SpaDES v1.2.0

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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")`.

Readme

Spatial Discrete Event Simulation (SpaDES)

Develop and run spatially explicit discrete event simulation models

Easily implement a variety of simulation 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 framework that facilitates modularity, and easily enables the user to include additional functionality by running user-built simulation modules. Included are numerous tools to rapidly visualize raster and other maps.

Website: http://SpaDES.PredictiveEcology.org

Wiki: https://github.com/PredictiveEcology/SpaDES/wiki

Installation

Building packages from source requires the appropriate development libraries for your operating system (e.g., Windows users should install Rtools).

The suggested package fastshp can be installed with:

install.packages("fastshp", repos = "http://rforge.net", type = "source")

Current stable release

Build Status AppVeyor Build Status Coverage Status CRAN_Status_Badge Downloads DOI

Install from CRAN:

install.packages("SpaDES")

Install from GitHub:

#install.packages("devtools")
library("devtools")
install_github("PredictiveEcology/SpaDES") # stable

Development version (unstable)

Build Status AppVeyor Build Status Coverage Status

Install from GitHub:

#install.packages("devtools")
library("devtools")
install_github("PredictiveEcology/SpaDES", ref = "development") # unstable

Getting started

Vignettes:

Available via our wiki or via browseVignettes(package="SpaDES").

Wiki:

https://github.com/PredictiveEcology/SpaDES/wiki

Q&A Forum:

https://groups.google.com/d/forum/spades-users

Reporting bugs

Contact us via the package GitHub site: https://github.com/PredictiveEcology/SpaDES/issues.


Copyright (C) 2016 Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada

Functions in SpaDES

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

Type Package
URL http://spades.predictiveecology.org, https://github.com/PredictiveEcology/SpaDES
Date 2016-06-24
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' 'mergeRaster.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 2016-06-24 17:20:13 UTC; achubaty
Repository CRAN
Date/Publication 2016-06-24 20:16:16

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