Calculate daily mortality and reproduction (Mid-level - Main function) — calculate_mortality

Calculates daily mortality probability and reproductive energy loss (natural mortality, fishing mortality, predation mortality, starvation, and weight-dependent survival) for a single time step.

Usage

calculate_mortality_reproduction(
  current_weight,
  temperature,
  day_of_year,
  processed_mortality_params,
  initial_weight = NULL
)

Arguments

current_weight: Current fish weight (g)
temperature: Water temperature (deg C)
day_of_year: Day of year (1-365)
processed_mortality_params: List with processed mortality parameters
initial_weight: Initial weight for relative calculations (optional)

Value

A named list with five elements:

mortality: Named list with seven numeric scalars (all daily rates, 0–1): survival_rate, combined_mortality, natural_mortality, fishing_mortality, predation_mortality, weight_effect (increment to mortality due to low body weight), and temperature_effect (increment due to thermal stress).
reproduction: NULL if no spawn pattern is defined in processed_mortality_params; otherwise a named list with weight_loss (g), energy_loss (J), spawn_fraction (0–1), and remaining_weight (g).
day_of_year: Integer. Day of year, as supplied.
current_weight: Numeric. Fish weight (g), as supplied.
temperature: Numeric. Water temperature (\(^\circ\)C), as supplied.

Experimental

Mortality rate modelling is an **experimental feature** under active development. This function can be called directly to compute daily mortality probability for a single time step, but **mortality rates are not yet integrated** into the main `run_fb4()` simulation loop. Full integration (automatic daily mortality application, population survival tracking, and result reporting) is planned for a future release. The API may change.

Note: **spawning energy loss** (reproductive cost) *is* already integrated into `run_fb4()` and applies automatically when `reproduction_data` is supplied to the `Bioenergetic` object.

Examples

params <- list(
  base_mortality      = 0.001,
  natural_mortality   = 0.001,
  fishing_mortality   = 0.0005,
  predation_mortality = 0.0002,
  weight_threshold    = 10,
  starvation_factor   = 2,
  optimal_temp        = 18,
  thermal_tolerance   = 8,
  stress_factor       = 1.5,
  spawn_pattern       = NULL
)
calculate_mortality_reproduction(current_weight = 100, temperature = 15,
                                 day_of_year = 180,
                                 processed_mortality_params = params)
#> $mortality
#> $mortality$survival_rate
#> [1] 0.9983008
#> 
#> $mortality$combined_mortality
#> [1] 0.0016992
#> 
#> $mortality$natural_mortality
#> [1] 0.001
#> 
#> $mortality$fishing_mortality
#> [1] 5e-04
#> 
#> $mortality$predation_mortality
#> [1] 2e-04
#> 
#> $mortality$weight_effect
#> [1] 0
#> 
#> $mortality$temperature_effect
#> [1] 0
#> 
#> 
#> $reproduction
#> NULL
#> 
#> $day_of_year
#> [1] 180
#> 
#> $current_weight
#> [1] 100
#> 
#> $temperature
#> [1] 15
#>