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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

1,077

Version

2.0.5

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

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

Homepage

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

Maintainer

Last Published

April 25th, 2024

Functions in SpaDES.core (2.0.5)

Copy,simList-method

Copy for simList class objects

Add a module to a moduleList

Plot,simList-method

Plot method for simList objects

.addChangedAttr,simList-method

.addChangedAttr for simList objects

Plot wrapper intended for use in a SpaDES module

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

Simple wrapper around data.table::rbindlist

SpaDES.core-package

Categorized overview of the SpaDES.core package

Check use and existence of parameters passed to simulation.

.checkCacheRepo,list-method

.checkCacheRepo for simList objects

.cacheMessage,simList-method

.cacheMessage for simList objects

Add simulation dependencies

checkModuleLocal

Check for the existence of a module locally

.addTagsToOutput,simList-method

.addTagsToOutput for simList objects

Check for the existence of a remote module

Simulation checkpoints.

all.equal.simList

All equal method for simList objects

Methods for .wrap and .unwrap

Zip a simList and various files

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

Named list of core SpaDES modules

Alternative way to define events in SpaDES.core

Define an output object of a module

Filter objects by class

Calculate checksum for a module's data files

A citation method for SpaDES modules

.fillOutputRows

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

Build edge list for module dependency graph

.findElementsInEnv

Find all references to sim$

Build a module dependency graph

Determine module load order

convertToPackage

Convert standard module code into an R package

Define an input object that the module expects.

Determine the largest timestep unit in a simulation

Attach missing attributes from x to y

Create new SpaDES project

Define a new module.

.getModuleInputObjects

Extract the user-defined .inputObjects function from a module

defineParameter

Define a parameter used in a module

Create a copy of an existing module

.fileExtensions

File extensions map

Open a file for editing

.identifyChildModules

Identify child modules from a recursive list

Extract a url from module metadata

Create new module code file

Extract filename (without extension) of a file

Guess package of a function

initialize,simList-method

Generate a simList object

strip GitHub repo info from vector of packages

.depsPruneEdges

Prune edges to remove cycles in module dependencies

clearCache,simList-method

clearCache for simList objects

Simulation module dependency diagram

Build a module dependency graph

Find objects if passed as character strings

Download a module from a SpaDES module GitHub repository

scheduleConditionalEvent

Schedule a conditional simulation event

Download module data

Get copies of sample files for examples and tests

Process a simulation event

Schedule a simulation event

Prepend module name to a message

Blank (template) event list

.parseElems,simList-method

.parseElems for simList class objects

._inputObjectsDF

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

Check is module uses module namespacing

Get and set global simulation parameters

Generate simulation file name

getModuleVersion

Find the latest module version from a SpaDES module repository

Initialize a new simulation

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

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

Save a whole simList object to disk

moduleCodeFiles

Extract the full file paths for R source code

Calculate module coverage of unit tests

Save objects using .saveObjects in params slot of simInit

Defaults values used in defineModule

.moduleDeps-class

The .moduleDeps class

A slightly modified version of getOption()

objSize.simList

Object size for simList

Parse and extract a module's version

Classes defined in SpaDES

Write simulation event info to file

Create empty fileTable for inputs and outputs

Simulation event diagram

Extract or replace an object from the simulation environment

.prepareOutput,simList-method

.prepareOutput for simList objects

Identify synonyms in a simList

Simulation object dependency diagram

.callingModuleName

Namespacing within SpaDES

Default (empty) metadata

Chose verb conjugation for "to be"

.tagsByClass,simList-method

.tagsByClass for simList objects

Generate random strings

.robustDigest,simList-method

.robustDigest for simList objects

Metadata accessors

memoryUseThisSession

Estimate memory used with system("ps")

.preDigestByClass,simList-method

Pre-digesting method for simList

Simulation modules and dependencies

Load a saved simList and ancillary files

Run a spatial discrete event simulation

Convert time units

.findModuleName

Identify module names up to a given recursive level

Find simList in a nested list

[,simList,character,ANY-method

Extract an intact simList but with subset of objects

makeMemoisable.simList

Make simList correctly work with memoise

Restart an interrupted simulation

Simulation event lists

progressInterval

Get and set simulation progress bar details

The .simDeps class

Determine the smallest timeunit in a simulation

Open all modules nested within a base directory

Get module or simulation package dependencies

suppliedElsewhere

Assess whether an object has or will be supplied from elsewhere

Parse and extract module metadata

Restart R programmatically

Create template testing structures for new modules

newModuleDocumentation

Create new module documentation

.modifySearchPath

Modify package order in search path

Create new module from template

Simulation inputs

Extract a module's parameters, inputs, or outputs

.parseModulePartial

Parse and initialize a module

Create new module code file

paramCheckOtherMods

Test and update a parameter against same parameter in other modules

The SpaDES.core package environment

Time usage in SpaDES

Get and set simulation parameters

tryCatch that keeps warnings, errors and value (result)

Determine which modules in a list are unparsed

The simList class

Determine the size of a remotely hosted file

Simple wrapper to load any Raster* object

Read raster to memory

show,simList-method

Get and set default working directories

SpaDES.core options

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

SpaDES time units

Objects exported from other packages

Runs a series of code checks during simInit()

Simulation environment

simInitAndSpades

Call simInit and spades together

Write RNG state info to file

Create a zip archive of a module subdirectory

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

Simulation outputs

Use GitHub actions for automated module checking

.runModuleInputObjects

Run module's .inputObjects