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


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Documentation for package ‘SpaDES.core’ version 0.2.5

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

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

-- A --

all.equal.simList All equal method for simLists
append_attr Add a module to a 'moduleList'
append_attr-method Add a module to a 'moduleList'

-- C --

Cache '.robustDigest' for 'simList' objects
cachePath Specify paths for modules, inputs, and outputs
cachePath-method Specify paths for modules, inputs, and outputs
cachePath<- Specify paths for modules, inputs, and outputs
cachePath<--method Specify paths for modules, inputs, and outputs
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 params passed to simulation.
checkParams-method Check use and existence of params 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 Metadata accessors
citation-method Metadata accessors
classFilter Filter objects by class
classFilter-method Filter objects by class
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
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, and outputs
dataPath-method Specify paths for modules, inputs, and outputs
dday SpaDES time units
defineModule Define a new module.
defineModule-method Define a new module.
defineParameter Define a parameter used in a module
defineParameter-method 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
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 Run an experiment using 'spades'
experiment-method Run an experiment using 'spades'
extractURL Extract a url from module metadata
extractURL-method Extract a url from module metadata

-- F --

fileName Extract filename (without extension) of a file

-- G --

G Get and set simulation globals.
G-method Get and set simulation globals.
G<- Get and set simulation globals.
G<--method Get and set simulation globals.
getModuleVersion Find the latest module version from a SpaDES module repository
getModuleVersion-method Find the latest module version from a SpaDES module repository
globals Get and set simulation globals.
globals-method Get and set simulation globals.
globals<- Get and set simulation globals.
globals<--method Get and set simulation globals.

-- I --

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

-- L --

loadFiles File extensions map
loadFiles-method File extensions map
loadPackages Load packages.
loadPackages-method Load packages.

-- 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
minTimeunit Determine the smallest timeunit in a simulation
minTimeunit-method Determine the smallest timeunit in a simulation
moduleCoverage Calculate module coverage of unit tests
moduleCoverage-method 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
moduleMetadata Parse and extract module metadata
moduleMetadata-method Parse and extract module metadata
modulePath Specify paths for modules, inputs, and outputs
modulePath-method Specify paths for modules, inputs, and outputs
modulePath<- Specify paths for modules, inputs, and outputs
modulePath<--method Specify paths for modules, inputs, and outputs
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

-- 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 Inputs and outputs
outputArgs-method Inputs and outputs
outputArgs<- Inputs and outputs
outputArgs<--method Inputs and outputs
outputObjects Metadata accessors
outputObjects-method Metadata accessors
outputPath Specify paths for modules, inputs, and outputs
outputPath-method Specify paths for modules, inputs, and outputs
outputPath<- Specify paths for modules, inputs, and outputs
outputPath<--method Specify paths for modules, inputs, and outputs
outputs Inputs and outputs
outputs-method Inputs and outputs
outputs<- Inputs and outputs
outputs<--method Inputs and outputs

-- P --

P Get and set simulation parameters.
packages Get module or simulation package dependencies
packages-method Get module or simulation package dependencies
paddedFloatToChar Convert numeric to character with padding
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, and outputs
paths-method Specify paths for modules, inputs, and outputs
paths<- Specify paths for modules, inputs, and outputs
paths<--method Specify paths for modules, inputs, and outputs
Plot-method Plot method for 'simList' objects
POM Use Pattern Oriented Modeling to fit unknown parameters
POM-method Use Pattern Oriented Modeling to fit unknown parameters
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 --

rasterToMemory Read raster to memory
rasterToMemory-method Read raster to memory
remoteFileSize Determine the size of a remotely hosted file
reqdPkgs Metadata accessors
reqdPkgs-method Metadata accessors
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'
saveSimList File extensions map
scheduleConditionalEvent Schedule a conditional simulation event
scheduleEvent Schedule a simulation event
setProgressBar Progress bar
show-method Show an Object
simInit Initialize a new simulation
simInit-method Initialize a new simulation
simInitAndExperiment Call 'simInit' and 'spades' or 'experiment' together
simInitAndSpades Call 'simInit' and 'spades' or 'experiment' together
simList The 'simList' class
simList-accessors-envir Simulation environment
simList-accessors-events Simulation event lists
simList-accessors-inout Inputs and outputs
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, and outputs
simList-accessors-times Time usage in 'SpaDES'
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
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 --

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'
updateList Update elements of a named list with elements of a second named list
updateList-method Update elements of a named list with elements of a second named list

-- Z --

zipModule Create a zip archive of a module subdirectory
zipModule-method Create a zip archive of a module subdirectory

-- 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
.highest Event priority
.last Event priority
.lowest Event priority
.normal Event priority
.objSizeInclEnviros-method '.objSizeInclEnviros' for 'simList' objects
.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