biomod2 (version 2.0.0)

BIOMOD_RangeSize: Analysis of the range size changes

Description

This function allows to estimate the proportion and relative number of pixels (or habitat) lost, gained and stable for the time slice considered in species-climate modelling under future scenarios.

Usage

## S3 method for class 'data.frame,data.frame':
BIOMOD_RangeSize(CurrentPred, FutureProj,  SpChange.Save=NULL)
## S3 method for class 'array,array':
BIOMOD_RangeSize(CurrentPred, FutureProj,  SpChange.Save=NULL)
## S3 method for class 'RasterStack,RasterStack':
BIOMOD_RangeSize(CurrentPred, FutureProj,  SpChange.Save=NULL)

Arguments

CurrentPred

a data.frame of n (number of models) columns OR an array formated as an output of BIOMOD_Projection function OR a RasterStack (a layer by model) giving the current state of the

FutureProj

a data.frame of n (number of models) columns OR an array formated as an output of BIOMOD_Projection function OR a RasterStack (a layer by model) giving the future projections o

SpChange.Save

the name given to the new object storing the results

Value

• A list of two items is created: Compt.By.Species and Diff.By.Pixel ; Compt.By.Species is the summary of this function; Diff.By.Pixel is in the same form than your input data.
• Compt.By.Species
  stores the summary of range change for each species (sorted by rows). The first four columns are absolute values whereas the next 3 ones are relative values:
• Disa
  represents the number of pixels predicted to be lost by the given species.
• Stable0
  is the number of pixels which are not currently occupied by the given species and not predicted to be.
• Stable1
  represents the number of pixels currently occupied by the given species, and predicted to remain occupied into the future.
• Gain
  represents the number of pixels which are currently not occupied by the given species but predicted to be into the future.
• PercLoss
  corresponds to the percentage of currently occupied sites to be lost (Disa/(Disa+Stable1)
• PercGain
  corresponds to the percentage of new sites considering the species' current distribution size (Gain/(Disa+Stable1). For example, if the there are 30 sites currently occupied and 15 new sites are projected to be occupied in future, it makes PercGain=+50(%).
• SpeciesRangeChange
  it is the overall projection outcome, equal to PercGain-PercLoss. It does not assess for any migration shifts as it strictly compares the range sizes between current and future states.
• CurrentRangeSize
  represents the modelled current range size (number of pixels occupied) of the given species.
• FutureRangeSize0Disp
  represents the future modelled range size assuming no migration of the given species.
• FutureRangeSize1Disp
  represents the future modelled range size assuming migration of the given species (depending on the datasets given in input, if Migration has been used or not).
• Diff.By.Pixel
  the summary of range change for each species (sorted by columns and with the pixel in rows). For each species, a pixel could have four different values : -2 if the given pixel is predicted to be lost by the species. -1 if the given pixel is predicted to be stable for the species. 0 is the given pixel was not occupied, and will not be in the future. 1 if the given pixel was not occupied, and is predicted to be into the future. This table could be easily plotted into GIS software in order to represent the pattern of change for the selected species (or even with the level.plot() function).

Details

Note that this function is only relevant if you make projections on the same area with the same resolution and for a different time slice (past or future) than for the current data.

Examples

# 0. Load data & Selecting Data

# species occurances
species_occ <- read.csv(system.file("external/species/species_occ.csv",package="biomod2"))

# we consider only presences of MyocastorCoypus species
myRespName <- 'MyocastorCoypus'
myRespCoord <- species_occ[which(!is.na(species_occ[,myRespName])),c('x','y')]
myResp <- as.numeric(na.omit(species_occ[,myRespName]))

# Environemental variables extracted from BIOCLIM (bio_3, bio_4, bio_7, bio_11 & bio_12)
myExpl = raster::stack(system.file("external/climat/current/bio3.grd",package="biomod2"),
                       system.file("external/climat/current/bio4.grd",package="biomod2"),
                       system.file("external/climat/current/bio7.grd",package="biomod2"),
                       system.file("external/climat/current/bio11.grd",package="biomod2"),
                       system.file("external/climat/current/bio12.grd",package="biomod2"))

# 1. Formating Data
myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
                                     expl.var = myExpl,
                                     resp.xy = myRespCoord,
                                     resp.name = myRespName,
                                     PA.nb.rep = 1,
                                     PA.nb.absences = 200,
                                     PA.strategy = 'random')
                                                                     
# 2. Defining Models Options using default options.
myBiomodOption <- BIOMOD_ModelingOptions()

# 3. Doing Modelisation

myBiomomodModelOut <- BIOMOD_Modeling( myBiomodData, 
                                       models = c('CTA','RF'), 
                                       models.options = myBiomodOption, 
                                       models.eval.meth ='TSS')
                                       
                                       
# 4.1 Projection on current environemental conditions

myBiomomodProjection <- BIOMOD_Projection(modeling.output = myBiomomodModelOut,
                                          new.env = myExpl,
                                          proj.name = 'current',
                                          selected.models = 'all',
                                          binary.meth = 'TSS',
                                          compress = FALSE,
                                          build.clamping.mask = FALSE)
                                          
# 4.2 Projection on future environemental conditions

myExpl2050 = raster::stack(system.file("external/climat/future/bio3.grd",package="biomod2"),
                           system.file("external/climat/future/bio4.grd",package="biomod2"),
                           system.file("external/climat/future/bio7.grd",package="biomod2"),
                           system.file("external/climat/future/bio11.grd",package="biomod2"),
                           system.file("external/climat/future/bio12.grd",package="biomod2"))

myBiomomodProjection2050 <- BIOMOD_Projection(modeling.output = myBiomomodModelOut,
                                              new.env = myExpl2050,
                                              proj.name = 't2050',
                                              selected.models = 'all',
                                              binary.meth = 'TSS',
                                              compress = FALSE,
                                              build.clamping.mask = FALSE)

# 5. Detect where our species occurances state is forecasted to change

# load binary projections
# here is rasters objects ('.grd')
currentPred <- stack("MyocastorCoypus/proj_current/proj_current_MyocastorCoypus_TSSbin")
futurePred <- stack("MyocastorCoypus/proj_t2050/proj_t2050_MyocastorCoypus_TSSbin")


# call the Range size function
myBiomodRangeSize <- BIOMOD_RangeSize(
                          CurrentPred=currentPred,
                          FutureProj=futurePred)

# see the results
myBiomodRangeSize$Compt.By.Models

#plot(myBiomodRangeSize$Diff.By.Pixel)