Skip to contents

All functions

abies
A data set containing localities and environmental condition of an Abies (fir tree) species in California, USA
backg
A data set containing environmental conditions of background points
calib_area()
Delimit calibration area for constructing species distribution models
correct_colinvar()
Collinearity reduction of predictor variables
data_bpdp()
Calculate data to construct partial dependence surface plots
data_pdp()
Calculate data to construct partial dependence plots
env_outliers()
Integration of outliers detection methods in environmental space
esm_gam()
Fit and validate Generalized Additive Models based on Ensembles of Small Models approach
esm_gau()
Fit and validate Gaussian Process models based on Ensembles of Small Models approach
esm_gbm()
Fit and validate Generalized Boosted Regression models based on Ensembles of Small Models approach
esm_glm()
Fit and validate Generalized Linear Models based on Ensembles of Small Models approach
esm_max()
Fit and validate Maximum Entropy Models based on Ensemble of Small of Model approach
esm_net()
Fit and validate Neural Networks based on Ensembles of Small of Models approach
esm_svm()
Fit and validate Support Vector Machine models based on Ensembles of Small of Models approach
extra_eval()
Measure model extrapolation based on Shape extrapolation metric
extra_truncate()
Truncate suitability predictions based on an extrapolation value
fit_ensemble()
Ensemble model fitting and validation
fit_gam()
Fit and validate Generalized Additive Models
fit_gau()
Fit and validate Gaussian Process models
fit_gbm()
Fit and validate Generalized Boosted Regression models
fit_glm()
Fit and validate Generalized Linear Models
fit_max()
Fit and validate Maximum Entropy models
fit_net()
Fit and validate Neural Networks models
fit_raf()
Fit and validate Random Forests models
fit_svm()
Fit and validate Support Vector Machine models
get_block()
Transform a spatial partition layer to the same spatial properties as environmental variables
hespero
A data set containing localities of Hesperocyparis stephensonii species in California, USA
homogenize_na()
Homogenize cells with NAs across all layers
interp()
Raster interpolation between two time periods
msdm_posteriori()
Methods to correct overprediction of species distribution models based on occurrences and suitability patterns.
msdm_priori()
Create spatial predictor variables to reduce overprediction of species distribution models
occfilt_env()
Perform environmental filtering on species occurrences
occfilt_geo()
Perform geographical filtering on species occurrences
occfilt_select()
Select filtered occurrences
part_random()
Conventional data partitioning methods
part_sband()
Spatial band cross-validation
part_sblock()
Spatial block cross-validation
part_senv()
Environmental and spatial cross-validation
plot_res()
Plot different resolutions to be used in part_sblock
p_bpdp()
Bivariate partial dependence plot
p_extra()
Graphical exploration of extrapolation or suitability pattern in the environmental and geographical space
p_pdp()
Partial Dependent Plot
sample_background()
Sample background points
sample_pseudoabs()
Sample pseudo-absences
sdm_directory()
Create directories for saving the outputs of the flexsdm
sdm_eval()
Calculate different model performance metrics
sdm_extract()
Extract environmental data values from a spatial raster based on x and y coordinates
sdm_predict()
Spatial predictions from individual and ensemble models
sdm_summarize()
Merge model performance tables
sdm_varimp()
Calculate permutation-based variable importance scores for SDMs
spp
A data set containing presences and absences of three virtual species
tune_gbm()
Fit and validate Generalized Boosted Regression models with exploration of hyper-parameters that optimize performance
tune_max()
Fit and validate Maximum Entropy models with exploration of hyper-parameters that optimize performance
tune_net()
Fit and validate Neural Networks models with exploration of hyper-parameters
tune_raf()
Fit and validate Random Forest models with exploration of hyper-parameters that optimize performance
tune_svm()
Fit and validate Support Vector Machine models with exploration of hyper-parameters that optimize performance