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SpaDES (version 1.1.3)

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

1.1.3

License

GPL-3

Issues

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Stars

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Repository

https://github.com/PredictiveEcology/SpaDES

Maintainer

Alex M Chubaty

Last Published

April 18th, 2016

Functions in SpaDES (1.1.3)

Create empty fileTable for inputs and outputs

Importing some grid functions

.makeSpadesPlot

Make a .spadesPlot class object

Open all modules nested within a base directory

Clear plotting device

getModuleVersion

Find the latest module version from a SpaDES module repository

Check for the existence of a remote module

Specify paths for modules, inputs, and outputs

Generate random strings

Calculate checksums for a module's data files

.updateSpadesPlot

Merge two SpaDES Plot objects

Copy a simList object

Define a new module.

show,simList-method

Save objects using .saveObjects in params slot of simInit

Assess whether a list of extents are all equal

Heading between spatial points.

Simulation environment

Vectorized wrapped normal density function

.spadesPlottables-class

The .spadesPlottables class

Copy or move objects from one environment to another

Determine which modules in a list are unparsed

Get and set simulation parameters.

The simList class

Compare module version against SpaDES package version and warn if incompatible

Determine the smallest timeunit in a simulation

Check use and existence of params passed to simulation.

divergentColors

Divergent colour palette

SELES - Initiate agents

Check filepath.

Parse arguments and find environments

Get simulation package dependencies

Plot spatial grobs (using grid package)

nlayers,list-method

Find the number of layers in a Spatial Object

Remove any reference to environments in a simList

.spadesGrob-class

The .spadesGrob class

.identifyGrobToPlot

Identify where to get the grob from

.depsPruneEdges

Prune edges to remove cycles in module dependencies

SpaDES time units

Process a simulation event

.arrangement-class

The .arrangement class

Convert time units

paddedFloatToChar

Convert numeric to character with padding

Assign to the internal SpaDES environment.

Open a new plotting window

Get the name of a source-ed file

Download module data

SELES - Number of Agents to initiate

Convert plotArgs to list of lists

Classes defined in SpaDES

Filter objects by class

Calculate the hashes of multiple files

Default (empty) metadata

Is an object defined in the .spades environment?

Extract the file extension of a file

defineParameter

Define a parameter used in a module

The simList_ class

Build a module dependency graph

doEvent.checkpoint

Simulation checkpoints.

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

SELES - Probability of Initiation

Get objects from the internal SpaDES environment

Determine the largest timestep unit in a simulation

.fileExtensions

File extensions map

Simulation event diagram

.fillOutputRows

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

Calculate module coverage of unit tests

List simulation objects and their structure

Add a module to a moduleList

Get colours for plotting Raster* objects.

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

SELES - Transitioning to next time step

Parse and extract module metadata

Schedule a simulation event

Read raster to memory

Download a module from a SpaDES module GitHub repository

Identify pixels in a circle around a SpatialPoints* object.

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

.arrangeViewports

Determine optimal plotting arrangement of plot objects

.moduleDeps-class

The .moduleDeps class

Prepare raster for plotting

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

Simulate a spread process on a landscape.

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

.spadesPlot-class

The .spadesPlot class

Run an experiment using spades

Extracts the object names

Create new module from template.

Extract filename (without extension) of a file

.makeColorMatrix

Convert Raster to color matrix useable by raster function for plotting

Split a raster into multiple tiles.

Produce a raster of a random Gaussian process.

Extract or replace an object from the simulation environment

Dummy maps included with SpaDES

The SpaDES environment

Sort a any named object with dotted names first

Simulation module dependency diagram

Categorized overview of the SpaDES package

Mouse interactions with Plots

Extract the layer names of Spatial Objects

Simulation object dependency diagram

SELES - Agent Location at initiation

Make an optimal layout of plots

Normalize filepath

Display a simple, interactive shiny app of the simList

specificNumPerPatch

specificNumPerPatch

clearStubArtifacts

Clear erroneous archivist artifacts

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

Specify where to plot

List simulation objects

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

Cache method for simList class objects

initialize,simList-method

Generate a simList object

rasterizeReduced

Convert reduced representation to full raster

Determine module load order

Add simulation dependencies

Time usage in SpaDES

Make SpatialLines object from two SpatialPoints objects

.spadesPlotObjects-class

The .spadesPlotObjects class

Convert grid.locator units

spatialObjects-class

The spatialObjects class

Wrap coordinates or pixels in a torus-like fashion

Create a zip archive of a module subdirectory

currentModule,.simList-method

Simulation event lists

Run a spatial discrete event simulation

Build edge list for module dependency graph

.emptyEventList

Blank (template) event list

The .simDeps class

Initialize a new simulation

Simulation modules and dependencies

Parse and initialize a module

Set colours for plotting Raster* objects.

Inputs and outputs