h3sdm workflow for a single model

Introduction

This vignette demonstrates a complete workflow for species distribution modeling (SDM) for a single species using h3sdm. We cover data preparation, model fitting, spatial cross-validation, prediction, and feature importance.

Load packages

library(h3sdm)
library(sf)
library(terra)
library(dplyr)
library(ggplot2)
library(tidymodels)
library(spatialsample)
library(DALEX)
library(themis)

1. Define the Area of Interest

cr <- cr_outline_c

2. Load Environmental Predictors

bio <- terra::rast(system.file("extdata", "bioclim_current.tif", package = "h3sdm"))
names(bio) <- gsub(".*bio_", "bio", names(bio))

3. Create the Hexagonal Grid

The hexagonal grid is the backbone of the h3sdm workflow. All subsequent steps — predictor extraction, presence assignment, and pseudo-absence generation — are built on top of it. The resolution controls the spatial scale of the analysis. At resolution 7, each hexagon covers approximately 514 ha, which is appropriate for many vertebrate species.

h7 <- h3sdm_get_grid(cr, res = 7)

4. Prepare Predictors

Environmental variables are extracted for every hexagon in the grid. Here we use three WorldClim bioclimatic variables: Bio1 (Annual Mean Temperature), Bio12 (Annual Precipitation), and Bio15 (Precipitation Seasonality).

bio_predictors <- h3sdm_extract_num(bio, h7)
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predictors <- h3sdm_predictors(bio_predictors) |>
  dplyr::select(h3_address, bio1, bio12, bio15, geometry)

ggplot() +
  theme_minimal() +
  geom_sf(data = predictors, aes(fill = bio1)) +
  scale_fill_viridis_c(option = "B")

5. Species Occurrence Data

Presence hexagons are generated using h3sdm_pres(), which downloads occurrence records and assigns them to hexagons. Multiple records within the same hexagon are consolidated into a single presence, reducing spatial sampling bias. Since each hexagon represents an area (~514 ha at resolution 7), this better reflects how organisms actually occupy space.

Pseudo-absences are then generated with h3sdm_pa(). They are placed outside the known distribution — excluding hexagons with presences and their immediate neighbors (buffer_k = 1) — and are selected using k-means clustering in environmental space. This ensures pseudo-absences represent the full range of environmental conditions available in the study area, not just their geographic distribution. Since there are approximately 100 presence hexagons, we request 300 pseudo-absences (3×).

pres <- h3sdm_pres("Silverstoneia flotator", cr, res = 7, limit = 10000)

records <- h3sdm_pa(pres, predictors, n_pseudoabs = 300)

table(records$presence)
#> 
#>   0   1 
#> 300 129

ggplot() +
  theme_minimal() +
  geom_sf(data = records, aes(fill = presence)) +
  scale_fill_manual(
    name = "Presence/Absence",
    values = c("red", "blue"),
    labels = c("Absence", "Presence")
  )

6. Combine Records and Predictors

dat <- h3sdm_data(records, predictors)

7. Spatial Cross-Validation

scv <- h3sdm_spatial_cv(dat, v = 5, repeats = 1)
autoplot(scv) + theme_minimal()

8. Define Recipe and Model

receta <- h3sdm_recipe(dat) |>
  themis::step_downsample(presence)

modelo <- parsnip::logistic_reg() |>
  parsnip::set_engine("glm") |>
  parsnip::set_mode("classification")

9. Create Workflow

wf <- h3sdm_workflow(modelo, receta)

10. Fit the Model

presence_data <- dat |>
  dplyr::filter(presence == 1)

f <- h3sdm_fit_model(wf, scv, presence_data)

11. Evaluate Model Performance

evaluation_metrics <- h3sdm_eval_metrics(
  fitted_model  = f$cv_model,
  presence_data = presence_data
)
evaluation_metrics
#> # A tibble: 8 × 6
#>   .metric  .estimator  mean std_err conf_low conf_high
#>   <chr>    <chr>      <dbl>   <dbl>    <dbl>     <dbl>
#> 1 accuracy binary     0.692  0.0266    0.640     0.744
#> 2 f_meas   binary     0.748  0.0522    0.646     0.851
#> 3 kap      binary     0.281  0.0605    0.162     0.399
#> 4 roc_auc  binary     0.751  0.0371    0.679     0.824
#> 5 sens     binary     0.669  0.0302    0.609     0.728
#> 6 spec     binary     0.766  0.0956    0.579     0.953
#> 7 tss      binary     0.486 NA        NA        NA    
#> 8 boyce    binary     0.572 NA        NA        NA

ggplot(evaluation_metrics, aes(.metric, mean)) +
  theme_minimal() +
  geom_col(width = 0.03, color = "dodgerblue3", fill = "dodgerblue3") +
  geom_point(size = 3, color = "orange") +
  ylim(0, 1)

12. Make Predictions

p <- h3sdm_predict(f, predictors)

ggplot() +
  theme_minimal() +
  geom_sf(data = p, aes(fill = prediction)) +
  scale_fill_viridis_c(name = "Habitat\nsuitability", option = "B", direction = -1)

13. Model Interpretation

e <- h3sdm_explain(f$final_model, data = dat)
#> Preparation of a new explainer is initiated
#>   -> model label       :  h3sdm workflow 
#>   -> data              :  429  rows  6  cols 
#>   -> target variable   :  429  values 
#>   -> predict function  :  custom_predict 
#>   -> predicted values  :  No value for predict function target column. (  default  )
#>   -> model_info        :  package Model of class: workflow package unrecognized , ver. Unknown , task regression (  default  ) 
#>   -> predicted values  :  numerical, min =  0.00405074 , mean =  0.4461539 , max =  0.9734401  
#>   -> residual function :  difference between y and yhat (  default  )
#>   -> residuals         :  numerical, min =  -0.9734401 , mean =  -0.1454546 , max =  0.8487902  
#>   A new explainer has been created!

predictors_to_evaluate <- setdiff(names(e$data), c("h3_address", "x", "y", "presence"))

var_imp <- DALEX::model_parts(
  explainer = e,
  variables = predictors_to_evaluate
)
plot(var_imp)

pdp_glm <- ingredients::partial_dependence(e, variables = c("bio12", "bio1", "bio15"))
plot(pdp_glm)

14. Future Scenario Predictions

bio_future <- terra::rast(system.file("extdata", "bioclim_future.tif", package = "h3sdm"))
names(bio_future) <- c("bio1", "bio12", "bio15")

bio_future_predictors <- h3sdm_extract_num(bio_future, h7)
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predictors_future <- h3sdm_predictors(bio_future_predictors)

p_future <- h3sdm_predict(f, predictors_future)

ggplot() +
  theme_minimal() +
  geom_sf(data = p_future, aes(fill = prediction)) +
  scale_fill_viridis_c(name = "Habitat\nsuitability", option = "B", direction = -1)

Conclusions

This vignette demonstrated a complete SDM workflow using h3sdm, including data preparation with a hexagonal grid, presence assignment, environmentally stratified pseudo-absence generation, model fitting with spatial cross-validation, performance evaluation, predictions, and variable importance analysis for both current and future climate scenarios.