v4.2-5 - 2023 Modeling options and Tuning #327
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…ions.dataset classes
…reated using TABLE_MODELS (to be stored at some point)
… to biomod2_classes_0
…m_RunModelsLoop_0
…ultiple GAM, MAXENT to be tested
…, missing at least MAXENT part)
Removed RF do.classif parameter to only use type
…ult or bigboss and set custom values for a few options
… and colnames of calib.lines)
Generalized the removal of unnecessary columns in tuning dataset
- give datatype to ensemble forecasting writeRaster - parallelize ensemble modeling - correct examples in functions documentation - correct getters (variables importance and built models)
Merge branch 'master' into devel_current # Conflicts: # DESCRIPTION # R/BIOMOD_Modeling.R # R/BIOMOD_ModelingOptions.R # R/biomod2_classes_1.R # R/biomod2_classes_4.R # R/bm_RunModelsLoop.R # README.md # docs/404.html # docs/articles/examples_1_mainFunctions.html # docs/articles/examples_2_secundaryFunctions.html # docs/articles/index.html # docs/articles/news.html # docs/articles/vignette_pseudoAbsences.html # docs/articles/vignette_variability.html # docs/authors.html # docs/index.html # docs/reference/BIOMOD.ensemble.models.out.html # docs/reference/BIOMOD.formated.data.PA.html # docs/reference/BIOMOD.formated.data.html # docs/reference/BIOMOD.models.options.html # docs/reference/BIOMOD.models.out.html # docs/reference/BIOMOD.projection.out.html # docs/reference/BIOMOD.stored.data.html # docs/reference/BIOMOD_ConvertOldRun-deprecated.html # docs/reference/BIOMOD_CrossValidation-deprecated.html # docs/reference/BIOMOD_EnsembleForecasting.html # docs/reference/BIOMOD_EnsembleModeling.html # docs/reference/BIOMOD_FormatingData.html # docs/reference/BIOMOD_LoadModels.html # docs/reference/BIOMOD_Modeling.html # docs/reference/BIOMOD_ModelingOptions.html # docs/reference/BIOMOD_PresenceOnly.html # docs/reference/BIOMOD_Projection.html # docs/reference/BIOMOD_RangeSize.html # docs/reference/BIOMOD_Tuning.html # docs/reference/BIOMOD_cv-deprecated.html # docs/reference/BIOMOD_presenceonly-deprecated.html # docs/reference/BIOMOD_tuning-deprecated.html # docs/reference/BinaryTransformation-deprecated.html # docs/reference/CustomIndexMaker-deprecated.html # docs/reference/DataSpecies.html # docs/reference/FilteringTransformation-deprecated.html # docs/reference/Find.Optim.Stat-deprecated.html # docs/reference/Print_Default_ModelingOptions-deprecated.html # docs/reference/ProbDensFunc-deprecated.html # docs/reference/bioclim_current.html # docs/reference/bioclim_future.html # docs/reference/biomod2-deprecated.html # docs/reference/biomod2_ensemble_model.html # docs/reference/biomod2_model.html # docs/reference/bm_BinaryTransformation.html # docs/reference/bm_CVnnet.html # docs/reference/bm_CrossValidation.html # docs/reference/bm_FindOptimStat.html # docs/reference/bm_MakeFormula.html # docs/reference/bm_PlotEvalBoxplot.html # docs/reference/bm_PlotEvalMean.html # docs/reference/bm_PlotRangeSize.html # docs/reference/bm_PlotResponseCurves.html # docs/reference/bm_PlotVarImpBoxplot.html # docs/reference/bm_PseudoAbsences.html # docs/reference/bm_RunModelsLoop.html # docs/reference/bm_SRE.html # docs/reference/bm_SampleBinaryVector.html # docs/reference/bm_SampleFactorLevels.html # docs/reference/bm_VariablesImportance.html # docs/reference/calculate.stat-deprecated.html # docs/reference/check_duplicated_cells.html # docs/reference/dot-categorical2numeric.html # docs/reference/dot-check_bytes_format.html # docs/reference/dot-get_categorical_names.html # docs/reference/dot-get_env_class.html # docs/reference/dot-load_gam_namespace.html # docs/reference/dot-transform.outputs.array-deprecated.html # docs/reference/dot-transform.outputs.list-deprecated.html # docs/reference/dot-transform_model.as.col.html # docs/reference/getStatOptimValue-deprecated.html # docs/reference/getters.bm.html # docs/reference/getters.out.html # docs/reference/index.html # docs/reference/load_stored_object.html # docs/reference/makeFormula-deprecated.html # docs/reference/models_scores_graph-deprecated.html # docs/reference/plot.html # docs/reference/predict.bm.html # docs/reference/predict.em.html # docs/reference/predict2.bm.html # docs/reference/predict2.em.html # docs/reference/rast.has.values.html # docs/reference/response.plot-deprecated.html # docs/reference/response.plot2-deprecated.html # docs/reference/sample.factor.levels-deprecated.html # docs/reference/sre-deprecated.html # docs/reference/summary.html # docs/reference/update_objects-deprecated.html # docs/reference/variables_importance-deprecated.html # docs/reference/zzz_bm.html # man/BIOMOD_Modeling.Rd # man/BIOMOD_ModelingOptions.Rd # vignettes/news.Rmd
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v4.2-5 Modeling Options and Tuning patch
Major changes
BIOMOD.options.defaultandBIOMOD.options.datasetclasses, retrieving default parameters and values withformalArgsfunctionModelsTableandOptionsBigbossdatasets containing single models informations and pre-defined modeling optionsBIOMOD_ModelingOptionstobm_ModelingOptionsbm_ModelingOptionsdirectly inBIOMOD_Modelingand add relatedOPT.[...]parametersBIOMOD_Tuningtobm_Tuningand adapt it to match with new modeling optionsbm_RunModelsLoopin a more generalized way dealing with new modeling optionsMinor changes
BIOMOD_PresenceOnlyfunction and addBOYCEandMPAindices intobm_FindOptimStatfunctionFLT4Sdatatype only when EMcv is activated, otherwise useINT2S