hdi_table — hdi_table • CheckEM

Generates a summary table for species data with Highest Density Interval (HDI) statistics and comparisons against species-specific maximum lengths.

Usage

hdi_table(species_data, max_lengths)

Arguments

species_data: A dataframe with species data, including columns for family, genus, species, scientific_name, and length_mm (length measurements in millimeters).
max_lengths: A dataframe with species-specific maximum lengths. It must include the column scientific_name to match the species and length_max_mm for the maximum length in millimeters.

Value

A dataframe summarizing the HDI statistics for each species, including:

family: Family of the species.
genus: Genus of the species.
species: Species name.
scientific_name: Scientific name of the species.
species_length_max_mm: Maximum length (in millimeters) from the provided species-specific data.
hdci_99_lower_bound: Lower bound of the 99% HDI for the species' length measurements.
hdci_99_upper_bound: Upper bound of the 99% HDI for the species' length measurements.
num_measurements: Number of individual length measurements (rows) for the species.
highest_metric: Indicates whether the maximum length (from FishBase) or the HDI upper bound is higher.
num_lengths_over_max: The count of lengths that exceed the species-specific maximum length.
num_lengths_over_hdi_upper: The count of lengths that exceed the 99% HDI upper bound.
num_lengths_smaller_hdi_lower: The count of lengths that are smaller than the 99% HDI lower bound.

Details

This function calculates HDI statistics (99% interval) for each species' length data, compares these statistics with species-specific maximum lengths (provided separately), and creates a summary dataframe. The summary includes family, genus, species, scientific name, species length max, HDI bounds, number of individuals measured, and metrics like the number of lengths exceeding the max or HDI upper bound.

The function first loops through each species in the species_data, calculates the 99% HDI using the ggdist::median_hdci() function, and compares the species' maximum length (from max_lengths) with the HDI statistics. It then appends the results for each species into a final dataframe.

Examples

# Example usage
species_data <- data.frame(family = c("Acanthuridae"), genus = c("Acanthurus"),
                           species = c("triostegus"), scientific_name = c("Acanthurus triostegus"),
                           length_mm = c(120, 130, 125, 140, 135, 290, 200, 260, 150, 190, 280))
max_lengths <- data.frame(scientific_name = c("Acanthurus triostegus"), length_max_mm = c(270))

hdi_table(species_data, max_lengths)
#> Error in loadNamespace(x): there is no package called ‘ggdist’