simInitAnd: Run 'simInit' and 'Experiment' in one step

In PredictiveEcology/SpaDES.experiment: Simulation Experiments Within The SpaDES Ecosystem

Description

Run simInit and Experiment in one step

Usage

simInitAndExperiment(
  times,
  params,
  modules,
  objects,
  paths,
  inputs,
  outputs,
  loadOrder,
  notOlderThan,
  replicates,
  dirPrefix,
  substrLength,
  saveExperiment,
  experimentFile,
  clearSimEnv,
  cl,
  ...
)

Arguments

times	A named list of numeric simulation start and end times (e.g., times = list(start = 0.0, end = 10.0)).
params	A list of lists of the form list(moduleName=list(param1=value, param2=value)). See details.
modules	A named list of character strings specifying 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 file ‘caribou.R’, located at the specified modulePath(simList) (see below).
objects	(optional) A vector of object names (naming objects that are in the calling environment of the simInit, which is often the .GlobalEnv unless used programmatically – NOTE: this mechanism will fail if object name is in a package dependency), or a named list of data objects to be passed into the simList (more reliable). These objects will be accessible from the simList as a normal list, e.g,. mySim$obj.
paths	An optional named list with up to 4 named elements, modulePath, inputPath, outputPath, and cachePath. See details. NOTE: Experimental feature now allows for multiple modulePaths to be specified in a character vector. The modules will be searched for sequentially in the first modulePath, then if it doesn't find it, in the second etc.
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 (numeric), loadTime (numeric). See inputs and vignette("ii-modules") section about inputs.
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 (numeric) and eventPriority (numeric). If eventPriority is not set, it defaults to .last(). If eventPriority is set to a low value, e.g., 0, 1, 2 and saveTime is start(sim), it should give "initial conditions". See outputs and vignette("ii-modules") section about outputs.
loadOrder	An optional list of module names specifying the order in which to load the modules. If not specified, the module load order will be determined automatically.
notOlderThan	A time, as in from Sys.time(). This is passed into the Cache function that wraps .inputObjects. If the module uses the .useCache parameter and it is set to TRUE or ".inputObjects", then the .inputObjects will be cached. Setting notOlderThan = Sys.time() will cause the cached versions of .inputObjects to be refreshed, i.e., rerun.
replicates	The number of replicates to run of the same simList. See details and examples.
dirPrefix	String vector. This will be concatenated as a prefix on the directory names. See details and examples.
substrLength	Numeric. While making outputPath for each spades call, this is the number of characters kept from each factor level. See details and examples.
saveExperiment	Logical. Should params, modules, inputs, sim, and resulting experimental design be saved to a file. If TRUE are saved to a single list called experiment. Default TRUE.
experimentFile	String. Filename if saveExperiment is TRUE; saved to outputPath(sim) in .RData format. See Details.
clearSimEnv	Logical. If TRUE, then the envir(sim) of each simList in the return list is emptied. This is to reduce RAM load of large return object. Default FALSE.
cl	A cluster object. Optional. This would generally be created using parallel::makeCluster or equivalent. This is an alternative way, instead of beginCluster(), to use parallelism for this function, allowing for more control over cluster use.
...	Passed to spades. Specifically, debug, .plotInitialTime, .saveInitialTime, cache and/or notOlderThan. Caching is still experimental. It is tested to work under some conditions, but not all. See details.

Details

simInitAndExperiment cannot pass modules or params to experiment because these are also in simInit. If the experiment is being used to vary these arguments, it must be done separately (i.e., simInit then experiment).

PredictiveEcology/SpaDES.experiment documentation built on Dec. 3, 2019, 4:59 p.m.