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SpaDES (version 1.1.1)

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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Version

Install

install.packages('SpaDES')

Monthly Downloads

484

Version

1.1.1

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/PredictiveEcology/SpaDES

Maintainer

Alex M Chubaty

Last Published

February 16th, 2016

Functions in SpaDES (1.1.1)

.arrangement-class

The .arrangement class

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

Check filepath.

Filter objects by class

SELES - Transitioning to next time step

.depsPruneEdges

Prune edges to remove cycles in module dependencies

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

.identifyGrobToPlot

Identify where to get the grob from

Remove any reference to environments in a simList

.makeColorMatrix

Convert Raster to color matrix useable by raster function for plotting

Build edge list for module dependency graph

Default (empty) metadata

Time usage in SpaDES

nlayers,list-method

Find the number of layers in a Spatial Object

Create new module from template.

Parse arguments and find environments

doEvent.checkpoint

Simulation checkpoints.

Clear plotting device

Download module data

Cache method for simList class objects

Importing some grid functions

Process a simulation event

Get objects from the internal SpaDES environment

Make an optimal layout of plots

Plot spatial grobs (using grid package)

initialize,simList-method

Generate a simList object

Define a new module.

Determine the largest timestep unit in a simulation

Determine which modules in a list are unparsed

defineParameter

Define a parameter used in a module

SELES - Agent Location at initiation

List simulation objects and their structure

Heading between spatial points.

Convert plotArgs to list of lists

.moduleDeps-class

The .moduleDeps class

Simulate a spread process on a landscape.

Split a raster into multiple tiles.

Simulation environment

List simulation objects

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

Assess whether a list of extents are all equal

SELES - Probability of Initiation

.updateSpadesPlot

Merge two SpaDES Plot objects

Get simulation package dependencies

Simulation object dependency diagram

Simulation module dependency diagram

Produce a raster of a random Gaussian process.

Add a module to a moduleList

Wrap coordinates or pixels in a torus-like fashion

Identify pixels in a circle around a SpatialPoints* object.

Build a module dependency graph

Open a new plotting window

Check use and existence of params passed to simulation.

.makeSpadesPlot

Make a .spadesPlot class object

Run a spatial discrete event simulation

show,simList-method

Save objects using .saveObjects in params slot of simInit

Calculate the hashes of multiple files

Determine module load order

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

.arrangeViewports

Determine optimal plotting arrangement of plot objects

Parse and extract module metadata

Make SpatialLines object from two SpatialPoints objects

Parse and initialize a module

The .simDeps class

Copy or move objects from one environment to another

Initialize a new simulation

divergentColors

Divergent colour palette

Get and set simulation parameters.

Download a module from a SpaDES module GitHub repository

Is an object defined in the .spades environment?

Prepare raster for plotting

paddedFloatToChar

Convert numeric to character with padding

Sort a any named object with dotted names first

Mouse interactions with Plots

Convert time units

SpaDES time units

Inputs and outputs

.spadesPlottables-class

The .spadesPlottables class

Generate random strings

Simulation event diagram

Set colours for plotting Raster* objects.

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

Classes defined in SpaDES

.spadesGrob-class

The .spadesGrob class

The simList_ class

SELES - Number of Agents to initiate

Extract or replace an object from the simulation environment

Convert grid.locator units

Specify where to plot

Vectorized wrapped normal density function

Create empty fileTable for inputs and outputs

getModuleVersion

Find the latest module version from a SpaDES module repository

Simulation event lists

Dummy maps included with SpaDES

Open all modules nested within a base directory

spatialObjects-class

The spatialObjects class

Assign to the internal SpaDES environment.

clearStubArtifacts

Clear erroneous archivist artifacts

rasterizeReduced

Convert reduced representation to full raster

Extract the layer names of Spatial Objects

Read raster to memory

Specify paths for modules, inputs, and outputs

.spadesPlotObjects-class

The .spadesPlotObjects class

Add simulation dependencies

Get the name of a source-ed file

Schedule a simulation event

Normalize filepath

Create a zip archive of a module subdirectory

.spadesPlot-class

The .spadesPlot class

The simList class

Compare module version against SpaDES package version and warn if incompatible

Categorized overview of the SpaDES package

Check for the existence of a remote module

Simulation modules and dependencies

SELES - Initiate agents

Extracts the object names

Load simulation objects according to filelist

specificNumPerPatch

specificNumPerPatch

Calculate checksums for a module's data files

Get colours for plotting Raster* objects.

Calculate module coverage of unit tests

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

Determine the smallest timeunit in a simulation

The SpaDES environment