R: Core Utilities for Developing and Running Spatially Explicit Discrete Event Models

# Core Utilities for Developing and Running Spatially Explicit Discrete Event Models

## Documentation for package ‘SpaDES.core’ version 3.0.4

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

## Help Pages

A B C D E F G I K L M N O P R S T U W Z misc

SpaDES.core-package | Categorized overview of the 'SpaDES.core' package

## -- A --

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
append_attr-method | Append attributes

## -- B --

bindrows | Simple wrapper around 'data.table::rbindlist'

## -- C --

Cache | '.robustDigest' for 'simList' objects
cachePath | Specify paths for modules, inputs, outputs, and temporary rasters
cachePath-method | Specify paths for modules, inputs, outputs, and temporary rasters
cachePath<- | Specify paths for modules, inputs, outputs, and temporary rasters
cachePath<--method | Specify paths for modules, inputs, outputs, and temporary rasters
checkModule | Check for the existence of a remote module
checkModule-method | Check for the existence of a remote module
checkModuleLocal | Check for the existence of a module locally
checkModuleLocal-method | Check for the existence of a module locally
checkModulePath | Check module path
checkObject | Check for existence of object(s) referenced by a 'objects' slot of a 'simList' object
checkObject-method | 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.
checkParams-method | Check use and existence of parameters passed to simulation.
checkpointFile | Simulation checkpoints
checkpointFile-method | Simulation checkpoints
checkpointFile<- | Simulation checkpoints
checkpointFile<--method | Simulation checkpoints
checkpointInterval | Simulation checkpoints
checkpointInterval-method | Simulation checkpoints
checkpointInterval<- | Simulation checkpoints
checkpointInterval<--method | Simulation checkpoints
checkpointLoad | Simulation checkpoints
checksums | Calculate checksum for a module's data files
checkTimeunit | Convert time units
checkTimeunit-method | Convert time units
citation | A citation method for 'SpaDES' modules
citation-method | A citation method for 'SpaDES' modules
classFilter | Filter objects by class
classFilter-method | Filter objects by class
clearCache-method | 'clearCache' for 'simList' objects
clearCacheEventsOnly | Convenience wrapper around 'clearCache' for SpaDES events
completed | Simulation event lists
completed-method | Simulation event lists
completed<- | Simulation event lists
completed<--method | Simulation event lists
conditionalEvents | Simulation event lists
conditionalEvents-method | Simulation event lists
convertTimeunit | Convert time units
convertToPackage | Convert standard module code into an R package
Copy-method | Copy for 'simList' class objects
copyModule | Create a copy of an existing module
copyModule-method | Create a copy of an existing module
createDESCRIPTIONandDocs | Convert standard module code into an R package
createsOutput | Define an output object of a module
createsOutput-method | Define an output object of a module
current | Simulation event lists
current-method | Simulation event lists
current<- | Simulation event lists
current<--method | Simulation event lists

## -- D --

dataPath | Specify paths for modules, inputs, outputs, and temporary rasters
dataPath-method | Specify paths for modules, inputs, outputs, and temporary rasters
dday | SpaDES time units
defineEvent | Alternative way to define events in SpaDES.core
defineModule | Define a new module.
defineModule-method | Define a new module.
defineParameter | Define a parameter used in a module
depends | Simulation modules and dependencies
depends-method | Simulation modules and dependencies
depends<- | Simulation modules and dependencies
depends<--method | Simulation modules and dependencies
depsEdgeList | Build edge list for module dependency graph
depsEdgeList-method | Build edge list for module dependency graph
depsGraph | Build a module dependency graph
depsGraph-method | Build a module dependency graph
dhour | SpaDES time units
dmin | SpaDES time units
dmonth | SpaDES time units
dmonths | SpaDES time units
dmonths-method | SpaDES time units
dNA | SpaDES time units
dNA-method | SpaDES time units
doCallSafe | Memory safe alternative to 'do.call'
documentation | Metadata accessors
documentation-method | Metadata accessors
doEvent.checkpoint | Simulation checkpoints
downloadData | Download module data
downloadData-method | Download module data
downloadModule | Download a module from a SpaDES module GitHub repository
downloadModule-method | Download a module from a SpaDES module GitHub repository
dsecond | SpaDES time units
dweek | SpaDES time units
dweeks | SpaDES time units
dweeks-method | SpaDES time units
dyear | SpaDES time units
dyears | SpaDES time units
dyears-method | SpaDES time units

## -- E --

elapsedTime | Time usage in 'SpaDES'
elapsedTime.simList | Time usage in 'SpaDES'
end | Time usage in 'SpaDES'
end.simList | Time usage in 'SpaDES'
end<- | Time usage in 'SpaDES'
end<--method | Time usage in 'SpaDES'
envir | Simulation environment
envir-method | Simulation environment
envir<- | Simulation environment
envir<--method | Simulation environment
eventDiagram | Simulation event diagram
eventDiagram-method | Simulation event diagram
events | Simulation event lists
events-method | Simulation event lists
events<- | Simulation event lists
events<--method | Simulation event lists
expectsInput | Define an input object that the module expects.
expectsInput-method | Define an input object that the module expects.
experiment | Zip a 'simList' and various files
experiment2 | Zip a 'simList' and various files
extractURL | Extract a url from module metadata
extractURL-method | Extract a url from module metadata

## -- F --

figurePath | Specify paths for modules, inputs, outputs, and temporary rasters
figurePath-method | Specify paths for modules, inputs, outputs, and temporary rasters
fileName | Extract filename (without extension) of a file
findObjects | Extract or replace an object from the simulation environment

## -- G --

G | Get and set global simulation parameters
G-method | Get and set global simulation parameters
G<- | Get and set global simulation parameters
G<--method | Get and set global simulation parameters
getMapPath | Get copies of sample files for examples and tests
getModuleVersion | Find the latest module version from a SpaDES module repository
getModuleVersion-method | Find the latest module version from a SpaDES module repository
getSampleModules | Get copies of sample files for examples and tests
globals | Get and set global simulation parameters
globals-method | Get and set global simulation parameters
globals<- | Get and set global simulation parameters
globals<--method | Get and set global simulation parameters

## -- I --

initialize-method | Generate a 'simList' object
inputArgs | Simulation inputs
inputArgs-method | Simulation inputs
inputArgs<- | Simulation inputs
inputArgs<--method | Simulation inputs
inputObjects | Metadata accessors
inputObjects-method | Metadata accessors
inputPath | Specify paths for modules, inputs, outputs, and temporary rasters
inputPath-method | Specify paths for modules, inputs, outputs, and temporary rasters
inputPath<- | Specify paths for modules, inputs, outputs, and temporary rasters
inputPath<--method | Specify paths for modules, inputs, outputs, and temporary rasters
inputs | Simulation inputs
inputs-method | Simulation inputs
inputs<- | Simulation inputs
inputs<--method | Simulation inputs
inSeconds | Convert time units

## -- K --

keepCache-method | 'clearCache' for 'simList' objects

## -- L --

loadFiles | File extensions map
loadFiles-method | File extensions map
loadPackages | Zip a 'simList' and various files
loadSimList | Load a saved 'simList' and ancillary files
logPath | Specify paths for modules, inputs, outputs, and temporary rasters
logPath-method | Specify paths for modules, inputs, outputs, and temporary rasters

## -- M --

makeMemoisable.simList | Make 'simList' correctly work with 'memoise'
maxTimeunit | Determine the largest timestep unit in a simulation
maxTimeunit-method | Determine the largest timestep unit in a simulation
memoryUse | Estimate memory used with 'system("ps")'
memoryUseThisSession | Estimate memory used with 'system("ps")'
minTimeunit | Determine the smallest timeunit in a simulation
minTimeunit-method | 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
moduleDiagram-method | Simulation module dependency diagram
moduleGraph | Build a module dependency graph
moduleGraph-method | Build a module dependency graph
moduleInputs | Extract a module's parameters, inputs, or outputs
moduleInputs-method | Extract a module's parameters, inputs, or outputs
moduleMetadata | Parse and extract module metadata
moduleMetadata-method | Parse and extract module metadata
moduleObjects | Extract or replace an object from the simulation environment
moduleOutputs | Extract a module's parameters, inputs, or outputs
moduleOutputs-method | Extract a module's parameters, inputs, or outputs
moduleParams | Extract a module's parameters, inputs, or outputs
moduleParams-method | Extract a module's parameters, inputs, or outputs
modulePath | Specify paths for modules, inputs, outputs, and temporary rasters
modulePath-method | Specify paths for modules, inputs, outputs, and temporary rasters
modulePath<- | Specify paths for modules, inputs, outputs, and temporary rasters
modulePath<--method | Specify paths for modules, inputs, outputs, and temporary rasters
modules | Simulation modules and dependencies
modules-method | Simulation modules and dependencies
modules<- | Simulation modules and dependencies
modules<--method | Simulation modules and dependencies
moduleVersion | Parse and extract a module's version
moduleVersion-method | Parse and extract a module's version

## -- N --

newModule | Create new module from template
newModule-method | Create new module from template
newModuleCode | Create new module from template
newModuleCode-method | Create new module from template
newModuleDocumentation | Create new module from template
newModuleDocumentation-method | Create new module from template
newModuleTests | Create template testing structures for new modules
newModuleTests-method | Create template testing structures for new modules
newObjectsCreated | Show which objects were first created in a 'simInit' or 'spades' call
newProgressBar | Progress bar
newProject | Create new SpaDES project
newProject-method | Create new SpaDES project
newProjectCode | Create new module code file
newProjectCode-method | Create new module code file
noEventWarning | Text for no event with that name

## -- O --

objectDiagram | Simulation object dependency diagram
objectDiagram-method | Simulation object dependency diagram
objectsCreated | Show which objects were first created in a 'simInit' or 'spades' call
objectSynonyms | Identify synonyms in a 'simList'
objs | Extract or replace an object from the simulation environment
objs-method | Extract or replace an object from the simulation environment
objs<- | Extract or replace an object from the simulation environment
objs<--method | Extract or replace an object from the simulation environment
objSize.simList | Object size for 'simList'
openModules | Open all modules nested within a base directory
openModules-method | Open all modules nested within a base directory
outputArgs | Simulation outputs
outputArgs-method | Simulation outputs
outputArgs<- | Simulation outputs
outputArgs<--method | Simulation outputs
outputObjectNames | Metadata accessors
outputObjectNames-method | Metadata accessors
outputObjects | Metadata accessors
outputObjects-method | Metadata accessors
outputPath | Specify paths for modules, inputs, outputs, and temporary rasters
outputPath-method | Specify paths for modules, inputs, outputs, and temporary rasters
outputPath<- | Specify paths for modules, inputs, outputs, and temporary rasters
outputPath<--method | Specify paths for modules, inputs, outputs, and temporary rasters
outputs | Simulation outputs
outputs-method | Simulation outputs
outputs<- | Simulation outputs
outputs<--method | Simulation outputs

## -- P --

P | Get and set simulation parameters
P<- | Get and set simulation parameters
packages | Get module or simulation package dependencies
packages-method | Get module or simulation package dependencies
paramCheckOtherMods | Test and update a parameter against same parameter in other modules
parameters | Get and set simulation parameters
parameters-method | Get and set simulation parameters
params | Get and set simulation parameters
params-method | Get and set simulation parameters
params<- | Get and set simulation parameters
params<--method | Get and set simulation parameters
paths | Specify paths for modules, inputs, outputs, and temporary rasters
paths-method | Specify paths for modules, inputs, outputs, and temporary rasters
paths<- | Specify paths for modules, inputs, outputs, and temporary rasters
paths<--method | Specify paths for modules, inputs, outputs, and temporary rasters
Plot-method | Plot method for 'simList' objects
Plots | 'Plot' wrapper intended for use in a SpaDES module
POM | Zip a 'simList' and various files
priority | Event priority
progressInterval | Get and set simulation progress bar details
progressInterval-method | Get and set simulation progress bar details
progressInterval<- | Get and set simulation progress bar details
progressInterval<--method | Get and set simulation progress bar details
progressType | Get and set simulation progress bar details
progressType-method | Get and set simulation progress bar details
progressType<- | Get and set simulation progress bar details
progressType<--method | Get and set simulation progress bar details

## -- R --

rasterCreate | Simple wrapper to load any Raster* object
rasterCreate.default | Simple wrapper to load any Raster* object
rasterPath | Specify paths for modules, inputs, outputs, and temporary rasters
rasterPath-method | Specify paths for modules, inputs, outputs, and temporary rasters
rasterPath<- | Specify paths for modules, inputs, outputs, and temporary rasters
rasterPath<--method | Specify paths for modules, inputs, outputs, and temporary rasters
rasterToMemory | Read raster to memory
rasterToMemory-method | Read raster to memory
registerOutputs | Simulation outputs
remoteFileSize | Determine the size of a remotely hosted file
reqdPkgs | Metadata accessors
reqdPkgs-method | Metadata accessors
restartOrSimInitAndSpades | Restart an interrupted simulation
restartR | Restart R programmatically
restartSpades | Restart an interrupted simulation
rndstr | Generate random strings
rndstr-method | Generate random strings

## -- S --

simList-accessors-packages | Get module or simulation package dependencies
savedSimEnv | Retrieve environment for saving interrupted simulations
saveFiles | Save objects using '.saveObjects' in 'params' slot of 'simInit'
saveSim | Save a whole 'simList' object to disk
saveSimList | Save a whole 'simList' object to disk
saveState | Restart an interrupted simulation
scheduleConditionalEvent | Schedule a conditional simulation event
scheduleEvent | Schedule a simulation event
scratchPath | Specify paths for modules, inputs, outputs, and temporary rasters
scratchPath-method | Specify paths for modules, inputs, outputs, and temporary rasters
scratchPath<- | Specify paths for modules, inputs, outputs, and temporary rasters
scratchPath<--method | Specify paths for modules, inputs, outputs, and temporary rasters
sessInfo | Metadata accessors
sessInfo-method | Metadata accessors
setProgressBar | Progress bar
show-method | Show an Object
showCache-method | 'clearCache' for 'simList' objects
simFile | Generate simulation file name
simInit | Initialize a new simulation
simInit-method | Initialize a new simulation
simInit2 | Initialize a new simulation
simInitAndExperiment | Zip a 'simList' and various files
simInitAndSpades | 'simInitAndSpades2' is a convenience wrapper for 'do.call(simInitAndSpades, listOfArgs)', i.e., a user can pass a list of all the arguments.
simInitAndSpades2 | 'simInitAndSpades2' is a convenience wrapper for 'do.call(simInitAndSpades, listOfArgs)', i.e., a user can pass a list of all the arguments.
simInitDefaults | Initialize a new simulation
simList | The 'simList' class
simList-accessors-envir | Simulation environment
simList-accessors-events | Simulation event lists
simList-accessors-inout | Simulation inputs
simList-accessors-metadata | Metadata accessors
simList-accessors-modules | Simulation modules and dependencies
simList-accessors-objects | Extract or replace an object from the simulation environment
simList-accessors-params | Get and set simulation parameters
simList-accessors-paths | Specify paths for modules, inputs, outputs, and temporary rasters
simList-accessors-times | Time usage in 'SpaDES'
simList-class | The 'simList' class
simList_ | The 'simList' class
simList_-class | The 'simList' class
spades | 'spades2' is a convenience wrapper for 'do.call(spades, listOfArgs)', i.e., a user can pass a list of all the arguments.
spades-method | 'spades2' is a convenience wrapper for 'do.call(spades, listOfArgs)', i.e., a user can pass a list of all the arguments.
SpaDES.core | Categorized overview of the 'SpaDES.core' package
spades2 | 'spades2' is a convenience wrapper for 'do.call(spades, listOfArgs)', i.e., a user can pass a list of all the arguments.
spadesClasses | Classes defined in SpaDES
spadesOptions | 'SpaDES.core' options
spadesTimes | Convert time units
start | Time usage in 'SpaDES'
start.simList | Time usage in 'SpaDES'
start<- | Time usage in 'SpaDES'
start<--method | Time usage in 'SpaDES'
suppliedElsewhere | Assess whether an object has or will be supplied from elsewhere

## -- T --

terraPath | Specify paths for modules, inputs, outputs, and temporary rasters
terraPath-method | Specify paths for modules, inputs, outputs, and temporary rasters
terraPath<- | Specify paths for modules, inputs, outputs, and temporary rasters
terraPath<--method | Specify paths for modules, inputs, outputs, and temporary rasters
time.simList | Time usage in 'SpaDES'
time<- | Time usage in 'SpaDES'
time<--method | Time usage in 'SpaDES'
times | Time usage in 'SpaDES'
times-method | Time usage in 'SpaDES'
times<- | Time usage in 'SpaDES'
times<--method | Time usage in 'SpaDES'
timeunit | Time usage in 'SpaDES'
timeunit-method | Time usage in 'SpaDES'
timeunit<- | Time usage in 'SpaDES'
timeunit<--method | Time usage in 'SpaDES'
timeunits | Time usage in 'SpaDES'
timeunits-method | Time usage in 'SpaDES'

## -- U --

unmakeMemoisable.simList_ | Make 'simList' correctly work with 'memoise'
unzipSimList | Load a saved 'simList' and ancillary files
updateList | Update elements of a named list with elements of a second named list
use_gha | Use GitHub actions for automated module checking

## -- W --

writeEventInfo | Write simulation event info to file
writeRNGInfo | Write RNG state info to file

## -- Z --

zipModule | Create a zip archive of a module subdirectory
zipModule-method | Create a zip archive of a module subdirectory
zipSimList | Zip a 'simList' and various files

## -- misc --

.addChangedAttr-method | '.addChangedAttr' for 'simList' objects
.addTagsToOutput-method | '.addTagsToOutput' for 'simList' objects
.cacheMessage-method | '.cacheMessage' for 'simList' objects
.checkCacheRepo-method | '.checkCacheRepo' for 'simList' objects
.checkpointSave | Simulation checkpoints
.fileExtensions | File extensions map
.findSimList | Find 'simList' in a nested list
.first | Event priority
.guessPkgFun | Guess package of a function
.highest | Event priority
.last | Event priority
.lowest | Event priority
.normal | Event priority
.parseElems-method | '.parseElems' for 'simList' class objects
.preDigestByClass-method | Pre-digesting method for 'simList'
.prepareOutput-method | '.prepareOutput' for 'simList' objects
.quickCheck | The 'SpaDES.core' variable to switch between quick and robust checking
.rndstr | Generate random strings
.robustDigest-method | '.robustDigest' for 'simList' objects
.saveFileExtensions | File extensions map
.spadesTimes | Convert time units
.tagsByClass-method | '.tagsByClass' for 'simList' objects
.unwrap..moduleDeps | Methods for '.wrap' and '.unwrap'
.unwrap..simDeps | Methods for '.wrap' and '.unwrap'
.unwrap.simList | Methods for '.wrap' and '.unwrap'
.wrap..moduleDeps | Methods for '.wrap' and '.unwrap'
.wrap..simDeps | Methods for '.wrap' and '.unwrap'
.wrap.simList | Methods for '.wrap' and '.unwrap'
[-method | Extract an intact 'simList' but with subset of objects