## these tests are fairly heavy, so don't run during automated tests
#########################################################
# Simple case, no variation in rasQuality, numeric advectionDir and advectionMag
#########################################################
# \donttest{
library(terra)
origDTThreads <- data.table::setDTthreads(2L)
origNcpus <- options(Ncpus = 2L)
maxDim <- 10000
ras <- terra::rast(terra::ext(c(0, maxDim, 0, maxDim)), res = 100, vals = 0)
rasQuality <- terra::rast(ras)
rasQuality[] <- 1
rasAbundance <- terra::rast(rasQuality)
rasAbundance[] <- 0
# startPixel <- middlePixel(rasAbundance)
startPixel <- sample(seq(terra::ncell(rasAbundance)), 30)
rasAbundance[startPixel] <- 1000
advectionDir <- 70
advectionMag <- 4 * res(rasAbundance)[1]
meanDist <- 2600
# Test the dispersal kernel -- create a function
plotDispersalKernel <- function(out, meanAdvectionMag) {
out[, disGroup := round(distance / 100) * 100]
freqs <- out[, .N, by = "disGroup"]
freqs[, `:=`(cumSum = cumsum(N), N = N)]
plot(freqs$disGroup, freqs$cumSum, # addTo = "CumulativeNumberSettled",
main = "Cumulative Number Settled") # can plot the distance X number
abline(v = meanAdvectionMag + meanDist)
newTitle <- "Number Settled By Distance"
plot(freqs$disGroup, freqs$N, # addTo = gsub(" ", "", newTitle),
main = newTitle) # can plot the distance X number
abline(v = meanAdvectionMag + meanDist)
# should be 0.63:
freqs[disGroup == meanAdvectionMag + meanDist, cumSum] / tail(freqs, 1)[, cumSum]
mtext(side = 3, paste("Average habitat quality: ",
round(mean(rasQuality[], na.rm = TRUE), 2)),
outer = TRUE, line = -2, cex = 2)
}
out <- spread3(rasAbundance = rasAbundance,
rasQuality = rasQuality,
advectionDir = advectionDir,
advectionMag = advectionMag,
meanDist = meanDist, verbose = 2,
plot.it = interactive())
plotDispersalKernel(out, advectionMag)
# The next examples are potentially time consuming; avoid on automated testing
if (interactive()) {
#########################################################
### The case of variable quality raster
#########################################################
rasQuality <- terra::rast(system.file("extdata", "rasQuality.tif",
package = "SpaDES.tools"))
terra::crs(rasQuality) <- system.file("extdata", "targetCRS.rds", package = "SpaDES.tools") |>
readRDS() |>
slot("projargs")
mask <- rasQuality < 5
rasQuality[mask[] %in% TRUE] <- 0
# rescale so min is 0.75 and max is 1
rasQuality[] <- rasQuality[] / (reproducible::maxFn(rasQuality) * 4) + 1 / 4
rasAbundance <- terra::rast(rasQuality)
rasAbundance[] <- 0
startPixel <- sample(seq(ncell(rasAbundance)), 300)
rasAbundance[startPixel] <- 1000
advectionDir <- 75
advectionMag <- 4 * res(rasAbundance)[1]
meanDist <- 2600
out <- spread3(rasAbundance = rasAbundance,
rasQuality = rasQuality,
advectionDir = advectionDir,
advectionMag = advectionMag,
meanDist = meanDist, verbose = 2,
plot.it = interactive())
if (interactive()) {
plotDispersalKernel(out, advectionMag)
}
###############################################################################
### The case of variable quality raster, raster for advectionDir & advectionMag
###############################################################################
maxDim <- 10000
ras <- terra::rast(terra::ext(c(0, maxDim, 0, maxDim)), res = 100, vals = 0)
rasQuality <- terra::rast(ras)
rasQuality[] <- 1
rasAbundance <- terra::rast(rasQuality)
rasAbundance[] <- NA
# startPixel <- middlePixel(rasAbundance)
startPixel <- sample(seq(ncell(rasAbundance)), 25)
rasAbundance[startPixel] <- 1000
# raster for advectionDir
advectionDir <- terra::rast(system.file("extdata", "advectionDir.tif",
package = "SpaDES.tools"))
crs(advectionDir) <- crs(rasQuality)
# rescale so min is 0.75 and max is 1
advectionDir[] <- advectionDir[] / (reproducible::maxFn(advectionDir)) * 180
# raster for advectionMag
advectionMag <- terra::rast(system.file("extdata", "advectionMag.tif",
package = "SpaDES.tools"))
crs(advectionMag) <- crs(rasQuality)
# rescale so min is 0.75 and max is 1
advectionMag[] <- advectionMag[] / (reproducible::maxFn(advectionMag)) * 600
out <- spread3(rasAbundance = rasAbundance,
rasQuality = rasQuality,
advectionDir = advectionDir,
advectionMag = advectionMag,
meanDist = meanDist, verbose = 2,
plot.it = interactive())
if (interactive()) {
names(advectionDir) <- "Wind direction"
names(advectionMag) <- "Wind speed"
names(rasAbundance) <- "Initial abundances"
terra::plot(c(advectionDir, advectionMag, rasAbundance))
plotDispersalKernel(out, mean(advectionMag[]))
}
#########################################
# save iterations to a stack to make animated GIF
########################################
tmpStack <- tempfile(pattern = "stackToAnimate", fileext = ".tif")
out <- spread3(rasAbundance = rasAbundance,
rasQuality = rasQuality,
advectionDir = advectionDir,
advectionMag = advectionMag,
meanDist = 2600, verbose = 2,
plot.it = interactive(), saveStack = tmpStack)
## This animates the series of images into an animated GIF
if (require(animation, quietly = TRUE)) {
out2 <- terra::rast(tmpStack)
gifName <- file.path(tempdir(), "animation.gif")
# Only works on some systems; may need to configure
# Works on Windows without system adjustments
if (identical(.Platform$OS.type, "windows"))
saveGIF(interval = 0.1, movie.name = gifName, expr = {
for (i in seq(length(names(out2)))) terra::plot(out2[[i]])
})
}
}
# clean up
data.table::setDTthreads(origDTThreads)
options(Ncpus = origNcpus)
# }
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