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SpaDES.core

Core functionality for Spatial Discrete Event Simulation (SpaDES)

Website: https://SpaDES.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

869

Version

1.0.9

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

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

Homepage

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

Maintainer

Alex Chubaty

Last Published

September 30th, 2021

Functions in SpaDES.core (1.0.9)

.addChangedAttr,simList-method

.addChangedAttr for simList objects

Test whether there should be any plotting from .plot parameter

Add a module to a moduleList

Copy,simList-method

Copy for simList class objects

.addTagsToOutput,simList-method

.addTagsToOutput for simList objects

all.equal.simList

All equal method for simLists

Add simulation dependencies

clearCache,simList-method

clearCache for simList objects

Plot,simList-method

Plot method for simList objects

Create a copy of an existing module

Check use and existence of params passed to simulation.

doEvent.checkpoint

Simulation checkpoints.

Plot wrapper intended for use in a SpaDES module

checkModuleLocal

Check for the existence of a module locally

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

Download module data

Simulation event diagram

Download a module from a SpaDES module GitHub repository

Define an output object of a module

Define an input object that the module expects.

.checkCacheRepo,list-method

.checkCacheRepo for simList objects

Named list of core SpaDES modules

.depsPruneEdges

Prune edges to remove cycles in module dependencies

SpaDES.core-package

Categorized overview of the SpaDES.core package

Process a simulation event

Find objects if passed as character strings

Calculate checksum for a module's data files

Filter objects by class

.findElementsInEnv

Find all references to sim$

Simple wrapper around data.table::rbindlist

Define a new module.

.cacheMessage,simList-method

.cacheMessage for simList objects

.findModuleName

Identify module names up to a given recursive level

Check for the existence of a remote module

Build a module dependency graph

Deprecated functions

defineParameter

Define a parameter used in a module

Get and set global simulation parameters

Determine module load order

Extract a url from module metadata

.getModuleInputObjects

Extract the user-defined .inputObjects function from a module

.fillOutputRows

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

Open a file for editing

.fileExtensions

File extensions map

Check is module uses module namespacing

.identifyChildModules

Identify Child Modules from a recursive list

Find simList in a nested list

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

Build edge list for module dependency graph

Defaults values used in defineModule

getModuleVersion

Find the latest module version from a SpaDES module repository

A slightly modified version of getOption

.moduleDeps-class

The .moduleDeps class

moduleCodeFiles

Extract the full file paths for R source code

Determine the largest timestep unit in a simulation

memoryUseThisSession

Estimate memory used with system("ps")

Calculate module coverage of unit tests

Parse and extract a module's version

newModuleDocumentation

Create new module documentation

Blank (template) event list

Create new module from template

Attach missing attributes from x to y

Extract filename (without extension) of a file

initialize,simList-method

Generate a simList object

Create empty fileTable for inputs and outputs

Build a module dependency graph

Simulation module dependency diagram

Default (empty) metadata

Create new module code file

Get module or simulation package dependencies

Open all modules nested within a base directory

Create template testing structures for new modules

.callingModuleName

Namespacing within SpaDES

objSize.simList

Object size for simList

.modifySearchPath

Modify package order in search path

Determine the smallest timeunit in a simulation

Simulation object dependency diagram

Get and set default working directories

Schedule a simulation event

Simulation environment

.tagsByClass,simList-method

.tagsByClass for simList objects

Simulation event lists

progressInterval

Get and set simulation progress bar details

Identify synonyms in a simList

Convert time units

Extract or replace an object from the simulation environment

Simple wrapper to load any Raster* object This wraps either raster::raster, raster::stack, or raster::brick, allowing a single function to be used to create a new object of the same class as a template.

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

.preDigestByClass,simList-method

Pre-digesting method for simList

Determine the size of a remotely hosted file

.runModuleInputObjects

Run module's .inputObjects

The SpaDES.core package environment

Save objects using .saveObjects in params slot of simInit

._inputObjectsDF

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

Restart R programmatically

Initialize a new simulation

simInitAndSpades

Call simInit and spades together

.robustDigest,simList-method

.robustDigest for simList objects

Runs a series of code checks during simInit

show,simList-method

Create new module code file

Create new SpaDES project

Prepend module name to a message

Load a saved simList and ancillary files

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

Restart an interrupted simulation

Generate random strings

The .simDeps class

Generate simulation file name

.parseModulePartial

Parse and initialize a module

makeMemoisable.simList

Make simList correctly work with memoise

Simulation modules and dependencies

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

Parse and extract module metadata

Extract a module's parameters, inputs, or outputs

Get and set simulation parameters

Time usage in SpaDES

Use GitHub actions for automated module checking

Run a spatial discrete event simulation

Classes defined in SpaDES

Determine which modules in a list are unparsed

The simList class

Simulation outputs

tryCatch that keeps warnings, errors and value (result)

Write RNG state info to file

Create a zip archive of a module subdirectory

SpaDES time units

SpaDES.core options

.prepareOutput,simList-method

.prepareOutput for simList objects

.parseElems,simList-method

.parseElems for simList class objects

Chose verb conjugation for "to be"

suppliedElsewhere

Assess whether an object has or will be supplied from elsewhere

Write simulation event info to file

Metadata accessors

Objects exported from other packages

scheduleConditionalEvent

Schedule a conditional simulation event

Read raster to memory

Simulation inputs

Save a whole simList object to disk