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SpaDES.core

Core functionality for Spatial Discrete Event Simulation (SpaDES)

Website: http://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) # stable

Development version (unstable)

Install from GitHub:

#install.packages("devtools")
library("devtools")
install_github("PredictiveEcology/SpaDES.core", ref = "development", dependencies = TRUE) # unstable

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Version

Install

install.packages('SpaDES.core')

Monthly Downloads

853

Version

0.2.4

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

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

Homepage

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

Maintainer

Alex Chubaty

Last Published

February 3rd, 2019

Functions in SpaDES.core (0.2.4)

checkModuleLocal

Check for the existence of a module locally

Define an output object of a module

Add a module to a moduleList

Define a new module.

Copy,simList-method

Copy for simList class objects

Create empty fileTable for inputs and outputs

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

.addChangedAttr,simList-method

.addChangedAttr for simList class objects

Get and set simulation globals.

Add simulation dependencies

.cacheMessage,simList-method

cacheMessage for simList class objects

.identifyChildModules

Identify Child Modules from a recursive list

.addTagsToOutput,simList-method

addTagsToOutput for simList class objects

Check for the existence of a remote module

.checkCacheRepo,list-method

checkCacheRepo for simList class objects

all.equal.simList

All equal method for simLists

.findModuleName

Identify module names up to a given recursive level

Find objects if passed as character strings

Calculate checksum for a module's data files

Determine the smallest timeunit in a simulation

Create a copy of an existing module

initialize,simList-method

Generate a simList object

Filter objects by class

Simulation object dependency diagram

.modifySearchPath

Modify package order in search path

Identify synonyms in a simList

Process a simulation event

Use Pattern Oriented Modeling to fit unknown parameters

.depsPruneEdges

Prune edges to remove cycles in module dependencies

defineParameter

Define a parameter used in a module

._inputObjectsDF

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

The SpaDES.core package environment

Simulation event diagram

Define an input object that the module expects.

.preDigestByClass,simList-method

Pre-digesting method for simList

Named list of core SpaDES modules

.fileExtensions

File extensions map

Build a module dependency graph

Calculate module coverage of unit tests

Extract filename (without extension) of a file

Determine module load order

Open a file for editing

.getModuleInputObjects

Extract the user-defined .inputObjects function from a module

Defaults values used in defineModule

Extract or replace an object from the simulation environment

Open all modules nested within a base directory

.robustDigest,simList-method

.robustDigest for simList class objects

getModuleVersion

Find the latest module version from a SpaDES module repository

Inputs and outputs

makeMemoisable.simList

Make simList correctly work with memoise

Build edge list for module dependency graph

Determine the largest timestep unit in a simulation

.moduleDeps-class

The .moduleDeps class

Simulation module dependency diagram

progressInterval

Get and set simulation progress bar details

Create new module from template

Metadata accessors

Create new module code file

Runs a series of code checks during simInit

objSize.simList

Object size for simLists

Read raster to memory

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

Blank (template) event list

.objSizeInclEnviros,simList-method

objSizeInclEnviros for simList class objects

.tagsByClass,simList-method

tagsByClass for simList class objects

Default (empty) metadata

Get and set simulation parameters.

Find simList in a nested list

The .simDeps class

SpaDES time units

.parseElems,simList-method

.parseElems for simList class objects

Convert time units

Build a module dependency graph

Parse and extract module metadata

newModuleDocumentation

Create new module documentation

Simulation modules and dependencies

Specify paths for modules, inputs, and outputs

Create template testing structures for new modules

.prepareOutput,simList-method

.prepareOutput for simList

suppliedElsewhere

Assess whether an object has or will be supplied from elsewhere

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

Schedule a simulation event

scheduleConditionalEvent

Schedule a conditional simulation event

Create a zip archive of a module subdirectory

Chose verb conjugation for "to be"

Plot,simList-method

Plot method for simList objects

Determine the size of a remotely hosted file

SpaDES.core-package

Categorized overview of the SpaDES.core package

Initialize a new simulation

Generate random strings

Check use and existence of params passed to simulation.

doEvent.checkpoint

Simulation checkpoints.

Simulation environment

Download module data

simInitAndSpades

Call simInit and spades or experiment together

Download a module from a SpaDES module GitHub repository

Run an experiment using spades

Simulation event lists

The simList_ class

Classes defined in SpaDES

Extract a url from module metadata

.fillOutputRows

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

.findElementsInEnv

Find all references to sim$

Run a spatial discrete event simulation

Check is module uses module namespacing

A slightly modified version of getOption

tryCatch that keeps warnings, errors and value (result)

Attach missing attributes from x to y

Parse and extract a module's version

Determine which modules in a list are unparsed

.callingModuleName

Namespacing within SpaDES

Get module or simulation package dependencies

paddedFloatToChar

Convert numeric to character with padding

Prepend module name to a message

.parseModulePartial

Parse and initialize a module

.runModuleInputObjects

Run module's .inputObjects

Save objects using .saveObjects in params slot of simInit

Get and set default working directories

show,simList-method

Time usage in SpaDES

The simList class

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