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SpaDES (version 1.1.0)

Develop and Run Spatially Explicit Discrete Event Simulation Models

Description

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")`.

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Version

Install

install.packages('SpaDES')

Monthly Downloads

331

Version

1.1.0

License

GPL-3

Issues

Pull Requests

Stars

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Repository

https://github.com/PredictiveEcology/SpaDES

Maintainer

Alex M Chubaty

Last Published

January 26th, 2016

Functions in SpaDES (1.1.0)

Filter objects by class

Get the name of a source-ed file

Load simulation objects according to filelist

Simulation event diagram

rasterizeReduced

Convert reduced representation to full raster

Copy or move objects from one environment to another

Run a spatial discrete event simulation

Categorized overview of the SpaDES package

Dummy maps included with SpaDES

Identify pixels in a circle around a SpatialPoints* object.

Make an optimal layout of plots

Extracts the object names

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

divergentColors

Divergent colour palette

Add a module to a moduleList

Convert grid.locator units

Parse and initialize a module

SELES - Agent Location at initiation

.arrangeViewports

Determine optimal plotting arrangement of plot objects

.spadesGrob-class

The .spadesGrob class

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

Process a simulation event

Check for the existence of a remote module

Check use and existence of params passed to simulation.

Build a module dependency graph

Split a raster into multiple tiles.

SELES - Transitioning to next time step

Parse and extract module metadata

Determine module load order

Read raster to memory

Vectorized wrapped normal density function

SELES - Probability of Initiation

Determine the smallest timeunit in a simulation

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

.makeColorMatrix

Convert Raster to color matrix useable by raster function for plotting

Determine the largest timestep unit in a simulation

Create new module from template.

Download module data

Normalize filepath

Download a module from a SpaDES module GitHub repository

Calculate the hashes of multiple files

Importing some grid functions

Specify paths for modules, inputs, and outputs

SELES - Number of Agents to initiate

.spadesPlottables-class

The .spadesPlottables class

Get simulation package dependencies

Specify where to plot

Calculate module coverage of unit tests

Clear plotting device

initialize,simList-method

Generate a simList object

clearStubArtifacts

Clear erroneous archivist artifacts

Get and set simulation parameters.

Build edge list for module dependency graph

getModuleVersion

Find the latest module version from a SpaDES module repository

Open a new plotting window

.makeSpadesPlot

Make a .spadesPlot class object

Wrap coordinates or pixels in a torus-like fashion

Default (empty) metadata

doEvent.checkpoint

Simulation checkpoints.

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

The simList_ class

Determine which modules in a list are unparsed

Assign to the internal SpaDES environment.

Calculate checksums for a module's data files

defineParameter

Define a parameter used in a module

Is an object defined in the .spades environment?

Plot spatial grobs (using grid package)

Create empty fileTable for inputs and outputs

Get objects from the internal SpaDES environment

Schedule a simulation event

Simulation event lists

Convert plotArgs to list of lists

The SpaDES environment

List simulation objects and their structure

nlayers,list-method

Find the number of layers in a Spatial Object

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

Extract or replace an object from the simulation environment

Mouse interactions with Plots

.spadesPlotObjects-class

The .spadesPlotObjects class

Convert time units

Heading between spatial points.

paddedFloatToChar

Convert numeric to character with padding

The simList class

Add simulation dependencies

spatialObjects-class

The spatialObjects class

Simulation modules and dependencies

.arrangement-class

The .arrangement class

Simulation object dependency diagram

Inputs and outputs

List simulation objects

Assess whether a list of extents are all equal

Generate random strings

The .simDeps class

.depsPruneEdges

Prune edges to remove cycles in module dependencies

Sort a any named object with dotted names first

Check filepath.

Parse arguments and find environments

.moduleDeps-class

The .moduleDeps class

specificNumPerPatch

specificNumPerPatch

.identifyGrobToPlot

Identify where to get the grob from

Open all modules nested within a base directory

show,simList-method

Set colours for plotting Raster* objects.

Simulation environment

Get and set simulation times.

.spadesPlot-class

The .spadesPlot class

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

Cache method for simList class objects

Define a new module.

Produce a raster of a random Gaussian process.

.updateSpadesPlot

Merge two SpaDES Plot objects

Classes defined in SpaDES

Extract the layer names of Spatial Objects

Get colours for plotting Raster* objects.

Make SpatialLines object from two SpatialPoints objects

Remove any reference to environments in a simList

SpaDES time units

SELES - Initiate agents

Simulation module dependency diagram

Prepare raster for plotting

Initialize a new simulation

Save objects using .saveObjects in params slot of simInit

Create a zip archive of a module subdirectory

Simulate a spread process on a landscape.