SpaDES: Develop and Run Spatially Explicit Discrete Event Simulation Models
Version 1.3.1

Implement a variety of event-based models, with a focus on spatially explicit models. These include raster-based, event-based, and agent-based models. The core simulation components are built upon a discrete event simulation (DES) framework that facilitates modularity, and easily enables the user to include additional functionality by running user-built simulation modules. Included are numerous tools to visualize raster and other maps. The suggested package 'fastshp' can be installed with `install.packages("fastshp", repos = "http://rforge.net", type = "source")`.

Browse man pages Browse package API and functions Browse package files

AuthorAlex M Chubaty [aut, cre], Eliot J B McIntire [aut], Yong Luo [ctb], Steve Cumming [ctb], Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Date of publication2016-10-07 18:42:54
MaintainerAlex M Chubaty <alexander.chubaty@canada.ca>
LicenseGPL-3
Version1.3.1
URL http://spades.predictiveecology.org https://github.com/PredictiveEcology/ SpaDES
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SpaDES")

Man pages

addDepends: Add simulation dependencies
addin_newModule: Rstudio addin to create a new module
adj: Fast 'adjacent' function, and Just In Time compiled version
append_attr: Add a module to a 'moduleList'
arrangement-class: The '.arrangement' class
arrangeViewports: Determine optimal plotting arrangement of plot objects
assignSpaDES: Assign to the internal SpaDES environment.
cache: Cache method for simList class objects
changeObjEnv: Copy or move objects from one environment to another
checkModule: Check for the existence of a remote module
checkObject: Check for existence of object(s) referenced by a 'objects'...
checkParams: Check use and existence of params passed to simulation.
checkPath: Check filepath.
checkpoint: Simulation checkpoints.
checksums: Calculate checksums for a module's data files
cir: Identify pixels in a circle or ring (donut) around an object.
classFilter: Filter objects by class
clearPlot: Clear plotting device
clearStubArtifacts: Clear erroneous archivist artifacts
copy: Copy a simList object
createsOutput: Define an output object of a module
crw: Move
defineModule: Define a new module.
defineParameter: Define a parameter used in a module
depsEdgeList: Build edge list for module dependency graph
depsGraph: Build a module dependency graph
depsLoadOrder: Determine module load order
depsPruneEdges: Prune edges to remove cycles in module dependencies
dev: Specify where to plot
digest: Calculate the hashes of multiple files
directions: Calculate distances and directions between many points and...
distances: Calculate distances and directions between many points and...
divergentColors: Divergent colour palette
doEvent: Process a simulation event
downloadData: Download module data
downloadModule: Download a module from a SpaDES module GitHub repository
dwrpnorm2: Vectorized wrapped normal density function
emptyEventList: Blank (template) event list
emptyMetadata: Default (empty) metadata
equalExtent: Assess whether a list of extents are all equal
eventDiagram: Simulation event diagram
existsSpaDES: Is an object defined in the .spades environment?
expectsInput: Define an input object that the module expects.
experiment: Run an experiment using 'spades'
fileEdit: Open a file for editing
fileExt: Extract the file extension of a file
fileName: Extract filename (without extension) of a file
fileTable: Create empty fileTable for inputs and outputs
fillInputRows: An internal function for coercing a data.frame to inputs()
fillOutputRows: An internal function for coercing a data.frame to inputs()
findFactors: Find factors
findObjects: Find objects if passed as character strings
ganttStatus: ganttStatus
gaussmap: Produce a 'raster' of a random Gaussian process.
getColors: Get colours for plotting Raster* objects.
getFileName: Get the name of a 'source'-ed file
getModuleVersion: Find the latest module version from a SpaDES module...
getSpaDES: Get objects from the internal SpaDES environment
globals: Get and set simulation globals.
grid-functions: Importing some grid functions
heading: Heading between spatial points.
identifyGrobToPlot: Identify where to get the grob from
initialize-method: Generate a 'simList' object
initiateAgents: 'SELES' - Initiate agents
inputObjects: Create an empty (template) inputObjects and outputObjects...
inRange: Test whether a number lies within range '[a,b]'
layerNames: Extract the layer names of Spatial Objects
loadFiles: File extensions map
loadPackages: Load packages.
ls-method: List simulation objects
ls_str-method: List simulation objects and their structure
makeColorMatrix: Convert Raster to color matrix useable by raster function for...
makeDigestible: Remove any reference to environments in a 'simList'
makeLayout: Make an optimal layout of plots
makeLines: Make 'SpatialLines' object from two 'SpatialPoints' objects
makeList: Convert 'plotArgs' to list of lists
makeSpadesPlot: Make a '.spadesPlot' class object
makeViewports: Make viewports
maxTimeunit: Determine the largest timestep unit in a simulation
mergeRaster: Merge split raster tiles into a single raster layer.
minTimeunit: Determine the smallest timeunit in a simulation
moduleCoverage: Calculate module coverage of unit tests
moduleDeps-class: The '.moduleDeps' class
moduleDiagram: Simulation module dependency diagram
moduleGraph: Build a module dependency graph
moduleMetadata: Parse and extract module metadata
namespacing: Namespacing within SpaDES
newModule: Create new module from template.
newModuleCode: Create new module code file
newModuleDocumentation: Create new module documentation
newModuleTests: Create template testing structures for new modules
newPlot: Open a new plotting window
newProgressBar: Progress bar
normPath: Normalize filepath
numLayers: Find the number of layers in a Spatial Object
objectDiagram: Simulation object dependency diagram
objectNames: Extracts the object names
objects: Extract or replace an object from the simulation environment
openModules: Open all modules nested within a base directory
packages: Get simulation package dependencies
paddedFloatToChar: Convert numeric to character with padding
params: Get and set simulation parameters.
parseArgs: Parse arguments and find environments
parseModule: Parse and initialize a module
patchSize: Patch size
paths: Default paths to use for a simulation
Plot: Plot: Fast, optimally arranged, multipanel plotting function...
plotGrob: Plot spatial grobs (using 'grid' package)
Plot-internal: Internal functions used by Plot
POM: Use Pattern Oriented Modeling to fit unknown parameters
prepareRaster: Prepare raster for plotting
priority: Event priority
progress: Get and set simulation progress bar details
randomPolygons: randomPolygons
rasterizeReduce: Convert reduced representation to full raster
rasterToMemory: Read raster to memory
rings: Identifies all cells within a ring around the focal cells
rndstr: Generate random strings
saveFiles: Save objects using '.saveObjects' in 'params' slot of...
scheduleEvent: Schedule a simulation event
SELESagentLocation: 'SELES' - Agent Location at initiation
SELESnumAgents: SELES - Number of Agents to initiate
SELESprobInit: 'SELES' - Probability of Initiation
SELEStransitions: 'SELES' - Transitioning to next time step
setColors: Set colours for plotting Raster* objects.
shine: Display a simple, interactive shiny app of the simList
show-method: Show an Object
sim2gantt: sim2gantt
simDeps-class: The '.simDeps' class
simInit: Initialize a new simulation
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-paths: Specify paths for modules, inputs, and outputs
simList-accessors-times: Time usage in 'SpaDES'
simList_-class: The 'simList_' class
simList-class: The 'simList' class
sortDotsFirst: Sort a any named object with dotted names first
spades: Run a spatial discrete event simulation
spades-classes: Classes defined in SpaDES
spadesEnv: The SpaDES environment
spadesGrob-class: The '.spadesGrob' class
spadesMaps: Dummy maps included with 'SpaDES'
spadesMouseClicks: Mouse interactions with Plots
SpaDES-package: Categorized overview of the 'SpaDES' package
spadesPlot-class: The '.spadesPlot' class
spadesPlotObjects-class: The '.spadesPlotObjects' class
spadesPlottables-class: The '.spadesPlottables' class
spadesTime: SpaDES time units
spatialObjects-class: The 'spatialObjects' class
specnumperpatch-probs: Initiate a specific number of agents in a map of patches
splitRaster: Split a RasterLayer into multiple tiles
spokes: Identify outward radiating spokes from initial points
spread: Simulate a spread process on a landscape.
timeConversion: Convert time units
unittrim: Convert 'grid.locator' units
unparsed: Determine which modules in a list are unparsed
updateList: Update elements of a named list with elements of a second...
updateSpadesPlot: Merge two SpaDES Plot objects
versionWarning: Compare module version against SpaDES package version and...
wrap: Wrap coordinates or pixels in a torus-like fashion
zipModule: Create a zip archive of a module subdirectory

Functions

# Man page
$ Man page
$,simList-method Man page
$<- Man page
$<-,simList-method Man page
.Plot Man page
.Plot,.spadesGrob-method Man page
.addDepends Man page
.addDepends,.simList,.moduleDeps-method Man page
.arrangeViewports Man page
.arrangeViewports,.spadesPlot-method Man page
.arrangement Man page
.arrangement-class Man page
.assignSpaDES Man page
.assignSpaDES,character,ANY-method Man page
.assignSpaDES,character,missing-method Man page
.callingFrameTimeunit Man page
.callingFrameTimeunit,.simList-method Man page
.callingFrameTimeunit,NULL-method Man page
.callingModuleName Man page
.callingModuleName,.simList-method Man page
.checkpointSave Man page
.clickCoord Man page
.convertSpatialToPlotGrob Man page
.convertSpatialToPlotGrob,spatialObjects,.spadesGrob-method Man page
.depsLoadOrder Man page
.depsLoadOrder,simList,igraph-method Man page
.depsPruneEdges Man page
.depsPruneEdges,data.table-method Man page
.emptyEventList Man page
.emptyEventList,missing,missing,missing,missing-method Man page
.emptyEventList,numeric,character,character,numeric-method Man page
.emptyEventListCols Man page
.emptyEventListDT Man page
.emptyEventListNA Man page
.emptyEventListObj Man page
.emptyMetadata Man page
.emptyMetadata,missing-method Man page
.existsSpaDES Man page
.existsSpaDES,ANY-method Man page
.fileEdit Man page
.fileExtensions Man page
.fileTableIn Man page
.fileTableIn,missing-method Man page
.fileTableInCols Man page
.fileTableOut Man page
.fileTableOut,missing-method Man page
.fileTableOutCols Man page
.fillInputRows Man page
.fillOutputRows Man page
.findFactors Man page
.findObjects Man page
.first Man page
.getSpaDES Man page
.getSpaDES,ANY-method Man page
.highest Man page
.identifyGrobToPlot Man page
.identifyGrobToPlot,.spadesGrob,list-method Man page
.inputObjects Man page
.inputObjects,missing-method Man page
.last Man page
.lowest Man page
.makeColorMatrix Man page
.makeColorMatrix,Raster,Extent,numeric-method Man page
.makeLayout Man page
.makeList Man page
.makeList,list-method Man page
.makeSpadesPlot Man page
.makeSpadesPlot,list,list-method Man page
.makeSpadesPlot,list,missing-method Man page
.makeSpadesPlot,missing,missing-method Man page
.makeViewports Man page
.moduleDeps Man page
.moduleDeps-class Man page
.normal Man page
.outputObjects Man page
.outputObjects,missing-method Man page
.parseArgs Man page
.parseModule Man page
.parseModule,simList,list-method Man page
.parseModulePartial Man page
.parseModulePartial,missing,missing,character,character-method Man page
.parseModulePartial,simList,list,missing,character-method Man page
.paths Man page
.plotGrob Man page
.plotGrob,SpatialLines-method Man page
.plotGrob,SpatialPoints-method Man page
.plotGrob,SpatialPolygons-method Man page
.plotGrob,matrix-method Man page
.pointDirection Man page
.pointDistance Man page
.prepareRaster Man page
.refreshGrob Man page
.refreshGrob,.spadesGrob-method Man page
.saveFileExtensions Man page
.sim2gantt Man page
.sim2gantt,simList,numeric,character,numeric-method Man page
.simDeps Man page
.simDeps-class Man page
.simList Man page
.simList-class Man page
.singleEventListDT Man page
.spadesEnv Man page
.spadesGrob Man page
.spadesGrob-class Man page
.spadesPlot Man page
.spadesPlot-class Man page
.spadesPlotObjects Man page
.spadesPlotObjects-class Man page
.spadesPlottables Man page
.spadesPlottables-class Man page
.spadesTimes Man page
.unittrim Man page
.unparsed Man page
.unparsed,list-method Man page
.updateGrobGPTextAxis Man page
.updateGrobGPTextAxis,.spadesGrob-method Man page
.updateSpadesPlot Man page
.updateSpadesPlot,.spadesPlot,list-method Man page
.updateSpadesPlot,.spadesPlot,missing-method Man page
.xyAxes Man page
.xyAxes,.spadesGrob,.arrangement-method Man page
@importClassesFrom Man page
NetLogoRClasses Man page
P Man page
P,.simList-method Man page
POM Man page
POM,simList,character-method Man page
Plot Man page
Plot,ANY-method Man page
Plot,simList-method Man page
PlotHelpers Man page
SpaDES Man page
SpaDES-package Man page
[[ Man page
[[,simList,ANY,ANY-method Man page
[[<- Man page
[[<-,simList,ANY,ANY,ANY-method Man page
addin_newModule Man page Source code
adj Man page
adj.raw Man page Source code
agentLocation Man page Source code
append_attr Man page
append_attr,list,list-method Man page
cache Man page
cache,ANY-method Man page
cachePath Man page
cachePath,.simList-method Man page
cachePath<- Man page
cachePath<-,.simList-method Man page
changeObjEnv Man page
changeObjEnv,character,environment,environment,logical-method Man page
changeObjEnv,character,environment,environment,missing-method Man page
changeObjEnv,character,environment,missing,logical-method Man page
changeObjEnv,character,environment,missing,missing-method Man page
changeObjEnv,character,missing,environment,logical-method Man page
changeObjEnv,character,missing,environment,missing-method Man page
changeObjEnv,list,ANY,ANY,ANY-method Man page
checkModule Man page
checkModule,character,character-method Man page
checkModule,character,missing-method Man page
checkObject Man page
checkObject,missing,ANY,missing,ANY-method Man page
checkObject,simList,character,missing,character-method Man page
checkObject,simList,character,missing,missing-method Man page
checkObject,simList,missing,ANY,missing-method Man page
checkObject,simList,missing,Raster,character-method Man page
checkParams Man page
checkParams,simList,list,list,character-method Man page
checkPath Man page
checkPath,NULL,ANY-method Man page
checkPath,character,logical-method Man page
checkPath,character,missing-method Man page
checkPath,missing,ANY-method Man page
checkTimeunit Man page
checkTimeunit,character,environment-method Man page
checkTimeunit,character,missing-method Man page
checkpointFile Man page
checkpointFile,.simList-method Man page
checkpointFile<- Man page
checkpointFile<-,.simList-method Man page
checkpointInterval Man page
checkpointInterval,.simList-method Man page
checkpointInterval<- Man page
checkpointInterval<-,.simList-method Man page
checkpointLoad Man page Source code
checkpointSave Source code
checksums Man page
checksums,character,character,logical-method Man page
checksums,character,character,missing-method Man page
cir Man page
cir,RasterLayer,SpatialPoints,missing-method Man page
cir,RasterLayer,matrix,missing-method Man page
cir,RasterLayer,missing,missing-method Man page
cir,RasterLayer,missing,numeric-method Man page
classFilter Man page
classFilter,character,character,character,environment-method Man page
classFilter,character,character,character,missing-method Man page
classFilter,character,character,missing,environment-method Man page
classFilter,character,character,missing,missing-method Man page
clearCache Man page
clearCache,ANY-method Man page
clearPlot Man page
clearPlot,missing,logical-method Man page
clearPlot,missing,missing-method Man page
clearPlot,numeric,logical-method Man page
clearPlot,numeric,missing-method Man page
clearStubArtifacts Man page
clearStubArtifacts,ANY-method Man page
clickCoord Source code
clickCoordinates Man page Source code
clickExtent Man page Source code
clickValues Man page Source code
completed Man page
completed,.simList,character-method Man page
completed,.simList,missing-method Man page
completed<- Man page
completed<-,.simList-method Man page
convertTimeunit Man page
convertTimeunit,numeric,character,environment-method Man page
convertTimeunit,numeric,character,missing-method Man page
convertTimeunit,numeric,missing,missing-method Man page
copy Man page
copy,simList,logical-method Man page
copy,simList,missing-method Man page
createsOutput Man page
createsOutput,ANY,ANY,ANY-method Man page
createsOutput,character,character,character-method Man page
crw Man page
crw,SpatialPoints-method Man page
crw,SpatialPointsDataFrame-method Man page
current Man page
current,.simList,character-method Man page
current,.simList,missing-method Man page
current<- Man page
current<-,.simList-method Man page
currentModule Man page
currentModule,.simList-method Man page
dNA Man page
dNA,ANY-method Man page
dday Man page Source code
defineModule Man page
defineModule,.simList,list-method Man page
defineParameter Man page
defineParameter,character,character,ANY,ANY,ANY,character-method Man page
defineParameter,character,character,ANY,missing,missing,characte Man page
defineParameter,missing,missing,missing,missing,missing,missing- Man page
depends Man page
depends,.simList-method Man page
depends<- Man page
depends<-,.simList-method Man page
depsEdgeList Man page
depsEdgeList,simList,logical-method Man page
depsEdgeList,simList,missing-method Man page
depsGraph Man page
depsGraph,simList,logical-method Man page
depsGraph,simList,missing-method Man page
dev Man page Source code
dhour Man page Source code
digest Man page
digest,character-method Man page
directionFromEachPoint Man page Source code
distanceFromEachPoint Man page Source code
divergentColors Man page
divergentColors,character,character,numeric,numeric-method Man page
divergentColours Man page
dmonth Man page Source code
dmonths Man page
dmonths,numeric-method Man page
doEvent Man page
doEvent,simList,ANY-method Man page
doEvent,simList,missing-method Man page
doEvent.checkpoint Man page Source code
doEvent.load Source code
doEvent.progress Source code
doEvent.save Source code
downloadData Man page
downloadData,character,character,logical-method Man page
downloadData,character,character,missing-method Man page
downloadData,character,missing,logical-method Man page
downloadData,character,missing,missing-method Man page
downloadModule Man page
downloadModule,character,ANY,ANY,ANY,ANY,ANY-method Man page
downloadModule,character,character,character,character,logical,l Man page
downloadModule,character,missing,missing,missing,missing,missing Man page
dsecond Man page Source code
dweek Man page Source code
dweeks Man page
dweeks,numeric-method Man page
dwrpnorm2 Man page Source code
dyear Man page Source code
dyears Man page
dyears,numeric-method Man page
end Man page
end,.simList,character-method Man page
end,.simList,missing-method Man page
end<- Man page
end<-,.simList-method Man page
envir Man page
envir,simList-method Man page
envir<- Man page
envir<-,simList-method Man page
equalExtent Man page
equalExtent,list-method Man page
eventDiagram Man page
eventDiagram,simList,missing,character-method Man page
eventDiagram,simList,missing,missing-method Man page
eventDiagram,simList,numeric,character-method Man page
events Man page
events,.simList,character-method Man page
events,.simList,missing-method Man page
events<- Man page
events<-,.simList-method Man page
expectsInput Man page
expectsInput,ANY,ANY,ANY,ANY-method Man page
expectsInput,character,character,character,character-method Man page
expectsInput,character,character,character,missing-method Man page
experiment Man page
experiment,simList-method Man page
fileEdit Source code
fileExt Man page Source code
fileExtensions Source code
fileName Man page Source code
fillInputRows Source code
fillOutputRows Source code
findFactors Source code
findObjects Man page Source code
first Source code
ganttStatus Man page
ganttStatus,character-method Man page
gaussMap Man page Source code
getColors Man page
getColors,ANY-method Man page
getColors,Raster-method Man page
getColors,SpatialPoints-method Man page
getColours Man page
getFileName Man page
getFileName,logical-method Man page
getModuleVersion Man page
getModuleVersion,character,character-method Man page
getModuleVersion,character,missing-method Man page
globals Man page
globals,.simList-method Man page
globals<- Man page
globals<-,.simList-method Man page
gpar Man page
gpar,ANY-method Man page
griddedClasses Man page
heading Man page
heading,SpatialPoints,SpatialPoints-method Man page
heading,SpatialPoints,matrix-method Man page
heading,matrix,SpatialPoints-method Man page
heading,matrix,matrix-method Man page
highest Source code
inRange Man page Source code
inSeconds Man page
inSeconds,NULL,missing-method Man page
inSeconds,character,environment-method Man page
inSeconds,character,missing-method Man page
initialize,simList-method Man page
initiateAgents Man page
initiateAgents,Raster,missing,Raster,ANY,missing-method Man page
initiateAgents,Raster,missing,missing,ANY,missing-method Man page
initiateAgents,Raster,missing,missing,ANY,numeric-method Man page
initiateAgents,Raster,numeric,Raster,ANY,missing-method Man page
initiateAgents,Raster,numeric,missing,ANY,missing-method Man page
inputArgs Man page
inputArgs,.simList-method Man page
inputArgs<- Man page
inputArgs<-,.simList-method Man page
inputPath Man page
inputPath,.simList-method Man page
inputPath<- Man page
inputPath<-,.simList-method Man page
inputs Man page
inputs,.simList-method Man page
inputs<- Man page
inputs<-,.simList-method Man page
last Source code
layerNames Man page
layerNames,.spadesPlot-method Man page
layerNames,ANY-method Man page
layerNames,Raster-method Man page
layerNames,igraph-method Man page
layerNames,list-method Man page
loadFiles Man page
loadFiles,missing,ANY-method Man page
loadFiles,missing,missing-method Man page
loadFiles,simList,missing-method Man page
loadPackages Man page
loadPackages,NULL-method Man page
loadPackages,character-method Man page
loadPackages,list-method Man page
lowest Source code
ls,simList-method Man page
ls.simList Man page Source code
ls.str,missing,simList-method Man page
ls.str,simList,missing-method Man page
ls.str.simList Man page Source code
makeColourMatrix Man page
makeDigestible Man page
makeDigestible,simList-method Man page
makeLayout Source code
makeLines Man page
makeLines,SpatialPoints,SpatialPoints-method Man page
makeViewports Source code
matchedPointDirection Source code
maxTimeunit Man page
maxTimeunit,simList-method Man page
mergeRaster Man page
mergeRaster,list-method Man page
minTimeunit Man page
minTimeunit,list-method Man page
minTimeunit,simList-method Man page
moduleCoverage Man page
moduleCoverage,character,character-method Man page
moduleCoverage,character,missing-method Man page
moduleDiagram Man page
moduleDiagram,simList,character,logical-method Man page
moduleDiagram,simList,missing,ANY-method Man page
moduleGraph Man page
moduleGraph,simList,logical-method Man page
moduleGraph,simList,missing-method Man page
moduleMetadata Man page
moduleMetadata,ANY,missing,simList-method Man page
moduleMetadata,character,character,ANY-method Man page
moduleMetadata,character,missing,missing-method Man page
modulePath Man page
modulePath,.simList-method Man page
modulePath<- Man page
modulePath<-,.simList-method Man page
modules Man page
modules,.simList-method Man page
modules<- Man page
modules<-,.simList-method Man page
move Man page Source code
newModule Man page
newModule,character,character-method Man page
newModule,character,missing-method Man page
newModuleCode Man page
newModuleCode,character,character,logical,character,character-me Man page
newModuleDocumentation Man page
newModuleDocumentation,character,character,logical,character,cha Man page
newModuleDocumentation,character,character,missing,ANY,ANY-metho Man page
newModuleDocumentation,character,missing,logical,ANY,ANY-method Man page
newModuleDocumentation,character,missing,missing,ANY,ANY-method Man page
newModuleTests Man page
newModuleTests,character,character,logical-method Man page
newPlot Man page Source code
newProgressBar Man page Source code
normPath Man page
normPath,NULL-method Man page
normPath,character-method Man page
normPath,list-method Man page
normPath,missing-method Man page
normal Source code
numAgents Man page Source code
numLayers Man page
numLayers,.spadesPlot-method Man page
numLayers,ANY-method Man page
numLayers,Raster-method Man page
numLayers,Spatial-method Man page
numLayers,list-method Man page
objectDiagram Man page
objectDiagram,simList-method Man page
objectNames Man page Source code
objects,simList-method Man page
objects.simList Man page Source code
objs Man page
objs,simList-method Man page
objs<- Man page
objs<-,simList-method Man page
onAttach Source code
onLoad Source code
onUnload Source code
openModules Man page
openModules,character,character-method Man page
openModules,character,missing-method Man page
openModules,missing,character-method Man page
openModules,missing,missing-method Man page
openModules,simList,missing-method Man page
outputArgs Man page
outputArgs,.simList-method Man page
outputArgs<- Man page
outputArgs<-,.simList-method Man page
outputPath Man page
outputPath,.simList-method Man page
outputPath<- Man page
outputPath<-,.simList-method Man page
outputs Man page
outputs,.simList-method Man page
outputs<- Man page
outputs<-,.simList-method Man page
p Man page Source code
packages Man page
packages,.simList-method Man page
paddedFloatToChar Man page Source code
parameters Man page
parameters,.simList-method Man page
params Man page
params,.simList-method Man page
params<- Man page
params<-,.simList-method Man page
parseArgs Source code
patchSize Man page Source code
paths Man page Source code
paths,.simList-method Man page
paths<- Man page
paths<-,.simList-method Man page
pointDirection Source code
pointDistance Man page Source code
prepareRaster Source code
priority Man page
probInit Man page Source code
progressInterval Man page
progressInterval,.simList-method Man page
progressInterval<- Man page
progressInterval<-,.simList-method Man page
progressType Man page
progressType,.simList-method Man page
progressType<- Man page
progressType<-,.simList-method Man page
randomPolygons Man page Source code
rasterToMemory Man page
rasterToMemory,ANY-method Man page
rasterizeReduced Man page Source code
rePlot Man page Source code
rings Man page
rings,RasterLayer-method Man page
rndstr Man page
rndstr,missing,missing,logical-method Man page
rndstr,missing,missing,missing-method Man page
rndstr,missing,numeric,logical-method Man page
rndstr,missing,numeric,missing-method Man page
rndstr,numeric,missing,logical-method Man page
rndstr,numeric,missing,missing-method Man page
rndstr,numeric,numeric,logical-method Man page
rndstr,numeric,numeric,missing-method Man page
saveFileExtensions Source code
saveFiles Man page Source code
scheduleEvent Man page
scheduleEvent,simList,NULL,character,character,numeric-method Man page
scheduleEvent,simList,numeric,character,character,missing-method Man page
scheduleEvent,simList,numeric,character,character,numeric-method Man page
setColors Man page
setColors,RasterLayer,character,missing-method Man page
setColors,RasterLayer,character,numeric-method Man page
setColors<- Man page
setColors<-,Raster,missing,list-method Man page
setColors<-,RasterLayer,missing,character-method Man page
setColors<-,RasterLayer,numeric,character-method Man page
setColors<-,RasterStack,numeric,list-method Man page
setColours Man page
setProgressBar Source code
shine Man page
shine,simList-method Man page
show,simList-method Man page
showCache Man page
showCache,ANY-method Man page
simInit Man page
simInit,ANY,ANY,ANY,ANY,ANY,ANY,ANY,ANY-method Man page
simInit,ANY,ANY,ANY,character,ANY,ANY,ANY,ANY-method Man page
simInit,ANY,ANY,character,ANY,ANY,ANY,ANY,ANY-method Man page
simInit,list,list,list,list,list,data.frame,data.frame,character Man page
simList Man page
simList-accessors-envir Man page
simList-accessors-events Man page
simList-accessors-inout Man page
simList-accessors-modules Man page
simList-accessors-objects Man page
simList-accessors-params Man page
simList-accessors-paths Man page
simList-accessors-times Man page
simList-class Man page
simList_ Man page
simList_-class Man page
sortDotsFirst Man page Source code
spades Man page
spades,ANY,ANY,ANY,logical-method Man page
spades,simList,ANY,ANY,missing-method Man page
spades-package Man page
spadesClasses Man page
spadesMaps Man page
spadesTimes Man page Source code
spatialObjects Man page
spatialObjects-class Man page
specificNumPerPatch Man page Source code
splitRaster Man page
splitRaster,RasterLayer,integer,integer,missing,character-method Man page
splitRaster,RasterLayer,integer,integer,missing,missing-method Man page
splitRaster,RasterLayer,integer,integer,numeric,character-method Man page
splitRaster,RasterLayer,numeric,numeric,integer,character-method Man page
splitRaster,RasterLayer,numeric,numeric,integer,missing-method Man page
splitRaster,RasterLayer,numeric,numeric,missing,character-method Man page
splitRaster,RasterLayer,numeric,numeric,missing,missing-method Man page
splitRaster,RasterLayer,numeric,numeric,numeric,character-method Man page
splitRaster,RasterLayer,numeric,numeric,numeric,missing-method Man page
spokes Man page
spokes,RasterLayer,SpatialPoints,missing-method Man page
spread Man page
spread,RasterLayer-method Man page
start Man page
start,.simList,character-method Man page
start,.simList,missing-method Man page
start<- Man page
start<-,.simList-method Man page
time Man page
time,.simList,character-method Man page
time,.simList,missing-method Man page
time<- Man page
time<-,.simList-method Man page
times Man page
times,.simList-method Man page
times<- Man page
times<-,.simList-method Man page
timeunit Man page
timeunit,.simList-method Man page
timeunit<- Man page
timeunit<-,.simList-method Man page
timeunits Man page
timeunits,.simList-method Man page
transitions Man page Source code
unittrim Source code
updateList Man page
updateList,NULL,NULL-method Man page
updateList,NULL,list-method Man page
updateList,list,NULL-method Man page
updateList,list,list-method Man page
versionWarning Man page
versionWarning,character-method Man page
wrap Man page
wrap,SpatialPoints,ANY,missing-method Man page
wrap,SpatialPointsDataFrame,Extent,logical-method Man page
wrap,SpatialPointsDataFrame,Raster,logical-method Man page
wrap,SpatialPointsDataFrame,matrix,logical-method Man page
wrap,matrix,Extent,missing-method Man page
wrap,matrix,Raster,missing-method Man page
wrap,matrix,matrix,missing-method Man page
zipModule Man page
zipModule,character,character,character-method Man page
zipModule,character,character,missing-method Man page
zipModule,character,missing,character-method Man page
zipModule,character,missing,missing-method Man page

Files

inst
inst/examples
inst/examples/example_experiment.R
inst/examples/example_splitRaster.R
inst/examples/example_spokes.R
inst/examples/example_POM.R
inst/examples/example_cir.R
inst/sampleModules
inst/sampleModules/randomLandscapes
inst/sampleModules/randomLandscapes/randomLandscapes.R
inst/sampleModules/fireSpread
inst/sampleModules/fireSpread/fireSpread.R
inst/sampleModules/SpaDES_sampleModules
inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.R
inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.Rmd
inst/sampleModules/caribouMovement
inst/sampleModules/caribouMovement/caribouMovement.R
inst/maps
inst/maps/percentPine.tif
inst/maps/forestAge.tif
inst/maps/forestCover.tif
inst/maps/DEM.tif
inst/maps/habitatQuality.tif
inst/rstudio
inst/rstudio/addins.dcf
inst/figs
inst/figs/SpaDES-overview-diagram.png
inst/doc
inst/doc/ii-modules.R
inst/doc/ii-modules.html
inst/doc/iii-plotting.R
inst/doc/ii-modules.Rmd
inst/doc/iii-plotting.html
inst/doc/i-introduction.R
inst/doc/i-introduction.Rmd
inst/doc/i-introduction.html
inst/doc/iii-plotting.Rmd
tests
tests/testthat
tests/testthat/test-save.R
tests/testthat/Rplots.pdf
tests/testthat/test-adj.R
tests/testthat/test-module-deps-methods.R
tests/testthat/test-simList.R
tests/testthat/test-updateList.R
tests/testthat/test-spread.R
tests/testthat/test-experiment.R
tests/testthat/test-splitRaster.R
tests/testthat/test-examples.R
tests/testthat/test-cache.R
tests/testthat/test-paths.R
tests/testthat/test-mapReduce.R
tests/testthat/test-downloadModule.R
tests/testthat/test-simulation.R
tests/testthat/test-checkPath.R
tests/testthat/test-load.R
tests/testthat/test-Plot.R
tests/testthat/test-checkpoint.R
tests/testthat/test-inRange.R
tests/testthat/test-timeunits.R
tests/testthat/test-environment.R
tests/testthat/test-module-template.R
tests/test-all.R
NAMESPACE
demo
demo/spades-simulation.R
demo/00Index
NEWS
R
R/splitRaster.R
R/simList-accessors.R
R/spades-package.R
R/load.R
R/moduleMetadata.R
R/copy.R
R/misc-methods.R
R/plotting.R
R/helpers.R
R/moduleCoverage.R
R/plotting-classes.R
R/check.R
R/SELES.R
R/plotting-helpers.R
R/simList-class.R
R/plotting-colours.R
R/agent.R
R/mapReduce.R
R/initialize.R
R/checkpoint.R
R/environment.R
R/simulation.R
R/spades-classes.R
R/mergeRaster.R
R/progress.R
R/movement.R
R/experiment.R
R/cache.R
R/plotting-other.R
R/shine.R
R/module-repository.R
R/save.R
R/module-dependencies-class.R
R/neighbourhood.R
R/numerical-comparisons.R
R/plotting-diagrams.R
R/probability.R
R/POM.R
R/spread-process.R
R/zzz.R
R/module-template.R
R/module-dependencies-methods.R
R/rstudio-addins.R
R/times.R
R/priority.R
vignettes
vignettes/bibliography.bib
vignettes/ii-modules.Rmd
vignettes/i-introduction.Rmd
vignettes/iii-plotting.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/updateList.Rd
man/depsGraph.Rd
man/spadesPlotObjects-class.Rd
man/loadFiles.Rd
man/unittrim.Rd
man/paths.Rd
man/newModuleCode.Rd
man/SELESnumAgents.Rd
man/getColors.Rd
man/Plot-internal.Rd
man/shine.Rd
man/getSpaDES.Rd
man/parseModule.Rd
man/saveFiles.Rd
man/distances.Rd
man/params.Rd
man/findFactors.Rd
man/checkModule.Rd
man/specnumperpatch-probs.Rd
man/progress.Rd
man/rndstr.Rd
man/normPath.Rd
man/minTimeunit.Rd
man/grid-functions.Rd
man/newPlot.Rd
man/ganttStatus.Rd
man/updateSpadesPlot.Rd
man/identifyGrobToPlot.Rd
man/makeColorMatrix.Rd
man/patchSize.Rd
man/SELEStransitions.Rd
man/spadesMouseClicks.Rd
man/doEvent.Rd
man/simList-accessors-times.Rd
man/globals.Rd
man/equalExtent.Rd
man/prepareRaster.Rd
man/moduleMetadata.Rd
man/newModuleDocumentation.Rd
man/spadesPlottables-class.Rd
man/makeSpadesPlot.Rd
man/clearStubArtifacts.Rd
man/emptyEventList.Rd
man/checkpoint.Rd
man/fileEdit.Rd
man/getFileName.Rd
man/existsSpaDES.Rd
man/rasterizeReduce.Rd
man/simInit.Rd
man/checkObject.Rd
man/Plot.Rd
man/assignSpaDES.Rd
man/spokes.Rd
man/maxTimeunit.Rd
man/copy.Rd
man/classFilter.Rd
man/loadPackages.Rd
man/setColors.Rd
man/getModuleVersion.Rd
man/moduleDeps-class.Rd
man/depsLoadOrder.Rd
man/checkParams.Rd
man/eventDiagram.Rd
man/unparsed.Rd
man/newModule.Rd
man/simList-accessors-events.Rd
man/SpaDES-package.Rd
man/newProgressBar.Rd
man/SELESprobInit.Rd
man/fileExt.Rd
man/emptyMetadata.Rd
man/versionWarning.Rd
man/initiateAgents.Rd
man/simList-accessors-paths.Rd
man/ls-method.Rd
man/objects.Rd
man/sortDotsFirst.Rd
man/inRange.Rd
man/dev.Rd
man/createsOutput.Rd
man/makeList.Rd
man/depsPruneEdges.Rd
man/splitRaster.Rd
man/show-method.Rd
man/arrangeViewports.Rd
man/rasterToMemory.Rd
man/namespacing.Rd
man/simList-accessors-envir.Rd
man/sim2gantt.Rd
man/zipModule.Rd
man/expectsInput.Rd
man/plotGrob.Rd
man/objectDiagram.Rd
man/simList-accessors-modules.Rd
man/digest.Rd
man/spadesEnv.Rd
man/numLayers.Rd
man/downloadData.Rd
man/defineModule.Rd
man/moduleDiagram.Rd
man/dwrpnorm2.Rd
man/simList_-class.Rd
man/cir.Rd
man/experiment.Rd
man/cache.Rd
man/heading.Rd
man/spadesMaps.Rd
man/directions.Rd
man/fillInputRows.Rd
man/inputObjects.Rd
man/fillOutputRows.Rd
man/fileName.Rd
man/addDepends.Rd
man/spades.Rd
man/defineParameter.Rd
man/clearPlot.Rd
man/fileTable.Rd
man/spadesGrob-class.Rd
man/simDeps-class.Rd
man/packages.Rd
man/wrap.Rd
man/append_attr.Rd
man/spades-classes.Rd
man/moduleGraph.Rd
man/timeConversion.Rd
man/depsEdgeList.Rd
man/POM.Rd
man/makeLayout.Rd
man/spadesTime.Rd
man/layerNames.Rd
man/downloadModule.Rd
man/checkPath.Rd
man/paddedFloatToChar.Rd
man/simList-accessors-inout.Rd
man/parseArgs.Rd
man/checksums.Rd
man/objectNames.Rd
man/divergentColors.Rd
man/arrangement-class.Rd
man/priority.Rd
man/randomPolygons.Rd
man/spadesPlot-class.Rd
man/scheduleEvent.Rd
man/makeDigestible.Rd
man/mergeRaster.Rd
man/crw.Rd
man/ls_str-method.Rd
man/newModuleTests.Rd
man/moduleCoverage.Rd
man/makeViewports.Rd
man/openModules.Rd
man/adj.Rd
man/findObjects.Rd
man/makeLines.Rd
man/changeObjEnv.Rd
man/simList-class.Rd
man/SELESagentLocation.Rd
man/initialize-method.Rd
man/rings.Rd
man/spatialObjects-class.Rd
man/addin_newModule.Rd
man/spread.Rd
man/gaussmap.Rd
SpaDES documentation built on May 19, 2017, 2:09 p.m.