SpaDES v1.1.4

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by Alex M Chubaty

Develop and Run Spatially Explicit Discrete Event Simulation Models

Easily implement a variety of simulation models, with a focus on spatially explicit agent based models. These include raster-based, event-based, and agent-based models. The core simulation components are built upon a discrete event simulation 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")`.

Functions in SpaDES

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

Type Package
URL https://github.com/PredictiveEcology/SpaDES
Date 2016-04-20
Additional_repositories http://rforge.net
License GPL-3
VignetteBuilder knitr, rmarkdown
BugReports https://github.com/PredictiveEcology/SpaDES/issues
ByteCompile yes
Collate 'agent.R' 'SELES.R' 'misc-methods.R' 'module-dependencies-class.R' 'helpers.R' 'simList-class.R' 'check.R' 'priority.R' 'environment.R' 'checkpoint.R' 'copy.R' 'experiment.R' 'initialize.R' 'simulation.R' 'load.R' 'mapReduce.R' 'module-dependencies-methods.R' 'moduleMetadata.R' 'module-repository.R' 'module-template.R' 'moduleCoverage.R' 'movement.R' 'neighbourhood.R' 'numerical-comparisons.R' 'plotting-classes.R' 'plotting-colours.R' 'times.R' 'simList-accessors.R' 'plotting-diagrams.R' 'plotting-helpers.R' 'plotting-other.R' 'plotting.R' 'probability.R' 'progress.R' 'save.R' 'shine.R' 'spades-classes.R' 'spades-package.R' 'splitRaster.R' 'spread-process.R' 'zzz.R'
RoxygenNote 5.0.1
NeedsCompilation no
Packaged 2016-04-20 16:35:44 UTC; achubaty
Repository CRAN
Date/Publication 2016-04-20 21:19:54

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