Fish Bioenergetics 4.0 Official Parameters Database

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

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.

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.

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. doi:10.1080/03632415.2017.1377558

See also

Bioenergetic, run_fb4

Examples

data(fish4_parameters)
head(names(fish4_parameters))
#> [1] "Alosa pseudoharengus"           "Gadus morhua"                  
#> [3] "Brevoortia tyrannus"            "Thymallus arcticus baicalensis"
#> [5] "Clupea harengus"                "Anchoa mitchilli"              
salmon_info <- fish4_parameters[["Oncorhynchus mykiss"]]
names(salmon_info$life_stages)
#> [1] "juvenile" "adult"    "adult_3" 
juvenile_params <- salmon_info$life_stages$juvenile
names(juvenile_params$consumption)
#> [1] "CEQ" "CA"  "CB"  "CQ"  "CTO" "CTM" "CTL" "CK1" "CK4"