Learn R Programming

⚠️There's a newer version (2.1.8) of this package.Take me there.

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

Copy Link

Version

Install

install.packages('SpaDES.core')

Monthly Downloads

842

Version

0.2.6

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

September 13th, 2019

Functions in SpaDES.core (0.2.6)

Add simulation dependencies

Add a module to a moduleList

Copy,simList-method

Copy for simList class objects

all.equal.simList

All equal method for simLists

.addTagsToOutput,simList-method

.addTagsToOutput for simList objects

.cacheMessage,simList-method

.cacheMessage for simList objects

Plot,simList-method

Plot method for simList objects

.addChangedAttr,simList-method

.addChangedAttr for simList objects

Use Pattern Oriented Modeling to fit unknown parameters

SpaDES.core-package

Categorized overview of the SpaDES.core package

Check use and existence of params passed to simulation.

Filter objects by class

Define an output object of a module

Calculate checksum for a module's data files

checkModuleLocal

Check for the existence of a module locally

Download module data

Create empty fileTable for inputs and outputs

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

Extract filename (without extension) of a file

Start and/or setup a parallel cluster

doEvent.checkpoint

Simulation checkpoints.

getModuleVersion

Find the latest module version from a SpaDES module repository

Create a copy of an existing module

Named list of core SpaDES modules

defineParameter

Define a parameter used in a module

Check for the existence of a remote module

.checkCacheRepo,list-method

.checkCacheRepo for simList objects

Build edge list for module dependency graph

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

Build a module dependency graph

.fillOutputRows

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

.identifyChildModules

Identify Child Modules from a recursive list

Get and set simulation globals.

Define a new module.

Default (empty) metadata

.findElementsInEnv

Find all references to sim$

Simulation event diagram

.depsPruneEdges

Prune edges to remove cycles in module dependencies

Process a simulation event

Extract a url from module metadata

Open a file for editing

Determine module load order

initialize,simList-method

Generate a simList object

Define an input object that the module expects.

Parse and extract module metadata

Find simList in a nested list

Blank (template) event list

Determine the largest timestep unit in a simulation

Determine the smallest timeunit in a simulation

Download a module from a SpaDES module GitHub repository

Find objects if passed as character strings

Calculate module coverage of unit tests

.modifySearchPath

Modify package order in search path

.objSizeInclEnviros,simList-method

.objSizeInclEnviros for simList objects

Run an experiment using spades

Attach missing attributes from x to y

Create new module code file

.preDigestByClass,simList-method

Pre-digesting method for simList

newModuleDocumentation

Create new module documentation

Parse and extract a module's version

Simulation event lists

.parseModulePartial

Parse and initialize a module

Simulation environment

Simulation object dependency diagram

The SpaDES.core package environment

.getModuleInputObjects

Extract the user-defined .inputObjects function from a module

Inputs and outputs

Generate random strings

Simulation modules and dependencies

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

Specify paths for modules, inputs, and outputs

show,simList-method

Restart an interrupted simulation

.prepareOutput,simList-method

.prepareOutput for simList objects

Chose verb conjugation for "to be"

Get and set default working directories

.fileExtensions

File extensions map

Metadata accessors

Schedule a simulation event

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

Get module or simulation package dependencies

scheduleConditionalEvent

Schedule a conditional simulation event

Open all modules nested within a base directory

The simList_ class

Classes defined in SpaDES

.findModuleName

Identify module names up to a given recursive level

.callingModuleName

Namespacing within SpaDES

tryCatch that keeps warnings, errors and value (result)

Determine which modules in a list are unparsed

Create template testing structures for new modules

Create new module from template

objSize.simList

Object size for simList

._inputObjectsDF

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

.parseElems,simList-method

.parseElems for simList class objects

Simulation module dependency diagram

Check is module uses module namespacing

Build a module dependency graph

paddedFloatToChar

Convert numeric to character with padding

Prepend module name to a message

makeMemoisable.simList

Make simList correctly work with memoise

Get and set simulation parameters.

Defaults values used in defineModule

.robustDigest,simList-method

.robustDigest for simList objects

Runs a series of code checks during simInit

Read raster to memory

Determine the size of a remotely hosted file

Run a spatial discrete event simulation

A slightly modified version of getOption

Create a zip archive of a module subdirectory

The .simDeps class

Time usage in SpaDES

.moduleDeps-class

The .moduleDeps class

Identify synonyms in a simList

Extract or replace an object from the simulation environment

progressInterval

Get and set simulation progress bar details

.runModuleInputObjects

Run module's .inputObjects

The simList class

SpaDES time units

suppliedElsewhere

Assess whether an object has or will be supplied from elsewhere

Convert time units

Initialize a new simulation

Save objects using .saveObjects in params slot of simInit

.tagsByClass,simList-method

.tagsByClass for simList objects

simInitAndSpades

Call simInit and spades or experiment together