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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) doi:10.1111/ele.13994, Barros et al. (2022) doi: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

841

Version

2.0.3

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

November 10th, 2023

Functions in SpaDES.core (2.0.3)

.addTagsToOutput,simList-method

.addTagsToOutput for simList objects

Plot wrapper intended for use in a SpaDES module

.addChangedAttr,simList-method

.addChangedAttr for simList objects

SpaDES.core-package

Categorized overview of the SpaDES.core package

Plot,simList-method

Plot method for simList objects

Add a module to a moduleList

Copy,simList-method

Copy for simList class objects

Simple wrapper around data.table::rbindlist

.checkCacheRepo,list-method

.checkCacheRepo for simList objects

Calculate checksum for a module's data files

Check use and existence of parameters passed to simulation.

A citation method for SpaDES modules

.cacheMessage,simList-method

.cacheMessage for simList objects

Simulation checkpoints.

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

checkModuleLocal

Check for the existence of a module locally

Check for the existence of a remote module

convertToPackage

Convert standard module code into an R package

defineParameter

Define a parameter used in a module

Define a new module.

Create a copy of an existing module

Alternative way to define events in SpaDES.core

Methods for .wrap and .unwrap

Filter objects by class

Define an output object of a module

Build a module dependency graph

Find objects if passed as character strings

Build edge list for module dependency graph

clearCache,simList-method

clearCache for simList objects

Zip a simList and various files

Open a file for editing

Process a simulation event

.depsPruneEdges

Prune edges to remove cycles in module dependencies

Determine module load order

strip GitHub repo info from vector of packages

Named list of core SpaDES modules

Create empty fileTable for inputs and outputs

Simulation event diagram

Define an input object that the module expects.

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

Default (empty) metadata

.fillOutputRows

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

Extract filename (without extension) of a file

.findElementsInEnv

Find all references to sim$

Load a saved simList and ancillary files

makeMemoisable.simList

Make simList correctly work with memoise

Parse and extract module metadata

Extract a module's parameters, inputs, or outputs

initialize,simList-method

Generate a simList object

Simulation module dependency diagram

getModuleVersion

Find the latest module version from a SpaDES module repository

A slightly modified version of getOption()

.identifyChildModules

Identify child modules from a recursive list

Find simList in a nested list

Extract a url from module metadata

Build a module dependency graph

.findModuleName

Identify module names up to a given recursive level

Attach missing attributes from x to y

Download module data

Guess package of a function

Download a module from a SpaDES module GitHub repository

Blank (template) event list

.getModuleInputObjects

Extract the user-defined .inputObjects function from a module

Get copies of sample files for examples and tests

Determine the smallest timeunit in a simulation

Get and set simulation parameters

Create new module code file

paramCheckOtherMods

Test and update a parameter against same parameter in other modules

Create template testing structures for new modules

newModuleDocumentation

Create new module documentation

Create new SpaDES project

.modifySearchPath

Modify package order in search path

.parseElems,simList-method

.parseElems for simList class objects

.fileExtensions

File extensions map

moduleCodeFiles

Extract the full file paths for R source code

Calculate module coverage of unit tests

Parse and extract a module's version

.callingModuleName

Namespacing within SpaDES

Open all modules nested within a base directory

objSize.simList

Object size for simList

Check is module uses module namespacing

Simulation object dependency diagram

._inputObjectsDF

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

Extract or replace an object from the simulation environment

Identify synonyms in a simList

.parseModulePartial

Parse and initialize a module

Get module or simulation package dependencies

Prepend module name to a message

Read raster to memory

Simple wrapper to load any Raster* object

scheduleConditionalEvent

Schedule a conditional simulation event

.moduleDeps-class

The .moduleDeps class

Schedule a simulation event

memoryUseThisSession

Estimate memory used with system("ps")

Get and set global simulation parameters

Determine the largest timestep unit in a simulation

Create new module from template

Create new module code file

Save objects using .saveObjects in params slot of simInit

Save a whole simList object to disk

Defaults values used in defineModule

.robustDigest,simList-method

.robustDigest for simList objects

Generate random strings

Simulation event lists

Simulation inputs

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

.preDigestByClass,simList-method

Pre-digesting method for simList

The SpaDES.core package environment

Restart an interrupted simulation

simInitAndSpades

Call simInit and spades together

Simulation environment

.prepareOutput,simList-method

.prepareOutput for simList objects

Restart R programmatically

Get and set default working directories

Objects exported from other packages

Determine the size of a remotely hosted file

progressInterval

Get and set simulation progress bar details

Runs a series of code checks during simInit()

Initialize a new simulation

.runModuleInputObjects

Run module's .inputObjects

Generate simulation file name

Classes defined in SpaDES

show,simList-method

Run a spatial discrete event simulation

The .simDeps class

The simList class

Time usage in SpaDES

Write simulation event info to file

SpaDES.core options

SpaDES time units

Chose verb conjugation for "to be"

tryCatch that keeps warnings, errors and value (result)

Simulation outputs

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

Determine which modules in a list are unparsed

Metadata accessors

Simulation modules and dependencies

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

Use GitHub actions for automated module checking

[,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

Convert time units

Write RNG state info to file

Create a zip archive of a module subdirectory

.tagsByClass,simList-method

.tagsByClass for simList objects

Add simulation dependencies

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

all.equal.simList

All equal method for simList objects