Core Utilities for Developing and Running Spatially Explicit Discrete Event Models

Documentation for package ‘SpaDES.core’ version 2.0.5

Help Pages

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

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	Add a module to a 'moduleList'
append_attr-method	Add a module to a 'moduleList'

-- 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
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
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
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
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 code file
newModuleCode-method	Create new module code file
newModuleDocumentation	Create new module documentation
newModuleDocumentation-method	Create new module documentation
newModuleTests	Create template testing structures for new modules
newModuleTests-method	Create template testing structures for new modules
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

-- O --

objectDiagram	Simulation object dependency diagram
objectDiagram-method	Simulation object dependency diagram
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
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
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
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
simInitAndExperiment	Zip a 'simList' and various files
simInitAndSpades	Call 'simInit' and 'spades' together
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	Run a spatial discrete event simulation
spades-method	Run a spatial discrete event simulation
SpaDES.core	Categorized overview of the 'SpaDES.core' package
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
.robustDigest-method	'.robustDigest' for 'simList' objects
.saveFileExtensions	File extensions map
.spadesTimes	Convert time units
.tagsByClass-method	'.tagsByClass' for 'simList' objects
.unwrap.simList	Methods for '.wrap' and '.unwrap'
.wrap.simList	Methods for '.wrap' and '.unwrap'
[-method	Extract an intact 'simList' but with subset of objects