R/BIOMOD_RangeSize.R
BIOMOD_RangeSize.Rd
This function allows to calculate the absolute number of locations (pixels) lost, stable and gained, as well as the corresponding relative proportions, between two (or more) binary projections of (ensemble) species distribution models (which can represent new time scales or environmental scenarios for example).
BIOMOD_RangeSize(
proj.current,
proj.future,
models.chosen = "all",
metric.binary = NULL
)
a BIOMOD.projection.out
object containing the initial projection(s)
of the (ensemble) species distribution model(s)
a BIOMOD.projection.out
object containing the final binary projection(s)
of the (ensemble) species distribution model(s)
a vector
containing model names to be kept, must be either
all
or a sub-selection of model names that can be obtained with the
get_projected_models
function
(optional, default NULL
)
A vector
containing evaluation metric selected to transform predictions into binary
values, must be among POD
, FAR
, POFD
, SR
, ACCURACY
,
BIAS
, ROC
, TSS
, KAPPA
, OR
, ORSS
, CSI
,
ETS
, BOYCE
, MPA
A BIOMOD.rangesize.out
containing principaly two objects :
a data.frame
containing the summary of range change for each
comparison
Loss
: number of pixels predicted to be lost
Stable_Abs
: number of pixels not currently occupied and not predicted to be
Stable_Pres
: number of pixels currently occupied and predicted to remain
occupied
Gain
: number of pixels predicted to be gained
PercLoss
: percentage of pixels currently occupied and predicted to be lost
(Loss / (Loss + Stable_Pres)
)
PercGain
: percentage of pixels predicted to be gained compare to the
number of pixels currently occupied (Gain / (Loss + Stable_Pres)
)
SpeciesRangeChange
: percentage of pixels predicted to change (loss or gain)
compare to the number of pixels currently occupied (PercGain - PercLoss
)
CurrentRangeSize
: number of pixels currently occupied
FutureRangeSize0Disp
: number of pixels predicted to be occupied, assuming
no migration
FutureRangeSize1Disp
: number of pixels predicted to be occupied, assuming
migration
an object in the same form than the input data (proj.current
and
proj.future
) and containing a value for each point/pixel of each comparison among :
-2
: predicted to be lost
-1
: predicted to remain occupied
0
: predicted to remain unoccupied
1
: predicted to be gained
an object in the same form than the input data (proj.current
and
proj.future
) and containing a value for each point/pixel of each comparison obtain with :
Future - 2* Current
for binary data
Future - Current
for nonbinary after rescaling Future and Current from 0 to 1.
BIOMOD_Projection
, BIOMOD_EnsembleForecasting
,
bm_PlotRangeSize
Other Main functions:
BIOMOD_EnsembleForecasting()
,
BIOMOD_EnsembleModeling()
,
BIOMOD_FormatingData()
,
BIOMOD_LoadModels()
,
BIOMOD_Modeling()
,
BIOMOD_Projection()
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.name = myRespName,
resp.var = myResp,
resp.xy = myRespXY,
expl.var = myExpl)
# 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',
build.clamping.mask = TRUE)
# --------------------------------------------------------------- #
# 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')
# Compute differences
myBiomodRangeSize <- BIOMOD_RangeSize(proj.current = myBiomodProj,
proj.future = myBiomodProjectionFuture,
metric.binary = "TSS")
# Represent main results
bm_PlotRangeSize(bm.range = myBiomodRangeSize)