SpaDES v1.3.1

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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")`.

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", dependencies = TRUE) # 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", dependencies = TRUE) # 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
changeObjEnv Copy or move objects from one environment to another
checkModule Check for the existence of a remote module
.arrangeViewports Determine optimal plotting arrangement of plot objects
adj.raw Fast `adjacent` function, and Just In Time compiled version
append_attr Add a module to a moduleList
.assignSpaDES Assign to the internal SpaDES environment.
addin_newModule Rstudio addin to create a new module
.addDepends Add simulation dependencies
clearStubArtifacts Clear erroneous archivist artifacts
classFilter Filter objects by class
checkPath Check filepath.
checkParams Check use and existence of params passed to simulation.
doEvent.checkpoint Simulation checkpoints.
copy Copy a simList object
checksums Calculate checksums for a module's data files
clearPlot Clear plotting device
createsOutput Define an output object of a module
cir Identify pixels in a circle or ring (donut) around an object.
distanceFromEachPoint Calculate distances and directions between many points and many grid cells
dev Specify where to plot
depsEdgeList Build edge list for module dependency graph
depsGraph Build a module dependency graph
move Move
directionFromEachPoint Calculate distances and directions between many points and many grid cells
defineParameter Define a parameter used in a module
.depsLoadOrder Determine module load order
digest Calculate the hashes of multiple files
.depsPruneEdges Prune edges to remove cycles in module dependencies
.existsSpaDES Is an object defined in the .spades environment?
equalExtent Assess whether a list of extents are all equal
downloadData Download module data
eventDiagram Simulation event diagram
divergentColors Divergent colour palette
.emptyEventList Blank (template) event list
doEvent Process a simulation event
downloadModule Download a module from a SpaDES module GitHub repository
.emptyMetadata Default (empty) metadata
dwrpnorm2 Vectorized wrapped normal density function
.findFactors Find factors
findObjects Find objects if passed as character strings
.fileEdit Open a file for editing
fileExt Extract the file extension of a file
.fillInputRows An internal function for coercing a data.frame to inputs()
.fillOutputRows An internal function for coercing a data.frame to inputs()
expectsInput Define an input object that the module expects.
experiment Run an experiment using spades
fileName Extract filename (without extension) of a file
.fileTableIn Create empty fileTable for inputs and outputs
.identifyGrobToPlot Identify where to get the grob from
heading Heading between spatial points.
globals Get and set simulation globals.
gpar Importing some grid functions
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 repository
ganttStatus ganttStatus
.getSpaDES Get objects from the internal SpaDES environment
gaussMap Produce a raster of a random Gaussian process.
loadPackages Load packages.
ls.simList List simulation objects
.makeColorMatrix Convert Raster to color matrix useable by raster function for plotting
ls.str.simList List simulation objects and their structure
layerNames Extract the layer names of Spatial Objects
inRange Test whether a number lies within range [a,b]
.fileExtensions File extensions map
.inputObjects Create an empty (template) inputObjects and outputObjects data.frames
initiateAgents SELES - Initiate agents
initialize,simList-method Generate a simList object
cache Cache method for simList class objects
mergeRaster Merge split raster tiles into a single raster layer.
maxTimeunit Determine the largest timestep unit in a simulation
moduleDiagram Simulation module dependency diagram
moduleGraph Build a module dependency graph
normPath Normalize filepath
numLayers Find the number of layers in a Spatial Object
POM Use Pattern Oriented Modeling to fit unknown parameters
newModuleDocumentation Create new module documentation
.prepareRaster Prepare raster for plotting
newModuleTests Create template testing structures for new modules
objectDiagram Simulation object dependency diagram
objectNames Extracts the object names
numAgents SELES - Number of Agents to initiate
probInit SELES - Probability of Initiation
envir Simulation environment
simList_-class The simList_ class
times Time usage in SpaDES
sortDotsFirst Sort a any named object with dotted names first
checkObject Check for existence of object(s) referenced by a objects slot of a simList object
makeDigestible Remove any reference to environments in a simList
.makeLayout Make an optimal layout of plots
moduleMetadata Parse and extract module metadata
packages Get simulation package dependencies
.callingModuleName Namespacing within SpaDES
paddedFloatToChar Convert numeric to character with padding
progressInterval Get and set simulation progress bar details
.first Event priority
.makeSpadesPlot Make a .spadesPlot class object
.makeViewports Make viewports
newModuleCode Create new module code file
newModule Create new module from template.
objs Extract or replace an object from the simulation environment
openModules Open all modules nested within a base directory
.plotGrob Plot spatial grobs (using grid package)
Plot Plot: Fast, optimally arranged, multipanel plotting function with SpaDES
rasterToMemory Read raster to memory
minTimeunit Determine the smallest timeunit in a simulation
rings Identifies all cells within a ring around the focal cells
moduleCoverage Calculate module coverage of unit tests
.parseModulePartial Parse and initialize a module
randomPolygons randomPolygons
patchSize Patch size
rasterizeReduced Convert reduced representation to full raster
simInit Initialize a new simulation
.sim2gantt sim2gantt
rndstr Generate random strings
transitions SELES - Transitioning to next time step
saveFiles Save objects using .saveObjects in params slot of simInit
setColors<- Set colours for plotting Raster* objects.
spades Run a spatial discrete event simulation
.spadesEnv The SpaDES environment
inputs Inputs and outputs
events Simulation event lists
spadesMaps Dummy maps included with SpaDES
scheduleEvent Schedule a simulation event
clickValues Mouse interactions with Plots
agentLocation SELES - Agent Location at initiation
spadesClasses Classes defined in SpaDES
SpaDES-package Categorized overview of the SpaDES package
.makeList Convert plotArgs to list of lists
makeLines Make SpatialLines object from two SpatialPoints objects
newProgressBar Progress bar
newPlot Open a new plotting window
.parseArgs Parse arguments and find environments
params Get and set simulation parameters.
.paths Default paths to use for a simulation
.convertSpatialToPlotGrob Internal functions used by Plot
shine Display a simple, interactive shiny app of the simList
show,simList-method Show an Object
modules Simulation modules and dependencies
paths Specify paths for modules, inputs, and outputs
specificNumPerPatch Initiate a specific number of agents in a map of patches
versionWarning Compare module version against SpaDES package version and warn if incompatible
dyears SpaDES time units
wrap Wrap coordinates or pixels in a torus-like fashion
updateList Update elements of a named list with elements of a second named list
.updateSpadesPlot Merge two SpaDES Plot objects
spread Simulate a spread process on a landscape.
inSeconds Convert time units
splitRaster Split a RasterLayer into multiple tiles
spokes Identify outward radiating spokes from initial points
.unittrim Convert grid.locator units
zipModule Create a zip archive of a module subdirectory
.unparsed Determine which modules in a list are unparsed
.arrangement-class The .arrangement class
defineModule Define a new module.
.moduleDeps-class The .moduleDeps class
.simDeps-class The .simDeps class
setColors<- Set colours for plotting Raster* objects.
.spadesPlot-class The .spadesPlot class
.spadesPlotObjects-class The .spadesPlotObjects class
.simList-class The simList class
.spadesGrob-class The .spadesGrob class
.spadesPlottables-class The .spadesPlottables class
spatialObjects-class The spatialObjects class
No Results!

Vignettes of SpaDES

Name
bibliography.bib
i-introduction.Rmd
ii-modules.Rmd
iii-plotting.Rmd
No Results!

Last month downloads

Details

Type Package
URL http://spades.predictiveecology.org, https://github.com/PredictiveEcology/ SpaDES
Date 2016-10-07
Additional_repositories http://rforge.net
License GPL-3
VignetteBuilder knitr, rmarkdown
BugReports https://github.com/PredictiveEcology/SpaDES/issues
ByteCompile yes
Collate 'priority.R' 'environment.R' 'misc-methods.R' 'module-dependencies-class.R' 'helpers.R' 'simList-class.R' 'POM.R' 'agent.R' 'SELES.R' 'cache.R' 'check.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' 'rstudio-addins.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 2016-10-07 16:22:11 UTC; achubaty
Repository CRAN
Date/Publication 2016-10-07 18:42:54

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