Specify the growth model for Rceattle

Usage

build_growth(fun = "empirical", growth_age_L1 = NA, linkages = NULL)

Arguments

fun: Growth function. Either a string (GROWTH_FUNS: "empirical" (default), "vonBertalanffy", "Richards") or the equivalent integer code (0, 1, 2). The canonical string form is stored on the returned object.
growth_age_L1: Von Bertalanffy / Richards anchor age (the age at which mean length equals L1). Matches SS3's Growth_Age_for_L1 control input. Scalar (recycled across species) or a length-nspp vector for per-species values. Default NA inherits data_list$growth_age_L1 if supplied (e.g. from the SS3 converter), otherwise falls back to max(0.5, minage[sp]) so minage >= 1 models stay backwards-compatible and minage = 0 models pick up an SS3-consistent half-year anchor.
linkages: Optional named list of linkage_spec() objects keyed by parameter name (must be one of GROWTH_LINKAGE_PARAMS). The mean-growth keys (K, L1, Linf, m) accept arbitrary one-sided formulas and produce year-varying offsets applied inside growth.hpp. The SD-endpoint keys (sd_L1, sd_Linf) only honor intercept-bearing formulas (typically ~ 1) – they thread init, bounds, and priors onto the underlying growth_log_sd parameter, giving the SDs the same prior/fix/initial-value contract as the mean parameters. Slope rows on SD specs raise a warning and have no effect; slope-only formulas (~ 0 + temp) error. Materialization into the global linkage table happens inside fit_mod() once data_list$env_data is in scope.

Value

A list of switches defining the growth model.

Examples

if (FALSE) { # \dontrun{
# Sex-specific von Bertalanffy with temperature on K, by species + sex
build_growth(
  fun = "vonBertalanffy",   # or fun = 1
  linkages = list(
    K = linkage_spec(
      formula = ~ temp,
      by      = ~ species + sex,
      priors  = list(temp = normal(0, 1))
    )
  )
)
} # }