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A B C D E F G L M N P R S U V Z misc
| biomod2-package | Species Distribution Modeling within an Ensemble Forecasting framework |
| ANN_biomod2_model | biomod2 models objects class and functions |
| ANN_biomod2_model-class | biomod2 models objects class and functions |
| array-method | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
| BinaryTransformation | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
| BinaryTransformation, | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
| BinaryTransformation-method | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
| BIOMOD.EnsembleModeling.out | BIOMOD_EnsembleModeling() outputs objects class |
| BIOMOD.EnsembleModeling.out-class | BIOMOD_EnsembleModeling() outputs objects class |
| BIOMOD.formated.data | BIOMOD_FormatingData() outputs objects class |
| BIOMOD.formated.data-class | BIOMOD_FormatingData() outputs objects class |
| BIOMOD.formated.data-method | BIOMOD_FormatingData() outputs objects class |
| BIOMOD.formated.data.PA | BIOMOD_FormatingData() outputs objects class |
| BIOMOD.formated.data.PA-class | BIOMOD_FormatingData() outputs objects class |
| BIOMOD.Model.Options-class | BIOMOD_ModelingOptions outputs objects class |
| BIOMOD.models.out-class | BIOMOD_modelling() outputs objects class |
| BIOMOD.projection.out | BIOMOD_Projection() outputs objects class |
| BIOMOD.projection.out-class | BIOMOD_Projection() outputs objects class |
| BIOMOD.stored.array | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.array-class | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.data | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.data-class | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.data.frame | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.data.frame-class | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.files | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.files-class | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.formated.data | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.formated.data-class | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.models.options | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.models.options-class | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.models.out | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.models.out-class | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.raster.stack | BIOMOD.stored.xxx objects class |
| BIOMOD.stored.raster.stack-class | BIOMOD.stored.xxx objects class |
| biomod2 | Species Distribution Modeling within an Ensemble Forecasting framework |
| biomod2_ensemble_model | biomod2 models objects class and functions |
| biomod2_ensemble_model-class | biomod2 models objects class and functions |
| biomod2_model | biomod2 models objects class and functions |
| biomod2_model-class | biomod2 models objects class and functions |
| BIOMOD_ConvertOldRun | Convert objects and outputs from BIOMOD.xx into biomod2.xx objects and outputs |
| BIOMOD_cv | Custom models cross-validation procedure |
| BIOMOD_EnsembleForecasting | Ensemble projections of species over space and time |
| BIOMOD_EnsembleModeling | Create and evaluate an ensemble set of models and predictions |
| BIOMOD_FormatingData | Initialize the datasets for usage in 'biomod2' |
| BIOMOD_LoadModels | Load models built within BIOMOD_Modeling function |
| BIOMOD_Modeling | Run a range of species distribution models |
| BIOMOD_ModelingOptions | Configure the modeling options for each selected model |
| BIOMOD_presenceonly | evaluate models with presences only metrics |
| BIOMOD_Projection | Project the calibrated models within 'biomod2' into new space or time |
| BIOMOD_RangeSize | Analysis of the range size changes |
| BIOMOD_RangeSize-method | Analysis of the range size changes |
| BIOMOD_RangeSize-methods | Analysis of the range size changes |
| BIOMOD_tuning | Tune models parameters |
| calculate.stat | Calculate evaluation metrics based on a misclassification table |
| check_data_range | biomod2 models objects class and functions |
| CTA_biomod2_model | biomod2 models objects class and functions |
| CTA_biomod2_model-class | biomod2 models objects class and functions |
| CustomIndexMaker | Replace default package Index help file by a custom one. |
| data.frame-method | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
| DF_to_ARRAY | Convert a biomod2 data.frame (or list) into array |
| disk.pseudo.abs.selection | biomod2 internal functions |
| disk.pseudo.abs.selection-method | biomod2 internal functions |
| EMca_biomod2_model | biomod2 models objects class and functions |
| EMca_biomod2_model-class | biomod2 models objects class and functions |
| EMci_biomod2_model | biomod2 models objects class and functions |
| EMci_biomod2_model-class | biomod2 models objects class and functions |
| EMcv_biomod2_model | biomod2 models objects class and functions |
| EMcv_biomod2_model-class | biomod2 models objects class and functions |
| EMmean_biomod2_model | biomod2 models objects class and functions |
| EMmean_biomod2_model-class | biomod2 models objects class and functions |
| EMmedian_biomod2_model | biomod2 models objects class and functions |
| EMmedian_biomod2_model-class | biomod2 models objects class and functions |
| EMwmean_biomod2_model | biomod2 models objects class and functions |
| EMwmean_biomod2_model-class | biomod2 models objects class and functions |
| evaluate | biomod2 modelling outputs evaluation |
| FDA_biomod2_model | biomod2 models objects class and functions |
| FDA_biomod2_model-class | biomod2 models objects class and functions |
| FilteringTransformation | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
| FilteringTransformation-method | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
| FilteringTransformation-methods | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
| Find.Optim.Stat | Calculate the best score according to a given evaluation method |
| free | BIOMOD.projection.out getters |
| free-method | BIOMOD.projection.out getters |
| full_suffling | data set shuffling tool |
| GAM_biomod2_model | biomod2 models objects class and functions |
| GAM_biomod2_model-class | biomod2 models objects class and functions |
| GBM_biomod2_model | biomod2 models objects class and functions |
| GBM_biomod2_model-class | biomod2 models objects class and functions |
| getEMalgos | biomod2 deprecated functions |
| getEMalgos-method | biomod2 deprecated functions |
| getEMbuiltModels | biomod2 deprecated functions |
| getEMbuiltModels-method | biomod2 deprecated functions |
| getEMeval | biomod2 deprecated functions |
| getEMeval-method | biomod2 deprecated functions |
| getEMkeptModels | biomod2 deprecated functions |
| getEMkeptModels-method | biomod2 deprecated functions |
| getEM_needed_models | biomod2 deprecated functions |
| getEM_needed_models-method | biomod2 deprecated functions |
| getFormalModel | biomod2 deprecated functions |
| getFormalModel-method | biomod2 deprecated functions |
| getModelsBuiltModels | biomod2 deprecated functions |
| getModelsBuiltModels-method | biomod2 deprecated functions |
| getModelsEvaluations | biomod2 deprecated functions |
| getModelsEvaluations-method | biomod2 deprecated functions |
| getModelsInputData | biomod2 deprecated functions |
| getModelsInputData-method | biomod2 deprecated functions |
| getModelsOptions | biomod2 deprecated functions |
| getModelsOptions-method | biomod2 deprecated functions |
| getModelsPrediction | biomod2 deprecated functions |
| getModelsPrediction-method | biomod2 deprecated functions |
| getModelsPredictionEval | biomod2 deprecated functions |
| getModelsPredictionEval-method | biomod2 deprecated functions |
| getModelsVarImport | biomod2 deprecated functions |
| getModelsVarImport-method | biomod2 deprecated functions |
| getProjection | biomod2 deprecated functions |
| getProjection-method | biomod2 deprecated functions |
| getScalingModel | biomod2 deprecated functions |
| getScalingModel-method | biomod2 deprecated functions |
| getStatOptimValue | get the optimal score of evaluation statistical metrics |
| get_built_models | BIOMOD.models.out getters |
| get_built_models-method | BIOMOD.models.out getters |
| get_calib_lines | BIOMOD.models.out getters |
| get_calib_lines-method | BIOMOD.models.out getters |
| get_evaluations | BIOMOD.models.out getters |
| get_evaluations-method | BIOMOD.models.out getters |
| get_formal_data | BIOMOD.models.out getters |
| get_formal_data-method | BIOMOD.models.out getters |
| get_formal_model | biomod2 models objects class and functions |
| get_formal_model-method | biomod2 models objects class and functions |
| get_kept_models | BIOMOD.EnsembleModeling.out getters |
| get_kept_models-method | BIOMOD.EnsembleModeling.out getters |
| get_needed_models | BIOMOD.EnsembleModeling.out getters |
| get_needed_models-method | BIOMOD.EnsembleModeling.out getters |
| get_options | BIOMOD.models.out getters |
| get_options-method | BIOMOD.models.out getters |
| get_predictions | BIOMOD.models.out getters |
| get_predictions-method | BIOMOD.models.out getters |
| get_projected_models | BIOMOD.projection.out getters |
| get_projected_models-method | BIOMOD.projection.out getters |
| get_scaling_model | biomod2 models objects class and functions |
| get_scaling_model-method | biomod2 models objects class and functions |
| get_variables_importance | BIOMOD.models.out getters |
| get_variables_importance-method | BIOMOD.models.out getters |
| get_var_range | biomod2 models objects class and functions |
| get_var_type | biomod2 models objects class and functions |
| GLM_biomod2_model | biomod2 models objects class and functions |
| GLM_biomod2_model-class | biomod2 models objects class and functions |
| level.plot | Plot 2-dimensional data for visualizing distribution of species or environment |
| LIST_to_ARRAY | Convert a biomod2 data.frame (or list) into array |
| load_stored_object | BIOMOD.stored.objects functions |
| load_stored_object-method | BIOMOD.stored.objects functions |
| makeFormula | Standardized formula maker |
| MARS_biomod2_model | biomod2 models objects class and functions |
| MARS_biomod2_model-class | biomod2 models objects class and functions |
| matrix-method | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
| MAXENT.Phillips.2_biomod2_model | biomod2 models objects class and functions |
| MAXENT.Phillips.2_biomod2_model-class | biomod2 models objects class and functions |
| MAXENT.Phillips_biomod2_model | biomod2 models objects class and functions |
| MAXENT.Phillips_biomod2_model-class | biomod2 models objects class and functions |
| models_scores_graph | Produce models evaluation bi-dimensional graph |
| multiple.plot | Plot and compare prediction maps within BIOMOD |
| numeric-method | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
| plot-method | BIOMOD_FormatingData() outputs objects class |
| plot-method | BIOMOD_Projection() outputs objects class |
| predict-method | biomod2 models objects class and functions |
| Print_Default_ModelingOptions | Get default values of BIOMOD inner models' options |
| ProbDensFunc | Probability Density Function |
| Projection | biomod2 internal functions |
| Projection-method | biomod2 internal functions |
| random.pseudo.abs.selection | biomod2 internal functions |
| random.pseudo.abs.selection-method | biomod2 internal functions |
| randomise_data | data set shuffling tool |
| RasterBrick-method | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
| RasterLayer-method | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
| RasterStack-method | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold |
| response.plot | Analysis of the response curves of a model within Biomod |
| response.plot2 | Function for for plotting predicted responses from species distribution models in 2 or 3 dimensions |
| RF_biomod2_model | biomod2 models objects class and functions |
| RF_biomod2_model-class | biomod2 models objects class and functions |
| sample.factor.levels | Tool to ensure the sampling of all levels of a factorial variable |
| SampleMat2 | Sample binary vector |
| show-method | BIOMOD_EnsembleModeling() outputs objects class |
| show-method | BIOMOD_ModelingOptions outputs objects class |
| show-method | BIOMOD_FormatingData() outputs objects class |
| show-method | BIOMOD_modelling() outputs objects class |
| show-method | BIOMOD_Projection() outputs objects class |
| show-method | biomod2 models objects class and functions |
| sre | Surface Range Envelope |
| sre.pseudo.abs.selection | biomod2 internal functions |
| sre.pseudo.abs.selection-method | biomod2 internal functions |
| SRE_biomod2_model | biomod2 models objects class and functions |
| SRE_biomod2_model-class | biomod2 models objects class and functions |
| update_objects | update biomod2 objects |
| user.defined.pseudo.abs.selection | biomod2 internal functions |
| user.defined.pseudo.abs.selection-method | biomod2 internal functions |
| variables_importance | Variables importance calculation |
| zzz_bm | Dummy function to clean working directory after package checks |
| .Models.prepare.data | biomod2 internal functions |
| .Models.prepare.data-method | biomod2 internal functions |
| .Projection.do.proj | biomod2 internal functions |
| .Projection.do.proj-method | biomod2 internal functions |
| .transform.outputs.array | Reshape biomod2 objects |
| .transform.outputs.list | Reshape biomod2 objects |