summary_sdm: Calculates performance across resamples

In caretSDM: Build Species Distribution Modeling using 'caret'

Calculates performance across resamples

Description

This function is used in caret::trainControl(summaryFunction=summary_sdm) to calculate performance metrics across resamples.

Usage

summary_sdm(data, lev = NULL, model = NULL, custom_fun=NULL)

summary_sdm_presence_only(data, lev, threshold)

validate_on_independent_data(model, data_independent, obs_col_name)

Arguments

data	A data.frame with observed and predicted values.
lev	A character vector of factors levels for the response.
model	Models names taken from train object.
custom_fun	A custom function to be applied in models (not yet implemented).
threshold	Threshold for presence-only models.
data_independent	independent data.frame to calculate metrics.
obs_col_name	The name of the column with observed values.

Details

See ?caret::defaultSummary for more details and options to pass on caret::trainControl.

Value

A input_sdm or a predictions object.

Author(s)

Luíz Fernando Esser ([e-mail]) https://luizfesser.wordpress.com

See Also

train_sdm

Examples

# Create sdm_area object:
sa <- sdm_area(parana, cell_size = 100000, crs = 6933)

# Include predictors:
sa <- add_predictors(sa, bioc) |> select_predictors(c("bio1", "bio12"))

# Include scenarios:
sa <- add_scenarios(sa)

# Create occurrences:
oc <- occurrences_sdm(occ, crs = 6933) |> join_area(sa)

# Create input_sdm:
i <- input_sdm(oc, sa)

# Pseudoabsence generation:
i <- pseudoabsences(i, method = "random")

# Custom trainControl:
ctrl_sdm <- caret::trainControl(method = "repeatedcv",
                                number = 2,
                                repeats = 1,
                                classProbs = TRUE,
                                returnResamp = "all",
                                summaryFunction = summary_sdm,
                                savePredictions = "all")

# Train models:
i <- train_sdm(i, algo = c("naive_bayes"), ctrl=ctrl_sdm) |>
suppressWarnings()

caretSDM documentation built on Aug. 29, 2025, 5:17 p.m.