BIOMOD.options.dataset: 'bm_ModelingOptions' output object class

In biomodhub/biomod2: Ensemble Platform for Species Distribution Modeling

bm_ModelingOptions output object class

Description

Class returned by bm_ModelingOptions (a list of BIOMOD.options.dataset more exactly), and used by BIOMOD_Modeling

Usage

## S4 method for signature 'character'
BIOMOD.options.dataset(
  mod,
  typ,
  pkg,
  fun,
  strategy,
  user.val = NULL,
  user.base = NULL,
  tuning.fun = NULL,
  bm.format = NULL,
  calib.lines = NULL
)

## S4 method for signature 'BIOMOD.options.dataset'
show(object)

## S4 method for signature 'BIOMOD.options.dataset'
print(x, dataset = "_allData_allRun")

Arguments

mod	a character corresponding to the model name to be computed, must be either ANN, CTA, FDA, GAM, GBM, GLM, MARS, MAXENT, MAXNET, RF, SRE, XGBOOST
typ	a character corresponding to the data type to be used, must be either binary, binary.PA, abundance, compositional
pkg	a character corresponding to the package containing the model function to be called
fun	a character corresponding to the model function name to be called
strategy	a character corresponding to the method to select models' parameters values, must be either default, bigboss, user.defined, tuned
user.val	(optional, default NULL) A list containing parameters values
user.base	(optional, default NULL) A character, default or bigboss used when strategy = 'user.defined'. It sets the bases of parameters to be modified by user defined values.
tuning.fun	(optional, default NULL) A character corresponding to the model function name to be called through train function for tuning parameters
bm.format	(optional, default NULL) A BIOMOD.formated.data or BIOMOD.formated.data.PA object returned by the BIOMOD_FormatingData function
calib.lines	(optional, default NULL) A data.frame object returned by get_calib_lines or bm_CrossValidation functions, to explore the distribution of calibration and validation datasets
object	a BIOMOD.options.dataset object
x	a BIOMOD.options.dataset object
dataset	a character corresponding to the name of a dataset contained in the arg.values slot

Slots

model

a character corresponding to the model

type

a character corresponding to the data type (binary, binary.PA, abundance, compositional)

package

a character corresponding to the package containing the model function to be called

func

a character corresponding to the model function name to be called

args.names

a vector containing character corresponding to the model function arguments

args.default

a list containing for each dataset the default values for all arguments listed in args.names

args.values

a list containing for each dataset the to-be-used values for all arguments listed in args.names

Author(s)

Maya Gueguen

See Also

BIOMOD.options.default, bm_ModelingOptions, bm_Tuning, BIOMOD_Modeling, bm_RunModelsLoop

Other Toolbox objects: BIOMOD.ensemble.models.out, BIOMOD.formated.data.PA, BIOMOD.formated.data, BIOMOD.models.options, BIOMOD.models.out, BIOMOD.options.default, BIOMOD.projection.out, BIOMOD.stored.data, biomod2_ensemble_model, biomod2_model

Examples

showClass("BIOMOD.options.dataset")

biomodhub/biomod2 documentation built on April 30, 2024, 2:32 a.m.