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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. The suggested package NLMR can be installed from the repository (https://PredictiveEcology.r-universe.dev).

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

853

Version

2.1.6

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

September 2nd, 2025

Functions in SpaDES.core (2.1.6)

.checkCacheRepo,list-method

.checkCacheRepo for simList objects

.cacheMessage,simList-method

.cacheMessage for simList objects

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

Check for the existence of a remote module

checkModulePath

Check module path

checkModuleLocal

Check for the existence of a module locally

Append attributes

Simple wrapper around data.table::rbindlist

Check use and existence of parameters passed to simulation.

Simulation checkpoints

Alternative way to define events in SpaDES.core

A citation method for SpaDES modules

Define an output object of a module

Filter objects by class

Methods for .wrap and .unwrap

Named list of core SpaDES modules

Calculate checksum for a module's data files

convertToPackage

Convert standard module code into an R package

Create a copy of an existing module

clearCache,simList-method

clearCache for simList objects

Zip a simList and various files

Build edge list for module dependency graph

.depsPruneEdges

Prune edges to remove cycles in module dependencies

Define a new module.

defineParameter

Define a parameter used in a module

strip GitHub repo info from vector of packages

Process a simulation event

Find objects if passed as character strings

Download module data

Extract a url from module metadata

Default (empty) metadata

Build a module dependency graph

Download a module from a SpaDES module GitHub repository

Simulation event diagram

Define an input object that the module expects.

Determine module load order

Blank (template) event list

Open a file for editing

.findModuleName

Identify module names up to a given recursive level

Extract filename (without extension) of a file

Guess package of a function

.knownDotParams

Reserved module parameter names

.getModuleInputObjects

Extract the user-defined .inputObjects function from a module

getModuleVersion

Find the latest module version from a SpaDES module repository

Find simList in a nested list

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

.fillOutputRows

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

.fileExtensions

File extensions map

initialize,simList-method

Generate a simList object

Get and set global simulation parameters

.findElementsInEnv

Find all references to sim$

Load a saved simList and ancillary files

Create empty fileTable for inputs and outputs

Simulation module dependency diagram

._inputObjectsDF

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

Check is module uses module namespacing

A slightly modified version of getOption()

.identifyChildModules

Identify child modules from a recursive list

Attach missing attributes from x to y

Determine the smallest timeunit in a simulation

Determine the largest timestep unit in a simulation

moduleCodeFiles

Extract the full file paths for R source code

makeMemoisable.simList

Make simList correctly work with memoise

memoryUseThisSession

Estimate memory used with system("ps")

.moduleDeps-class

The .moduleDeps class

.modifySearchPath

Modify package order in search path

Get copies of sample files for examples and tests

Calculate module coverage of unit tests

Create new module code file

Extract a module's parameters, inputs, or outputs

Defaults values used in defineModule

Create template testing structures for new modules

Create new module from template

Create new SpaDES project

Parse and extract a module's version

Text for no event with that name

Build a module dependency graph

Parse and extract module metadata

.callingModuleName

Namespacing within SpaDES

Open all modules nested within a base directory

objSize.simList

Object size for simList

Get module or simulation package dependencies

Simulation object dependency diagram

Identify synonyms in a simList

.parseElems,simList-method

.parseElems for simList class objects

Prepend module name to a message

Extract or replace an object from the simulation environment

Get and set simulation parameters

paramCheckOtherMods

Test and update a parameter against same parameter in other modules

.prepareOutput,simList-method

.prepareOutput for simList objects

.parseModulePartial

Parse and initialize a module

.preDigestByClass,simList-method

Pre-digesting method for simList

progressInterval

Get and set simulation progress bar details

Read raster to memory

Simple wrapper to load any Raster* object

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

The SpaDES.core package environment

Runs a series of code checks during simInit()

Determine the size of a remotely hosted file

Restart R programmatically

Objects exported from other packages

Save objects using .saveObjects in params slot of simInit

Generate random strings

.robustDigest,simList-method

.robustDigest for simList objects

Restart an interrupted simulation

Save a whole simList object to disk

.runModuleInputObjects

Run module's .inputObjects

show,simList-method

Retrieve environment for saving interrupted simulations

Generate simulation file name

The .simDeps class

Schedule a simulation event

simInitAndSpades2

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

scheduleConditionalEvent

Schedule a conditional simulation event

Initialize a new simulation

Get and set default working directories

newObjectsCreated

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

Simulation modules and dependencies

Simulation inputs

Metadata accessors

Simulation event lists

The simList class

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

Simulation environment

Simulation outputs

Time usage in SpaDES

Determine which modules in a list are unparsed

[,simList,character,ANY-method

Extract an intact simList but with subset of objects

suppliedElsewhere

Assess whether an object has or will be supplied from elsewhere

Classes defined in SpaDES

Convert time units

.tagsByClass,simList-method

.tagsByClass for simList objects

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

tryCatch that keeps warnings, errors and value (result)

SpaDES time units

SpaDES.core options

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

Write RNG state info to file

Write simulation event info to file

Create a zip archive of a module subdirectory

Use GitHub actions for automated module checking

Chose verb conjugation for "to be"

Copy,simList-method

Copy for simList class objects

.addChangedAttr,simList-method

.addChangedAttr for simList objects

.addTagsToOutput,simList-method

.addTagsToOutput for simList objects

Add simulation dependencies

all.equal.simList

All equal method for simList objects

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

Plot,simList-method

Plot method for simList objects

Plot wrapper intended for use in a SpaDES module

SpaDES.core-package

Categorized overview of the SpaDES.core package

FilterRecursive

Recursively Filter a list