BIOMOD.models.out: 'BIOMOD_Modeling()' output object class
In biomodhub/biomod2: Ensemble Platform for Species Distribution Modeling

BIOMOD.models.out

R Documentation

`BIOMOD_Modeling()` output object class

Description

Class returned by BIOMOD_Modeling, and used by BIOMOD_LoadModels, BIOMOD_PresenceOnly, BIOMOD_Projection and BIOMOD_EnsembleModeling

Usage

## S4 method for signature 'BIOMOD.models.out'
show(object)

Arguments

object

a BIOMOD.models.out object

Slots

modeling.id: a character corresponding to the name (ID) of the simulation set
dir.name: a character corresponding to the modeling folder
sp.name: a character corresponding to the species name
data.type: a character corresponding to the data type
expl.var.names: a vector containing names of explanatory variables
models.computed: a vector containing names of computed models
models.failed: a vector containing names of failed models
has.evaluation.data: a logical value defining whether evaluation data is given
scale.models: a logical value defining whether models have been rescaled or not
formated.input.data: a BIOMOD.stored.formated.data-class object containing informations from BIOMOD_FormatingData object
calib.lines: a BIOMOD.stored.data.frame-class object containing calibration lines
models.options: a BIOMOD.stored.options-class object containing informations from bm_ModelingOptions object
models.evaluation: a BIOMOD.stored.data.frame-class object containing models evaluation
variables.importance: a BIOMOD.stored.data.frame-class object containing variables importance
models.prediction: a BIOMOD.stored.data.frame-class object containing models predictions
models.prediction.eval: a BIOMOD.stored.data.frame-class object containing models predictions for evaluation data
link: a character containing the file name of the saved object
call: a language object corresponding to the call used to obtain the object

Author(s)

Damien Georges

Examples


showClass("BIOMOD.models.out")

## ----------------------------------------------------------------------- #
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)



## ----------------------------------------------------------------------- #
# 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', 'AUCroc'),
                                    var.import = 3,
                                    seed.val = 42)
myBiomodModelOut

biomodhub/biomod2 documentation built on July 4, 2025, 6:15 p.m.