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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-and-priors").

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 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-and-priors").

linkages

Optional named list of linkage_spec() objects keyed by M parameter name (currently the only valid key is "M1"). Each spec describes how 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 M1
build_M1(
  M1_model = "sex_age_invariant",
  linkages = list(
    M1 = linkage_spec(
      formula = ~ temp,
      by      = ~ species,
      priors  = list(temp = normal(0, 0.5))
    )
  )
)
} # }