####################################
## external functions importation ##
####################################

### generic methods importation
#import("graphics")
#import("stats")
import("methods") 
import("raster")
import("sp")
import("ggplot2")
import("parallel")

importFrom("abind", abind, asub)
import("reshape")
#importFrom("gbm", gbm, gbm.perf)
import("gbm")
importFrom("MASS",stepAIC)
#importFrom("mda", fda, mars)
import("mda")
import("earth")
#importFrom("nnet", nnet)
import("nnet")
#importFrom("parallel", detectCores) # for gbm package
import("pROC") # import the whole package to get S3 Methods
#importFrom("rpart", prune, rpart)
import("rpart")
importFrom("randomForest",randomForest)
#import("randomForest")
### raster package is at time consider as dependencie
#importFrom(raster, addLayer, calc, canProcessInMemory, cellFromXY, cv, extract, inMemory, maxValue, minValue, ncell, nlayers, predict, raster, rasterOptions, reclassify, readAll, sampleRandom, stack, Which, writeRaster)
importFrom(rasterVis, levelplot)
#importFrom(RColorBrewer, brewer.pal)
### sp package is at time consider as dependencie
#importFrom(sp, coordinates, read.asciigrid, SpatialPointsDataFrame, spplot)
#import("survivial") # for gbm package
#import("spline") # for gbm package
#importFrom("gam", s)
#import("maxent")

### imports for ecospat.xxx functions (to be removed at some point?)
importFrom("dismo", kfold)
importFrom("PresenceAbsence", presence.absence.accuracy)
## importFrom("caret", trainControl, twoClassSummary)
## importFrom("ENMeval", ENMevaluate)

importFrom("grDevices", "colorRampPalette", "colors", "dev.new",
           "dev.off", "gray", "jpeg", "pdf", "png", "postscript",
           "rainbow", "tiff")
importFrom("graphics", "abline", "axis", "layout", "legend", "par",
           "plot.new", "points", "polygon", "rug")
importFrom("stats", "as.formula", "binomial", "cor", "formula", "glm",
           "median", "na.omit", "qt", "sd", "terms")
importFrom("utils", "combn", "read.csv", "str", "write.table") 


####################################
##       biomod2 exports	  	  ##
####################################

### To export automaticaly all classes, methods and functions ###
#exportPattern("^[[:alpha:]]+")
#exportClassPattern("^[[:alpha:]]+")

### To export only user level functions ###

##### Classes
exportClasses(
	BIOMOD.EnsembleModeling.out,
	BIOMOD.formated.data,
	BIOMOD.formated.data.PA,
	BIOMOD.Model.Options,
	BIOMOD.models.out,
	BIOMOD.projection.out

)

#exportClasses(
#	BIOMOD.stored.array, 
#	BIOMOD.stored.data,
#	BIOMOD.stored.data.frame,
#	BIOMOD.stored.files,
#	BIOMOD.stored.formated.data,
#	BIOMOD.stored.models.options, 
#	BIOMOD.stored.models.out,
#	BIOMOD.stored.raster.stack
#)

exportClasses(
	biomod2_model,
	biomod2_ensemble_model,
	ANN_biomod2_model,
	CTA_biomod2_model,
	FDA_biomod2_model,
	GAM_biomod2_model,
	GBM_biomod2_model,
	GLM_biomod2_model,
	MARS_biomod2_model,
	MAXENT.Phillips_biomod2_model,
  MAXENT.Tsuruoka_biomod2_model,
	RF_biomod2_model,
	SRE_biomod2_model,
	EMca_biomod2_model,
	EMci_biomod2_model,
	EMcv_biomod2_model,
	EMmean_biomod2_model,
	EMmedian_biomod2_model,
	EMwmean_biomod2_model
)

##### Methods & Functions

## user level
exportMethods(
	BinaryTransformation,
	BIOMOD_RangeSize,
	FilteringTransformation,
	free,
	plot,
	predict,
	RemoveProperly,
	show
)

export(
	BinaryTransformation,
	BIOMOD_RangeSize,
	FilteringTransformation,
	free,
	plot,
	predict,
	RemoveProperly,
	show
)

exportMethods(
	get_built_models,
	get_evaluations,
	get_calib_lines,
	get_formal_data,
	get_formal_model, 
	get_kept_models,
	get_needed_models,
	get_options,
	get_predictions,
	get_projected_models,
	get_scaling_model,
	get_variables_importance
)

export(
	get_built_models,
	get_evaluations,
	get_calib_lines,
	get_formal_data,
	get_formal_model, 
	get_kept_models,
	get_needed_models,
	get_options,
	get_predictions,
	get_projected_models,
	get_scaling_model,
	get_variables_importance
)

export(
	BIOMOD_ConvertOldRun,
	BIOMOD_EnsembleForecasting,
	BIOMOD_EnsembleModeling,
	BIOMOD_FormatingData,
	BIOMOD_LoadModels,
	BIOMOD_Modeling,
	BIOMOD_ModelingOptions, 
	BIOMOD_Projection,
	calculate.stat,
	DF_to_ARRAY,
	evaluate,
	Find.Optim.Stat,
	full_suffling,
	getStatOptimValue,
	level.plot,
	LIST_to_ARRAY,
	makeFormula,
	models_scores_graph,
	multiple.plot,
	Print_Default_ModelingOptions,
	ProbDensFunc,
	randomise_data,
	response.plot2,
	sre,
	update_objects,
	variables_importance,
  .create.maxent.bg.dir,
	BIOMOD_cv,
	BIOMOD_presenceonly,
	BIOMOD_tuning,
  sample.factor.levels
)

## to be hidden
exportMethods(
	disk.pseudo.abs.selection,
	load_stored_object,
	Projection,
	random.pseudo.abs.selection,
	sre.pseudo.abs.selection,
	user.defined.pseudo.abs.selection,
	.Models.prepare.data,
	.Projection.do.proj, 
	.transform.outputs
)

exportMethods(
	getEMalgos, 
	getEMbuiltModels, 
	getEMeval, 
	getEMkeptModels, 
	getEM_needed_models, 
	getFormalModel, 
	getModelsBuiltModels, 
	getModelsEvaluations, 
	getModelsInputData, 
	getModelsOptions, 
	getModelsPrediction, 
	getModelsPredictionEval, 
	getModelsVarImport, 
	getProjection,
	getScalingModel
)

export(
	check_data_range,
	CustomIndexMaker,
	get_var_range, 
	get_var_type,
	response.plot,
	SampleMat2
	#test_slots,
	#update.objects_BIOMOD.formated.data,
	#update.objects_biomod2_model,
	#update.objects_BIOMOD.models.out
)





