Simulation inputs

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

Arguments

sim: A simList object from which to extract element(s) or in which to replace element(s).
value: The object to be stored at the slot. See Details.

Value

Returns or sets the value(s) of the input or output slots in the simList object.

Details

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.

inputs function or argument in `simInit`

inputs 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 module

Any 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' }

Examples

#######################
# inputs
#######################

# Start with a basic empty simList
sim <- simInit()
#> Setting:
#>   options(
#>     reproducible.cachePath = '/tmp/RtmpAzfvD1/myProject/cache'
#>     spades.inputPath = '/tmp/RtmpAzfvD1/myProject/inputs'
#>     spades.outputPath = '/tmp/RtmpAzfvD1/myProject/outputs'
#>     spades.modulePath = '/tmp/RtmpAzfvD1/myProject/modules'
#>     spades.scratchPath = '/tmp/RtmpAzfvD1/SpaDES/scratch'
#>   )
#> Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.

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     fun package objectName loadTime loaded
#> 1 /tmp/RtmpAzfvD1/inputs/test.rds readRDS    base       test        0     NA
#>   arguments intervals
#> 1        NA        NA
simOut <- spades(sim)
#> Aug19 19:59:29       Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Aug19 19:59:29 chckpn  total elpsd: 0.00099 secs | 0 checkpoint init 0
#> Aug19 19:59:29 save    total elpsd: 0.0027 secs | 0 save init 0
#> Aug19 19:59:29 prgrss  total elpsd: 0.0043 secs | 0 progress init 0
#> Aug19 19:59:29 load    total elpsd: 0.0058 secs | 0 load init 0
#> Aug19 19:59:29 load    total elpsd: 0.0072 secs | 0 load inputs 0
#> Aug19 19:59:29 load   test read from /tmp/RtmpAzfvD1/inputs/test.rds using readRDS
#> simList saved in
#>  SpaDES.core:::.pkgEnv$.sim 
#> It will be deleted at next spades() call.
inputs(simOut) # confirm it was loaded
#>                              file     fun package objectName loadTime loaded
#> 1 /tmp/RtmpAzfvD1/inputs/test.rds readRDS    base       test        0   TRUE
#>   arguments intervals
#> 1        NA        NA
simOut$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)
}
#> Please note that rgdal will be retired by the end of 2023,
#> plan transition to sf/stars/terra functions using GDAL and PROJ
#> at your earliest convenience.
#> 
#> rgdal: version: 1.5-32, (SVN revision 1176)
#> Geospatial Data Abstraction Library extensions to R successfully loaded
#> Loaded GDAL runtime: GDAL 3.0.4, released 2020/01/28
#> Path to GDAL shared files: /usr/share/gdal
#> GDAL binary built with GEOS: TRUE 
#> Loaded PROJ runtime: Rel. 6.3.1, February 10th, 2020, [PJ_VERSION: 631]
#> Path to PROJ shared files: /usr/share/proj
#> Linking to sp version:1.5-0
#> To mute warnings of possible GDAL/OSR exportToProj4() degradation,
#> use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.
#> Setting:
#>   options(
#>     reproducible.cachePath = '/tmp/RtmpAzfvD1/myProject/cache'
#>     spades.inputPath = '/tmp/RtmpAzfvD1/myProject/inputs'
#>     spades.outputPath = '/tmp/RtmpAzfvD1/myProject/outputs'
#>     spades.modulePath = '/tmp/RtmpAzfvD1/myProject/modules'
#>     spades.scratchPath = '/tmp/RtmpAzfvD1/SpaDES/scratch'
#>   )
#> Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Aug19 19:59:29 simInit:       DEM read from /home/runner/work/_temp/Library/quickPlot/maps/DEM.tif using raster(inMemory=FALSE)
#> Aug19 19:59:29 simInit:       forestAge read from /home/runner/work/_temp/Library/quickPlot/maps/forestAge.tif using raster(inMemory=FALSE)
#> Aug19 19:59:29 simInit:       forestCover read from /home/runner/work/_temp/Library/quickPlot/maps/forestCover.tif using raster(inMemory=FALSE)
#> Aug19 19:59:29 simInit:       habitatQuality read from /home/runner/work/_temp/Library/quickPlot/maps/habitatQuality.tif using raster(inMemory=FALSE)
#> Aug19 19:59:29 simInit:       percentPine read from /home/runner/work/_temp/Library/quickPlot/maps/percentPine.tif using raster(inMemory=FALSE)
#> Aug19 19:59:29       Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Aug19 19:59:29 chckpn  total elpsd: 9e-04 secs | 0 checkpoint init 0
#> Aug19 19:59:29 save    total elpsd: 0.0025 secs | 0 save init 0
#> Aug19 19:59:29 prgrss  total elpsd: 0.0042 secs | 0 progress init 0
#> Aug19 19:59:29 load    total elpsd: 0.0056 secs | 0 load init 0
#> Aug19 19:59:29 load    total elpsd: 0.007 secs | 0 load inputs 0
#> Aug19 19:59:29 load   Maps1 read from /home/runner/work/_temp/Library/quickPlot/maps/DEM.tif using raster(inMemory=FALSE)
#> Aug19 19:59:29 load   Maps2 read from /home/runner/work/_temp/Library/quickPlot/maps/forestAge.tif using raster(inMemory=FALSE)
#> Aug19 19:59:29 load   Maps3 read from /home/runner/work/_temp/Library/quickPlot/maps/forestCover.tif using raster(inMemory=FALSE)
#> Aug19 19:59:29 load   Maps4 read from /home/runner/work/_temp/Library/quickPlot/maps/habitatQuality.tif using raster(inMemory=FALSE)
#> Aug19 19:59:29 load   Maps5 read from /home/runner/work/_temp/Library/quickPlot/maps/percentPine.tif using raster(inMemory=FALSE)
#> Aug19 19:59:29 load    total elpsd: 0.046 secs | 10 load inputs 0
#> Aug19 19:59:29 load   Maps5 read from /home/runner/work/_temp/Library/quickPlot/maps/percentPine.tif using raster(inMemory=FALSE)  at time 10
#> simList saved in
#>  SpaDES.core:::.pkgEnv$.sim 
#> It will be deleted at next spades() call.

# 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))
#> Setting:
#>   options(
#>     reproducible.cachePath = '/tmp/RtmpAzfvD1/myProject/cache'
#>     spades.inputPath = '/tmp/RtmpAzfvD1/myProject/inputs'
#>     spades.outputPath = '/tmp/RtmpAzfvD1/myProject/outputs'
#>     spades.modulePath = '/tmp/RtmpAzfvD1/myProject/modules'
#>     spades.scratchPath = '/tmp/RtmpAzfvD1/SpaDES/scratch'
#>   )
#> Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
a <- spades(a)
#> Aug19 19:59:29       Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Aug19 19:59:29 chckpn  total elpsd: 0.00088 secs | 0 checkpoint init 0
#> Aug19 19:59:29 save    total elpsd: 0.0024 secs | 0 save init 0
#> Aug19 19:59:29 prgrss  total elpsd: 0.0041 secs | 0 progress init 0
#> Aug19 19:59:29 load    total elpsd: 0.0057 secs | 0 load init 0
#> Aug19 19:59:29 load    total elpsd: 0.0072 secs | 1 load inputs 0
#> Aug19 19:59:29 load   a loaded into simList
#> simList saved in
#>  SpaDES.core:::.pkgEnv$.sim 
#> It will be deleted at next spades() call.
identical(a1, a$a)
#> [1] TRUE

end(a) <- 3
a <- spades(a) # different object (a2) loaded onto a$a
#> Aug19 19:59:29       Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Aug19 19:59:29 load    total elpsd: 0.024 secs | 2 load inputs 0
#> Aug19 19:59:29 load   a loaded into simList
#> simList saved in
#>  SpaDES.core:::.pkgEnv$.sim 
#> It will be deleted at next spades() call.
identical(a2, a$a)
#> [1] TRUE

# Clean up after
unlink(tmpdir, recursive = TRUE)

Arguments

Value

Details

inputs function or argument in simInit

.inputObjects function placed inside module

See also

Examples

inputs function or argument in `simInit`

`.inputObjects` function placed inside module