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.

Details

This function is particularly 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 (…) : All the following arguments are optional.

models: a character vector defining the names of models (e.g c(‘GLM’, ‘GAM’, ‘RF’) ) you want to load (models subselection)
run.eval: a character vector defining the names of evaluation run (e.g c(‘RUN1’, ‘Full’) ) you want to load (repetition subselection)
data.set: a character vector defining the names of data.set (e.g c(‘PA1’, ‘PA2’)) you want to load (pseudo absences subselection)
path: the path to file where the species folder is. To be filled if species folder is different from your working directory)

Examples

Run this code

# NOT RUN {
# species occurrences
DataSpecies <- read.csv(system.file("external/species/mammals_table.csv",
                                    package="biomod2"), row.names = 1)
head(DataSpecies)

# the name of studied species
myRespName <- 'GuloGulo'

# the presence/absences data for our species
myResp <- as.numeric(DataSpecies[,myRespName])

# the XY coordinates of species data
myRespXY <- DataSpecies[,c("X_WGS84","Y_WGS84")]


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

# 1. Formatting Data
myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
                                     expl.var = myExpl,
                                     resp.xy = myRespXY,
                                     resp.name = myRespName)


# 2. Defining Models Options using default options.
myBiomodOption <- BIOMOD_ModelingOptions()

# 3. Doing Modelisation

myBiomodModelOut <- BIOMOD_Modeling( myBiomodData,
                                       models = c('RF'),
                                       models.options = myBiomodOption,
                                       NbRunEval=2,
                                       DataSplit=70,
                                       models.eval.meth = c('TSS'),
                                       SaveObj = TRUE,
                                       do.full.models = FALSE)

# 4. Loading some models built

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

myLoadedModels

# }