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SpaDES.core

Core functionality for Spatial Discrete Event System (SpaDES).

This package provides the core framework for a discrete event system to implement a complete data-to-decisions, reproducible workflow (e.g., McIntire et al. (2022) https://doi.org/10.1111/ele.13994, Barros et al. (2022) https://doi.org/10.1111/2041-210X.14034). The core components facilitate the development of modular pieces, and enable the user to include additional functionality by running user-built modules. Includes conditional scheduling, restart after interruption, packaging of reusable modules, tools for developing arbitrary automated workflows, automated interweaving of modules of different temporal resolution, and tools for visualizing and understanding the within-project dependencies.

Website: https://SpaDES-core.PredictiveEcology.org

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

Installation

Current stable release

Install from CRAN:

install.packages("SpaDES.core")

Install from GitHub:

#install.packages("devtools")
library("devtools")
install_github("PredictiveEcology/SpaDES.core", dependencies = TRUE) # master

Development version (unstable)

Install from GitHub:

#install.packages("devtools")
library("devtools")
install_github("PredictiveEcology/SpaDES.core", ref = "development", dependencies = TRUE)

Contributions

Please see CONTRIBUTING.md for information on how to contribute to this project.

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Version

Install

install.packages('SpaDES.core')

Monthly Downloads

372

Version

3.2.1

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/PredictiveEcology/SpaDES.core

Homepage

https://spades-core.predictiveecology.org/

Maintainer

Eliot J B

Last Published

August 29th, 2026

Functions in SpaDES.core (3.2.1)

.addTagsToOutput,simList-method

.addTagsToOutput for simList objects

Test whether there should be any plotting from .plots module parameter

Add simulation dependencies

SpaDES.core-package

Categorized overview of the SpaDES.core package

Plot wrapper intended for use in a SpaDES module

Copy,simList-method

Copy for simList class objects

all.equal.simList

All equal method for simList objects

Plot,simList-method

Plot method for simList objects

.addChangedAttr,simList-method

.addChangedAttr for simList objects

FilterRecursive

Recursively Filter a list

Check for the existence of a remote module

Append attributes

checkModuleLocal

Check for the existence of a module locally

.checkCacheRepo,list-method

.checkCacheRepo for simList objects

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

.cacheMessage,simList-method

.cacheMessage for simList objects

checkModulePath

Check module path

Check use and existence of parameters passed to simulation.

Simple wrapper around data.table::rbindlist

checkModuleMetadata

Statically check a SpaDES module file for malformed metadata

clearCacheEventsOnly

Convenience wrapper around clearCache for SpaDES events

clearCache,simList-method

clearCache for simList objects

Calculate checksum for a module's data files

Simulation checkpoints

Named list of core SpaDES modules

Create a copy of an existing module

A citation method for SpaDES modules

convertToPackage

Convert standard module code into an R package

codeCheckModule

Statically check a SpaDES module's source code (v2)

Filter objects by class

Methods for .wrap and .unwrap

Build edge list for module dependency graph

Define an output object of a module

Alternative way to define events in SpaDES.core

Build a module dependency graph

Determine module load order

Zip a simList and various files

Define a new module.

defineParameter

Define a parameter used in a module

.depsPruneEdges

Prune edges to remove cycles in module dependencies

.fnsReachableFrom

Transitive closure of module-local functions reachable from a starting function

Guess package of a function

Memory safe alternative to do.call

.knownDotParams

Reserved module parameter names

.charLiteralsIn

Collect character-string literals appearing in a parsed expression

Find objects if passed as character strings

Finish initialization of a simList after the .inputObjects phase

strip GitHub repo info from vector of packages

Fill in unspecified dotParams for a module

Process a simulation event

Download a module from a SpaDES module GitHub repository

Process one event with recovery wrapping

Download module data

.restartResolveSim

Resolve the sim argument for the restart functions

.restartModuleToReparse

Identify the module whose source should be re-parsed on restart

.restartRefreshBindings

Re-establish the mod/P active bindings for re-parsed modules (shared)

.restartRestoreEventObjs

Restore one recovered event's object state on restart (shared rewind core)

.runInputObjectsPhase

Run (or resume) a simList's .inputObjects phase

.reparseModules

Re-parse module source into a simList

Blank (template) event list

Open a file for editing

Extract a url from module metadata

Define an input object that the module expects.

Simulation event diagram

.findElementsInEnv

Find all references to sim$

Create empty fileTable for inputs and outputs

.fillOutputRows

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

Default (empty) metadata

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

Extract filename (without extension) of a file

Get and set global simulation parameters

Get copies of sample files for examples and tests

findProjectPath

Find the project root directory

getModuleVersion

Find the latest module version from a SpaDES module repository

Find simList in a nested list

.identifyChildModules

Identify child modules from a recursive list

.getModuleInputObjects

Extract the user-defined .inputObjects function from a module

.findModuleName

Identify module names up to a given recursive level

A slightly modified version of getOption()

Check is module uses module namespacing

Determine the largest timestep unit in a simulation

initialize,simList-method

Generate a simList object

memoryUseThisSession

Estimate memory used with system("ps")

.fileExtensions

File extensions map

makeMemoisable.simList

Make simList correctly work with memoise

Load a saved simList and ancillary files

inputObjectNames

Per-module input object names

._inputObjectsDF

Create an empty data.frame object for use with inputObjects or outputObjects

Attach missing attributes from x to y

Determine the smallest timeunit in a simulation

Simulation module dependency diagram

Defaults values used in defineModule

.moduleDeps-class

The .moduleDeps class

Extract a module's parameters, inputs, or outputs

Build a module dependency graph

moduleCodeFiles

Extract the full file paths for R source code

Parse and extract module metadata

Calculate module coverage of unit tests

.modifySearchPath

Modify package order in search path

Parse and extract a module's version

Create new module code file

Identify synonyms in a simList

Text for no event with that name

Create template testing structures for new modules

Simulation object dependency diagram

Create new module from template

Create new SpaDES project

.callingModuleName

Namespacing within SpaDES

objSize.simList

Object size for simList

.parseModulePartial

Parse and initialize a module

Get module or simulation package dependencies

.preDigestByClass,simList-method

Pre-digesting method for simList

.parseElems,simList-method

.parseElems for simList class objects

Extract or replace an object from the simulation environment

Open all modules nested within a base directory

paramCheckOtherMods

Test and update a parameter against same parameter in other modules

Get and set simulation parameters

The SpaDES.core package environment

Prepend module name to a message

Objects exported from other packages

.prepareOutput,simList-method

.prepareOutput for simList objects

Read raster to memory

progressInterval

Get and set simulation progress bar details

Restart R programmatically

Determine the size of a remotely hosted file

The SpaDES.core variable to switch between quick and robust checking

Simple wrapper to load any Raster* object

.robustDigest,simList-method

.robustDigest for simList objects

saveSimOnExitSimInit

Save the simList on exit from simInit, mirroring saveSimOnExit()

Runs a series of code checks during simInit()

Save objects using .saveObjects in params slot of simInit

Generate random strings

scheduleConditionalEvent

Schedule a conditional simulation event

Restart an interrupted simulation

Retrieve environment for saving interrupted simulations

Save a whole simList object to disk

.runModuleInputObjects

Run module's .inputObjects

Generate simulation file name

The .simDeps class

Initialize a new simulation

.simInitMessageHandler

Calling handlers that prefix simInit-phase messages/warnings

Simulation environment

simInitAndSpades2

simInitAndSpades2 is a convenience wrapper for do.call(simInitAndSpades, listOfArgs), i.e., a user can pass a list of all the arguments.

Schedule a simulation event

Get and set default working directories

show,simList-method

Simulation event lists

Time usage in SpaDES

Simulation modules and dependencies

Simulation inputs

Metadata accessors

newObjectsCreated

Show which objects were first created in a simInit or spades call

Specify paths for modules, inputs, outputs, and temporary rasters

Simulation outputs

The simList class

Pick the singular or plural form for a message

Determine which modules in a list are unparsed

SpaDES time units

suppliedElsewhere

Assess whether an object has or will be supplied from elsewhere

spades2 is a convenience wrapper for do.call(spades, listOfArgs), i.e., a user can pass a list of all the arguments.

SpaDES.core options

[,simList,character,ANY-method

Extract an intact simList but with subset of objects

.tagsByClass,simList-method

.tagsByClass for simList objects

Convert time units

tryCatch that keeps warnings, errors and value (result)

Classes defined in SpaDES

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

Create a zip archive of a module subdirectory

Chose verb conjugation for "to be"

Write simulation event info to file

Write RNG state info to file

Use GitHub actions for automated module checking