File extensions map

Source: R/load.R, R/save.R

How to load various types of files in R.

This function has two roles:

  1. to proceed with the loading of files that are in a simList; or

  2. as a shortcut to simInit(inputs = filelist).

A data.frame with information on how to load various types of files in R, containing the columns:

  • exts: the file extension;

  • fun: the function to use for files with this file extension;

  • package: the package from which to load fun.

.fileExtensions()

loadFiles(sim, filelist, ...)

# S4 method for class 'simList,missing'
loadFiles(sim, filelist, ...)

# S4 method for class 'missing,ANY'
loadFiles(sim, filelist, ...)

# S4 method for class 'missing,missing'
loadFiles(sim, filelist, ...)

.saveFileExtensions()

Arguments

sim

simList object.

filelist

list or data.frame to call loadFiles directly from the filelist as described in Details

...

Additional arguments.

Value

data.frame of file extension, package, and function mappings

the modified sim, invisibly.

data.frame

Note

Generally not intended to be used by users.

See also

inputs()

Author

Eliot McIntire and Alex Chubaty

Examples

# \donttest{
library(SpaDES.core)

# Load random maps included with package
filelist <- data.frame(
  files = dir(getMapPath(tempdir()), full.names = TRUE),
  functions = "rasterToMemory",
  package = "SpaDES.core"
)
sim1 <- loadFiles(filelist = filelist) # loads all the maps to sim1 simList
#> Setting:
#>   options(
#>     reproducible.cachePath = '/tmp/Rtmp45trFG/reproducible/cache'
#>     spades.inputPath = '/tmp/Rtmp45trFG/SpaDES/inputs'
#>     spades.outputPath = '/tmp/Rtmp45trFG/SpaDES/outputs'
#>     spades.modulePath = '/tmp/Rtmp45trFG/SpaDES/modules'
#>     spades.scratchPath = '/tmp/Rtmp45trFG/SpaDES/scratch'
#>   )
#> Nov21 04:22:34 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Nov21 04:22:34 simInit DEM read from /tmp/Rtmp45trFG/maps/DEM.tif using rasterToMemory
#> Nov21 04:22:34 simInit forestAge read from /tmp/Rtmp45trFG/maps/forestAge.tif using rasterToMemory
#> Nov21 04:22:34 simInit forestCover read from /tmp/Rtmp45trFG/maps/forestCover.tif using rasterToMemory
#> Nov21 04:22:34 simInit habitatQuality read from /tmp/Rtmp45trFG/maps/habitatQuality.tif using rasterToMemory
#> Nov21 04:22:34 simInit percentPine read from /tmp/Rtmp45trFG/maps/percentPine.tif using rasterToMemory
#> Elpsed time for simInit: 0.144654 secs

# Second, more sophisticated. All maps loaded at time = 0, and the last one is reloaded
#  at time = 10 and 20 (via "intervals").
# Also, pass the single argument as a list to all functions...
#  specifically, when add "native = TRUE" as an argument to the raster function
files <- dir(getMapPath(tempdir()), full.names = TRUE)
arguments <- I(rep(list(lyrs = 1), length(files)))
filelist <- data.frame(
   files = files,
   functions = "terra::rast",
   objectName = NA,
   arguments = arguments,
   loadTime = 0,
   intervals = c(rep(NA, length(files)-1), 10)
)

sim2 <- loadFiles(filelist = filelist) # only does the time = 0 loading; see next
#> Setting:
#>   options(
#>     reproducible.cachePath = '/tmp/Rtmp45trFG/reproducible/cache'
#>     spades.inputPath = '/tmp/Rtmp45trFG/SpaDES/inputs'
#>     spades.outputPath = '/tmp/Rtmp45trFG/SpaDES/outputs'
#>     spades.modulePath = '/tmp/Rtmp45trFG/SpaDES/modules'
#>     spades.scratchPath = '/tmp/Rtmp45trFG/SpaDES/scratch'
#>   )
#> Nov21 04:22:34 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Nov21 04:22:34 simInit DEM read from /tmp/Rtmp45trFG/maps/DEM.tif using rast(inMemory=FALSE)
#> Nov21 04:22:34 simInit forestAge read from /tmp/Rtmp45trFG/maps/forestAge.tif using rast(inMemory=FALSE)
#> Nov21 04:22:34 simInit forestCover read from /tmp/Rtmp45trFG/maps/forestCover.tif using rast(inMemory=FALSE)
#> Nov21 04:22:34 simInit habitatQuality read from /tmp/Rtmp45trFG/maps/habitatQuality.tif using rast(inMemory=FALSE)
#> Nov21 04:22:34 simInit percentPine read from /tmp/Rtmp45trFG/maps/percentPine.tif using rast(inMemory=FALSE)
#> Elpsed time for simInit: 0.06026769 secs
end(sim2) <- 10
sim2 <- spades(sim2) # loads the object at time 10
#> Nov21 04:22:34 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Nov21 04:22:34 chckpn:init total elpsd: 0.061 secs | 0 checkpoint init 0
#> Nov21 04:22:34 save  :init total elpsd: 0.063 secs | 0 save init 0
#> Nov21 04:22:34 prgrss:init total elpsd: 0.065 secs | 0 progress init 0
#> Nov21 04:22:34 load  :init total elpsd: 0.067 secs | 0 load init 0
#> Nov21 04:22:34 load  :inputs total elpsd: 0.068 secs | 10 load inputs 0
#> Nov21 04:22:34 load  :inputs percentPine read from /tmp/Rtmp45trFG/maps/percentPine.tif using rast(inMemory=FALSE)
#> Nov21 04:22:34 load  :inputs    at time 10
#> simList saved in
#> SpaDES.core:::savedSimEnv()$.sim
#> It will be deleted at next spades() call.

# if we extend the end time and continue running, it will load an object scheduled
#  at time = 10, and it will also schedule a new object loading at 20 because
#  interval = 10
end(sim2) <- 20
sim2 <- spades(sim2) # loads the percentPine map 2 more times, once at 10, once at 20
#> Nov21 04:22:34 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Nov21 04:22:34 load  :inputs total elpsd: 0.085 secs | 20 load inputs 0
#> Nov21 04:22:34 load  :inputs percentPine read from /tmp/Rtmp45trFG/maps/percentPine.tif using rast(inMemory=FALSE)
#> Nov21 04:22:34 load  :inputs    at time 20
#> simList saved in
#> SpaDES.core:::savedSimEnv()$.sim
#> It will be deleted at next spades() call.
# }