R: Analysis of R Code for Reproducible Research and Code Comprehension

# Analysis of R Code for Reproducible Research and Code Comprehension

## Documentation for package ‘CodeDepends’ version 0.6.7

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

## Help Pages

$-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