Package index • SpaDES.core

All functions
`Copy(<simList>)`	Copy for `simList` class objects
`Plot(<simList>)`	Plot method for `simList` objects
`Plots()`	`Plot` wrapper intended for use in a SpaDES module
`SpaDES.core` `SpaDES.core-package`	Categorized overview of the `SpaDES.core` package
`.addChangedAttr(<simList>)`	`.addChangedAttr` for `simList` objects
`.addTagsToOutput(<simList>)`	`.addTagsToOutput` for `simList` objects
`all(<equal.simList>)`	All equal method for `simList` objects
`anyPlotting()`	Test whether there should be any plotting from `.plots` module parameter
`append_attr()`	Append attributes
`bindrows()`	Simple wrapper around `data.table::rbindlist`
`.cacheMessage(<simList>)`	`.cacheMessage` for `simList` objects
`.checkCacheRepo(<list>)`	`.checkCacheRepo` for `simList` objects
`checkModule()`	Check for the existence of a remote module
`checkModuleLocal()`	Check for the existence of a module locally
`checkModulePath()`	Uses "." if getPath not set
`checkObject()`	Check for existence of object(s) referenced by a `objects` slot of a `simList` object
`checkParams()`	Check use and existence of parameters passed to simulation.
`checkpointFile()` `checkpointFile<-`() `checkpointInterval()` `checkpointInterval<-`() `doEvent.checkpoint()` `checkpointLoad()` `.checkpointSave()`	Simulation checkpoints
`checksums()`	Calculate checksum for a module's data files
`citation()`	A citation method for `SpaDES` modules
`classFilter()`	Filter objects by class
`clearCache(<simList>)` `showCache(<simList>)` `keepCache(<simList>)`	`clearCache` for `simList` objects
`convertToPackage()`	Convert standard module code into an R package
`copyModule()`	Create a copy of an existing module
`createsOutput()`	Define an output object of a module
`.wrap(<simList>)` `.wrap(<.simDeps>)` `.unwrap(<.simDeps>)` `.wrap(<.moduleDeps>)` `.unwrap(<.moduleDeps>)` `.unwrap(<simList>)`	Methods for `.wrap` and `.unwrap`
`defineEvent()`	Alternative way to define events in SpaDES.core
`defineModule()`	Define a new module.
`defineParameter()`	Define a parameter used in a module
`zipSimList()` `experiment()` `experiment2()` `POM()` `simInitAndExperiment()` `loadPackages()`	Zip a `simList` and various files
`depsEdgeList()`	Build edge list for module dependency graph
`depsGraph()`	Build a module dependency graph
`.guessPkgFun()`	Guess package of a function
`downloadData()`	Download module data
`downloadModule()`	Download a module from a SpaDES module GitHub repository
`eventDiagram()`	Simulation event diagram
`expectsInput()`	Define an input object that the module expects.
`extractURL()`	Extract a url from module metadata
`fileName()`	Extract filename (without extension) of a file
`.findSimList()`	Find `simList` in a nested list
`getModuleVersion()`	Find the latest module version from a SpaDES module repository
`getMapPath()` `getSampleModules()`	Get copies of sample files for examples and tests
`globals()` `globals<-`() `G()` `G<-`()	Get and set global simulation parameters
`initialize(<simList>)` `initialize(<simList_>)`	Generate a `simList` object
`.fileExtensions()` `loadFiles()` `.saveFileExtensions()`	File extensions map
`loadSimList()` `unzipSimList()`	Load a saved `simList` and ancillary files
`makeMemoisable(<simList>)` `unmakeMemoisable(<simList_>)`	Make `simList` correctly work with `memoise`
`maxTimeunit()`	Determine the largest timestep unit in a simulation
`memoryUseThisSession()` `memoryUse()`	Estimate memory used with `system("ps")`
`minTimeunit()`	Determine the smallest timeunit in a simulation
`moduleCodeFiles()`	Extract the full file paths for R source code
`moduleCoverage()`	Calculate module coverage of unit tests
`moduleDefaults`	Defaults values used in `defineModule`
`moduleDiagram()`	Simulation module dependency diagram
`moduleGraph()`	Build a module dependency graph
`moduleMetadata()`	Parse and extract module metadata
`moduleParams()` `moduleInputs()` `moduleOutputs()`	Extract a module's parameters, inputs, or outputs
`moduleVersion()`	Parse and extract a module's version
`newModule()` `newModuleCode()` `newModuleDocumentation()`	Create new module from template
`newModuleTests()`	Create template testing structures for new modules
`newProject()`	Create new SpaDES project
`newProjectCode()`	Create new module code file
`noEventWarning()`	Text for no event with that name
`objSize(<simList>)`	Object size for `simList`
`objectDiagram()`	Simulation object dependency diagram
`objectSynonyms()`	Identify synonyms in a `simList`
`objs()` `objs<-`() `moduleObjects()` `findObjects()`	Extract or replace an object from the simulation environment
`openModules()`	Open all modules nested within a base directory
`packages()`	Get module or simulation package dependencies
`paramCheckOtherMods()`	Test and update a parameter against same parameter in other modules
`params()` `params<-`() `P()` `P<-`() `parameters()`	Get and set simulation parameters
`.parseElems(<simList>)`	`.parseElems` for `simList` class objects
`.preDigestByClass(<simList>)`	Pre-digesting method for `simList`
`.prepareOutput(<simList>)`	`.prepareOutput` for `simList` objects
`.first()` `.highest()` `.last()` `.lowest()` `.normal()`	Event priority
`progressInterval()` `progressInterval<-`() `progressType()` `progressType<-`()	Get and set simulation progress bar details
`newProgressBar()` `setProgressBar()`	Progress bar
`.quickCheck`	The `SpaDES.core` variable to switch between quick and robust checking
`rasterCreate()`	Simple wrapper to load any `Raster*` object
`rasterToMemory()`	Read raster to memory
`remoteFileSize()`	Determine the size of a remotely hosted file
`restartR()`	Restart R programmatically
`restartSpades()`	Restart an interrupted simulation
`.rndstr()` `rndstr()`	Generate random strings
`.robustDigest(<simList>)`	`.robustDigest` for `simList` objects
`saveFiles()`	Save objects using `.saveObjects` in `params` slot of `simInit`
`saveSimList()`	Save a whole `simList` object to disk
`savedSimEnv()`	Retrieve environment for saving interrupted simulations
`scheduleConditionalEvent()`	Schedule a conditional simulation event
`scheduleEvent()`	Schedule a simulation event
`show(<simList>)`	Show an Object
`simFile()`	Generate simulation file name
`simInit()` `simInit2()` `simInitDefaults()`	Initialize a new simulation
`simInitAndSpades2()` `simInitAndSpades()`	`simInitAndSpades2` is a convenience wrapper for `do.call(simInitAndSpades, listOfArgs)`, i.e., a user can pass a list of all the arguments.
`envir()` `envir<-`()	Simulation environment
`events()` `events<-`() `conditionalEvents()` `current()` `current<-`() `completed()` `completed<-`()	Simulation event lists
`inputs()` `inputs<-`() `inputArgs()` `inputArgs<-`()	Simulation inputs
`inputObjects()` `outputObjects()` `outputObjectNames()` `reqdPkgs()` `documentation()` `sessInfo()`	Metadata accessors
`modules()` `modules<-`() `depends()` `depends<-`()	Simulation modules and dependencies
`newObjectsCreated()`	Show which objects were first created in a `simInit` or `spades` call
`outputs()` `outputs<-`() `registerOutputs()` `outputArgs()` `outputArgs<-`()	Simulation outputs
`paths()` `paths<-`() `cachePath()` `cachePath<-`() `inputPath()` `inputPath<-`() `outputPath()` `outputPath<-`() `figurePath()` `logPath()` `modulePath()` `modulePath<-`() `scratchPath()` `scratchPath<-`() `rasterPath()` `rasterPath<-`() `terraPath()` `terraPath<-`() `dataPath()`	Specify paths for modules, inputs, outputs, and temporary rasters
`times()` `times<-`() `time(<simList>)` `time<-`() `end()` `end<-`() `start()` `start<-`() `timeunit()` `timeunit<-`() `timeunits()` `elapsedTime()`	Time usage in `SpaDES`
`simList-class` `simList` `simList_-class` `simList_`	The `simList` class
`spadesClasses`	Classes defined in SpaDES
`spades2()` `spades()`	`spades2` is a convenience wrapper for `do.call(spades, listOfArgs)`, i.e., a user can pass a list of all the arguments.
`spadesOptions()`	`SpaDES.core` options
`dhour()` `dmin()` `dday()` `dyears()` `dmonths()` `dweeks()` `dweek()` `dmonth()` `dyear()` `dsecond()` `dNA()`	SpaDES time units
`[`(<simList>,<character>,<ANY>)	Extract an intact `simList` but with subset of objects
`suppliedElsewhere()`	Assess whether an object has or will be supplied from elsewhere
`.tagsByClass(<simList>)`	`.tagsByClass` for `simList` objects
`inSeconds()` `convertTimeunit()` `.spadesTimes` `spadesTimes()` `checkTimeunit()`	Convert time units
`updateList()`	Update elements of a named list with elements of a second named list
`use_gha()`	Use GitHub actions for automated module checking
`writeEventInfo()`	Write simulation event info to file
`writeRNGInfo()`	Write RNG state info to file
`zipModule()`	Create a zip archive of a module subdirectory

Reference

All functions