biomod2 (version 2.0.0)

BIOMOD_LoadModels: Load models built within BIOMOD_Modeling function

Description

This function was implemented to help biomod2 users to load individual models built during the BIOMOD_Modeling step.

Usage

BIOMOD_LoadModels(bm.out, ... )

Arguments

bm.out

a "BIOMOD.models.out" returned by BIOMOD_Modeling

...

additional arguments (see details)

Value

• A character vector filled with the loaded models names.

itemize

• models:

sQuote

• GLM
• GAM
• RF
• RUN1
• Full
• PA1
• PA2

item

• run.eval:
• data.set:
• path:

Details

This function is particulary useful when you plane to make some response plot analyses. It will induce models, built at BIOMOD_Modeling step, loading in your working space. If you run this function referencing only bm.out argument, all models built will be loaded. However, you can make a models subselection using the additional arguments (see below). Additional arguments (...) :

See Also

BIOMOD_Modeling

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 = 2,
                                     PA.nb.absences = 200,
                                     PA.strategy = 'random')
                                                                     
# 2. Defining Models Options using default options.
myBiomodOption <- BIOMOD_ModelingOptions()

# 3. Doing Modelisation

myBiomodModelOut <- BIOMOD_Modeling( myBiomodData, 
                                       models = c('SRE','CTA','RF'), 
                                       models.options = myBiomodOption, 
                                       NbRunEval=1, 
                                       DataSplit=80, 
                                       Yweights=NULL, 
                                       VarImport=3, 
                                       models.eval.meth = c('TSS','ROC'),
                                       SaveObj = TRUE )
                                       
# 4. Loading some models built

myLoadedModels <- BIOMOD_LoadModels(myBiomodModelOut, models='RF')

myLoadedModels