R: Build Species Distribution Modeling using 'caret'

# Build Species Distribution Modeling using 'caret'

## Documentation for package ‘caretSDM’ version 1.8.3

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

A B C D E F G I J M N O P R S T U V W

## -- A --

add_ensembles | Ensemble Species Distribution Models
add_input_sdm | 'input_sdm'
add_models | Train SDM models
add_occurrences | Occurrences Managing
add_predictions | Predict SDM models in new data
add_predictors | Add predictors to 'sdm_area'
add_scenarios | Add scenarios to 'sdm_area'
add_sdm_area | Create a 'sdm_area' object
algorithms | Caret Algorithms
algorithms_used | Train SDM models

## -- B --

background | Obtain Background data
background_data | Obtain Background data
background_method | Obtain Background data
bioc | Bioclimatic Variables
buffer_sdm | Create buffer around occurrences

## -- C --

correlate_sdm | Correlation between projections

## -- D --

data_clean | Presence data cleaning routine

## -- E --

ensemble_sdm | Ensemble Species Distribution Models

## -- 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 | Ensemble Species Distribution Models
get_models | Train SDM models
get_occurrences | Occurrences Managing
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_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_sdm_area | 'is_class' functions to check caretSDM data classes.

## -- J --

join_area | Join Area

## -- M --

mapview_ensembles | S3 Methods for plot and mapview
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
multicollinearity_sdm | Multicollinearity Analysis
mutate.input_sdm | Tidyverse methods for caretSDM objects
mutate.sdm_area | Tidyverse methods for caretSDM objects

## -- N --

n_background | Obtain Background data
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_background | S3 Methods for plot and mapview
plot_ensembles | S3 Methods for plot and mapview
plot_grid | S3 Methods for plot and mapview
plot_niche | 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
prediction_change_sdm | Prediction Change Analysis
predict_sdm | Predict SDM models in new data
print.ensembles | Print method for ensembles
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'
scen_rs | Bioclimatic Variables
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 | Multicollinearity Analysis
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
summary_sdm_presence_only | Calculates performance across resamples

## -- T --

test_variables_names | Predictors Names Managing
train_sdm | Train SDM models
tsne_sdm | tSNE
tuneGrid_sdm | Retrieve tuneGrid from models

## -- U --

use_esm | Ensemble of Small Models (ESM) in caretSDM
use_mem | MacroEcological Models (MEM) in caretSDM

## -- V --

validate_on_independent_data | Calculates performance across resamples
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_background | Write caretSDM 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