BIOMOD_ModelingOptions {biomod2}R Documentation

Configure the modeling options for each selected model

Description

Parametrize and/or tune biomod2's single models options.

Usage

BIOMOD_ModelingOptions(
  GLM = NULL,
  GBM = NULL,
  GAM = NULL,
  CTA = NULL,
  ANN = NULL,
  SRE = NULL,
  FDA = NULL,
  MARS = NULL,
  RF = NULL,
  MAXENT = NULL,
  XGBOOST = NULL
)

bm_DefaultModelingOptions()

Arguments

GLM

(optional, default NULL)
A list containing GLM options

GBM

(optional, default NULL)
A list containing GBM options

GAM

(optional, default NULL)
A list containing GAM options

CTA

(optional, default NULL)
A list containing CTA options

ANN

(optional, default NULL)
A list containing ANN options

SRE

(optional, default NULL)
A list containing SRE options

FDA

(optional, default NULL)
A list containing FDA options

MARS

(optional, default NULL)
A list containing MARS options

RF

(optional, default NULL)
A list containing RF options

MAXENT

(optional, default NULL)
A list containing MAXENT options

XGBOOST

(optional, default NULL)
A list containing XGBOOST options

Details

This function allows advanced user to change some default parameters of biomod2 inner models.
10 single models are available within the package, and their options can be set with this function through list objects.

The bm_DefaultModelingOptions function prints all default parameter values for all available models.
This output can be copied and pasted to be used as is (with wanted changes) as function arguments (see Examples).

Below is the detailed list of all modifiable parameters for each available model.

Value

A BIOMOD.models.options object that can be used to build species distribution model(s) with the BIOMOD_Modeling function.

GLM

(glm)

GBM

(default gbm)

Please refer to gbm help file for more details.

GAM

(gam or gam)

CTA

(rpart)

Please refer to rpart help file for more details.

ANN

(nnet)

SRE

(bm_SRE)

FDA

(fda)

Please refer to fda help file for more details.

MARS

(earth)

Please refer to earth help file for more details.

RF

(randomForest)

MAXENT

(https://biodiversityinformatics.amnh.org/open_source/maxent/)

XGBOOST

(default xgboost)

Please refer to xgboost help file for more details.

Author(s)

Damien Georges, Wilfried Thuiller

See Also

BIOMOD_Tuning, BIOMOD_Modeling

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

Examples

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)



# ---------------------------------------------------------------#
# Print default modeling options
bm_DefaultModelingOptions()

# Create default modeling options
myBiomodOptions <- BIOMOD_ModelingOptions()
myBiomodOptions

# # Part (or totality) of the print can be copied and customized
# # Below is an example to compute quadratic GLM and select best model with 'BIC' criterium
# myBiomodOptions <- BIOMOD_ModelingOptions(
#   GLM = list(type = 'quadratic',
#              interaction.level = 0,
#              myFormula = NULL,
#              test = 'BIC',
#              family = 'binomial',
#              control = glm.control(epsilon = 1e-08,
#                                    maxit = 1000,
#                                    trace = FALSE)))
# myBiomodOptions
# 
# # It is also possible to give a specific GLM formula
# myForm <- 'Sp277 ~ bio3 + log(bio10) + poly(bio16, 2) + bio19 + bio3:bio19'
# myBiomodOptions <- BIOMOD_ModelingOptions(GLM = list(myFormula = formula(myForm)))
# myBiomodOptions



[Package biomod2 version 4.2-4 Index]