library(terra)
# Load species occurrences (6 species available)
data(DataSpecies)
head(DataSpecies)
# Select the name of the studied species
myRespName <- 'GuloGulo'
# Get corresponding presence/absence data
myResp <- as.numeric(DataSpecies[, myRespName])
# Get corresponding XY coordinates
myRespXY <- DataSpecies[, c('X_WGS84', 'Y_WGS84')]
# Load environmental variables extracted from BIOCLIM (bio_3, bio_4, bio_7, bio_11 & bio_12)
data(bioclim_current)
myExpl <- terra::rast(bioclim_current)
# \dontshow{
myExtent <- terra::ext(0,30,45,70)
myExpl <- terra::crop(myExpl, myExtent)
# }
# ---------------------------------------------------------------#
file.out <- paste0(myRespName, "/", myRespName, ".AllModels.models.out")
if (file.exists(file.out)) {
myBiomodModelOut <- get(load(file.out))
} else {
# Format Data with true absences
myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
expl.var = myExpl,
resp.xy = myRespXY,
resp.name = myRespName)
# Model single models
myBiomodModelOut <- BIOMOD_Modeling(bm.format = myBiomodData,
modeling.id = 'AllModels',
models = c('RF', 'GLM'),
CV.strategy = 'random',
CV.nb.rep = 2,
CV.perc = 0.8,
OPT.strategy = 'bigboss',
metric.eval = c('TSS','ROC'),
var.import = 3,
seed.val = 42)
}
models.proj <- get_built_models(myBiomodModelOut, algo = "RF")
# Project single models
myBiomodProj <- BIOMOD_Projection(bm.mod = myBiomodModelOut,
proj.name = 'CurrentRangeSize',
new.env = myExpl,
models.chosen = models.proj,
metric.binary = 'all')
# ---------------------------------------------------------------#
# Load environmental variables extracted from BIOCLIM (bio_3, bio_4, bio_7, bio_11 & bio_12)
data(bioclim_future)
myExplFuture <- terra::rast(bioclim_future)
# \dontshow{
myExtent <- terra::ext(0,30,45,70)
myExplFuture <- terra::crop(myExplFuture, myExtent)
# }
# Project onto future conditions
myBiomodProjectionFuture <- BIOMOD_Projection(bm.mod = myBiomodModelOut,
proj.name = 'FutureRangeSize',
new.env = myExplFuture,
models.chosen = models.proj,
metric.binary = 'TSS')
# Load current and future binary projections
CurrentProj <- get_predictions(myBiomodProj,
metric.binary = "TSS",
model.as.col = TRUE)
FutureProj <- get_predictions(myBiomodProjectionFuture,
metric.binary = "TSS",
model.as.col = TRUE)
# Compute differences
myBiomodRangeSize <- BIOMOD_RangeSize(proj.current = CurrentProj, proj.future = FutureProj)
# ---------------------------------------------------------------#
myBiomodRangeSize$Compt.By.Models
plot(myBiomodRangeSize$Diff.By.Pixel)
# Represent main results
bm_PlotRangeSize(bm.range = myBiomodRangeSize)
Run the code above in your browser using DataLab