Develop and Run Spatially Explicit Discrete Event Simulation Models

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Documentation for package ‘SpaDES’ version 1.3.1

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

SpaDES-package Categorized overview of the 'SpaDES' package
spades-package Categorized overview of the 'SpaDES' package

-- A --

addin_newModule Rstudio addin to create a new module
adj Fast 'adjacent' function, and Just In Time compiled version
adj.raw Fast 'adjacent' function, and Just In Time compiled version
agentLocation 'SELES' - Agent Location at initiation
append_attr Add a module to a 'moduleList'
append_attr-method Add a module to a 'moduleList'

-- C --

cache Cache method for simList class objects
cache-method Cache method for simList class 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
changeObjEnv Copy or move objects from one environment to another
changeObjEnv-method Copy or move objects from one environment to another
checkModule Check for the existence of a remote module
checkModule-method Check for the existence of a remote module
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.
checkPath Check filepath.
checkPath-method Check filepath.
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 checksums for a module's data files
checksums-method Calculate checksums for a module's data files
checkTimeunit Convert time units
checkTimeunit-method Convert time units
cir Identify pixels in a circle or ring (donut) around an object.
cir-method Identify pixels in a circle or ring (donut) around an object.
classFilter Filter objects by class
classFilter-method Filter objects by class
clearCache Cache method for simList class objects
clearCache-method Cache method for simList class objects
clearPlot Clear plotting device
clearPlot-method Clear plotting device
clearStubArtifacts Clear erroneous archivist artifacts
clearStubArtifacts-method Clear erroneous archivist artifacts
clickCoordinates Mouse interactions with Plots
clickExtent Mouse interactions with Plots
clickValues Mouse interactions with Plots
completed Simulation event lists
completed-method Simulation event lists
completed<- Simulation event lists
completed<--method Simulation event lists
convertTimeunit Convert time units
convertTimeunit-method Convert time units
copy Copy a simList object
copy-method Copy a simList object
createsOutput Define an output object of a module
createsOutput-method Define an output object of a module
crw Move
crw-method Move
current Simulation event lists
current-method Simulation event lists
current<- Simulation event lists
current<--method Simulation event lists

-- D --

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
dev Specify where to plot
dhour SpaDES time units
directionFromEachPoint Calculate distances and directions between many points and many grid cells
distanceFromEachPoint Calculate distances and directions between many points and many grid cells
divergentColors Divergent colour palette
divergentColors-method Divergent colour palette
divergentColours Divergent colour palette
dmonth SpaDES time units
dmonths SpaDES time units
dmonths-method SpaDES time units
dNA SpaDES time units
dNA-method SpaDES time units
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
dwrpnorm2 Vectorized wrapped normal density function
dyear SpaDES time units
dyears SpaDES time units
dyears-method SpaDES time units

-- E --

end Time usage in 'SpaDES'
end-method 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
equalExtent Assess whether a list of extents are all equal
equalExtent-method Assess whether a list of extents are all equal
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'

-- F --

fileExt Extract the file extension of a file
fileName Extract filename (without extension) of a file
findObjects Find objects if passed as character strings

-- G --

gaussMap Produce a 'raster' of a random Gaussian process.
getColors Get colours for plotting Raster* objects.
getColors-method Get colours for plotting Raster* objects.
getColours Get colours for plotting Raster* objects.
getFileName Get the name of a 'source'-ed file
getFileName-method Get the name of a 'source'-ed file
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.
gpar Importing some grid functions
gpar-method Importing some grid functions

-- H --

heading Heading between spatial points.
heading-method Heading between spatial points.

-- I --

initialize-method Generate a 'simList' object
initiateAgents 'SELES' - Initiate agents
initiateAgents-method 'SELES' - Initiate agents
inputArgs Inputs and outputs
inputArgs-method Inputs and outputs
inputArgs<- Inputs and outputs
inputArgs<--method Inputs and outputs
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
inRange Test whether a number lies within range '[a,b]'
inSeconds Convert time units
inSeconds-method Convert time units

-- L --

layerNames Extract the layer names of Spatial Objects
layerNames-method Extract the layer names of Spatial Objects
loadFiles File extensions map
loadFiles-method File extensions map
loadPackages Load packages.
loadPackages-method Load packages.
ls-method List simulation objects
ls.simList List simulation objects
ls.str-method List simulation objects and their structure
ls.str.simList List simulation objects and their structure

-- M --

makeLines Make 'SpatialLines' object from two 'SpatialPoints' objects
makeLines-method Make 'SpatialLines' object from two 'SpatialPoints' objects
maxTimeunit Determine the largest timestep unit in a simulation
maxTimeunit-method Determine the largest timestep unit in a simulation
mergeRaster Merge split raster tiles into a single raster layer.
mergeRaster-method Merge split raster tiles into a single raster layer.
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
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
move Move

-- 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
newPlot Open a new plotting window
newProgressBar Progress bar
normPath Normalize filepath
normPath-method Normalize filepath
numAgents SELES - Number of Agents to initiate
numLayers Find the number of layers in a Spatial Object
numLayers-method Find the number of layers in a Spatial Object

-- O --

objectDiagram Simulation object dependency diagram
objectDiagram-method Simulation object dependency diagram
objects-method List simulation objects
objects.simList List simulation objects
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
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
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.
p Get and set simulation parameters.
P-method Get and set simulation parameters.
packages Get simulation package dependencies
packages-method Get 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.
patchSize Patch size
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 Plot: Fast, optimally arranged, multipanel plotting function with SpaDES
Plot-method Plot: Fast, optimally arranged, multipanel plotting function with SpaDES
pointDistance Calculate distances and directions between many points and many grid cells
POM Use Pattern Oriented Modeling to fit unknown parameters
POM-method Use Pattern Oriented Modeling to fit unknown parameters
priority Event priority
probInit 'SELES' - Probability of Initiation
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 --

randomPolygons randomPolygons
rasterizeReduced Convert reduced representation to full raster
rasterToMemory Read raster to memory
rasterToMemory-method Read raster to memory
rePlot Plot: Fast, optimally arranged, multipanel plotting function with SpaDES
rings Identifies all cells within a ring around the focal cells
rings-method Identifies all cells within a ring around the focal cells
rndstr Generate random strings
rndstr-method Generate random strings

-- S --

saveFiles Save objects using '.saveObjects' in 'params' slot of 'simInit'
scheduleEvent Schedule a simulation event
scheduleEvent-method Schedule a simulation event
setColors Set colours for plotting Raster* objects.
setColors-method Set colours for plotting Raster* objects.
setColors<- Set colours for plotting Raster* objects.
setColors<--method Set colours for plotting Raster* objects.
setColours Set colours for plotting Raster* objects.
shine Display a simple, interactive shiny app of the simList
shine-method Display a simple, interactive shiny app of the simList
show-method Show an Object
showCache Cache method for simList class objects
showCache-method Cache method for simList class objects
simInit Initialize a new simulation
simInit-method Initialize a new simulation
simList The 'simList' class
simList-accessors-envir Simulation environment
simList-accessors-events Simulation event lists
simList-accessors-inout Inputs and outputs
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 Categorized overview of the 'SpaDES' package
spades Run a spatial discrete event simulation
spades-method Run a spatial discrete event simulation
spadesClasses Classes defined in SpaDES
spadesMaps Dummy maps included with 'SpaDES'
spadesTimes Convert time units
spatialObjects The 'spatialObjects' class
spatialObjects-class The 'spatialObjects' class
specificNumPerPatch Initiate a specific number of agents in a map of patches
splitRaster Split a RasterLayer into multiple tiles
splitRaster-method Split a RasterLayer into multiple tiles
spokes Identify outward radiating spokes from initial points
spokes-method Identify outward radiating spokes from initial points
spread Simulate a spread process on a landscape.
spread-method Simulate a spread process on a landscape.
start Time usage in 'SpaDES'
start-method Time usage in 'SpaDES'
start<- Time usage in 'SpaDES'
start<--method Time usage in 'SpaDES'

-- T --

time Time usage in 'SpaDES'
time-method 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'
transitions 'SELES' - Transitioning to next time step

-- U --

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

-- V --

versionWarning Compare module version against SpaDES package version and warn if incompatible
versionWarning-method Compare module version against SpaDES package version and warn if incompatible

-- W --

wrap Wrap coordinates or pixels in a torus-like fashion
wrap-method Wrap coordinates or pixels in a torus-like fashion

-- Z --

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

-- misc --

$ Extract or replace an object from the simulation environment
$-method Extract or replace an object from the simulation environment
$<- Extract or replace an object from the simulation environment
$<--method Extract or replace an object from the simulation environment
.arrangement The '.arrangement' class
.arrangement-class The '.arrangement' class
.checkpointSave Simulation checkpoints.
.clickCoord Mouse interactions with Plots
.fileEdit Open a file for editing
.fileExtensions File extensions map
.fillInputRows An internal function for coercing a data.frame to inputs()
.fillOutputRows An internal function for coercing a data.frame to inputs()
.findObjects Find objects if passed as character strings
.first Event priority
.highest Event priority
.last Event priority
.lowest Event priority
.makeSpadesPlot Make a '.spadesPlot' class object
.makeSpadesPlot-method Make a '.spadesPlot' class object
.makeViewports Make viewports
.moduleDeps The '.moduleDeps' class
.moduleDeps-class The '.moduleDeps' class
.normal Event priority
.pointDirection Calculate distances and directions between many points and many grid cells
.pointDistance Calculate distances and directions between many points and many grid cells
.saveFileExtensions File extensions map
.simDeps The '.simDeps' class
.simDeps-class The '.simDeps' class
.simList The 'simList' class
.simList-class The 'simList' class
.spadesEnv The SpaDES environment
.spadesGrob The '.spadesGrob' class
.spadesGrob-class The '.spadesGrob' class
.spadesPlot The '.spadesPlot' class
.spadesPlot-class The '.spadesPlot' class
.spadesPlotObjects The '.spadesPlotObjects' class
.spadesPlotObjects-class The '.spadesPlotObjects' class
.spadesPlottables The '.spadesPlottables' class
.spadesPlottables-class The '.spadesPlottables' class
.spadesTimes Convert time units
.updateSpadesPlot Merge two SpaDES Plot objects
.updateSpadesPlot-method Merge two SpaDES Plot objects
[[ Extract or replace an object from the simulation environment
[[-method Extract or replace an object from the simulation environment
[[<- Extract or replace an object from the simulation environment
[[<--method Extract or replace an object from the simulation environment