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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

2.1.8

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 18th, 2025

Functions in SpaDES.core (2.1.8)

.addChangedAttr,simList-method

.addChangedAttr for simList objects

FilterRecursive

Recursively Filter a list

Plot wrapper intended for use in a SpaDES module

Add simulation dependencies

all.equal.simList

All equal method for simList objects

.addTagsToOutput,simList-method

.addTagsToOutput for simList objects

Plot,simList-method

Plot method for simList objects

Copy,simList-method

Copy for simList class objects

SpaDES.core-package

Categorized overview of the SpaDES.core package

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

checkModulePath

Check module path

Check for the existence of a remote module

checkModuleLocal

Check for the existence of a module locally

Check use and existence of parameters passed to simulation.

.cacheMessage,simList-method

.cacheMessage for simList objects

Simple wrapper around data.table::rbindlist

Append attributes

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

Simulation checkpoints

.checkCacheRepo,list-method

.checkCacheRepo for simList objects

Calculate checksum for a module's data files

Named list of core SpaDES modules

Create a copy of an existing module

Methods for .wrap and .unwrap

Filter objects by class

Define an output object of a module

Alternative way to define events in SpaDES.core

A citation method for SpaDES modules

clearCache,simList-method

clearCache for simList objects

convertToPackage

Convert standard module code into an R package

defineParameter

Define a parameter used in a module

Zip a simList and various files

strip GitHub repo info from vector of packages

Define a new module.

Build edge list for module dependency graph

Build a module dependency graph

Find objects if passed as character strings

Process a simulation event

.depsPruneEdges

Prune edges to remove cycles in module dependencies

Determine module load order

Define an input object that the module expects.

Default (empty) metadata

Download module data

Simulation event diagram

Guess package of a function

Extract a url from module metadata

Download a module from a SpaDES module GitHub repository

Open a file for editing

Blank (template) event list

.knownDotParams

Reserved module parameter names

Extract filename (without extension) of a file

Find simList in a nested list

.fillOutputRows

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

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

getModuleVersion

Find the latest module version from a SpaDES module repository

Create empty fileTable for inputs and outputs

.getModuleInputObjects

Extract the user-defined .inputObjects function from a module

.findModuleName

Identify module names up to a given recursive level

.findElementsInEnv

Find all references to sim$

Get and set global simulation parameters

Get copies of sample files for examples and tests

.identifyChildModules

Identify child modules from a recursive list

initialize,simList-method

Generate a simList object

.fileExtensions

File extensions map

Load a saved simList and ancillary files

._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()

Attach missing attributes from x to y

.modifySearchPath

Modify package order in search path

Determine the largest timestep unit in a simulation

makeMemoisable.simList

Make simList correctly work with memoise

moduleCodeFiles

Extract the full file paths for R source code

Calculate module coverage of unit tests

Determine the smallest timeunit in a simulation

memoryUseThisSession

Estimate memory used with system("ps")

Simulation module dependency diagram

Defaults values used in defineModule

.moduleDeps-class

The .moduleDeps class

.callingModuleName

Namespacing within SpaDES

Create template testing structures for new modules

Create new module from template

Parse and extract module metadata

Parse and extract a module's version

Build a module dependency graph

Create new SpaDES project

Create new module code file

Text for no event with that name

Extract a module's parameters, inputs, or outputs

.parseElems,simList-method

.parseElems for simList class objects

Identify synonyms in a simList

paramCheckOtherMods

Test and update a parameter against same parameter in other modules

Simulation object dependency diagram

Extract or replace an object from the simulation environment

Get and set simulation parameters

Open all modules nested within a base directory

objSize.simList

Object size for simList

Prepend module name to a message

Get module or simulation package dependencies

Simple wrapper to load any Raster* object

Read raster to memory

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

.prepareOutput,simList-method

.prepareOutput for simList objects

progressInterval

Get and set simulation progress bar details

.preDigestByClass,simList-method

Pre-digesting method for simList

.parseModulePartial

Parse and initialize a module

The SpaDES.core package environment

Restart R programmatically

Runs a series of code checks during simInit()

Generate random strings

Save objects using .saveObjects in params slot of simInit

.runModuleInputObjects

Run module's .inputObjects

.robustDigest,simList-method

.robustDigest for simList objects

Save a whole simList object to disk

Objects exported from other packages

Determine the size of a remotely hosted file

Restart an interrupted simulation

Schedule a simulation event

Initialize a new simulation

Retrieve environment for saving interrupted simulations

scheduleConditionalEvent

Schedule a conditional 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.

Generate simulation file name

show,simList-method

The .simDeps class

Get and set default working directories

Simulation event lists

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

The simList class

Time usage in SpaDES

Metadata accessors

Simulation modules and dependencies

newObjectsCreated

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

Simulation environment

Simulation inputs

Simulation outputs

Convert time units

SpaDES.core options

Classes defined in SpaDES

.tagsByClass,simList-method

.tagsByClass for simList objects

SpaDES time units

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

[,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

Determine which modules in a list are unparsed

tryCatch that keeps warnings, errors and value (result)

Write RNG state info to file

Use GitHub actions for automated module checking

Create a zip archive of a module subdirectory

Write simulation event info to file

Chose verb conjugation for "to be"

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