How to load various types of files in R.
This function has two roles:
to proceed with the loading of files that are in a simList; or
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 simList,missing
loadFiles(sim, filelist, ...)
# S4 method for missing,ANY
loadFiles(sim, filelist, ...)
# S4 method for missing,missing
loadFiles(sim, filelist, ...)
.saveFileExtensions()simList object.
list or data.frame to call loadFiles directly from the
filelist as described in Details
Additional arguments.
data.frame of file extension, package, and function mappings
the modified sim, invisibly.
data.frame
Generally not intended to be used by users.
# \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/RtmpNobduY/reproducible/cache'
#> spades.inputPath = '/tmp/RtmpNobduY/SpaDES/inputs'
#> spades.outputPath = '/tmp/RtmpNobduY/SpaDES/outputs'
#> spades.modulePath = '/tmp/RtmpNobduY/SpaDES/modules'
#> spades.scratchPath = '/tmp/RtmpNobduY/SpaDES/scratch'
#> )
#> Apr16 20:30:43 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Apr16 20:30:43 simInit DEM read from /tmp/RtmpNobduY/maps/DEM.tif using rasterToMemory
#> Apr16 20:30:43 simInit forestAge read from /tmp/RtmpNobduY/maps/forestAge.tif using rasterToMemory
#> Apr16 20:30:43 simInit forestCover read from /tmp/RtmpNobduY/maps/forestCover.tif using rasterToMemory
#> Apr16 20:30:43 simInit habitatQuality read from /tmp/RtmpNobduY/maps/habitatQuality.tif using rasterToMemory
#> Apr16 20:30:43 simInit percentPine read from /tmp/RtmpNobduY/maps/percentPine.tif using rasterToMemory
#> Elpsed time for simInit: 0.1407115 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/RtmpNobduY/reproducible/cache'
#> spades.inputPath = '/tmp/RtmpNobduY/SpaDES/inputs'
#> spades.outputPath = '/tmp/RtmpNobduY/SpaDES/outputs'
#> spades.modulePath = '/tmp/RtmpNobduY/SpaDES/modules'
#> spades.scratchPath = '/tmp/RtmpNobduY/SpaDES/scratch'
#> )
#> Apr16 20:30:43 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Apr16 20:30:43 simInit DEM read from /tmp/RtmpNobduY/maps/DEM.tif using rast(inMemory=FALSE)
#> Apr16 20:30:43 simInit forestAge read from /tmp/RtmpNobduY/maps/forestAge.tif using rast(inMemory=FALSE)
#> Apr16 20:30:43 simInit forestCover read from /tmp/RtmpNobduY/maps/forestCover.tif using rast(inMemory=FALSE)
#> Apr16 20:30:43 simInit habitatQuality read from /tmp/RtmpNobduY/maps/habitatQuality.tif using rast(inMemory=FALSE)
#> Apr16 20:30:43 simInit percentPine read from /tmp/RtmpNobduY/maps/percentPine.tif using rast(inMemory=FALSE)
#> Elpsed time for simInit: 0.05918622 secs
end(sim2) <- 10
sim2 <- spades(sim2) # loads the object at time 10
#> Apr16 20:30:43 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Apr16 20:30:43 chckpn:init total elpsd: 0.06 secs | 0 checkpoint init 0
#> Apr16 20:30:43 save :init total elpsd: 0.062 secs | 0 save init 0
#> Apr16 20:30:43 prgrss:init total elpsd: 0.064 secs | 0 progress init 0
#> Apr16 20:30:43 load :init total elpsd: 0.086 secs | 0 load init 0
#> Apr16 20:30:43 load :inputs total elpsd: 0.088 secs | 10 load inputs 0
#> Apr16 20:30:43 load :inputs percentPine read from /tmp/RtmpNobduY/maps/percentPine.tif using rast(inMemory=FALSE)
#> Apr16 20:30:43 load :inputs at time 10
#> simList saved in
#> SpaDES.core:::.pkgEnv$.sim
#> It will be deleted at next spades() call.
# if we extend the end time and continue running, it will load an object scheduled
# at time = 10, and it will also schedule a new object loading at 20 because
# interval = 10
end(sim2) <- 20
sim2 <- spades(sim2) # loads the percentPine map 2 more times, once at 10, once at 20
#> Apr16 20:30:43 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Apr16 20:30:43 load :inputs total elpsd: 0.11 secs | 20 load inputs 0
#> Apr16 20:30:43 load :inputs percentPine read from /tmp/RtmpNobduY/maps/percentPine.tif using rast(inMemory=FALSE)
#> Apr16 20:30:43 load :inputs at time 20
#> simList saved in
#> SpaDES.core:::.pkgEnv$.sim
#> It will be deleted at next spades() call.
# }