All functions

.addTagsToOutput

addTagsToOutput for simList class objects

append_attr

Add a module to a moduleList

.cacheMessage

cacheMessage for simList class objects

.checkCacheRepo

checkCacheRepo for simList class objects

checkModuleLocal

Check for the existence of a module locally

checkModule

Check for the existence of a remote module

checkObject

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

checkParams

Check use and existence of params passed to simulation.

doEvent.checkpoint checkpointLoad .checkpointSave checkpointFile checkpointFile<- checkpointInterval checkpointInterval<-

Simulation checkpoints.

checksums

Calculate checksums for a module's data files

classFilter

Filter objects by class

copyModule

Create a copy of an existing module

Copy

Copy for simList class objects

createsOutput

Define an output object of a module

defineModule

Define a new module.

defineParameter

Define a parameter used in a module

depsEdgeList

Build edge list for module dependency graph

depsGraph

Build a module dependency graph

downloadData

Download module data

downloadModule

Download a module from a SpaDES module GitHub repository

dwrpnorm2

Vectorized wrapped normal density function

eventDiagram

Simulation event diagram

expectsInput

Define an input object that the module expects.

experiment

Run an experiment using spades

fileExt

Extract the file extension of a file

fileName

Extract filename (without extension) of a file

F

F allows the user to access functions from their module. It should be unnecessary to use this as namespacing should take care of it. But, if the user wants to specify a function this way, it will work too. To access a function from within a module, you can use F(sim)$functionName.

getModuleVersion

Find the latest module version from a SpaDES module repository

globals globals<- G G<-

Get and set simulation globals.

initialize

Generate a simList object

.fileExtensions loadFiles .saveFileExtensions saveSimList

File extensions map

loadPackages

Load packages.

ls.simList ls objects.simList objects

List simulation objects

ls.str.simList ls.str

List simulation objects and their structure

maxTimeunit

Determine the largest timestep unit in a simulation

minTimeunit

Determine the smallest timeunit in a simulation

moduleCoverage

Calculate module coverage of unit tests

moduleDiagram

Simulation module dependency diagram

moduleGraph

Build a module dependency graph

moduleMetadata

Parse and extract module metadata

moduleVersion

Parse and extract a module's version

newModuleCode

Create new module code file

newModuleDocumentation

Create new module documentation

newModule

Create new module from template

newModuleTests

Create template testing structures for new modules

objectDiagram

Simulation object dependency diagram

objs

Extract or replace an object from the simulation environment

.objSizeInclEnviros

objSizeInclEnviros for simList class objects

openModules

Open all modules nested within a base directory

packages

Get module or simulation package dependencies

paddedFloatToChar

Convert numeric to character with padding

params params<- P parameters

Get and set simulation parameters.

.parseElems

.parseElems for simList class objects

Plot

Plot method for simList objects

POM

Use Pattern Oriented Modeling to fit unknown parameters

.preDigestByClass

Pre-digesting method for simList

.prepareOutput

prepareOutput for simList class objects

.first .highest .last .lowest .normal

Event priority

newProgressBar setProgressBar

Progress bar

progressInterval progressInterval<- progressType progressType<-

Get and set simulation progress bar details

rasterToMemory

Read raster to memory

rndstr

Generate random strings

.robustDigest

.robustDigest for simList class objects

saveFiles

Save objects using .saveObjects in params slot of simInit

scheduleEvent

Schedule a simulation event

show

Show an Object

simInit

Initialize a new simulation

envir envir<-

Simulation environment

events events<- current current<- completed completed<-

Simulation event lists

inputs inputs<- outputs outputs<- inputArgs inputArgs<- outputArgs outputArgs<-

Inputs and outputs

modules modules<- depends depends<-

Simulation modules and dependencies

paths paths<- cachePath cachePath<- inputPath inputPath<- outputPath outputPath<- modulePath modulePath<-

Specify paths for modules, inputs, and outputs

times times<- time time<- end end<- start start<- timeunit timeunit<- timeunits

Time usage in SpaDES

.simList-class

The simList class

spadesClasses

Classes defined in SpaDES

SpaDES.core-package

Categorized overview of the SpaDES.core package

spades

setMethod( "scheduleEvent", signature( sim = "simList", eventTime = "NULL", moduleName = "character", eventType = "character", eventPriority = "numeric" ), definition = function(sim, eventTime, moduleName, eventType, eventPriority) warning( paste( "Invalid or missing eventTime. This is usually", "caused by an attempt to scheduleEvent at time NULL", "or by using an undefined parameter." ) ) return(invisible(sim)) )

dyears dmonths dweeks dweek dmonth dyear dsecond dday dhour dNA

SpaDES time units

.tagsByClass

tagsByClass for simList class objects

inSeconds convertTimeunit .spadesTimes spadesTimes checkTimeunit

Convert time units

updateList

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

zipModule

Create a zip archive of a module subdirectory