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SpaDES (version 1.1.4)

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

1,226

Version

1.1.4

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/PredictiveEcology/SpaDES

Maintainer

Alex M Chubaty

Last Published

April 20th, 2016

Functions in SpaDES (1.1.4)

Get and set simulation parameters.

Normalize filepath

Extract or replace an object from the simulation environment

.arrangement-class

The .arrangement class

initialize,simList-method

Generate a simList object

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

Add a module to a moduleList

.fileExtensions

File extensions map

Importing some grid functions

.makeSpadesPlot

Make a .spadesPlot class object

SELES - Probability of Initiation

.moduleDeps-class

The .moduleDeps class

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

SELES - Transitioning to next time step

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

Determine module load order

Dummy maps included with SpaDES

Parse and extract module metadata

Remove any reference to environments in a simList

Extract the layer names of Spatial Objects

defineParameter

Define a parameter used in a module

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

Check filepath.

Generate random strings

Get the name of a source-ed file

show,simList-method

Add simulation dependencies

Initialize a new simulation

Determine the largest timestep unit in a simulation

Categorized overview of the SpaDES package

Calculate the hashes of multiple files

Prepare raster for plotting

Filter objects by class

.makeColorMatrix

Convert Raster to color matrix useable by raster function for plotting

Assess whether a list of extents are all equal

Parse arguments and find environments

Copy or move objects from one environment to another

Heading between spatial points.

Simulation environment

.spadesGrob-class

The .spadesGrob class

rasterizeReduced

Convert reduced representation to full raster

SELES - Agent Location at initiation

Default (empty) metadata

Determine which modules in a list are unparsed

Define a new module.

Determine the smallest timeunit in a simulation

.depsPruneEdges

Prune edges to remove cycles in module dependencies

Set colours for plotting Raster* objects.

Assign to the internal SpaDES environment.

doEvent.checkpoint

Simulation checkpoints.

Build edge list for module dependency graph

Time usage in SpaDES

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

Download module data

getModuleVersion

Find the latest module version from a SpaDES module repository

Convert grid.locator units

Download a module from a SpaDES module GitHub repository

Cache method for simList class objects

Compare module version against SpaDES package version and warn if incompatible

Calculate module coverage of unit tests

Read raster to memory

Extract filename (without extension) of a file

.spadesPlotObjects-class

The .spadesPlotObjects class

Specify where to plot

Schedule a simulation event

Open a new plotting window

List simulation objects and their structure

spatialObjects-class

The spatialObjects class

SpaDES time units

Classes defined in SpaDES

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

Simulation modules and dependencies

Make SpatialLines object from two SpatialPoints objects

currentModule,.simList-method

Simulation event lists

.emptyEventList

Blank (template) event list

Run an experiment using spades

Mouse interactions with Plots

Extracts the object names

.spadesPlottables-class

The .spadesPlottables class

The simList_ class

List simulation objects

paddedFloatToChar

Convert numeric to character with padding

.spadesPlot-class

The .spadesPlot class

Make an optimal layout of plots

Simulate a spread process on a landscape.

Check use and existence of params passed to simulation.

Clear plotting device

Extract the file extension of a file

Is an object defined in the .spades environment?

Save objects using .saveObjects in params slot of simInit

Process a simulation event

Display a simple, interactive shiny app of the simList

.updateSpadesPlot

Merge two SpaDES Plot objects

SELES - Initiate agents

Copy a simList object

Get colours for plotting Raster* objects.

Check for the existence of a remote module

The SpaDES environment

SELES - Number of Agents to initiate

Produce a raster of a random Gaussian process.

Open all modules nested within a base directory

The simList class

Run a spatial discrete event simulation

nlayers,list-method

Find the number of layers in a Spatial Object

Create a zip archive of a module subdirectory

Sort a any named object with dotted names first

.arrangeViewports

Determine optimal plotting arrangement of plot objects

Vectorized wrapped normal density function

Convert plotArgs to list of lists

.identifyGrobToPlot

Identify where to get the grob from

Simulation object dependency diagram

Parse and initialize a module

clearStubArtifacts

Clear erroneous archivist artifacts

.fillOutputRows

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

Simulation module dependency diagram

The .simDeps class

Plot spatial grobs (using grid package)

Wrap coordinates or pixels in a torus-like fashion

Convert time units

divergentColors

Divergent colour palette

Get objects from the internal SpaDES environment

Get simulation package dependencies

Specify paths for modules, inputs, and outputs

Split a raster into multiple tiles.

Identify pixels in a circle around a SpatialPoints* object.

Calculate checksums for a module's data files

Build a module dependency graph

Create empty fileTable for inputs and outputs

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

Simulation event diagram

Inputs and outputs

Create new module from template.

specificNumPerPatch

specificNumPerPatch