Introduction | The workhorses: readScript and getInputs | Symbols within formulas | Input collectors, function handlers, and customization | Dependency detection and script visualization | Variable dependency graphs | call graphs | Variable definitions timelines
Package: CodeDepends 0.6.7
Gabriel Becker
CodeDepends: Analysis of R Code for Reproducible Research and Code Comprehension
Tools for analyzing R expressions or blocks of code and determining the dependencies between them. It focuses on R scripts, but can be used on the bodies of functions. There are many facilities including the ability to summarize or get a high-level view of code, determining dependencies between variables, code improvement suggestions.
Authors:
CodeDepends_0.6.7.tar.gz
CodeDepends_0.6.7.zip(r-4.7)CodeDepends_0.6.7.zip(r-4.6)CodeDepends_0.6.7.zip(r-4.5)
CodeDepends_0.6.7.tgz(r-4.6-any)CodeDepends_0.6.7.tgz(r-4.5-any)
CodeDepends_0.6.7.tar.gz(r-4.7-any)CodeDepends_0.6.7.tar.gz(r-4.6-any)
CodeDepends_0.6.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CodeDepends/json (API)
| # Install 'CodeDepends' in R: |
| install.packages('CodeDepends', repos = c('https://duncantl.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/duncantl/codedepends/issues
Last updated from:5bf358ae2b. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 130 | ||
| source / vignettes | OK | 174 | ||
| linux-release-x86_64 | OK | 132 | ||
| macos-release-arm64 | OK | 191 | ||
| macos-oldrel-arm64 | OK | 154 | ||
| windows-devel | OK | 89 | ||
| windows-release | OK | 90 | ||
| windows-oldrel | OK | 91 | ||
| wasm-release | OK | 98 |
Exports:addRemoveIntermediatesapplyhandlerfactoryassignfunhandlerassignhandlerasVarNamecoercecolonshandlercounthandlerdatahandlerdefaultFuncHandlersdefhandlerdollarhandlerfilterhandlerfindWhenUnneededforhandlerformulahandlerfullnsehandlerfunchandlerfunshandlergetDependsThreadgetDetailedTimelinesgetExpressionThreadgetInputsgetPropagateChangesgetSectionDependsgetVariableDependsgetVariablesgroupbyhandlerguessTaskTypehighlightCodehistoryAsScriptinputCollectorlibreqhandlermakeCallGraphmakeTaskGraphmakeVariableGraphnoophandlernseafterfirstnsehandlerfactorynseonlyhandlerfactorypipehandlerreadAnnotatedScriptreadScriptrmhandlerrunUpToSectionscriptInfoseparateExpressionBlockssourceVariablesplitRedefinitionsspreadhandlersummarize_handlerfactoryupdatingScript
Dependencies:BiocGenericscodetoolsgenericsgraphXML
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| asVarName | asVarName |
| Determine the code block after which a variable can be explicitly removed | addRemoveIntermediates findWhenUnneeded |
| Specifying custom processing behavior, Function handlers and handler factories | applyhandlerfactory assignfunhandler assignhandler colonshandler counthandler datahandler defaultFuncHandlers defhandler dollarhandler filterhandler forhandler formulahandler fullnsehandler funchandler functionhandlers funshandler groupbyhandler libreqhandler noophandler nseafterfirst nsehandlerfactory nseonlyhandlerfactory pipehandler rmhandler spreadhandler summarize_handlerfactory |
| Compute which code blocks in a script are inputs to define a variable | getDependsThread getDependsThread,character-method getDependsThread,name-method getDependsThread,numeric-method |
| Compute and plot life cycle of variables in code | coerce,DetailedVariableTimeline,matrix-method getDetailedTimelines plot.DetailedVariableTimeline |
| Find the sequence of expressions needed to get to a certain point in the code | getExpressionThread |
| Get input and output variables and literals from R expressions | getInputs getInputs,ANY-method getInputs,function-method getInputs,Script-method getInputs,ScriptNode-method getInputs,ScriptNodeInfo-method scriptInfo |
| Determine which expressions to update when a variable changes | getPropagateChanges |
| Determine dependencies for code blocks | getSectionDepends getVariableDepends |
| Get the names of the variables used in code | getVariables getVariables,expression-method getVariables,Script-method getVariables,ScriptInfo-method getVariables,ScriptNode-method getVariables,ScriptNodeInfo-method |
| Guess the type of high-level task of a code block | guessTaskType |
| Display R code with highlighting of variables, links to functions and packages | highlightCode |
| Convert R interactive history to a Script object | historyAsScript |
| Create customized input/output collector for use in getInputs | inputCollector |
| Create a graph representing which functions call other functions | makeCallGraph makeCallGraph,character-method makeCallGraph,function-method makeCallGraph,list-method |
| Create a graph connecting the tasks within a script | makeTaskGraph |
| Create a graph describing the relationships between variables in a script | makeVariableGraph |
| Read the code blocks/chunks from a document | readAnnotatedScript readScript readScript,character-method readScript,connection-method readScript,missing-method readScript,XMLInternalDocument-method |
| Evaluate the code blocks up to a particular section of a document | runUpToSection |
| The Script class and elements | $,Script-method AnnotatedScript-class coerce,expression,ScriptNodeInfo-method coerce,language,ScriptNodeInfo-method coerce,Script,ScriptInfo-method coerce,ScriptNode,ScriptNodeInfo-method Script-class ScriptInfo-class ScriptNode-class ScriptNodeInfo-class [,Script,character,missing-method [,Script,vector,missing-method |
| Convert a script into individual top-level calls | separateExpressionBlocks |
| Evaluate code in document in order to define the specified variables | sourceVariable |
| Divide a script into separate lists of code based on redefinition of a variable | splitRedefinitions |
| Create a Script object that re-reads the original file as needed | coerce,DynScript,Script-method getInputs,DynScript-method updatingScript |
