# Develop and Run Spatially Explicit Discrete Event Simulation Models

## Documentation for package ‘SpaDES’ version 1.3.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

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