SpaDES: Develop and Run Spatially Explicit Discrete Event Simulation Models

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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")`.

Author
Alex 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 publication
2016-10-07 18:42:54
Maintainer
Alex M Chubaty <alexander.chubaty@canada.ca>
License
GPL-3
Version
1.3.1
URLs

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

Files in this package

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