fish4_parameters: Fish Bioenergetics 4.0 Official Parameters Database
In fb4package: 'Fish Bioenergetics 4.0' Model Implementation with High-Performance 'TMB' Backend

fish4_parameters

R Documentation

Fish Bioenergetics 4.0 Official Parameters Database

Description

Comprehensive database containing species-specific bioenergetic parameters for the Fish Bioenergetics 4.0 model. This database includes consumption, respiration, egestion, excretion, and predator energy density parameters for multiple fish species across different life stages.

Usage

fish4_parameters

Format

A list containing bioenergetic parameters for fish species with the following structure:

species_name: List for each species containing:
species_info: Basic taxonomic information (scientific name, common name, family, order)
life_stages: Named list of life stages (e.g., "juvenile", "adult", "larval") containing:
consumption: Consumption parameters (CA, CB, CQ, CTO, CTM, CTL, CK1, CK4, CEQ)
respiration: Respiration parameters (RA, RB, RQ, RTO, RTM, RTL, RK1, RK4, RK5, REQ)
activity: Activity multipliers (ACT, BACT)
sda: Specific Dynamic Action coefficient (SDA)
egestion: Egestion parameters (FA, FB, FG, EGEQ)
excretion: Excretion parameters (UA, UB, UG, EXEQ)
predator: Predator energy density parameters (Alpha1, Beta1, Alpha2, Beta2, Cutoff, ED_data, PREDEDEQ)
source: Literature source reference
notes: Additional notes about the parameters
sources: Vector of literature sources for the species

Details

The database contains parameters for fish species from multiple families including Salmonidae, Percidae, Centrarchidae, Cyprinidae, and others. Each species entry includes one or more life stages with complete or partial parameter sets.

Parameter Categories:

Consumption:: Temperature-dependent consumption model parameters
Respiration:: Metabolic rate and activity parameters
Egestion:: Waste production and defecation parameters
Excretion:: Nitrogenous waste excretion parameters
Predator Energy Density:: Weight-dependent energy content parameters

Temperature Parameters:

CTO, RTO:: Optimum temperature for consumption/respiration
CTM, RTM:: Maximum temperature for consumption/respiration
CTL, RTL:: Lethal temperature for consumption/respiration

Usage: This database is primarily used with the Bioenergetic constructor to create species-specific bioenergetic model objects. Parameters can be extracted using utility functions or accessed directly by species and life stage.

Source

Parameters extracted from Parameters_official.csv, the official species database bundled with the Fish Bioenergetics 4.0 ('FB4') Shiny application (<https://github.com/biofish/FishBioenergetics>). Converted to R list format via generate_fish4_parameters(). Original parameter values compiled from peer-reviewed literature; see the source field within each species entry for individual references.

References

Deslauriers, D., Chipps, S.R., Breck, J.E., Rice, J.A., Madenjian, C.P. (2017). Fish Bioenergetics 4.0: An R-based modeling application. Fisheries, 42(11), 586–596. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1080/03632415.2017.1377558")}

Examples

data(fish4_parameters)
head(names(fish4_parameters))
salmon_info <- fish4_parameters[["Oncorhynchus mykiss"]]
names(salmon_info$life_stages)
juvenile_params <- salmon_info$life_stages$juvenile
names(juvenile_params$consumption)

fb4package documentation built on May 8, 2026, 1:07 a.m.