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Get Life History Traits from FishLife

Source: R/get_traits.R
get_traits.Rd

Retrieves mean (un-logged) life history traits for the closest taxonomic match in the FishLife database. Traits are looked up by matching the supplied taxonomic hierarchy against the FishBase_and_RAM database bundled with marlin.

Usage

get_traits(
  Class = "predictive",
  Order = "predictive",
  Family = "predictive",
  Genus = "predictive",
  Species = "predictive"
)

Arguments

Class

Character. Taxonomic class (e.g. "Actinopterygii"). Default "predictive" (let FishLife infer from lower ranks).

Order

Character. Taxonomic order. Default "predictive".

Family

Character. Taxonomic family. Default "predictive".

Genus

Character. Genus name (e.g. "Lutjanus"). Default "predictive".

Species

Character. Species epithet (e.g. "campechanus"). Default "predictive". Supply at least Genus and Species for species-level lookup.

Value

A data frame with one row containing mean trait values for the closest taxonomic match, including columns for growth parameters (K, Linf, t0), natural mortality (M), maturity (tm), weight-length (a, b), Temperature, and closest_taxa_match (the matched taxon string from FishLife).

Details

Traits are returned on the natural scale (exponentiated from the log scale used internally by FishLife), except Temperature which is returned as-is. Useful for inspecting the life history that create_critter will use when scientific_name is supplied, or for populating custom parameter sets for less well-known species.

See also

create_critter, search_species

Examples

if (FALSE) { # \dontrun{
# Look up red snapper traits
traits <- get_traits(Genus = "Lutjanus", Species = "campechanus")
traits$K       # von Bertalanffy growth rate
traits$Linf    # asymptotic length (cm)
traits$M       # natural mortality rate
} # }