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Define M1 specifications

Source: R/0-build_srr_and_M.R
build_M1.Rd

Define M1 specifications

Usage

build_M1(
  M1_model = 0,
  M1_re = 0,
  updateM1 = FALSE,
  M1_use_prior = FALSE,
  M2_use_prior = FALSE,
  M_prior = 0.4,
  M_prior_sd = 0.35,
  M1_indices = NA,
  linkages = NULL
)

Arguments

M1_model

Vector or scalar specifying the M1 structural fixed- effects model. Either an integer code or the equivalent string alias (both forms are accepted; the integer code is canonical):

  • 0 / "fixed" – use the input M1_base (no estimation).

  • 1 / "sex_age_invariant" – estimate one M1_{spp}.

  • 2 / "sex_specific" – estimate M1_{spp, sex}.

  • 3 / "sex_age_specific" – estimate M1_{spp, sex, age}.

  • 4, 5 – soft-deprecated env-driven codes; use the linkages argument instead. See vignette("environmental-linkages").

M1_re

Vector or scalar specifying the M1 random-effects model. Either an integer code or the equivalent string alias: 0 / "none", 1 / "iid_age", 2 / "iid_year", 3 / "iid_age_year", 4 / "ar1_age", 5 / "ar1_year", 6 / "ar1_age_year".

updateM1

If using initial parameters, use M1 fixed effects from data (M1_base) instead. Default FALSE.

M1_use_prior

Vector or scalar; if TRUE, apply the lognormal M_prior / M_prior_sd to log_M1 directly.

M2_use_prior

Vector or scalar; if TRUE, apply the lognormal prior to M1 + M2 in multi-species models.

M_prior

Mean (natural-scale) of the lognormal prior on M.

M_prior_sd

SD (log-scale) of the lognormal prior on M.

M1_indices

Soft-deprecated. Vector of column indices into env_data (excluding Year) for environmentally linked M1 when M1_model %in% c(4, 5). Use the linkages argument instead; see vignette("environmental-linkages").

linkages

Optional named list of linkage_spec() objects keyed by M parameter name (currently the only valid key is "log_M1"). Each spec describes how log_M1 depends on environmental covariates and on stratifying factors (species, sex, age). The offset enters additively (on the log scale) inside the M1_at_age compute. A row's age_bin == NA broadcasts the offset across ages; specific values pin it to that age slice.

Value

A list of switches for defining the M1 model.

Examples

if (FALSE) { # \dontrun{
# Sex/age-invariant M with a temperature linkage on log_M1
build_M1(
  M1_model = "sex_age_invariant",
  linkages = list(
    log_M1 = linkage_spec(
      formula = ~ temp,
      by      = ~ species,
      priors  = list(temp = normal(0, 0.5))
    )
  )
)
} # }