

TimeoutException

TimeoutException represents timeout errors

displayCode

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

copyDirectory

Copies a directory

GString

Parses and evaluates a GString into a regular string

as.character.binmode

Converts a binary/octal/hexadecimal number into a string

popBackupFile

Drops a backup suffix from the backup pathname

captureOutput

Evaluate an R expression and captures the output

Arguments$getDoubles

Coerces to a double vector and validates

capture.Verbose

Captures output of a function

System

Static class to query information about the system

findFiles

Finds one or several files in multiple directories

mkdirs

Creates a directory including any necessary but nonexistent parent directories

commandArgs

Extract command-line arguments

convertComment.SmartComments

Converts a single smart comment to R code

queryRCmdCheck

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

Java$asByte

Converts a numeric to a Java byte

getLeaves.Options

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

Arguments$getNumerics

Coerces to a numeric vector and validates

touchFile

Updates the timestamp of a file

PERCENT< -PERCENT

Assignment operator for delayed assignments ('lazy future')

Arguments$getFilename

Gets and validates a filename

FileProgressBar

A progress bar that sets the size of a file accordingly

findSourceTraceback

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

dataFrame

Allocates a data frame with given column classes

getMessage.TimeoutException

Gets the message of the exception

draw.density

Draws a density curve

cmdArgs

Simple access to parsed command-line arguments

evaluate.Verbose

Evaluates a function and prints its results if above threshold

countLines

Counts the number of lines in a text file

extract.array

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

unwrap.array

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

capitalize

Capitalizes/decapitalizes each character string in a vector

Arguments$getWritablePathname

Gets a writable pathname

compressPDF

Compresses a PDF (into a new PDF)

Creates a vector of column classes used for tabular reading

Java$asInt

Converts an numeric to a Java integer

as.character.Options

Returns a character string version of this object

GString$getBuiltinDatetime

Gets the current date and time

GString$getBuiltinDate

Gets the current date

intervalsToSeq.matrix

Generates a vector of indices from a matrix of intervals

dimNA< -

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

isReplicated

Identifies all entries with replicated values

Settings

Class for applicational settings

Verbose

Class to writing verbose messages to a connection or file

writeRaw.Verbose

Writes objects if above threshold

compressFile

Compressing and decompressing files

Settings$findSettings

Searches for the settings file in one or several directories

Arguments$getIntegers

Coerces to a integer vector and validates

hpaste

Concatenating vectors into human-readable strings

moveInSearchPath

Moves a environment in the search path to another position

getThreshold.Verbose

Gets current verbose threshold

evaluate.GString

Parses and evaluates a GString

off.Verbose

Turn off the output

isModified.Settings

Checks if settings has been modified compared to whats on file

GString$getBuiltinRhome

Gets the path where R is installed

readWindowsShortcut

Reads a Microsoft Windows Shortcut (.lnk file)

Arguments$getCharacters

Coerces to a character vector and validates

Arguments$getReadablePathname

Gets a readable pathname

setStepLength.ProgressBar

Sets default step length

Arguments$getReadablePathnames

Gets a readable pathname

mapToIntervals.numeric

Maps values to intervals

arrayIndex

Converts vector indices to array indices

gcat

Parses, evaluates and outputs a GString

getRelativePath

Gets the relative pathname relative to a directory

shell.exec2

Open a file or URL using Windows File Associations

GString$getBuiltinUsername

Gets the username of the user running R

Sys.readlink2

Read File Symbolic Links (also on Windows)

subplots

Creates a grid of subplots

reset.VComments

Resets a VComments compiler

Arguments$getVector

Validates a vector

cleanup.FileProgressBar

Removes the progress file for a file progress bar

readTable

Reads a file in table format

getLoadedPathname.Settings

Gets the pathname of the settings file loaded

nbrOfOptions.Options

Gets the number of options set

finalizeSession

Function to call for finalizing the R session

System$findGhostscript

Searches for a Ghostview executable on the current system

Assert$check

Static method asserting that a generic condition is true

Java$readShort

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

updateLabels.TextStatusBar

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

pushTemporaryFile

Appends a temporary suffix to the pathname

doCall

Executes a function call with option to ignore unused arguments

saveAnywhere.Settings

Saves settings to file

copyFile

Copies a file atomically

createWindowsShortcut

Creates a Microsoft Windows Shortcut (.lnk file)

createLink

Creates a link to a file or a directory

Arguments$getIndices

Coerces to a integer vector and validates

Install R packages by name or URL

toUrl

Converts a pathname into a URL

hsize

Convert byte sizes into human-readable byte sizes

withLocale

Evaluate an R expression with locale set temporarily

getAbsolutePath

Gets the absolute pathname string

isPackageInstalled

Checks if a package is installed or not

Java$readUTF

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

withSink

Evaluate an R expression while temporarily diverting output

insert

Insert values to a vector at certain positions

isEof.connection

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

parse.SmartComments

Parses one single smart comment

isUrl

Checks if one or several pathnames is URLs

readRdHelp

Reads one or more Rd help files in a certain format

getTimestampFormat.Verbose

Gets the default timestamp format

detachPackage

Detaches packages by name

isZero

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

GString$getBuiltinRversion

Gets the current R version

increase.ProgressBar

Increases (steps) progress bar

newline.Verbose

Writes one or several empty lines

Java$readByte

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

R.utils-package

Package R.utils

patchCode

Patches installed and loaded packages and more

lastModified

Gets the time when the file was last modified

setLabels.TextStatusBar

Sets new values of given labels

SmartComments

Abstract class SmartComments

Java$writeShort

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

Arguments$getEnvironment

Gets an existing environment

getParent

Gets the string of the parent specified by this pathname

GString$getBuiltinHostname

Gets the hostname of the system running R

GString$getBuiltinTime

Gets the current time

fileAccess

Checks the permission of a file or a directory

printf.Verbose

Formats and prints object if above threshold

on.Verbose

Turn on the output

Java$writeUTF

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

printf

C-style formatted output

isOn.NullVerbose

Checks if the output is on

isVisible.NullVerbose

Checks if a certain verbose level will be shown or not

inAnyInterval.numeric

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

as.character.Verbose

Returns a character string version of this object

setValue.ProgressBar

Sets current value

onGarbageCollect

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

convertComment.VComments

Converts a verbose comment to R code

readBinFragments

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

Options

The Options class

renameFile

Renames a file (or a directory) atomically/safely

withRepos

Evaluate an R expression with repositories set temporarily

System$getHostname

Retrieves the computer name of the current host

eget

Gets a variable by name

update.ProgressBar

Updates progress bar

reassignInPackage

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

loadObject

Method to load object from a file or a connection

equals.Options

Checks if this object is equal to another Options object

file.info2

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

Java$writeByte

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

pushBackupFile

Appends a backup suffix to the pathname

newline.TextStatusBar

Writes a newline

isDone.ProgressBar

Checks if progress bar is completed

flush.TextStatusBar

Flushes the output

Assert$isVector

Static method asserting thatan object is a vector

mergeIntervals.numeric

Merges intervals

less.Verbose

Creates a cloned instance with a higher threshold

setTicks.ProgressBar

Sets values for which ticks should be visible

sourceDirectory

Sources files recursively to either local or global environment

isOn.Verbose

Checks if the output is on

popMessage.TextStatusBar

Adds a message above the status bar

isDirectory

Checks if the file specification is a directory

setOption.Options

Sets an option

print.GString

Prints the processed GString

names.Options

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

Arguments

Static class to validate and process arguments

reset.SmartComments

Resets a SmartComments compiler

withOptions

Evaluate an R expression with options set temporarily

onSessionExit

Registers a function to be called when the R session finishes

as.double.Verbose

Gets a numeric value of this object

loadAnywhere.Settings

Loads settings from file

str.Verbose

Prints the structure of an object if above threshold

loadToEnv

Method to load objects to a new environment

summary.Verbose

Generates a summary of an object if above threshold

System$parseDebian

Parses a string, file or connection for Debian formatted parameters

setProgress.ProgressBar

Sets current progress

env

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

ruler.Verbose

Writes a ruler

readTableIndex

Reads a single column from file in table format

tempvar

Gets a unique non-existing temporary variable name

GString$getVariableValue

Gets a variable value given a name and attributes

equals.Verbose

Checks if this object is equal to another

egsub

Global substitute of expression using regular expressions

isFile

Checks if the file specification is a file

tmpfile

Creates a temporary file with content

setOption

Sets a option in R

Arguments$getLogicals

Coerces to a logical vector and validates

isOpen.character

Checks if there is an open connection to a file

listDirectory

Gets the file names in the directory

System$findGraphicsDevice

Searches for a working PNG device

isAbsolutePath

Checks if this pathname is absolute

mout

Miscellaneous functions for outputting via message()

swapXY.density

Swaps x and y coordinates of a density object

resetWarnings

Resets recorded warnings

use

Attaches or loads packages

validate.VComments

Validates the compiled lines

mpager

A \"pager\" function that outputs to standard error

more.Verbose

Creates a cloned instance with a lower threshold

Assert$isMatrix

Static method asserting thatan object is a matrix

validate.SmartComments

Validates the compiled lines

update.FileProgressBar

Updates file progress bar

popTemporaryFile

Drops a temporary suffix from the temporary pathname

wrap.array

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

setLabel.TextStatusBar

Sets the value of a label

reset.ProgressBar

Reset progress bar

timestampOn.Verbose

Turns automatic timestamping on and off

System$openBrowser

Opens an HTML document using the OS default HTML browser

isPackageLoaded

Checks if a package is loaded or not

Java$readInt

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

intToBin

Converts an integer to a binary/octal/hexadecimal number

sourceTo

Parses and evaluates code from a file or a connection

promptAndSave.Settings

Prompt user to save modified settings

removeDirectory

Removes a directory

withSeed

Evaluate an R expression with a temporarily set random set

Arguments$getVerbose

Coerces to Verbose object

Assert$inherits

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

seqToIntervals

Gets all contigous intervals of a vector of indices

saveObject

Saves an object to a file or a connection

writeDataFrame.data.frame

Writes a data.frame to tabular text file

setTimestampFormat.Verbose

Sets the default timestamp format

resample

Sample values from a set of elements

splitByPattern

Splits a single character string by pattern

setMaxValue.ProgressBar

Sets maximum value

seqToHumanReadable

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

stext

Writes text in the margin along the sides of a plot

Java$writeInt

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

whichVector.logical

Identifies TRUE elements in a logical vector

toCamelCase

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

systemR

Launches another R process from within R

warnings.Verbose

Outputs any warnings recorded

update.TextStatusBar

Updates the status bar (visually)

parse.GString

Parses a GString

setThreshold.Verbose

Sets verbose threshold

useRepos

Sets package repositories

isVisible.Verbose

Checks if a certain verbose level will be shown or not

withCapture

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

withTimeout

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

writeBinFragments

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

writeRaw.MultiVerbose

Writes to each of the Verbose objects

pushState.Verbose

Pushes the current indentation state of the Verbose object