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.
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
Generated from the official Fish Bioenergetics 4.0 parameters CSV file
(Parameters_official.csv) using the generate_fish4_parameters() function.
Original parameters compiled from peer-reviewed literature sources.
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.
Examples
if (FALSE) { # \dontrun{
# Load the database
data(fish4_parameters)
# List available species
species_names <- names(fish4_parameters)
head(species_names)
# Get species information
salmon_info <- fish4_parameters[["Oncorhynchus mykiss"]]
print(salmon_info$species_info)
# Available life stages for a species
names(salmon_info$life_stages)
# Extract parameters for a specific life stage
juvenile_params <- salmon_info$life_stages$juvenile
print(juvenile_params$consumption)
# Use with Bioenergetic constructor
bio_obj <- Bioenergetic(
species_params = juvenile_params,
species_info = salmon_info$species_info
)
} # }