simInitAndSpades: Call 'simInit' and 'spades' together

In SpaDES.core: Core Utilities for Developing and Running Spatially Explicit Discrete Event Models

Call simInit and spades together

Description

These functions are convenience wrappers that may allow for more efficient caching. Passes all arguments to simInit(), then passes the created simList to spades().

Usage

simInitAndSpades(
  times,
  params,
  modules,
  objects,
  paths,
  inputs,
  outputs,
  loadOrder,
  notOlderThan,
  debug,
  progress,
  cache,
  .plots,
  .plotInitialTime,
  .saveInitialTime,
  events,
  ...
)

Arguments

times	A named list of numeric simulation start and end times (e.g., times = list(start = 0.0, end = 10.0, timeunit = "year")), with the final optional element, timeunit, overriding the default time unit used in the simulation which is the "smallest time unit" across all modules. See examples.
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 character vector 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.
debug	Optional tools for invoking debugging. Supplying a list will invoke the more powerful logging package. See details. Default is to use the value in getOption("spades.debug").
progress	Logical (TRUE or FALSE show a graphical progress bar), character ("graphical", "text") or numeric indicating the number of update intervals to show in a graphical progress bar.
cache	Logical. If TRUE, then the spades call will be cached. This means that if the call is made again with the same simList, then spades will return the return value from the previous run of that exact same simList. Default FALSE. See Details. See also the vignette on caching for examples.
.plots	Character. Sets the parameter of this name in all modules. See Plots() for possible values. The parameter is intended to slowly take over from .plotInitialTime as a mechanism to turn on or off plotting. For backwards compatibility, if .plotInitialTime is not set in this spades call, but this .plots is used, two things will happen: setting this without "screen" will turn off all plotting; setting this with "screen" will trigger plotting for any modules that use this parameter but will have no effect on other modules. To get plotting, therefore, it may be necessary to also set .plotInitialTime = start(sim).
.plotInitialTime	Numeric. Temporarily override the .plotInitialTime parameter for all modules. See Details.
.saveInitialTime	Numeric. Temporarily override the .plotInitialTime parameter for all modules. See Details.
events	A character vector or a named list of character vectors. If specified, the simulations will only do the events indicated here. If a named list, the names must correspond to the modules and the character vectors can be specific events within each of the named modules. With the list form, all unspecified modules will run all their events, including internal spades modules, e.g., save, that get invoked with the outputs argument in simInit. See example.
...	Arguments passed to simInit() and spades()

Value

Same as spades() (a simList) or

See Also

simInit(), spades()

SpaDES.core documentation built on June 22, 2024, 10:32 a.m.