biomod2 (version 4.1-2)

BIOMOD_LoadModels: Load species distribution models built with biomod2

Description

This function loads individual models built with BIOMOD_Modeling or BIOMOD_EnsembleModeling functions.

Usage

BIOMOD_LoadModels(bm.out, ...)

Value

A vector containing the names of the loaded models.

Arguments

bm.out

a BIOMOD.models.out or BIOMOD.ensemble.models.out object that can be obtained with the BIOMOD_Modeling or BIOMOD_EnsembleModeling functions

...

(optional, see Details))

Author

Damien Georges

Details

This function might be of particular use to load models and make response plot analyses.

Running the function providing only bm.out argument will load all models built by the BIOMOD_Modeling or BIOMOD_EnsembleModeling function. But a subselection of models can be done using the following additional arguments :

• models : a vector containing model names to be loaded, must be among GLM, GBM, GAM, CTA, ANN, SRE, FDA, MARS, RF, MAXENT.Phillips, MAXENT.Phillips.2

• run.eval : a vector containing repetition set to be loaded, must be among RUN1, RUN2, ..., Full

• data.set : a vector containing pseudo-absence set to be loaded, must be among PA1, PA2, ...
  
  

• path : a character corresponding to the location of the species folder (if different from the current working directory)
  
  

• full.name : a vector containing model names to be kept, must be either all or a sub-selection of model names
  
  

• as : a character to contain the loaded models

See Also

BIOMOD_Modeling, BIOMOD_EnsembleModeling

Other Main functions: BIOMOD_CrossValidation(), BIOMOD_EnsembleForecasting(), BIOMOD_EnsembleModeling(), BIOMOD_FormatingData(), BIOMOD_ModelingOptions(), BIOMOD_Modeling(), BIOMOD_PresenceOnly(), BIOMOD_Projection(), BIOMOD_RangeSize(), BIOMOD_Tuning()

Examples

# Load species occurrences (6 species available)
myFile <- system.file('external/species/mammals_table.csv', package = 'biomod2')
DataSpecies <- read.csv(myFile, row.names = 1)
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)
myFiles <- paste0('external/bioclim/current/bio', c(3, 4, 7, 11, 12), '.grd')
myExpl <- raster::stack(system.file(myFiles, package = 'biomod2'))

# \dontshow{
myExtent <- raster::extent(0,30,45,70)
myExpl <- raster::stack(raster::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)

  # Create default modeling options
  myBiomodOptions <- BIOMOD_ModelingOptions()

  # Model single models
  myBiomodModelOut <- BIOMOD_Modeling(bm.format = myBiomodData,
                                      modeling.id = 'AllModels',
                                      models = c('RF', 'GLM'),
                                      bm.options = myBiomodOptions,
                                      nb.rep = 2,
                                      data.split.perc = 80,
                                      metric.eval = c('TSS','ROC'),
                                      var.import = 3,
                                      do.full.models = FALSE,
                                      seed.val = 42)
}


# ---------------------------------------------------------------
# Loading some models built
myLoadedModels <- BIOMOD_LoadModels(bm.out = myBiomodModelOut, models = 'RF')
myLoadedModels