calculate_contaminant_accumulation: Calculate contaminant accumulation (Mid-level - Main...

In fb4package: 'Fish Bioenergetics 4.0' Model Implementation with High-Performance 'TMB' Backend

Calculate contaminant accumulation (Mid-level - Main function)

Description

Calculates daily contaminant dynamics (uptake, elimination, body burden) for a fish using one of three bioaccumulation models (CONTEQ 1-3).

Usage

calculate_contaminant_accumulation(
  respiration_o2,
  consumption,
  weight,
  temperature,
  current_concentration,
  processed_contaminant_params
)

Arguments

respiration_o2	Respiration in g O2/g/day
consumption	Vector of consumption by prey type (g/day)
weight	Fish weight (g)
temperature	Water temperature (deg C)
current_concentration	Current concentration in predator (ug/g)
processed_contaminant_params	List with processed contaminant parameters

Value

A named list with at least six elements (all numeric scalars unless noted):

clearance

Daily elimination of contaminant (ug/day).

uptake

Total daily uptake from food (ug/day); for CONTEQ 3 this is the sum of water and food uptake.

new_burden

Body burden at end of day (ug); floored at 0.

new_concentration

Whole-body concentration (ug/g wet weight); floored at 0.

weight

Fish weight (g), as supplied.

model_used

Integer. CONTEQ equation used (1, 2, or 3).

CONTEQ 3 (Arnot & Gobas 2004) appends two additional elements: uptake_water (ug/day from water) and uptake_food (ug/day from food).

Experimental

Contaminant modelling is an **experimental feature** under active development. This function can be called directly to compute daily bioaccumulation for a single time step, but it is **not yet integrated** into the main 'run_fb4()' simulation loop. Full integration (automatic contaminant tracking across all simulation days, inclusion in 'fb4_result' objects, and TMB backend support) is planned for a future release. The API may change.

Examples

# CONTEQ 1: food uptake only, no elimination
params <- list(
  CONTEQ = 1,
  prey_concentrations = c(0.05, 0.08),
  transfer_efficiency = c(0.8, 0.8)
)
calculate_contaminant_accumulation(
  respiration_o2 = 0.02, consumption = c(2.0, 1.0),
  weight = 100, temperature = 15,
  current_concentration = 0.1,
  processed_contaminant_params = params
)

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