Specify the growth model for Rceattle

Usage

build_growth(
  fun = "empirical",
  growth_age_L1 = NA,
  sd_plus_group = NA,
  linkages = NULL,
  sd_form = NA,
  plus_group_length = NA,
  plus_group_decay = NA,
  pop_lengths = NULL
)

Arguments

fun: Growth function: a string (GROWTH_FUNS: "empirical" (default), "vonBertalanffy", "Richards") or the equivalent integer code (0, 1, 2). The canonical string is stored on the returned object.
growth_age_L1: Von Bertalanffy / Richards anchor age, where mean length equals L1; SS3's Growth_Age_for_L1. Falls back to max(0.5, minage[sp]), which keeps minage >= 1 models backwards-compatible and gives minage = 0 models an SS3-consistent half-year anchor.
sd_plus_group: How the oldest age class's SD-at-age is treated, and only for estimated growth. "WHAM" (the fallback) pins the plus-group SD to the upper anchor exp(sd_Linf), the WHAM SDAA convention; "SS3" interpolates it by length like any interior age. Integer codes 1/2 are accepted. Where SS3's Growth_Age_for_L2 is 999 it pins the plus group to the upper anchor, which is "WHAM" here.
linkages: Optional named list of linkage_spec() objects keyed by parameter name (one of GROWTH_LINKAGE_PARAMS). The mean-growth keys (K, L1, Linf, m) take arbitrary one-sided formulas and make that parameter year-varying, as a per-year offset around its mean. The SD-endpoint keys (sd_L1, sd_Linf) honour only intercept-bearing formulas, typically ~ 1, threading init, bounds and priors onto the growth SD-at-age so the SDs get the same prior, fix and starting-value contract as the means. A slope row on an SD spec warns and has no effect; a slope-only formula (~ 0 + temp) is an error.
sd_form: What the two variability endpoints (sd_L1, sd_Linf) are: "SD" (the fallback), standard deviations of length-at-age in cm, SS3's CV_Growth_Pattern 2; or "CV", coefficients of variation, so the SD is CV x mean length, SS3 pattern 0.
plus_group_length: How the plus group's mean length is set: "M1" (the fallback), "none", "SS3.24" or "decay". See Details.
plus_group_decay: Annual decay rate for plus_group_length = "decay", SS3's positive Linf_decay, roughly the plus group's total mortality. Required for, and used only by, "decay".
pop_lengths: Population length bins (lower edges, cm) on which the age-length key, weight-at-length and maturity-at-length are computed before being summed into the data length bins: SS3's population length bins. Every data-bin lower edge must also be a population-bin edge. A vector applies to every species, a list gives one per species, and the fallback is the data bins.

Value

A list of switches defining the growth model.

Details

Every switch above takes a scalar, recycled across species, or a length-nspp vector for per-species values. Each defaults to NA, which inherits the matching field from data_list when it is set – so a refit, or a model built by the SS3 converter, keeps the original choice – and otherwise uses the fallback named with it.

Plus-group mean length. Fish older than the oldest age are pooled, so the plus group's mean length lies between the growth curve at the oldest age, L_A, and L-infinity:

"M1": mean of L_A + (a/n)(Linf - L_A) over a = 0..n (n = nages), weighted by survival at the oldest age's base M1.
"none": L_A (SS3 Linf_decay = -998).
"SS3.24": as "M1" with weights exp(-0.2 a) and a = 0..A, A the oldest age (SS3 Linf_decay = -999).
"decay": L_A and 2A further ages, each one more year along the von Bertalanffy curve, weighted by exp(-d a) with d = plus_group_decay (SS3 Linf_decay = d).

Under "none", "SS3.24" and "decay" the plus group also grows within the year like every other age, as SS3 does; under "M1" it keeps its Jan-1 length through the year.

Maturity-at-length is set in the data, not here: the per-species control columns L50_mat_len and slope_mat_len.

Examples

# \donttest{
# 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))
    )
  )
)
#> $fun
#> [1] "vonBertalanffy"
#> 
#> $linkages
#> $linkages$K
#> <Rceattle linkage spec>
#>   param:   K
#>   formula: ~temp
#>   prior:    temp ~ normal(0, 1)
#>   link:    log
#> 
#> 
#> $growth_model
#> [1] 1
#> 
#> $sd_plus_group
#> [1] NA
#> 
#> $growth_sd_style
#> [1] NA
#> 
#> $growth_age_L1
#> [1] NA
#> 
#> $sd_form
#> [1] NA
#> 
#> $growth_sd_form
#> [1] NA
#> 
#> $plus_group_length
#> [1] NA
#> 
#> $growth_plus_length
#> [1] NA
#> 
#> $plus_group_decay
#> [1] NA
#> 
#> $pop_lengths
#> NULL
#> 
# }