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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

842

Version

0.2.5

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

March 19th, 2019

Functions in SpaDES.core (0.2.5)

.addTagsToOutput,simList-method

.addTagsToOutput for simList objects

all.equal.simList

All equal method for simLists

Add a module to a moduleList

Calculate checksum for a module's data files

Filter objects by class

.cacheMessage,simList-method

.cacheMessage for simList objects

Create a copy of an existing module

Extract a url from module metadata

Named list of core SpaDES modules

Open a file for editing

Build a module dependency graph

.findElementsInEnv

Find all references to sim$

Determine module load order

Extract filename (without extension) of a file

.findModuleName

Identify module names up to a given recursive level

Plot,simList-method

Plot method for simList objects

SpaDES.core-package

Categorized overview of the SpaDES.core package

Create empty fileTable for inputs and outputs

checkModuleLocal

Check for the existence of a module locally

makeMemoisable.simList

Make simList correctly work with memoise

defineParameter

Define a parameter used in a module

getModuleVersion

Find the latest module version from a SpaDES module repository

Build edge list for module dependency graph

Get and set simulation globals.

Simulation module dependency diagram

Copy,simList-method

Copy for simList class objects

Use Pattern Oriented Modeling to fit unknown parameters

Define an output object of a module

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

Build a module dependency graph

Define a new module.

Check use and existence of params passed to simulation.

doEvent.checkpoint

Simulation checkpoints.

Attach missing attributes from x to y

.fileExtensions

File extensions map

Define an input object that the module expects.

Find simList in a nested list

Find objects if passed as character strings

.depsPruneEdges

Prune edges to remove cycles in module dependencies

.callingModuleName

Namespacing within SpaDES

Run an experiment using spades

.addChangedAttr,simList-method

.addChangedAttr for simList objects

Defaults values used in defineModule

Create template testing structures for new modules

objSize.simList

Object size for simList

.parseElems,simList-method

.parseElems for simList class objects

.moduleDeps-class

The .moduleDeps class

._inputObjectsDF

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

Parse and extract module metadata

Check is module uses module namespacing

Create new module from template

Parse and extract a module's version

Open all modules nested within a base directory

.objSizeInclEnviros,simList-method

.objSizeInclEnviros for simList objects

Prepend module name to a message

Simulation object dependency diagram

Process a simulation event

Download a module from a SpaDES module GitHub repository

Add simulation dependencies

.checkCacheRepo,list-method

.checkCacheRepo for simList objects

Blank (template) event list

Identify synonyms in a simList

Read raster to memory

Determine the size of a remotely hosted file

Get module or simulation package dependencies

Schedule a simulation event

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

Get and set default working directories

Extract or replace an object from the simulation environment

.parseModulePartial

Parse and initialize a module

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

The SpaDES.core package environment

.fillOutputRows

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

Check for the existence of a remote module

.identifyChildModules

Identify Child Modules from a recursive list

Generate random strings

show,simList-method

.robustDigest,simList-method

.robustDigest for simList objects

Start and/or setup a parallel cluster

initialize,simList-method

Generate a simList object

progressInterval

Get and set simulation progress bar details

Metadata accessors

Simulation modules and dependencies

Specify paths for modules, inputs, and outputs

Save objects using .saveObjects in params slot of simInit

Convert time units

Time usage in SpaDES

Calculate module coverage of unit tests

.modifySearchPath

Modify package order in search path

Download module data

tryCatch that keeps warnings, errors and value (result)

Default (empty) metadata

Create new module code file

newModuleDocumentation

Create new module documentation

.preDigestByClass,simList-method

Pre-digesting method for simList

scheduleConditionalEvent

Schedule a conditional simulation event

Simulation event lists

.prepareOutput,simList-method

.prepareOutput for simList objects

Runs a series of code checks during simInit

.runModuleInputObjects

Run module's .inputObjects

Simulation event diagram

Inputs and outputs

Classes defined in SpaDES

.getModuleInputObjects

Extract the user-defined .inputObjects function from a module

The .simDeps class

Run a spatial discrete event simulation

Chose verb conjugation for "to be"

Create a zip archive of a module subdirectory

Determine the largest timestep unit in a simulation

Determine the smallest timeunit in a simulation

paddedFloatToChar

Convert numeric to character with padding

Get and set simulation parameters.

Initialize a new simulation

A slightly modified version of getOption

simInitAndSpades

Call simInit and spades or experiment together

The simList class

Simulation environment

suppliedElsewhere

Assess whether an object has or will be supplied from elsewhere

The simList_ class

SpaDES time units

.tagsByClass,simList-method

.tagsByClass for simList objects

Determine which modules in a list are unparsed

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