All functions

Copy(<simList>)

Copy for simList class objects

POM()

Use Pattern Oriented Modeling to fit unknown parameters

Plot(<simList>)

Plot method for simList objects

SpaDES.core-package

Categorized overview of the SpaDES.core package

.addChangedAttr(<simList>)

.addChangedAttr for simList class objects

.addTagsToOutput(<simList>)

addTagsToOutput for simList class objects

all(<equal.simList>)

All equal method for simLists

append_attr()

Add a module to a moduleList

.cacheMessage(<simList>)

cacheMessage for simList class objects

.checkCacheRepo(<list>)

checkCacheRepo for simList class objects

checkModule()

Check for the existence of a remote module

checkModuleLocal()

Check for the existence of a module locally

checkObject()

Check for existence of object(s) referenced by a objects slot of a simList object

checkParams()

Check use and existence of params passed to simulation.

doEvent.checkpoint() checkpointLoad() .checkpointSave() checkpointFile() `checkpointFile<-`() checkpointInterval() `checkpointInterval<-`()

Simulation checkpoints.

checksums()

Calculate checksum for a module's data files

classFilter()

Filter objects by class

copyModule()

Create a copy of an existing module

createsOutput()

Define an output object of a module

defineModule()

Define a new module.

defineParameter()

Define a parameter used in a module

depsEdgeList()

Build edge list for module dependency graph

depsGraph()

Build a module dependency graph

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.

experiment()

Run an experiment using spades

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

globals() `globals<-`() G() `G<-`()

Get and set simulation globals.

initialize(<simList>)

Generate a simList object

.fileExtensions() loadFiles() .saveFileExtensions() saveSimList()

File extensions map

loadPackages()

Load packages.

ls.simList() ls(<simList>) objects.simList() objects(<simList>)

List simulation objects

ls.str.simList() ls.str(<missing>,<simList>) ls.str(<simList>,<missing>)

List simulation objects and their structure

makeMemoiseable(<simList>) unmakeMemoiseable(<simList_>)

Make simList correctly work with memoise

maxTimeunit()

Determine the largest timestep unit in a simulation

minTimeunit()

Determine the smallest timeunit in a simulation

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

moduleVersion()

Parse and extract a module's version

newModule()

Create new module from template

newModuleCode()

Create new module code file

newModuleDocumentation()

Create new module documentation

newModuleTests()

Create template testing structures for new modules

objSize(<simList>)

Object size for simLists

.objSizeInclEnviros(<simList>)

objSizeInclEnviros for simList class objects

objectDiagram()

Simulation object dependency diagram

objs() `objs<-`() `[[`(<simList>,<ANY>,<ANY>) `[[<-`(<simList>,<ANY>,<ANY>,<ANY>) `$`(<simList>) `$<-`(<simList>)

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

paddedFloatToChar()

Convert numeric to character with padding

params() `params<-`() 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

.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

rasterToMemory()

Read raster to memory

remoteFileSize()

Determine the size of a remotely hosted file

rndstr()

Generate random strings

.robustDigest(<simList>)

.robustDigest for simList class objects

saveFiles()

Save objects using .saveObjects in params slot of simInit

scheduleEvent()

Schedule a simulation event

show(<simList>)

Show an Object

simInit() simInitAndSpades()

Initialize a new simulation

envir() `envir<-`()

Simulation environment

events() `events<-`() current() `current<-`() completed() `completed<-`()

Simulation event lists

inputs() `inputs<-`() outputs() `outputs<-`() inputArgs() `inputArgs<-`() outputArgs() `outputArgs<-`()

Inputs and outputs

modules() `modules<-`() depends() `depends<-`()

Simulation modules and dependencies

paths() `paths<-`() cachePath() `cachePath<-`() inputPath() `inputPath<-`() outputPath() `outputPath<-`() modulePath() `modulePath<-`() dataPath()

Specify paths for modules, inputs, and outputs

times() `times<-`() time(<.simList>) `time<-`() end() `end<-`() start() `start<-`() timeunit() `timeunit<-`() timeunits()

Time usage in SpaDES

.simList-class

The simList class

spadesClasses

Classes defined in SpaDES

spades()

Run a spatial discrete event simulation

dyears() dmonths() dweeks() dweek() dmonth() dyear() dsecond() dday() dhour() dNA()

SpaDES time units

suppliedElsewhere()

Assess whether an object has or will be supplied from elsewhere

.tagsByClass(<simList>)

tagsByClass for simList class objects

inSeconds() convertTimeunit() .spadesTimes spadesTimes() checkTimeunit()

Convert time units

updateList()

Update elements of a named list with elements of a second named list

zipModule()

Create a zip archive of a module subdirectory