SpaDES: Develop and Run Spatially Explicit Discrete Event Simulation Models

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")`.

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
http://spades.predictiveecology.org, https://github.com/PredictiveEcology/ SpaDES

View on CRAN

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
$ Man page
$<- Man page
# Man page
.addDepends Man page
.addDepends,.simList,.moduleDeps-method Man page
addin_newModule Man page
adj Man page
adj.raw Man page
agentLocation Man page
append_attr Man page
append_attr,list,list-method Man page
.arrangement Man page
.arrangement-class Man page
.arrangeViewports Man page
.arrangeViewports,.spadesPlot-method Man page
.assignSpaDES Man page
.assignSpaDES,character,ANY-method Man page
.assignSpaDES,character,missing-method Man page
cache Man page
cache,ANY-method Man page
cachePath Man page
cachePath<- Man page
cachePath<-,.simList-method Man page
cachePath,.simList-method Man page
.callingFrameTimeunit Man page
.callingFrameTimeunit,NULL-method Man page
.callingFrameTimeunit,.simList-method Man page
.callingModuleName Man page
.callingModuleName,.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,character,logical-method Man page
checkPath,character,missing-method Man page
checkPath,missing,ANY-method Man page
checkPath,NULL,ANY-method Man page
checkpointFile Man page
checkpointFile<- Man page
checkpointFile<-,.simList-method Man page
checkpointFile,.simList-method Man page
checkpointInterval Man page
checkpointInterval<- Man page
checkpointInterval<-,.simList-method Man page
checkpointInterval,.simList-method Man page
checkpointLoad Man page
.checkpointSave Man page
checksums Man page
checksums,character,character,logical-method Man page
checksums,character,character,missing-method Man page
checkTimeunit Man page
checkTimeunit,character,environment-method Man page
checkTimeunit,character,missing-method Man page
cir Man page
cir,RasterLayer,matrix,missing-method Man page
cir,RasterLayer,missing,missing-method Man page
cir,RasterLayer,missing,numeric-method Man page
cir,RasterLayer,SpatialPoints,missing-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 Man page
clickCoordinates Man page
clickExtent Man page
clickValues Man page
completed Man page
completed<- Man page
completed,.simList,character-method Man page
completed<-,.simList-method Man page
completed,.simList,missing-method Man page
.convertSpatialToPlotGrob Man page
.convertSpatialToPlotGrob,spatialObjects,.spadesGrob-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,SpatialPointsDataFrame-method Man page
crw,SpatialPoints-method Man page
current Man page
current<- Man page
currentModule Man page
currentModule,.simList-method Man page
current,.simList,character-method Man page
current<-,.simList-method Man page
current,.simList,missing-method Man page
dday Man page
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<- Man page
depends<-,.simList-method 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
.depsLoadOrder Man page
.depsLoadOrder,simList,igraph-method Man page
.depsPruneEdges Man page
.depsPruneEdges,data.table-method Man page
dev Man page
dhour Man page
digest Man page
digest,character-method Man page
directionFromEachPoint Man page
distanceFromEachPoint Man page
divergentColors Man page
divergentColors,character,character,numeric,numeric-method Man page
divergentColours Man page
dmonth Man page
dmonths Man page
dmonths,numeric-method Man page
dNA Man page
dNA,ANY-method Man page
doEvent Man page
doEvent.checkpoint Man page
doEvent,simList,ANY-method Man page
doEvent,simList,missing-method Man page
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
dweek Man page
dweeks Man page
dweeks,numeric-method Man page
dwrpnorm2 Man page
dyear Man page
dyears Man page
dyears,numeric-method Man page
.emptyEventList Man page
.emptyEventListCols Man page
.emptyEventListDT Man page
.emptyEventList,missing,missing,missing,missing-method Man page
.emptyEventListNA Man page
.emptyEventList,numeric,character,character,numeric-method Man page
.emptyEventListObj Man page
.emptyMetadata Man page
.emptyMetadata,missing-method Man page
end Man page
end<- Man page
end,.simList,character-method Man page
end<-,.simList-method Man page
end,.simList,missing-method Man page
envir Man page
envir<- Man page
envir<-,simList-method 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<- Man page
events,.simList,character-method Man page
events<-,.simList-method Man page
events,.simList,missing-method Man page
.existsSpaDES Man page
.existsSpaDES,ANY-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 Man page
fileExt Man page
.fileExtensions Man page
fileName Man page
.fileTableIn Man page
.fileTableInCols Man page
.fileTableIn,missing-method Man page
.fileTableOut Man page
.fileTableOutCols Man page
.fileTableOut,missing-method Man page
.fillInputRows Man page
.fillOutputRows Man page
.findFactors Man page
findObjects Man page
.findObjects Man page
.first Man page
ganttStatus Man page
ganttStatus,character-method Man page
gaussMap Man page
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
.getSpaDES Man page
.getSpaDES,ANY-method Man page
globals Man page
globals<- Man page
globals<-,.simList-method Man page
globals,.simList-method Man page
gpar Man page
gpar,ANY-method Man page
griddedClasses Man page
heading Man page
heading,matrix,matrix-method Man page
heading,matrix,SpatialPoints-method Man page
heading,SpatialPoints,matrix-method Man page
heading,SpatialPoints,SpatialPoints-method Man page
.highest Man page
.identifyGrobToPlot Man page
.identifyGrobToPlot,.spadesGrob,list-method Man page
@importClassesFrom Man page
initialize,simList-method Man page
initiateAgents Man page
initiateAgents,Raster,missing,missing,ANY,missing-method Man page
initiateAgents,Raster,missing,missing,ANY,numeric-method Man page
initiateAgents,Raster,missing,Raster,ANY,missing-method Man page
initiateAgents,Raster,numeric,missing,ANY,missing-method Man page
initiateAgents,Raster,numeric,Raster,ANY,missing-method Man page
inputArgs Man page
inputArgs<- Man page
inputArgs<-,.simList-method Man page
inputArgs,.simList-method Man page
.inputObjects Man page
.inputObjects,missing-method Man page
inputPath Man page
inputPath<- Man page
inputPath<-,.simList-method Man page
inputPath,.simList-method Man page
inputs Man page
inputs<- Man page
inputs<-,.simList-method Man page
inputs,.simList-method Man page
inRange Man page
inSeconds Man page
inSeconds,character,environment-method Man page
inSeconds,character,missing-method Man page
inSeconds,NULL,missing-method Man page
.last Man page
layerNames Man page
layerNames,ANY-method Man page
layerNames,igraph-method Man page
layerNames,list-method Man page
layerNames,Raster-method Man page
layerNames,.spadesPlot-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,character-method Man page
loadPackages,list-method Man page
loadPackages,NULL-method Man page
.lowest Man page
ls.simList Man page
ls,simList-method Man page
ls.str,missing,simList-method Man page
ls.str.simList Man page
ls.str,simList,missing-method Man page
.makeColorMatrix Man page
.makeColorMatrix,Raster,Extent,numeric-method Man page
makeColourMatrix Man page
makeDigestible Man page
makeDigestible,simList-method Man page
.makeLayout Man page
makeLines Man page
makeLines,SpatialPoints,SpatialPoints-method 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
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
.moduleDeps Man page
.moduleDeps-class 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<- Man page
modulePath<-,.simList-method Man page
modulePath,.simList-method Man page
modules Man page
modules<- Man page
modules<-,.simList-method Man page
modules,.simList-method Man page
move Man page
NetLogoRClasses Man page
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
newProgressBar Man page
.normal Man page
normPath Man page
normPath,character-method Man page
normPath,list-method Man page
normPath,missing-method Man page
normPath,NULL-method Man page
numAgents Man page
numLayers Man page
numLayers,ANY-method Man page
numLayers,list-method Man page
numLayers,Raster-method Man page
numLayers,.spadesPlot-method Man page
numLayers,Spatial-method Man page
objectDiagram Man page
objectDiagram,simList-method Man page
objectNames Man page
objects.simList Man page
objects,simList-method Man page
objs Man page
objs<- Man page
objs<-,simList-method Man page
objs,simList-method Man page
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<- Man page
outputArgs<-,.simList-method Man page
outputArgs,.simList-method Man page
.outputObjects Man page
.outputObjects,missing-method Man page
outputPath Man page
outputPath<- Man page
outputPath<-,.simList-method Man page
outputPath,.simList-method Man page
outputs Man page
outputs<- Man page
outputs<-,.simList-method Man page
outputs,.simList-method Man page
p Man page
P Man page
packages Man page
packages,.simList-method Man page
paddedFloatToChar Man page
parameters Man page
parameters,.simList-method Man page
params Man page
params<- Man page
params<-,.simList-method Man page
params,.simList-method Man page
.parseArgs Man page
.parseModule Man page
.parseModulePartial Man page
.parseModulePartial,missing,missing,character,character-method Man page
.parseModulePartial,simList,list,missing,character-method Man page
.parseModule,simList,list-method Man page
patchSize Man page
paths Man page
.paths Man page
paths<- Man page
paths<-,.simList-method Man page
paths,.simList-method Man page
Plot Man page
.Plot Man page
Plot,ANY-method Man page
.plotGrob Man page
.plotGrob,matrix-method Man page
.plotGrob,SpatialLines-method Man page
.plotGrob,SpatialPoints-method Man page
.plotGrob,SpatialPolygons-method Man page
PlotHelpers Man page
Plot,simList-method Man page
.Plot,.spadesGrob-method Man page
.pointDirection Man page
pointDistance Man page
.pointDistance Man page
POM Man page
POM,simList,character-method Man page
.prepareRaster Man page
priority Man page
probInit Man page
progressInterval Man page
progressInterval<- Man page
progressInterval<-,.simList-method Man page
progressInterval,.simList-method Man page
progressType Man page
progressType<- Man page
progressType<-,.simList-method Man page
progressType,.simList-method Man page
P,.simList-method Man page
randomPolygons Man page
rasterizeReduced Man page
rasterToMemory Man page
rasterToMemory,ANY-method Man page
.refreshGrob Man page
.refreshGrob,.spadesGrob-method Man page
rePlot Man page
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 Man page
saveFiles Man page
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<- Man page
setColors,RasterLayer,character,missing-method Man page
setColors,RasterLayer,character,numeric-method Man page
setColors<-,RasterLayer,missing,character-method Man page
setColors<-,RasterLayer,numeric,character-method Man page
setColors<-,Raster,missing,list-method Man page
setColors<-,RasterStack,numeric,list-method Man page
setColours Man page
shine Man page
shine,simList-method Man page
showCache Man page
showCache,ANY-method Man page
show,simList-method Man page
.sim2gantt Man page
.sim2gantt,simList,numeric,character,numeric-method Man page
.simDeps Man page
.simDeps-class 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 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,ANY,ANY,ANY-method Man page
[[,simList,ANY,ANY-method Man page
.simList-class Man page
simList_-class Man page
simList-class Man page
$<-,simList-method Man page
$,simList-method Man page
.singleEventListDT Man page
sortDotsFirst Man page
spades Man page
SpaDES Man page
spades,ANY,ANY,ANY,logical-method Man page
spadesClasses Man page
.spadesEnv Man page
.spadesGrob Man page
.spadesGrob-class Man page
spadesMaps Man page
spades-package Man page
SpaDES-package Man page
.spadesPlot Man page
.spadesPlot-class Man page
.spadesPlotObjects Man page
.spadesPlotObjects-class Man page
.spadesPlottables Man page
.spadesPlottables-class Man page
spades,simList,ANY,ANY,missing-method Man page
spadesTimes Man page
.spadesTimes Man page
spatialObjects Man page
spatialObjects-class Man page
specificNumPerPatch Man page
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<- Man page
start,.simList,character-method Man page
start<-,.simList-method Man page
start,.simList,missing-method Man page
time Man page
time<- Man page
times Man page
times<- Man page
time,.simList,character-method Man page
time<-,.simList-method Man page
time,.simList,missing-method Man page
times<-,.simList-method Man page
times,.simList-method Man page
timeunit Man page
timeunit<- Man page
timeunits Man page
timeunit<-,.simList-method Man page
timeunit,.simList-method Man page
timeunits,.simList-method Man page
transitions Man page
.unittrim Man page
.unparsed Man page
.unparsed,list-method Man page
.updateGrobGPTextAxis Man page
.updateGrobGPTextAxis,.spadesGrob-method Man page
updateList Man page
updateList,list,list-method Man page
updateList,list,NULL-method Man page
updateList,NULL,list-method Man page
updateList,NULL,NULL-method Man page
.updateSpadesPlot Man page
.updateSpadesPlot,.spadesPlot,list-method Man page
.updateSpadesPlot,.spadesPlot,missing-method Man page
versionWarning Man page
versionWarning,character-method Man page
wrap Man page
wrap,matrix,Extent,missing-method Man page
wrap,matrix,matrix,missing-method Man page
wrap,matrix,Raster,missing-method Man page
wrap,SpatialPoints,ANY,missing-method Man page
wrap,SpatialPointsDataFrame,Extent,logical-method Man page
wrap,SpatialPointsDataFrame,matrix,logical-method Man page
wrap,SpatialPointsDataFrame,Raster,logical-method Man page
.xyAxes Man page
.xyAxes,.spadesGrob,.arrangement-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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.