Fill Species Traits Using FishBase

Populates key life-history traits in a data frame of species using FishBase, via the rfishbase package.

Usage

fillDefaultsFromFishBase(
  species_params,
  scientific_name_col = "Scientific_name",
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

species_params

A data frame containing at least a column with scientific names for each species. Other columns (e.g. common names or user-defined identifiers) may be included and will be preserved. This is typically a minimal table created at the start of model construction (e.g., from a species list), not yet a full species_params object.

scientific_name_col

A string giving the column name in species_params that holds the scientific names. Defaults to "Scientific_name".

overwrite

Logical (default = FALSE). If TRUE, existing values in the data frame are replaced by FishBase values. If FALSE, only missing values are filled.

verbose

Logical (default = TRUE). If TRUE, prints a summary of filled species.

Value

The same data frame, augmented with the following columns where data are available:

• a, b: Length–weight allometric coefficients

• Length: Maximum length (cm)

• w_max: Maximum weight (calculated from Length, a, and b)

• l_mat: Length at maturity (median)

• age_mat: Age at maturity (median)

• w_mat: Weight at maturity (from l_mat, a, and b)

Details

This function is typically used early in model setup, to populate a table of species names with biological parameters needed for Mizer models. It supports cases where only species names and scientific names are initially known.

This is a convenience function that queries FishBase through the rfishbase package. Traits are pulled from the estimate(), maturity(), and species() tables. Maturity traits are summarised by median within FishBase SpecCode groups. Derived weights are calculated from length–weight relationships.

Existing columns in the input will only be overwritten if overwrite = TRUE.

Note

Requires the rfishbase package. Install it with install.packages("rfishbase").

See also

rfishbase::estimate(), rfishbase::maturity(), rfishbase::species()

Examples

if (FALSE) { # \dontrun{
# Minimal example with only scientific names
species_df <- data.frame(
  Scientific_name = c("Merluccius merluccius", "Scomber scombrus")
)
enriched <- fillDefaultsFromFishBase(species_df)

# Optional: include user-defined species labels
species_df <- data.frame(
  species = c("Hake", "Mackerel"),
  Scientific_name = c("Merluccius merluccius", "Scomber scombrus")
)
enriched <- fillDefaultsFromFishBase(species_df)
} # }