SpaDES-package: Categorized overview of the `SpaDES` package

Description

This package allows implementation a variety of simulation-type models, with a focus on spatially explicit 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 various spatial data formats, as well as non-spatial data.

Bug reports: https://github.com/PredictiveEcology/SpaDES/issues

Module repository: https://github.com/PredictiveEcology/SpaDES-modules

Wiki: https://github.com/PredictiveEcology/SpaDES/wiki

Arguments

1 Spatial discrete event simulation (<code>SpaDES</code>)

A collection of top-level functions for doing spatial discrete event simulation.

1.1 Simulations

There are two workhorse functions that initialize and run a simulation, and third function for doing multiple spades runs:

`simInit`	Initialize a new simulation
`spades`	Run a discrete event simulation
`experiment`	Run multiple `spades` calls

1.2 Events

Within a module, important simulation functions include:

`scheduleEvent`	Schedule a simulation event
`removeEvent`	Remove an event from the simulation queue (not yet implemented)

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1.2 <code>simList</code> methods

Collections of commonly used functions to retrieve or set slots (and their elements) of a simList object are summarized further below.

1.2.1 Simulation parameters

`globals`	List of global simulation parameters.
`params`	Nested list of all simulation parameter.
`P`	Namespaced version of `params` (i.e., do not have to specify module name).

1.2.2 loading from disk, saving to disk

`inputs`	List of loaded objects used in simulation. (advanced)
`outputs`	List of objects to save during simulation. (advanced)

1.2.3 objects in simList

`ls`, `objects`	Names of objects referenced by the simulation environment.
`ls.str`	List the structure of the simList objects.
`objs`	List of objects referenced by the simulation environment.

1.2.4 Simulation paths

Accessor functions for the paths slot and its elements.

`cachePath`	Global simulation cache path.	`modulePath`
Global simulation module path.	`inputPath`	Global simulation input path.
`outputPath`	Global simulation output path.	`paths`
Global simulation paths (cache, modules, inputs, outputs).	`cachePath`	Global simulation cache path.

1.2.5 Simulation times

Accessor functions for the simtimes slot and its elements.

`time`	Current simulation time, in units of longest module.
`start`	Simulation start time, in units of longest module.
`end`	Simulation end time, in units of longest module.
`times`	List of all simulation times (current, start, end), in units of longest module..

1.2.6 Simulation event queues

Accessor functions for the events and completed slots. By default, the event lists are shown when the simList object is printed, thus most users will not require direct use of these methods.

`events`	Scheduled simulation events (the event queue). (advanced)
`current`	Currently executing event. (advanced)
`completed`	Completed simulation events. (advanced)

1.2.7 Modules and dependencies

Accessor functions for the depends, modules, and .loadOrder slots. These are included for advanced users.

`depends`	List of simulation module dependencies. (advanced)
`modules`	List of simulation modules to be loaded. (advanced)

1.2.8 simList environment

The simList has a slot called .envir which is an environment. All objects in the simList are actually in this environment, i.e., the simList is not entirely just a list. In R, environments use pass-by-reference semantics, which means that copying an simList object using normal R assignment operation, e.g., sim2 <- sim1, will not copy the objects contained within the .envir slot. The two objects sim1 and sim2 will shared identical objects within that slot. Sometimes, this not desired, and a true copy is required.

`envir`	Access the environment of the simList directly (advanced)
`copy`	Deep copy of a simList. (advanced)

1.2.9 Checkpointing

Accessor method	Module	Description
`checkpointFile`	`.checkpoint`	Name of the checkpoint file. (advanced)
`checkpointInterval`	`.checkpoint`	The simulation checkpoint interval. (advanced)

1.2.10 Progress Bar

`progressType`	`.progress`	Type of graphical progress bar used. (advanced)
`progressInterval`	`.progress`	Interval for the progress bar. (advanced)

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1.3 Module operations

Modules are the basic unit of SpaDES. These are generally created and stored locally, or are downloaded from remote repositories, including our SpaDES-modules repository on GitHub.

`checksums`	Verify (and optionally write) checksums for a module's data files.
`downloadModule`	Open all modules nested within a base directory
`getModuleVersion`	Get the latest module version # from module repository
`newModule`	Create new module from template
`newModuleDocumentation`	Create empty documentation for a new module
`openModules`	Open all modules nested within a base directory
`moduleMetadata`	Shows the module metadata
`zipModule`	Zip a module and its associated files

1.4 Module metadata

Each module requires several items to be defined. These comprise the metadata for that module (including default parameter specifications, inputs and outputs), and are currently written at the top of the module's .R file.

`defineModule`	Define the module metadata
`defineParameter`	Specify a parameter's name, value and set a default
`expectsInput`	Specify an input object's name, class, description, sourceURL and other specifications
`createsOutput`	Specify an output object's name, class, description and other specifications

1.5 Module dependencies

Once a set of modules have been chosen, the dependency information is automatically calculated once simInit is run. There are several functions to assist with dependency information:

`depsEdgeList`	Build edge list for module dependency graph
`depsGraph`	Build a module dependency graph using `igraph`

1.6 Exported <code>SpaDES</code> object classes

simList The 'simList' class

1.7 Caching

Caching can be done in a variety of ways, most of which are up to the module developer. However, the one most common usage would be to cache a simulation run. This might be useful if a simulation is very long, has been run once, and the goal is just to retrieve final results. This would be an alternative to manually saving the outputs.

See example in spades, achieved by using cache = TRUE argument.

`cache`	Caches a spades call, but often used as arg in `spades`
`showCache`	Shows information about the objects in the cache
`clearCache`	Removes objects from the cache
`clearStubArtifacts`	Removes some errors in cached files

A module developer can build caching into their module by creating cached versions of their functions.

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2 Module functions

A collection of functions that help with making modules, in addition to all the other R packages and code.

2.1 Spatial spreading/distances methods

Spatial contagion is a key phenomenon for spatially explicit simulation models. Contagion can be modelled using discrete approaches or continuous approaches. Several SpaDES functions assist with these:

`spread`	Contagious cellular automata
`rings`	Identify rings around focal cells (e.g., buffers and donuts)
`adj`	An optimized (i.e., faster) version of `adjacent`
`cir`	Identify pixels in a circle around a `SpatialPoints*` object
`distanceFromEachPoint`	Fast calculation of distance surfaces

2.2 Spatial agent methods

Agents have several methods and functions specific to them:

`crw`	Simple correlated random walk function
`heading`	Determines the heading between SpatialPoints*
`makeLines`	Makes `SpatialLines` object for, e.g., drawing arrows
`move`	A meta function that can currently only take "crw"
`specificNumPerPatch`	Initiate a specific number of agents per patch

2.3 GIS operations

In addition to the vast amount of GIS operations available in R (mostly from contributed packages such as sp, raster, maps, maptools and many others), we provide the following GIS-related functions:

equalExtent Assess whether a list of extents are all equal

2.4 Map-reduce - type operations

These functions convert between reduced and mapped representations of the same data. This allows compact representation of, e.g., rasters that have many individual pixels that share identical information.

rasterizeReduced Convert reduced representation to full raster

2.5 Colors in Raster* objects

We likely will not want the default colours for every map. Here are several helper functions to add to, set and get colors of Raster* objects:

`setColors`	Set colours for plotting `Raster*` objects
`getColors`	Get colours in a `Raster*` objects
`divergentColors`	Create a color palette with diverging colors around a middle

2.6 Random Map Generation

It is often useful to build dummy maps with which to build simulation models before all data are available. These dummy maps can later be replaced with actual data maps.

`gaussMap`	Creates a random map using gaussian random fields
`randomPolygons`	Creates a random polygon with specified number of classes

2.7 Checking for the existence of objects

SpaDES modules will often require the existence of objects in the simList. These are helpers for assessing this:

`checkObject`	Check for a existence of an object within a `simList`
`checkPath`	Checks the specified filepath for formatting consistencies

2.8 SELES-type approach to simulation

These functions are essentially skeletons and are not fully implemented. They are intended to make translations from SELES. You must know how to use SELES for these to be useful:

`agentLocation`	Agent location
`initiateAgents`	Initiate agents into a SpatialPointsDataFrame
`numAgents`	Number of agents
`probInit`	Probability of intiating an agent or event
`transitions`	Transition probability

2.9 Miscellaneous

Functions that may be useful within a SpaDES context

`inRange`	Test whether a number lies within range [a,b]
`layerNames`	Get layer names for numerous object classes
`loadPackages`	Simple wrapper for loading packages
`numLayers`	Return number of layers
`paddedFloatToChar`	Wrapper for padding (e.g., zeros) floating numbers to character
`updateList`	Update values in a named list

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3 Plotting

There are several user-accessible plotting functions that are optimized for modularity and speed of plotting:

Commonly used:

Plot The workhorse plotting function

Simulation diagrams:

`eventDiagram`	Gantt chart representing the events in a completed simulation.
`moduleDiagram`	Network diagram of simplified module (object) dependencies.
`objectDiagram`	Sequence diagram of detailed object dependencies.

Other useful plotting functions:

`clearPlot`	Helpful for resolving many errors
`clickValues`	Extract values from a raster object at the mouse click location(s)
`clickExtent`	Zoom into a raster or polygon map that was plotted with `Plot`
`clickCoordinates`	Get the coordinates, in map units, under mouse click
`dev`	Specify which device to plot on, making a non-RStudio one as default
`newPlot`	Open a new default plotting device
`rePlot`	Replots all elements of device for refreshing or moving plot

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4 File operations

In addition to R's file operations, we have added several here to aid in bulk loading and saving of files for simulation purposes:

`getFileName`	Get the name of current file
`loadFiles`	Load simulation objects according to a filelist
`rasterToMemory`	Read a raster from file to RAM
`saveFiles`	Save simulation objects according to outputs and params

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5 Sample data and modules included in package

Five maps and three modules are included within the SpaDES package

5.1 Data

Several dummy data sets are included for testing of functionality

spadesMaps Help showing included maps

5.2 Modules

Several dummy modules are included for testing of functionality. These can be found with file.path(find.package("SpaDES"), "sampleModules")

`randomLandscapes`	Imports, updates, and plots several raster map layers
`caribouMovement`	A simple agent-based (a.k.a., individual-based) model
`fireSpread`	A simple model of a spatial spread process

6 Package options

SpaDES uses the following options to configure behaviour:

spades.cachePath: The default local directory in which to cache simulation outputs. Default is a temporary directory (typically /tmp/SpaDES/cache).
spades.inputPath: The default local directory in which to look for simulation inputs. Default is a temporary directory (typically /tmp/SpaDES/inputs).
spades.lowMemory: If true, some functions will use more memory efficient (but slower) algorithms. Default FALSE.
spades.modulePath: The default local directory where modules and data will be downloaded and stored. Default is a temporary directory (typically /tmp/SpaDES/modules).
spades.moduleRepo: The default GitHub repository to use when downloading modules. Default "PredictiveEcology/SpaDES-modules".
spades.nCompleted: The maximum number of completed events to retain in the completed event queue. Default 1000L.
spades.outputPath: The default local directory in which to save simulation outputs. Default is a temporary directory (typically /tmp/SpaDES/outputs).
spades.tolerance: The default tolerance value used for floating point number comparisons. Default .Machine$double.eps^0.5.