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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) # 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

853

Version

0.2.7

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

November 25th, 2019

Functions in SpaDES.core (0.2.7)

Plot,simList-method

Plot method for simList objects

.checkCacheRepo,list-method

.checkCacheRepo for simList objects

SpaDES.core-package

Categorized overview of the SpaDES.core package

Copy,simList-method

Copy for simList class objects

.cacheMessage,simList-method

.cacheMessage for simList objects

.addChangedAttr,simList-method

.addChangedAttr for simList objects

.addTagsToOutput,simList-method

.addTagsToOutput for simList objects

all.equal.simList

All equal method for simLists

Add a module to a moduleList

Add simulation dependencies

doEvent.checkpoint

Simulation checkpoints.

.depsPruneEdges

Prune edges to remove cycles in module dependencies

Check use and existence of params passed to simulation.

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

Determine module load order

Open a file for editing

defineParameter

Define a parameter used in a module

checkModuleLocal

Check for the existence of a module locally

Deprecated functions

Check for the existence of a remote module

Extract filename (without extension) of a file

Extract a url from module metadata

Calculate checksum for a module's data files

Define an input object that the module expects.

._inputObjectsDF

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

Find simList in a nested list

initialize,simList-method

Generate a simList object

Create a copy of an existing module

Get and set global simulation parameters

Filter objects by class

Named list of core SpaDES modules

.identifyChildModules

Identify Child Modules from a recursive list

clearCache,simList-method

clearCache for simList objects

makeMemoisable.simList

Make simList correctly work with memoise

Determine the smallest timeunit in a simulation

getModuleVersion

Find the latest module version from a SpaDES module repository

Blank (template) event list

Download module data

Download a module from a SpaDES module GitHub repository

Process a simulation event

memoryUseThisSession

Estimate memory used with system("ps")

.getModuleInputObjects

Extract the user-defined .inputObjects function from a module

Determine the largest timestep unit in a simulation

.callingModuleName

Namespacing within SpaDES

Defaults values used in defineModule

Create template testing structures for new modules

Create new SpaDES project

Parse and extract module metadata

Parse and extract a module's version

.moduleDeps-class

The .moduleDeps class

Prepend module name to a message

.parseElems,simList-method

.parseElems for simList class objects

Build a module dependency graph

Build edge list for module dependency graph

Define an output object of a module

Create new module from template

Extract or replace an object from the simulation environment

Identify synonyms in a simList

Open all modules nested within a base directory

Determine the size of a remotely hosted file

Get module or simulation package dependencies

Read raster to memory

Default (empty) metadata

.fillOutputRows

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

Simulation event diagram

.findElementsInEnv

Find all references to sim$

.fileExtensions

File extensions map

.objSizeInclEnviros,simList-method

.objSizeInclEnviros for simList objects

Simulation object dependency diagram

Define a new module.

Create empty fileTable for inputs and outputs

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

.modifySearchPath

Modify package order in search path

Create new module code file

.preDigestByClass,simList-method

Pre-digesting method for simList

objSize.simList

Object size for simList

Calculate module coverage of unit tests

.prepareOutput,simList-method

.prepareOutput for simList objects

Save a whole simList object to disk

Save objects using .saveObjects in params slot of simInit

Initialize a new simulation

paddedFloatToChar

Convert numeric to character with padding

Runs a series of code checks during simInit

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

Generate random strings

.findModuleName

Identify module names up to a given recursive level

simInitAndSpades

Call simInit and spades together

Check is module uses module namespacing

Find objects if passed as character strings

.robustDigest,simList-method

.robustDigest for simList objects

Get and set default working directories

Get and set simulation parameters

Restart an interrupted simulation

Restart R programmatically

show,simList-method

Attach missing attributes from x to y

Simulation environment

A slightly modified version of getOption

SpaDES time units

Simulation module dependency diagram

Determine which modules in a list are unparsed

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

Simulation event lists

The .simDeps class

Build a module dependency graph

.runModuleInputObjects

Run module's .inputObjects

tryCatch that keeps warnings, errors and value (result)

Time usage in SpaDES

Convert time units

The simList class

Simulation modules and dependencies

newModuleDocumentation

Create new module documentation

The SpaDES.core package environment

Zip many of the files in a simList

Create new module code file

.parseModulePartial

Parse and initialize a module

progressInterval

Get and set simulation progress bar details

scheduleConditionalEvent

Schedule a conditional simulation event

Schedule a simulation event

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

suppliedElsewhere

Assess whether an object has or will be supplied from elsewhere

.tagsByClass,simList-method

.tagsByClass for simList objects

Inputs and outputs

Metadata accessors

Run a spatial discrete event simulation

Classes defined in SpaDES

Create a zip archive of a module subdirectory

Chose verb conjugation for "to be"