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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

Install from CRAN:

install.packages("SpaDES")

Install from GitHub:

#install.packages("devtools")
library("devtools")
install_github("PredictiveEcology/SpaDES", dependencies = TRUE) # stable

Development version (unstable)

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

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Version

Install

install.packages('SpaDES')

Monthly Downloads

484

Version

1.3.0

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/PredictiveEcology/SpaDES

Homepage

http://spades.predictiveecology.org

Maintainer

Alex M Chubaty

Last Published

October 6th, 2016

Functions in SpaDES (1.3.0)

Check for existence of object(s) referenced by a objects slot of a simList object

Check for the existence of a remote module

Cache method for simList class objects

Fast `adjacent` function, and Just In Time compiled version

Copy or move objects from one environment to another

Add a module to a moduleList

addin_newModule

Rstudio addin to create a new module

Assign to the internal SpaDES environment.

.arrangeViewports

Determine optimal plotting arrangement of plot objects

Check use and existence of params passed to simulation.

Check filepath.

Identify pixels in a circle or ring (donut) around an object.

Filter objects by class

Copy a simList object

Clear plotting device

Define an output object of a module

clearStubArtifacts

Clear erroneous archivist artifacts

doEvent.checkpoint

Simulation checkpoints.

Calculate checksums for a module's data files

Determine module load order

Build a module dependency graph

Specify where to plot

distanceFromEachPoint

Calculate distances and directions between many points and many grid cells

Calculate the hashes of multiple files

directionFromEachPoint

Calculate distances and directions between many points and many grid cells

Build edge list for module dependency graph

.depsPruneEdges

Prune edges to remove cycles in module dependencies

defineParameter

Define a parameter used in a module

Simulation event diagram

Is an object defined in the .spades environment?

Download a module from a SpaDES module GitHub repository

Vectorized wrapped normal density function

Download module data

.emptyEventList

Blank (template) event list

divergentColors

Divergent colour palette

Process a simulation event

Assess whether a list of extents are all equal

Default (empty) metadata

An internal function for coercing a data.frame to inputs()

Open a file for editing

Create empty fileTable for inputs and outputs

Extract the file extension of a file

Find objects if passed as character strings

Extract filename (without extension) of a file

Define an input object that the module expects.

Run an experiment using spades

.fillOutputRows

An internal function for coercing a data.frame to inputs()

Heading between spatial points.

.identifyGrobToPlot

Identify where to get the grob from

Create an empty (template) inputObjects and outputObjects data.frames

Create new module from template.

.makeSpadesPlot

Make a .spadesPlot class object

Test whether a number lies within range [a,b]

Create new module code file

Determine the largest timestep unit in a simulation

List simulation objects

.makeColorMatrix

Convert Raster to color matrix useable by raster function for plotting

Merge split raster tiles into a single raster layer.

Build a module dependency graph

Simulation module dependency diagram

Simulation object dependency diagram

Use Pattern Oriented Modeling to fit unknown parameters

Extracts the object names

Prepare raster for plotting

Add simulation dependencies

Produce a raster of a random Gaussian process.

Default paths to use for a simulation

Read raster to memory

.convertSpatialToPlotGrob

Internal functions used by Plot

Display a simple, interactive shiny app of the simList

show,simList-method

Identifies all cells within a ring around the focal cells

SpaDES time units

Get colours for plotting Raster* objects.

Get the name of a source-ed file

List simulation objects and their structure

Make SpatialLines object from two SpatialPoints objects

Convert plotArgs to list of lists

Get and set simulation globals.

Parse and extract module metadata

.callingModuleName

Namespacing within SpaDES

Importing some grid functions

Get simulation package dependencies

Extract the layer names of Spatial Objects

.fileExtensions

File extensions map

Remove any reference to environments in a simList

Make an optimal layout of plots

Open a new plotting window

Extract or replace an object from the simulation environment

Open all modules nested within a base directory

Plot: Fast, optimally arranged, multipanel plotting function with SpaDES

Plot spatial grobs (using grid package)

Generate random strings

Save objects using .saveObjects in params slot of simInit

Simulation event lists

Classes defined in SpaDES

Categorized overview of the SpaDES package

Inputs and outputs

Get and set simulation parameters.

Parse arguments and find environments

.parseModulePartial

Parse and initialize a module

rasterizeReduced

Convert reduced representation to full raster

Initialize a new simulation

paddedFloatToChar

Convert numeric to character with padding

Time usage in SpaDES

Sort a any named object with dotted names first

SELES - Agent Location at initiation

Schedule a simulation event

Run a spatial discrete event simulation

progressInterval

Get and set simulation progress bar details

The SpaDES environment

Split a RasterLayer into multiple tiles

Identify outward radiating spokes from initial points

getModuleVersion

Find the latest module version from a SpaDES module repository

Get objects from the internal SpaDES environment

initialize,simList-method

Generate a simList object

Determine the smallest timeunit in a simulation

SELES - Initiate agents

Calculate module coverage of unit tests

newModuleDocumentation

Create new module documentation

Normalize filepath

Create template testing structures for new modules

Find the number of layers in a Spatial Object

Convert grid.locator units

specificNumPerPatch

Initiate a specific number of agents in a map of patches

Determine which modules in a list are unparsed

SELES - Transitioning to next time step

Set colours for plotting Raster* objects.

Dummy maps included with SpaDES

Mouse interactions with Plots

Update elements of a named list with elements of a second named list

.updateSpadesPlot

Merge two SpaDES Plot objects

Simulate a spread process on a landscape.

Convert time units

Create a zip archive of a module subdirectory

SELES - Number of Agents to initiate

SELES - Probability of Initiation

The simList_ class

Simulation environment

Simulation modules and dependencies

Specify paths for modules, inputs, and outputs

Compare module version against SpaDES package version and warn if incompatible

Wrap coordinates or pixels in a torus-like fashion