SpaDES (version 1.3.1)

spades: Run a spatial discrete event simulation

Description

Based on code from chapter 7.8.3 of Matloff (2011): "Discrete event simulation". Here, we implement a simulation in a more modular fashion so it's 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).

Usage

spades(sim, debug = FALSE, progress = NA, cache, .plotInitialTime = NULL,
  .saveInitialTime = NULL, notOlderThan, ...)
# S4 method for simList,ANY,ANY,missing
spades(sim, debug = FALSE,
  progress = NA, cache, .plotInitialTime = NULL, .saveInitialTime = NULL,
  notOlderThan, ...)
# S4 method for ANY,ANY,ANY,logical
spades(sim, debug = FALSE, progress = NA,
  cache, .plotInitialTime = NULL, .saveInitialTime = NULL, notOlderThan,
  ...)

Arguments

sim

A simList simulation object, generally produced by simInit.

debug

Optional logical flag or character vector indicating what to print to console at each event. See details. Default is debug=FALSE.

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.

.plotInitialTime

Numeric. Temporarily override the .plotInitialTime parameter for all modules. See Details.

.saveInitialTime

Numeric. Temporarily override the .plotInitialTime parameter for all modules. See Details.

notOlderThan

Date. Passed to SpaDES::cache to update the cache. Default is NULL, meaning don't update the cache. If Sys.time() is provided then, it will force a recache. Ignored if cache is FALSE.

...

Any. Can be used to make a unique cache identity, such as "replicate = 1". This will be included in the SpaDES::cache call, so will be unique and thus spades will not use a cached copy as long as anything passed in ... is unique, i.e., not cached previously.

Value

Invisibly returns the modified simList object.

Details

The is the workhorse function in the SpaDES package. It runs simulations by implementing the rules outlined in the simList.

This function gives simple access to two sets of module parameters: .plotInitialTime and with .plotInitialTime. The primary use of these arguments is to temporarily turn off plotting and saving. "Temporary" means that the simList is not changed, so it can be used again with the simList values reinstated. To turn off plotting and saving, use .plotInitialTime = NA or .saveInitialTime = NA. NOTE: if a module did not use .plotInitialTime or .saveInitialTime, then these arguments will not do anything.

If cache is TRUE, this allows for a seamless way to "save" results of a simulation. The user does not have to intentionally do any saving manually. Instead, upon a call to spades in which the simList is identical, the function will simply return the result that would have come if it had been rerun. Use this with caution, as it will return exactly the result from a previous run, even if there is stochasticity internally. Caching is only based on the input simList. See also experiment for the same mechanism, but it can be used with replication.

If debug is specified, it can be Logical or character vector. In all cases, something will be printed to the console immediately before each event is being executed. If TRUE, then the event immediately following will be printed as it runs (equivalent to current(sim)). If a character string, then it can be one of the many simList accessors, such as events, params, or "simList" (print the entire simList), or any R expression. If an R expression if will be evaluated with access to the sim object. If this is more than one character string, then all will be printed to the screen in their sequence.

References

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

See Also

simInit, SpaDES

experiment for using replication with spades.

Examples

# NOT RUN {
 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)

 # Different debug options
 spades(mySim, debug = TRUE) # Fastest
 spades(mySim, debug = "simList")
 spades(mySim, debug = "print(table(sim$landscape$Fires[]))")

 # Can turn off plotting, and inspect the output simList instead
 out <- spades(mySim, .plotInitialTime = NA) # much faster
 completed(out) # shows completed events

 # use cache -- simInit should generally be rerun each time a spades call is made
 #   to guarantee that it is identical. Here, run spades call twice, first
 #   time to establish cache, second time to return cached result
 for(i in 1:2) {
   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"))
   )
   print(system.time(out <- spades(mySim, cache = TRUE)))
 }
# }
# NOT RUN {
# }