Accessor functions for the inputs slots in a simList object.
inputs(sim) # S4 method for simList inputs(sim) inputs(sim) <- value # S4 method for simList inputs(sim) <- value inputArgs(sim) # S4 method for simList inputArgs(sim) inputArgs(sim) <- value # S4 method for simList inputArgs(sim) <- value
| sim | A |
|---|---|
| value | The object to be stored at the slot. See Details. |
Returns or sets the value(s) of the input or output slots
in the simList object.
These functions are one of three mechanisms to add the information about which input files
to load in a spades call.
As arguments to a simInit call. Specifically, inputs or outputs.
See ?simInit.
With the outputs(simList) function call.
By adding a function called .inputObjects inside a module, which will be executed
during the simInit call. This last way is the most "modular" way to create
default data sets for your model.
See below for more details.
simInitinputs accepts a data.frame, with up to 7 columns.
Columns are:
file | required, a character string indicating the file path. There is no default. |
objectName | optional, character string indicating the name of the object
that the loaded file will be assigned to in the simList. This object
can therefore be accessed with sim$xxx in any module, where
objectName = "xxx". Defaults to the filename without file extension or
directory information. |
fun | optional, a character string indicating the function to use to
load that file. Defaults to the known extensions in SpaDES (found by
examining .fileExtensions()). The package and fun can be
jointly specified here as "packageName::functionName", e.g.,
"raster::raster". |
package | optional character string indicating the package in
which to find the fun); |
loadTime | optional numeric, indicating when in simulation time the file
should be loaded. The default is the highest priority at start(sim),
i.e., at the very start. |
interval | optional numeric, indicating at what interval should this same
exact file be reloaded from disk, e.g,. 10 would mean every 10 time units. The
default is NA or no interval, i.e, load the file only once as described in
loadTime |
arguments | is a list of lists of named arguments, one list for each
fun. For example, if fun="raster", arguments = list(native = TRUE)
will pass the argument "native = TRUE" to raster. If there is only one list,
then it is assumed to apply to all files and will be recycled as per normal R
rules of recycling for each fun. |
Currently, only file is required. All others will be filled with defaults
if not specified.
See the modules vignette for more details (browseVignettes("SpaDES.core")).
.inputObjects function placed inside moduleAny code placed inside a function called .inputObjects will be run during
simInit() for the purpose of creating any objects required by this module,
i.e., objects identified in the inputObjects element of defineModule.
This is useful if there is something required before simulation to produce the module
object dependencies, including such things as downloading default datasets, e.g.,
downloadData('LCC2005', modulePath(sim)).
Nothing should be created here that does not create an named object in inputObjects.
Any other initiation procedures should be put in the "init" eventType of the doEvent function.
Note: the module developer can use 'sim$.userSuppliedObjNames' inside the function to
selectively skip unnecessary steps because the user has provided those inputObjects in the
simInit call. e.g., the following code would look to see if the user had passed defaultColor
into during simInit. If the user had done this, then this function would not override
that value with 'red'. If the user has not passed in a value for defaultColor, then
the module will get it here:
if (!('defaultColor' %in% sim$.userSuppliedObjNames)) {
sim$defaultColor <- 'red'
}
SpaDES.core-package, specifically the section 1.2.2 on loading and saving.
Other functions to access elements of a 'simList' object:
.addDepends(),
doEvent.checkpoint(),
envir(),
events(),
globals(),
modules(),
objs(),
packages(),
params(),
paths(),
progressInterval(),
times()
####################### # inputs ####################### # Start with a basic empty simList sim <- simInit()#> #> #> #> #> #> #> #>test <- 1:10 library(igraph) # for %>% library(reproducible) # for checkPath tmpdir <- file.path(tempdir(), "inputs") %>% checkPath(create = TRUE) tmpFile <- file.path(tmpdir, "test.rds") saveRDS(test, file = tmpFile) inputs(sim) <- data.frame(file = tmpFile) # using only required column, "file" inputs(sim) # see that it is not yet loaded, but when it is scheduled to be loaded#> file #> 1 /private/var/folders/l2/hy6b0sl977bcd8695nt6j7s80000gn/T/RtmpRqC26y/inputs/test.rds #> fun package objectName loadTime loaded arguments intervals #> 1 readRDS base test 0 NA NA NA#>#> total elpsd: 0.0028 secs | 0 save init 0#> total elpsd: 0.0053 secs | 0 progress init 0#> total elpsd: 0.0073 secs | 0 load init 0#> total elpsd: 0.0091 secs | 0 load inputs 0#>#> simList saved in #> SpaDES.core:::.pkgEnv$.sim #>inputs(simOut) # confirm it was loaded#> file #> 1 /private/var/folders/l2/hy6b0sl977bcd8695nt6j7s80000gn/T/RtmpRqC26y/inputs/test.rds #> fun package objectName loadTime loaded arguments intervals #> 1 readRDS base test 0 TRUE NA NAsimOut$test#> [1] 1 2 3 4 5 6 7 8 9 10# can put data.frame for inputs directly inside simInit call allTifs <- dir(system.file("maps", package = "quickPlot"), full.names = TRUE, pattern = "tif") # next: .objectNames are taken from the filenames (without the extension) # This will load all 5 tifs in the SpaDES sample directory, using # the raster fuction in the raster package, all at time = 0 if (require("rgdal", quietly = TRUE)) { sim <- simInit( inputs = data.frame( files = allTifs, functions = "raster", package = "raster", loadTime = 0, stringsAsFactors = FALSE) ) ############################## #A fully described inputs object, including arguments: files <- dir(system.file("maps", package = "quickPlot"), full.names = TRUE, pattern = "tif") # arguments must be a list of lists. This may require I() to keep it as a list # once it gets coerced into the data.frame. arguments = I(rep(list(native = TRUE), length(files))) filelist = data.frame( objectName = paste0("Maps", 1:5), files = files, functions = "raster::raster", arguments = arguments, loadTime = 0, intervals = c(rep(NA, length(files) - 1), 10) ) inputs(sim) <- filelist spades(sim) }#> #> #> #> #> #> #> #> #> #> #>#> #> #> #> #> #> #> #>#>#>#>#>#>#> total elpsd: 0.00039 secs | 0 checkpoint init 0#> total elpsd: 0.0024 secs | 0 save init 0#> total elpsd: 0.016 secs | 0 progress init 0#> total elpsd: 0.023 secs | 0 load init 0#> total elpsd: 0.027 secs | 0 load inputs 0#>#>#>#>#>#> total elpsd: 0.1 secs | 10 load inputs 0#>#> simList saved in #> SpaDES.core:::.pkgEnv$.sim #># Example showing loading multiple objects from global environment onto the # same object in the simList, but at different load times a1 <- 1 a2 <- 2 # Note arguments must be a list of NROW(inputs), with each element itself being a list, # which is passed to do.call(fun[x], arguments[[x]]), where x is row number, one at a time args <- lapply(1:2, function(x) { list(x = paste0("a", x), envir = environment()) # may be necessary to specify in which envir a1, a2 # are located, if not in an interactive sessino }) inputs <- data.frame(objectName = "a", loadTime = 1:2, fun = "base::get", arguments = I(args)) a <- simInit(inputs = inputs, times = list(start = 0, end = 1))#> #> #> #> #> #> #> #>#> total elpsd: 0.00043 secs | 0 checkpoint init 0#> total elpsd: 0.0027 secs | 0 save init 0#> total elpsd: 0.0076 secs | 0 progress init 0#> total elpsd: 0.01 secs | 0 load init 0#> total elpsd: 0.013 secs | 1 load inputs 0#>#> simList saved in #> SpaDES.core:::.pkgEnv$.sim #>#> [1] TRUE#> total elpsd: 0.033 secs | 2 load inputs 0#>#> simList saved in #> SpaDES.core:::.pkgEnv$.sim #>#> [1] TRUE