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

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

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