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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

470

Version

3.0.4

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

January 11th, 2026

Functions in SpaDES.core (3.0.4)

Simulation checkpoints

.checkCacheRepo,list-method

.checkCacheRepo for simList objects

.cacheMessage,simList-method

.cacheMessage for simList objects

Check for the existence of a remote module

checkModulePath

Check module path

checkModuleLocal

Check for the existence of a module locally

Check use and existence of parameters passed to simulation.

Simple wrapper around data.table::rbindlist

Append attributes

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

createDESCRIPTIONandDocs

Convert standard module code into an R package

Calculate checksum for a module's data files

Named list of core SpaDES modules

convertToPackage

Convert standard module code into an R package

clearCache,simList-method

clearCache for simList objects

A citation method for SpaDES modules

Filter objects by class

Define an output object of a module

clearCacheEventsOnly

Convenience wrapper around clearCache for SpaDES events

Create a copy of an existing module

.depsPruneEdges

Prune edges to remove cycles in module dependencies

Build edge list for module dependency graph

defineParameter

Define a parameter used in a module

Alternative way to define events in SpaDES.core

Zip a simList and various files

Build a module dependency graph

Memory safe alternative to do.call

Determine module load order

Find objects if passed as character strings

Download module data

Simulation event diagram

.knownDotParams

Reserved module parameter names

Guess package of a function

Download a module from a SpaDES module GitHub repository

Default (empty) metadata

Blank (template) event list

Define a new module.

Methods for .wrap and .unwrap

.fillOutputRows

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

Extract filename (without extension) of a file

Define an input object that the module expects.

.findElementsInEnv

Find all references to sim$

Process a simulation event

Get copies of sample files for examples and tests

Extract a url from module metadata

Find simList in a nested list

Get and set global simulation parameters

initialize,simList-method

Generate a simList object

Create empty fileTable for inputs and outputs

Determine the largest timestep unit in a simulation

getModuleVersion

Find the latest module version from a SpaDES module repository

Check is module uses module namespacing

._inputObjectsDF

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

.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()

.identifyChildModules

Identify child modules from a recursive list

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

strip GitHub repo info from vector of packages

Open a file for editing

memoryUseThisSession

Estimate memory used with system("ps")

Attach missing attributes from x to y

.fileExtensions

File extensions map

moduleCodeFiles

Extract the full file paths for R source code

Determine the smallest timeunit in a simulation

Parse and extract a module's version

Calculate module coverage of unit tests

.modifySearchPath

Modify package order in search path

.callingModuleName

Namespacing within SpaDES

Defaults values used in defineModule

.moduleDeps-class

The .moduleDeps class

Text for no event with that name

Simulation module dependency diagram

Load a saved simList and ancillary files

Build a module dependency graph

makeMemoisable.simList

Make simList correctly work with memoise

Extract a module's parameters, inputs, or outputs

Create new SpaDES project

Create new module from template

Create template testing structures for new modules

Parse and extract module metadata

Simulation object dependency diagram

Extract or replace an object from the simulation environment

Open all modules nested within a base directory

Get module or simulation package dependencies

.prepareOutput,simList-method

.prepareOutput for simList objects

paramCheckOtherMods

Test and update a parameter against same parameter in other modules

progressInterval

Get and set simulation progress bar details

Identify synonyms in a simList

Create new module code file

The SpaDES.core package environment

.preDigestByClass,simList-method

Pre-digesting method for simList

Get and set simulation parameters

.parseElems,simList-method

.parseElems for simList class objects

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

Generate random strings

Restart an interrupted simulation

Determine the size of a remotely hosted file

Read raster to memory

objSize.simList

Object size for simList

.robustDigest,simList-method

.robustDigest for simList objects

.parseModulePartial

Parse and initialize a module

Prepend module name to a message

Objects exported from other packages

Simple wrapper to load any Raster* object

Save a whole simList object to disk

Restart R programmatically

Get and set default working directories

Runs a series of code checks during simInit()

The .simDeps class

show,simList-method

Save objects using .saveObjects in params slot of simInit

Retrieve environment for saving interrupted simulations

.runModuleInputObjects

Run module's .inputObjects

scheduleConditionalEvent

Schedule a conditional simulation event

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.

Simulation event lists

newObjectsCreated

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

Generate simulation file name

Simulation environment

Simulation modules and dependencies

Simulation outputs

Metadata accessors

Initialize a new simulation

Simulation inputs

.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.

suppliedElsewhere

Assess whether an object has or will be supplied from elsewhere

SpaDES.core options

The simList class

SpaDES time units

Time usage in SpaDES

Classes defined in SpaDES

[,simList,character,ANY-method

Extract an intact simList but with subset of objects

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

Use GitHub actions for automated module checking

Write simulation event info to file

Determine which modules in a list are unparsed

tryCatch that keeps warnings, errors and value (result)

Chose verb conjugation for "to be"

Create a zip archive of a module subdirectory

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

Write RNG state info to file

Convert time units

Copy,simList-method

Copy for simList class objects

all.equal.simList

All equal method for simList objects

SpaDES.core-package

Categorized overview of the SpaDES.core package

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

Plot,simList-method

Plot method for simList objects

Add simulation dependencies

.addTagsToOutput,simList-method

.addTagsToOutput for simList objects

Plot wrapper intended for use in a SpaDES module

.addChangedAttr,simList-method

.addChangedAttr for simList objects

FilterRecursive

Recursively Filter a list