Analysis of R Code for Reproducible Research and Code Comprehension

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Documentation for package ‘CodeDepends’ version 0.6.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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$-method	The Script class and elements
addRemoveIntermediates	Determine the code block after which a variable can be explicitly removed
AnnotatedScript-class	The Script class and elements
applyhandlerfactory	Specifying custom processing behavior, Function handlers and handler factories
assignfunhandler	Specifying custom processing behavior, Function handlers and handler factories
assignhandler	Specifying custom processing behavior, Function handlers and handler factories
asVarName	asVarName
coerce-method	The Script class and elements
coerce-method	Compute and plot life cycle of variables in code
coerce-method	Create a Script object that re-reads the original file as needed
colonshandler	Specifying custom processing behavior, Function handlers and handler factories
counthandler	Specifying custom processing behavior, Function handlers and handler factories
datahandler	Specifying custom processing behavior, Function handlers and handler factories
defaultFuncHandlers	Specifying custom processing behavior, Function handlers and handler factories
defhandler	Specifying custom processing behavior, Function handlers and handler factories
dollarhandler	Specifying custom processing behavior, Function handlers and handler factories
filterhandler	Specifying custom processing behavior, Function handlers and handler factories
findWhenUnneeded	Determine the code block after which a variable can be explicitly removed
forhandler	Specifying custom processing behavior, Function handlers and handler factories
formulahandler	Specifying custom processing behavior, Function handlers and handler factories
fullnsehandler	Specifying custom processing behavior, Function handlers and handler factories
funchandler	Specifying custom processing behavior, Function handlers and handler factories
functionhandlers	Specifying custom processing behavior, Function handlers and handler factories
funshandler	Specifying custom processing behavior, Function handlers and handler factories
getDependsThread	Compute which code blocks in a script are inputs to define a variable
getDependsThread-method	Compute which code blocks in a script are inputs to define a variable
getDetailedTimelines	Compute and plot life cycle of variables in code
getExpressionThread	Find the sequence of expressions needed to get to a certain point in the code
getInputs	Get input and output variables and literals from R expressions
getInputs-method	Get input and output variables and literals from R expressions
getInputs-method	Create a Script object that re-reads the original file as needed
getPropagateChanges	Determine which expressions to update when a variable changes
getSectionDepends	Determine dependencies for code blocks
getVariableDepends	Determine dependencies for code blocks
getVariables	Get the names of the variables used in code
getVariables-method	Get the names of the variables used in code
groupbyhandler	Specifying custom processing behavior, Function handlers and handler factories
guessTaskType	Guess the type of high-level task of a code block
highlightCode	Display R code with highlighting of variables, links to functions and packages
historyAsScript	Convert R interactive history to a Script object
inputCollector	Create customized input/output collector for use in getInputs
libreqhandler	Specifying custom processing behavior, Function handlers and handler factories
makeCallGraph	Create a graph representing which functions call other functions
makeCallGraph-method	Create a graph representing which functions call other functions
makeTaskGraph	Create a graph connecting the tasks within a script
makeVariableGraph	Create a graph describing the relationships between variables in a script
noophandler	Specifying custom processing behavior, Function handlers and handler factories
nseafterfirst	Specifying custom processing behavior, Function handlers and handler factories
nsehandlerfactory	Specifying custom processing behavior, Function handlers and handler factories
nseonlyhandlerfactory	Specifying custom processing behavior, Function handlers and handler factories
pipehandler	Specifying custom processing behavior, Function handlers and handler factories
plot.DetailedVariableTimeline	Compute and plot life cycle of variables in code
readAnnotatedScript	Read the code blocks/chunks from a document
readScript	Read the code blocks/chunks from a document
readScript-method	Read the code blocks/chunks from a document
rmhandler	Specifying custom processing behavior, Function handlers and handler factories
runUpToSection	Evaluate the code blocks up to a particular section of a document
Script-class	The Script class and elements
scriptInfo	Get input and output variables and literals from R expressions
ScriptInfo-class	The Script class and elements
ScriptNode-class	The Script class and elements
ScriptNodeInfo-class	The Script class and elements
separateExpressionBlocks	Convert a script into individual top-level calls
sourceVariable	Evaluate code in document in order to define the specified variables
splitRedefinitions	Divide a script into separate lists of code based on redefinition of a variable
spreadhandler	Specifying custom processing behavior, Function handlers and handler factories
summarize_handlerfactory	Specifying custom processing behavior, Function handlers and handler factories
updatingScript	Create a Script object that re-reads the original file as needed
[-method	The Script class and elements