Calculate contaminant accumulation (Mid-level - Main function) — calculate_contaminant

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
)
#> $clearance
#> [1] 0
#> 
#> $uptake
#> [1] 0.144
#> 
#> $new_burden
#> [1] 10.144
#> 
#> $new_concentration
#> [1] 0.10144
#> 
#> $weight
#> [1] 100
#> 
#> $model_used
#> [1] 1
#>