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biomod2 (version 4.1-2)

getters.out: Functions to extract informations from BIOMOD.models.out, BIOMOD.projection.out or BIOMOD.ensemble.models.out objects

Description

These functions allow the user to easily retrieve informations stored in the different biomod2 objects from the different modeling steps, such as modeling options and formated data, models used or not, predictions, evaluations, variables importance.

Usage

# S4 method for BIOMOD.models.out
get_options(obj)
# S4 method for BIOMOD.models.out
get_calib_lines(obj, as.data.frame = FALSE, ...)
# S4 method for BIOMOD.models.out
get_formal_data(obj, subinfo = NULL)
# S4 method for BIOMOD.models.out
get_predictions(
  obj,
  as.data.frame = FALSE,
  evaluation = FALSE,
  full.name = NULL,
  model = NULL,
  run.eval = NULL,
  data.set = NULL
)
# S4 method for BIOMOD.models.out
get_built_models(obj, ...)
# S4 method for BIOMOD.models.out
get_evaluations(obj, as.data.frame = FALSE, ...)
# S4 method for BIOMOD.models.out
get_variables_importance(obj, as.data.frame = FALSE, ...)
# S4 method for BIOMOD.projection.out
get_projected_models(obj)
# S4 method for BIOMOD.projection.out
free(obj)
# S4 method for BIOMOD.projection.out
get_predictions(
  obj,
  as.data.frame = FALSE,
  full.name = NULL,
  model = NULL,
  run.eval = NULL,
  data.set = NULL
)
# S4 method for BIOMOD.ensemble.models.out
get_formal_data(obj, subinfo = NULL)
# S4 method for BIOMOD.ensemble.models.out
get_built_models(obj, ...)
# S4 method for BIOMOD.ensemble.models.out
get_needed_models(obj, selected.models = "all", ...)
# S4 method for BIOMOD.ensemble.models.out
get_kept_models(obj, model, ...)
# S4 method for BIOMOD.ensemble.models.out
get_predictions(
  obj,
  as.data.frame = FALSE,
  evaluation = FALSE,
  full.name = NULL
)
# S4 method for BIOMOD.ensemble.models.out
get_built_models(obj, ...)
# S4 method for BIOMOD.ensemble.models.out
get_evaluations(obj, as.data.frame = FALSE, ...)
# S4 method for BIOMOD.ensemble.models.out
get_variables_importance(obj, as.data.frame = FALSE, ...)

Value

get_options

a BIOMOD.stored.models.options-class object from the models.options slot of a BIOMOD.models.out-class object

get_calib_lines

a BIOMOD.stored.array-class object from the calib.lines slot of a BIOMOD.models.out object

get_projected_models

a vector from the models.projected slot of a BIOMOD.projection.out object

get_predictions

a BIOMOD.stored.data object from the proj.out slot of a BIOMOD.models.out, BIOMOD.projection.out or BIOMOD.ensemble.models.out object

get_needed_models

a vector containing names of the needed models of a BIOMOD.ensemble.models.out object

get_kept_models

a vector containing names of the kept models of a BIOMOD.ensemble.models.out object

get_formal_data

depending on the subinfo parameter :

NULL

a BIOMOD.stored.formated.data-class (or BIOMOD.stored.models.out-class) object from the formated.input.data (or models.out) slot of a BIOMOD.models.out (or BIOMOD.ensemble.models.out) object

expl.var.names

a vector from the expl.var.names slot of a BIOMOD.models.out or BIOMOD.ensemble.models.out object

resp.var

a vector from the data.species slot of the formated.input.data slot of a BIOMOD.models.out or BIOMOD.ensemble.models.out object

expl.var

a data.frame from the data.env.var slot of the formated.input.data slot of a BIOMOD.models.out or BIOMOD.ensemble.models.out object

MinMax

a list of minimum and maximum values (or levels if factorial) of variable contained in the data.env.var slot of the formated.input.data slot of a BIOMOD.models.out or BIOMOD.ensemble.models.out object

eval.resp.var

a vector from the eval.data.species slot of the formated.input.data slot of a BIOMOD.models.out or BIOMOD.ensemble.models.out object

eval.expl.var

a data.frame from the eval.data.env.var slot of the formated.input.data slot of a BIOMOD.models.out or BIOMOD.ensemble.models.out object

get_built_models

a vector from the models.computed slot (or em.computed) of a BIOMOD.models.out (or BIOMOD.ensemble.models.out) object

get_evaluations

a BIOMOD.stored.array-class (or matrix) from the models.evaluation slot (or model_evaluation of each model in em.computed) of a BIOMOD.models.out (or BIOMOD.ensemble.models.out) object

get_variables_importance

a BIOMOD.stored.array-class from the variables.importance slot (or model_variables_importance of each model in em.models) of a BIOMOD.models.out (or BIOMOD.ensemble.models.out) object

Arguments

obj

a BIOMOD.models.out, BIOMOD.projection.out or BIOMOD.ensemble.models.out object

as.data.frame

a logical defining whether output should be returned as data.frame or array object

subinfo

a character corresponding to the information to be extracted, must be among NULL, expl.var.names, resp.var, expl.var, MinMax, eval.resp.var, eval.expl.var (see Details)

evaluation

a logical defining whether evaluation data should be used or not

full.name

a vector containing model names to be kept, must be either all or a sub-selection of model names

model

a character corresponding to the model name, must be either GLM, GBM, GAM, CTA, ANN, SRE, FDA, MARS, RF, MAXENT.Phillips, MAXENT.Phillips.2

run.eval

a vector containing repetition set to be loaded, must be among RUN1, RUN2, ..., Full

data.set

a vector containing pseudo-absence set to be loaded, must be among PA1, PA2, ...

selected.models

a vector containing names of the needed models of a BIOMOD.ensemble.models.out object

...

(optional, one or several of the following arguments depending on the selected function))

Author

Damien Georges

See Also

BIOMOD.models.out, BIOMOD.projection.out, BIOMOD.ensemble.models.out

Other Toolbox functions: getters.bm, load_stored_object(), predict.bm, predict.em, predict2.bm, predict2.em