Learn R Programming

⚠️There's a newer version (2.0.11) of this package.Take me there.

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") # stable

Development version (unstable)

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

Copy Link

Version

Install

install.packages('SpaDES')

Monthly Downloads

318

Version

1.2.0

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/PredictiveEcology/SpaDES

Homepage

http://spades.predictiveecology.org

Maintainer

Last Published

June 24th, 2016

Functions in SpaDES (1.2.0)

Add a module to a moduleList

Check for the existence of a remote module

Add simulation dependencies

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

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

.arrangement-class

The .arrangement class

Cache method for simList class objects

.arrangeViewports

Determine optimal plotting arrangement of plot objects

Assign to the internal SpaDES environment.

Copy or move objects from one environment to another

Filter objects by class

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

Clear plotting device

doEvent.checkpoint

Simulation checkpoints.

Calculate checksums for a module's data files

clearStubArtifacts

Clear erroneous archivist artifacts

Check filepath.

Check use and existence of params passed to simulation.

Define a new module.

defineParameter

Define a parameter used in a module

Assess whether a list of extents are all equal

Default (empty) metadata

Get colours for plotting Raster* objects.

Find objects if passed as character strings

Vectorized wrapped normal density function

.emptyEventList

Blank (template) event list

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

Get simulation package dependencies

Get objects from the internal SpaDES environment

paddedFloatToChar

Convert numeric to character with padding

Remove any reference to environments in a simList

rasterizeReduced

Convert reduced representation to full raster

Identifies all cells within a ring around the focal cells

Generate random strings

Read raster to memory

The simList_ class

Simulation environment

Get and set simulation parameters.

Specify where to plot

Specify paths for modules, inputs, and outputs

Calculate the hashes of multiple files

Download a module from a SpaDES module GitHub repository

Download module data

Make SpatialLines object from two SpatialPoints objects

Make an optimal layout of plots

Determine the largest timestep unit in a simulation

.spadesPlot-class

The .spadesPlot class

.spadesPlotObjects-class

The .spadesPlotObjects class

Copy a simList object

Build edge list for module dependency graph

Build a module dependency graph

Simulation event diagram

Is an object defined in the .spades environment?

Get the name of a source-ed file

List simulation objects

Simulation module dependency diagram

List simulation objects and their structure

Parse and extract module metadata

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

Importing some grid functions

Extract filename (without extension) of a file

Create empty fileTable for inputs and outputs

Process a simulation event

Heading between spatial points.

.fileExtensions

File extensions map

Normalize filepath

Simulation object dependency diagram

Extract or replace an object from the simulation environment

Simulation modules and dependencies

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

Convert plotArgs to list of lists

.makeSpadesPlot

Make a .spadesPlot class object

Create new module from template.

Open a new plotting window

Display a simple, interactive shiny app of the simList

Set colours for plotting Raster* objects.

Sort a any named object with dotted names first

Classes defined in SpaDES

Simulate a spread process on a landscape.

Split a RasterLayer into multiple tiles

SELES - Agent Location at initiation

currentModule,.simList-method

Simulation event lists

SELES - Number of Agents to initiate

Inputs and outputs

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

Determine which modules in a list are unparsed

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

Determine module load order

Run an experiment using spades

.identifyGrobToPlot

Identify where to get the grob from

.depsPruneEdges

Prune edges to remove cycles in module dependencies

Extract the file extension of a file

initialize,simList-method

Generate a simList object

Calculate module coverage of unit tests

.moduleDeps-class

The .moduleDeps class

The simList class

Time usage in SpaDES

.spadesPlottables-class

The .spadesPlottables class

SpaDES time units

Wrap coordinates or pixels in a torus-like fashion

Create a zip archive of a module subdirectory

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

SELES - Initiate agents

.fillOutputRows

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

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

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

Extract the layer names of Spatial Objects

Merge split raster tiles into a single raster layer.

Determine the smallest timeunit in a simulation

Extracts the object names

Open all modules nested within a base directory

Plot spatial grobs (using grid package)

Prepare raster for plotting

Save objects using .saveObjects in params slot of simInit

Schedule a simulation event

show,simList-method

Parse arguments and find environments

nlayers,list-method

Find the number of layers in a Spatial Object

Parse and initialize a module

SELES - Transitioning to next time step

SELES - Probability of Initiation

The .simDeps class

Initialize a new simulation

Mouse interactions with Plots

Dummy maps included with SpaDES

Convert time units

Convert grid.locator units

Categorized overview of the SpaDES package

Run a spatial discrete event simulation

.updateSpadesPlot

Merge two SpaDES Plot objects

Compare module version against SpaDES package version and warn if incompatible