Ensemble Platform for Species Distribution Modeling
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Documentation for package ‘biomod2’ version 4.2-5-2
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-- A --
| ANN_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()') |
-- B --
| bioclim_current | Bioclimatic variables for SDM based on current condition |
| bioclim_future | Bioclimatic variables for SDM based on future condition |
| BIOMOD.ensemble.models.out | 'BIOMOD_EnsembleModeling()' output object class |
| BIOMOD.ensemble.models.out-class | 'BIOMOD_EnsembleModeling()' output object class |
| BIOMOD.formated.data | 'BIOMOD_FormatingData()' output object class |
| BIOMOD.formated.data-class | 'BIOMOD_FormatingData()' output object class |
| BIOMOD.formated.data-method | 'BIOMOD_FormatingData()' output object class |
| BIOMOD.formated.data.PA | 'BIOMOD_FormatingData()' output object class (with pseudo-absences) |
| BIOMOD.formated.data.PA-class | 'BIOMOD_FormatingData()' output object class (with pseudo-absences) |
| BIOMOD.formated.data.PA-method | 'BIOMOD_FormatingData()' output object class (with pseudo-absences) |
| BIOMOD.models.options | 'bm_ModelingOptions' output object class |
| BIOMOD.models.options-class | 'bm_ModelingOptions' output object class |
| BIOMOD.models.out | 'BIOMOD_Modeling()' output object class |
| BIOMOD.models.out-class | 'BIOMOD_Modeling()' output object class |
| BIOMOD.options.dataset | 'bm_ModelingOptions' output object class |
| BIOMOD.options.dataset-class | 'bm_ModelingOptions' output object class |
| BIOMOD.options.dataset-method | 'bm_ModelingOptions' output object class |
| BIOMOD.options.default | 'bm_ModelingOptions' output object class |
| BIOMOD.options.default-class | 'bm_ModelingOptions' output object class |
| BIOMOD.options.default-method | 'bm_ModelingOptions' output object class |
| BIOMOD.projection.out | 'BIOMOD_Projection()' output object class |
| BIOMOD.projection.out-class | 'BIOMOD_Projection()' output object class |
| BIOMOD.stored.data | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class |
| BIOMOD.stored.data-class | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class |
| BIOMOD.stored.data.frame-class | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class |
| BIOMOD.stored.files-class | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class |
| BIOMOD.stored.formated.data-class | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class |
| BIOMOD.stored.models.out-class | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class |
| BIOMOD.stored.options-class | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class |
| BIOMOD.stored.SpatRaster-class | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class |
| biomod2_ensemble_model | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()') |
| biomod2_ensemble_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()') |
| biomod2_model | Single model output object class (when running 'BIOMOD_Modeling()') |
| biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()') |
| BIOMOD_EnsembleForecasting | Project ensemble species distribution models onto new environment |
| BIOMOD_EnsembleModeling | Create and evaluate an ensemble set of models and predictions |
| BIOMOD_FormatingData | Format input data, and select pseudo-absences if wanted, for usage in 'biomod2' |
| BIOMOD_LoadModels | Load species distribution models built with 'biomod2' |
| BIOMOD_Modeling | Run a range of species distribution models |
| BIOMOD_Projection | Project a range of calibrated species distribution models onto new environment |
| BIOMOD_RangeSize | Analyze the range size differences between projections of species distribution models |
| BIOMOD_RangeSize-method | Analyze the range size differences between projections of species distribution models |
| bm_BinaryTransformation | Convert probability values into binary values using a predefined threshold |
| bm_BinaryTransformation-method | Convert probability values into binary values using a predefined threshold |
| bm_CalculateStat | Calculate the best score according to a given evaluation method |
| bm_CrossValidation | Build cross-validation table |
| bm_CrossValidation_block | Build cross-validation table |
| bm_CrossValidation_block-method | Build cross-validation table |
| bm_CrossValidation_env | Build cross-validation table |
| bm_CrossValidation_env-method | Build cross-validation table |
| bm_CrossValidation_kfold | Build cross-validation table |
| bm_CrossValidation_kfold-method | Build cross-validation table |
| bm_CrossValidation_random | Build cross-validation table |
| bm_CrossValidation_random-method | Build cross-validation table |
| bm_CrossValidation_strat | Build cross-validation table |
| bm_CrossValidation_strat-method | Build cross-validation table |
| bm_CrossValidation_user.defined | Build cross-validation table |
| bm_CrossValidation_user.defined-method | Build cross-validation table |
| bm_FindOptimStat | Calculate the best score according to a given evaluation method |
| bm_MakeFormula | Standardized formula maker |
| bm_ModelingOptions | Configure the modeling options for each selected model |
| bm_PlotEvalBoxplot | Plot boxplot of evaluation scores |
| bm_PlotEvalMean | Plot mean evaluation scores |
| bm_PlotRangeSize | Plot species range change |
| bm_PlotResponseCurves | Plot response curves |
| bm_PlotVarImpBoxplot | Plot boxplot of variables importance |
| bm_PseudoAbsences | Select pseudo-absences |
| bm_PseudoAbsences_disk | Select pseudo-absences |
| bm_PseudoAbsences_disk-method | Select pseudo-absences |
| bm_PseudoAbsences_random | Select pseudo-absences |
| bm_PseudoAbsences_random-method | Select pseudo-absences |
| bm_PseudoAbsences_sre | Select pseudo-absences |
| bm_PseudoAbsences_sre-method | Select pseudo-absences |
| bm_PseudoAbsences_user.defined | Select pseudo-absences |
| bm_PseudoAbsences_user.defined-method | Select pseudo-absences |
| bm_RunModel | Loop to compute all single species distribution models |
| bm_RunModelsLoop | Loop to compute all single species distribution models |
| bm_SampleBinaryVector | Sample binary vector |
| bm_SampleFactorLevels | Sample all levels of a factorial variable |
| bm_SampleFactorLevels.data.frame | Sample all levels of a factorial variable |
| bm_SampleFactorLevels.raster | Sample all levels of a factorial variable |
| bm_SRE | Surface Range Envelope |
| bm_Tuning | Tune models parameters |
| bm_VariablesImportance | Variables' importance calculation |
-- C --
| CTA_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()') |
-- D --
| DataSpecies | Presence-Absence data to build test SDM |
-- E --
| EMca_biomod2_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()') |
| EMci_biomod2_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()') |
| EMcv_biomod2_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()') |
| EMmean_biomod2_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()') |
| EMmedian_biomod2_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()') |
| EMwmean_biomod2_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()') |
-- F --
| FDA_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()') |
| free | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| free-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
-- G --
| GAM_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()') |
| GBM_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()') |
| getters.bm | Functions to extract informations from 'biomod2_model' objects |
| getters.out | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_built_models | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_built_models-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_calib_lines | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_calib_lines-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_evaluations | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_evaluations-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_eval_data | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_eval_data-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_formal_data | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_formal_data-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_formal_model | Functions to extract informations from 'biomod2_model' objects |
| get_formal_model-method | Functions to extract informations from 'biomod2_model' objects |
| get_kept_models | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_kept_models-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_optim_value | Calculate the best score according to a given evaluation method |
| get_options | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_options-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_predictions | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_predictions-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_projected_models | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_projected_models-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_scaling_model | Functions to extract informations from 'biomod2_model' objects |
| get_scaling_model-method | Functions to extract informations from 'biomod2_model' objects |
| get_species_data | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_species_data-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_variables_importance | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| get_variables_importance-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects |
| GLM_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()') |
-- L --
| load_stored_object | Functions to load 'BIOMOD.stored.data' objects |
| load_stored_object-method | Functions to load 'BIOMOD.stored.data' objects |
-- M --
| MARS_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()') |
| MAXENT_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()') |
| MAXNET_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()') |
| ModelsTable | Single models package and functions |
-- O --
| OptionsBigboss | Bigboss pre-defined parameter values for single models |
-- P --
| plot-method | 'BIOMOD_Projection()' output object class |
| plot-method | 'plot' method for 'BIOMOD.formated.data' object class |
| predict-method | Functions to get predictions from 'biomod2_model' objects |
| predict.biomod2_model | Functions to get predictions from 'biomod2_model' objects |
| predict.bm | Functions to get predictions from 'biomod2_model' objects |
| predict.em | Functions to get predictions from 'biomod2_ensemble_model' objects |
| print-method | 'bm_ModelingOptions' output object class |
| print-method | 'bm_ModelingOptions' output object class |
-- R --
| RF_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()') |
-- S --
| show-method | 'BIOMOD_EnsembleModeling()' output object class |
| show-method | 'BIOMOD_FormatingData()' output object class |
| show-method | 'bm_ModelingOptions' output object class |
| show-method | 'BIOMOD_Modeling()' output object class |
| show-method | 'bm_ModelingOptions' output object class |
| show-method | 'BIOMOD_Projection()' output object class |
| show-method | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()') |
| show-method | Single model output object class (when running 'BIOMOD_Modeling()') |
| SRE_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()') |
| summary-method | 'summary' method for 'BIOMOD.formated.data' object class |
-- X --
| XGBOOST_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()') |