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SpaDES (version 1.0.1)

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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Install

install.packages('SpaDES')

Monthly Downloads

484

Version

1.0.1

License

GPL-3

Issues

Pull Requests

Stars

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Repository

https://github.com/PredictiveEcology/SpaDES

Maintainer

Alex M Chubaty

Last Published

August 10th, 2015

Functions in SpaDES (1.0.1)

Build a module dependency graph

Open a new plotting window

Cache method for simList class objects

Get colours for plotting Raster* objects.

Build edge list for module dependency graph

Simulation modules and dependencies

Add simulation dependencies

Open all modules nested within a base directory

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

.spadesPlot-class

The .spadesPlot class

show,simList-method

Set colours for plotting Raster* objects.

Check use and existence of params passed to simulation.

Remove any reference to environments in a simList

defineParameter

Define a parameter used in a module

Process a simulation event

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

Create new module from template.

Simulation module dependency diagram

.depsPruneEdges

Prune edges to remove cycles in module dependencies

Simulation event diagram

Make SpatialLines object from two SpatialPoints objects

Convert plotArgs to list of lists

Determine which modules in a list are unparsed

Extracts the object names

Make an optimal layout of plots

Assess whether a list of extents are all equal

Get the name of a source-ed file

SELES - Initiate agents

Load simulation objects according to filelist

Parse arguments and find environments

Determine module load order

Define a new module.

Plot spatial grobs (using grid package)

List simulation objects and their structure

Assign to the internal SpaDES environment.

List simulation objects

.identifyGrobToPlot

Identify where to get the grob from

Determine the largest timestep unit in a simulation

Extract the layer names of Spatial Objects

Identify pixels in a circle around a SpatialPoints* object.

Simulation event lists

Split a raster into multiple tiles.

.arrangement-class

The .arrangement class

Get objects from the internal SpaDES environment

SELES - Agent Location at initiation

doEvent.checkpoint

Simulation checkpoints.

Vectorized wrapped normal density function

Prepare raster for plotting

Schedule a simulation event

Simulate a spread process on a landscape.

.makeSpadesPlot

Make a .spadesPlot class object

Generate random strings

Classes defined in SpaDES

Parse and extract module metadata

Produce a raster of a random Gaussian process.

Heading between spatial points.

Categorized overview of the SpaDES package

paddedFloatToChar

Convert numeric to character with padding

.spatialObjects-class

The .spatialObjects class

.spadesGrob-class

The .spadesGrob class

Importing some grid functions

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

Inputs and outputs - adding file-based inputs and saving files

Simulation object dependency diagram

specificNumPerPatch

specificNumPerPatch

Create a zip archive of a module subdirectory

rasterizeReduced

Convert reduced representation to full raster

Sort a any named object with dotted names first

The .simDeps class

Clear plotting device

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

nlayers,list-method

Find the number of layers in a Spatial Object

.spadesPlotObjects-class

The .spadesPlotObjects class

SELES - Transitioning to next time step

Normalize filepath.

Run a spatial discrete event simulation

The SpaDES environment

Read raster to memory

.spadesPlottables-class

The .spadesPlottables class

Dummy maps included with SpaDES

Save simulation objects according to params

Parse and initialize a module

Get and set simulation times.

Extract or replace parts of an object from the simulation environment

SELES - Probability of Initiation

Get and set simulation parameters.

Specify paths for modules, inputs and outputs

.updateSpadesPlot

Merge two SpaDES Plot objects

Initialize a new simulation

Copy or move objects from one environment to another

Download a module from a SpaDES module GitHub repository

.moduleDeps-class

The .moduleDeps class

Check filepath.

SpaDES time units

Get simulation package dependencies

Convert grid.locator units

The simList class

Mouse interactions with Plots

Wrap coordinates or pixels in a torus-like fashion

.arrangeViewports

Determine optimal plotting arrangement of plot objects

Filter objects by class

Specify where to plot

Is an object defined in the .spades environment?

initialize,simList-method

Generate a simList object

Simulation environment

getModuleVersion

Find the latest module version from a SpaDES module repository

The simList_ class

SELES - Number of Agents to initiate

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

Add a module to a moduleList

Determine the smallest timeunit in a simulation

.makeColorMatrix

Convert Raster to color matrix useable by raster function for plotting

Convert time units