SpaDES (version 1.0.1)

simInit: Initialize a new simulation

Description

Create a new simulation object, preloaded with parameters, modules, times, etc.

Usage

simInit(times, params, modules, objects, paths, inputs, outputs, loadOrder)

## S3 method for class 'list,list,list,list,list,data.frame,ANY,character':
simInit(times,
  params, modules, objects, paths, inputs, outputs, loadOrder)


  ## S3 method for class 'list,list,list,list,list,data.frame,missing,character':
simInit(times,
  params, modules, objects, paths, inputs, loadOrder)

## S3 method for class 'list,list,list,list,list,data.frame,missing,missing':
simInit(times,
  params, modules, objects, paths, inputs)


  ## S3 method for class 'list,list,list,list,missing,data.frame,missing,character':
simInit(times,
  params, modules, objects, inputs, loadOrder)


  ## S3 method for class 'list,list,list,missing,list,data.frame,missing,character':
simInit(times,
  params, modules, paths, inputs, loadOrder)


  ## S3 method for class 'list,list,list,list,missing,data.frame,missing,missing':
simInit(times,
  params, modules, objects, inputs)


  ## S3 method for class 'list,list,list,missing,missing,data.frame,missing,character':
simInit(times,
  params, modules, inputs, loadOrder)


  ## S3 method for class 'list,list,list,missing,list,data.frame,missing,missing':
simInit(times,
  params, modules, paths, inputs)


  ## S3 method for class 'list,list,list,missing,missing,data.frame,missing,missing':
simInit(times,
  params, modules, inputs)

## S3 method for class 'list,list,list,list,list,missing,missing,missing':
simInit(times,
  params, modules, objects, paths, inputs)


  ## S3 method for class 'list,list,list,list,missing,missing,missing,character':
simInit(times,
  params, modules, objects, inputs, loadOrder)


  ## S3 method for class 'list,list,list,missing,list,missing,missing,character':
simInit(times,
  params, modules, paths, inputs, loadOrder)

## S3 method for class 'list,list,list,list,missing,missing,missing,missing':
simInit(times,
  params, modules, objects, inputs)


  ## S3 method for class 'list,list,list,missing,missing,missing,missing,character':
simInit(times,
  params, modules, inputs, loadOrder)

## S3 method for class 'list,list,list,missing,list,missing,missing,missing':
simInit(times,
  params, modules, paths, inputs)


  ## S3 method for class 'list,list,list,missing,missing,missing,missing,missing':
simInit(times,
  params, modules, inputs)

## S3 method for class 'list,list,list,list,list,missing,ANY,missing':
simInit(times, params,
  modules, objects, paths, outputs)

## S3 method for class 'list,list,list,list,missing,missing,ANY,character':
simInit(times,
  params, modules, objects, outputs, loadOrder)

## S3 method for class 'list,list,list,missing,list,missing,ANY,character':
simInit(times,
  params, modules, paths, outputs, loadOrder)

## S3 method for class 'list,list,list,list,missing,missing,ANY,missing':
simInit(times,
  params, modules, objects, outputs)

## S3 method for class 'list,list,list,missing,missing,missing,ANY,character':
simInit(times,
  params, modules, outputs, loadOrder)

## S3 method for class 'list,list,list,missing,list,missing,ANY,missing':
simInit(times,
  params, modules, paths, outputs)

## S3 method for class 'list,list,list,missing,missing,missing,ANY,missing':
simInit(times,
  params, modules, outputs)

## S3 method for class 'list,list,list,list,list,data.frame,ANY,missing':
simInit(times,
  params, modules, objects, paths, inputs, outputs)

## S3 method for class 'list,list,list,list,missing,data.frame,ANY,character':
simInit(times,
  params, modules, objects, inputs, outputs, loadOrder)

## S3 method for class 'list,list,list,missing,list,data.frame,ANY,character':
simInit(times,
  params, modules, paths, inputs, outputs, loadOrder)

## S3 method for class 'list,list,list,list,missing,data.frame,ANY,missing':
simInit(times,
  params, modules, objects, inputs, outputs)


  ## S3 method for class 'list,list,list,missing,missing,data.frame,ANY,character':
simInit(times,
  params, modules, inputs, outputs, loadOrder)

## S3 method for class 'list,list,list,missing,list,data.frame,ANY,missing':
simInit(times,
  params, modules, paths, inputs, outputs)


  ## S3 method for class 'list,list,list,missing,missing,data.frame,ANY,missing':
simInit(times,
  params, modules, inputs, outputs)

## S3 method for class 'ANY,ANY,ANY,character,ANY,ANY,ANY,ANY':
simInit(times, params,
  modules, objects, paths, inputs, outputs, loadOrder)


  ## S3 method for class 'missing,missing,missing,missing,missing,data.frame,missing,missing':
simInit(times,
  params, modules, objects, paths, inputs, outputs, loadOrder)


  ## S3 method for class 'missing,missing,missing,missing,missing,missing,missing,missing':
simInit(inputs,
  outputs)

## S3 method for class 'ANY,ANY,ANY,ANY,ANY,ANY,ANY,ANY':
simInit(times, params, modules,
  objects, paths, inputs, outputs, loadOrder)

Arguments

times

A named list of numeric simulation start and end times (e.g., times=list(start=0.0, end=10.0)).

params

A named list of simulation parameters and their values.

modules

A named list of character strings specfying the names of modules to be loaded for the simulation. Note: the module name should correspond to the R source file from which the module is loaded. Example: a module named "caribou" will be sourced form the f

objects

An optional list of data objects to be used in the simulation.

paths

An optional named list with up to 3 named elements, modulePath, inputPath, and outputPath. See details.

inputs

A data.frame. Can specify from 1 to 6 columns with following column names: objectName (character, required), file (character), fun (character), package (character), interval (

outputs

A data.frame. Can specify from 1 to 5 columns with following column names: objectName (character, required), file (character), fun (character), package (character), saveTime (

loadOrder

An optional list of module names specfiying the order in which to load the modules. If not specified, the module load order will be determined automatically.

Value

• A simList simulation object, pre-initialized from values specified in the arguments supplied.

Details

We implement a discrete event simulation in a more modular fashion so it is easier to add submodules to the simulation. We use S4 classes and methods, and use data.table instead of data.frame to implement the event queue (because it is much faster). paths specifies the location of the module source files, the data input files, and the saving output files. If no paths are specified, default is current working directory.

References

Matloff, N. (2011). The Art of R Programming (ch. 7.8.3). San Fransisco, CA: No Starch Press, Inc.. Retrieved from http://www.nostarch.com/artofr.htm

See Also

spades.

Examples

mySim <- simInit(
   times=list(start=0.0, end=2.0, timeunit="year"),
   params=list(.globals=list(stackName="landscape", burnStats="nPixelsBurned")),
   modules=list("randomLandscapes", "fireSpread", "caribouMovement"),
   paths=list(modulePath=system.file("sampleModules", package="SpaDES"))
 )
 spades(mySim)

# A little more complicated with inputs and outputs
 mapPath <- system.file("maps", package="SpaDES")
 mySim <- simInit(
   times=list(start=0.0, end=2.0, timeunit="year"),
   params=list(.globals=list(stackName="landscape", burnStats="nPixelsBurned")),
   modules=list("randomLandscapes", "fireSpread", "caribouMovement"),
   paths=list(modulePath=system.file("sampleModules", package="SpaDES"),
              outputPath=tempdir()),
   inputs=data.frame(
     files=
       dir(file.path(mapPath), full.names=TRUE, pattern="tif")[1:2],
     functions="raster",
     package="raster",
     loadTime=3,
     stringsAsFactors=FALSE),
   outputs=data.frame(
     expand.grid(objectName=c("caribou","landscape"),
     saveTime=1:2,
     stringsAsFactors = FALSE))
 )
 spades(mySim)