Build Species Distribution Modeling using 'caret'
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Documentation for package ‘caretSDM’ version 1.1.0.1
Help Pages
A B D F G I J M N O P R S T U V W
-- A --
| add_occurrences | Occurrences Managing |
| add_predictors | Add predictors to 'sdm_area' |
| add_scenarios | Add scenarios to 'sdm_area' |
| algorithms | Caret Algorithms |
| algorithms_used | Train SDM models |
-- B --
| bioc | Bioclimatic Variables |
| buffer_sdm | Create buffer around occurrences |
-- D --
| data_clean | Presence data cleaning routine |
-- F --
| filter.input_sdm | Tidyverse methods for caretSDM objects |
| filter.occurrences | Tidyverse methods for caretSDM objects |
| filter.sdm_area | Tidyverse methods for caretSDM objects |
| filter_species | Tidyverse methods for caretSDM objects |
-- G --
| GBIF_data | Retrieve Species data from GBIF |
| gcms_ensembles | Ensemble GCMs into one scenario |
| get_coords | Occurrences Managing |
| get_ensembles | Predict SDM models in new data |
| get_models | Train SDM models |
| get_pca_model | Predictors as PCA-axes |
| get_pdp_sdm | Model Response to Variables |
| get_predictions | Predict SDM models in new data |
| get_predictors | Add predictors to 'sdm_area' |
| get_predictor_names | Predictors Names Managing |
| get_predictor_names.input_sdm | Predictors Names Managing |
| get_predictor_names.sdm_area | Predictors Names Managing |
| get_scenarios_data | Add scenarios to 'sdm_area' |
| get_sdm_area | Create a 'sdm_area' object |
| get_tune_length | Train SDM models |
| get_validation_metrics | Train SDM models |
-- I --
| input_sdm | 'input_sdm' |
| is_input_sdm | 'is_class' functions to check caretSDM data classes. |
| is_models | 'is_class' functions to check caretSDM data classes. |
| is_occurrences | 'is_class' functions to check caretSDM data classes. |
| is_predictions | 'is_class' functions to check caretSDM data classes. |
| is_predictors | 'is_class' functions to check caretSDM data classes. |
| is_scenarios | 'is_class' functions to check caretSDM data classes. |
| is_sdm_area | 'is_class' functions to check caretSDM data classes. |
-- J --
| join_area | Join Area |
-- M --
| mapview_grid | S3 Methods for plot and mapview |
| mapview_occurrences | S3 Methods for plot and mapview |
| mapview_predictions | S3 Methods for plot and mapview |
| mapview_predictors | S3 Methods for plot and mapview |
| mapview_scenarios | S3 Methods for plot and mapview |
| mean_validation_metrics | Train SDM models |
| mutate.input_sdm | Tidyverse methods for caretSDM objects |
| mutate.sdm_area | Tidyverse methods for caretSDM objects |
-- N --
| n_pseudoabsences | Obtain Pseudoabsences |
| n_records | Occurrences Managing |
-- O --
| occ | Araucaria angustifolia occurrence data |
| occurrences_as_df | Occurrences Managing |
| occurrences_sdm | Occurrences Managing |
-- P --
| parana | Paraná State |
| pca_predictors | Predictors as PCA-axes |
| pca_summary | Predictors as PCA-axes |
| pdp_sdm | Model Response to Variables |
| plot_grid | S3 Methods for plot and mapview |
| plot_occurrences | S3 Methods for plot and mapview |
| plot_predictions | S3 Methods for plot and mapview |
| plot_predictors | S3 Methods for plot and mapview |
| plot_scenarios | S3 Methods for plot and mapview |
| predictors | Predictors Names Managing |
| predictors.input_sdm | Predictors Names Managing |
| predictors.sdm_area | Predictors Names Managing |
| predict_sdm | Predict SDM models in new data |
| print.input_sdm | Print method for input_sdm |
| print.models | Print method for models |
| print.occurrences | Print method for occurrences |
| print.predictions | Print method for predictions |
| pseudoabsences | Obtain Pseudoabsences |
| pseudoabsence_data | Obtain Pseudoabsences |
| pseudoabsence_method | Obtain Pseudoabsences |
-- R --
| rivs | Hydrologic Variables |
-- S --
| salm | Salminus brasiliensis occurrence data |
| scen | Bioclimatic Variables |
| scenarios_names | Add scenarios to 'sdm_area' |
| sdm_area | Create a 'sdm_area' object |
| sdm_as_raster | 'sdm_as_X' functions to transform 'caretSDM' data into other classes. |
| sdm_as_stars | 'sdm_as_X' functions to transform 'caretSDM' data into other classes. |
| sdm_as_terra | 'sdm_as_X' functions to transform 'caretSDM' data into other classes. |
| select.input_sdm | Tidyverse methods for caretSDM objects |
| select.sdm_area | Tidyverse methods for caretSDM objects |
| selected_variables | Calculate VIF |
| select_predictors | Tidyverse methods for caretSDM objects |
| select_scenarios | Add scenarios to 'sdm_area' |
| set_predictor_names | Predictors Names Managing |
| set_predictor_names.input_sdm | Predictors Names Managing |
| set_predictor_names.sdm_area | Predictors Names Managing |
| set_scenarios_names | Add scenarios to 'sdm_area' |
| set_variables_names | Predictors Names Managing |
| species_names | Occurrences Managing |
| summary_sdm | Calculates performance across resamples |
-- T --
| test_variables_names | Predictors Names Managing |
| train_sdm | Train SDM models |
| tsne_sdm | tSNE |
-- U --
| use_mem | MacroEcological Models (MEM) in caretSDM |
-- V --
| varImp_sdm | Calculation of variable importance for models |
| vif_predictors | Calculate VIF |
| vif_summary | Calculate VIF |
-- W --
| WorldClim_data | Download WorldClim v.2.1 bioclimatic data |
| write_ensembles | Write caretSDM data |
| write_gpkg | Write caretSDM data |
| write_gpkg.sdm_area | Write caretSDM data |
| write_grid | Write caretSDM data |
| write_models | Write caretSDM data |
| write_occurrences | Write caretSDM data |
| write_predictions | Write caretSDM data |
| write_predictors | Write caretSDM data |
| write_pseudoabsences | Write caretSDM data |
| write_validation_metrics | Write caretSDM data |