bm_ModelingOptions output object class

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

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

# S4 method for class '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

See also

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

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

Author

Maya Gueguen

Examples

showClass("BIOMOD.options.dataset")