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Map natural mortality parameters to a block structure

do_natmort_mapping.Rd

Constructs the M_blocks index array and the ln_M factor map used by the TMB/RTMB objective function to share or fix natural mortality parameters across population, region, year, season, age, and sex dimensions. Each unique combination of blocks is assigned a sequential integer ID; all cells within a block share the same ln_M parameter.

Usage

do_natmort_mapping(
  input_list,
  M_spec,
  M_popblk_spec_vals,
  M_regionblk_spec_vals,
  M_yearblk_spec_vals,
  M_seasblk_spec_vals,
  M_ageblk_spec_vals,
  M_sexblk_spec_vals
)

Arguments

input_list

Named list containing $data, $par, and $map sublists, as constructed by upstream setup functions.

M_spec

Character string controlling whether ln_M is estimated or fixed. One of:

"est_ln_M"

Freely estimate ln_M across all defined blocks.

"fix"

Fix all ln_M parameters by mapping them to NA.

M_popblk_spec_vals

List of integer vectors assigning population indices to blocks, e.g., list(1, 2) for two population-specific blocks or list(1:2) for a single shared block.

M_regionblk_spec_vals

List of integer vectors assigning region indices to blocks, e.g., list(1:3, 4:5) for two region blocks.

M_yearblk_spec_vals

List of integer vectors assigning year indices to blocks, e.g., list(1:10, 11:30) for two time periods.

M_seasblk_spec_vals

List of integer vectors assigning season indices to blocks, e.g., list(1, 2) for two season-specific rates.

M_ageblk_spec_vals

List of integer vectors assigning age indices to blocks, e.g., list(1:5, 6:10) for two age groups.

M_sexblk_spec_vals

List of integer vectors assigning sex indices to blocks. Use list(1:2) for a sex-invariant block or list(1, 2) for sex-specific mortality.

Value

The input input_list with two fields updated:

$map$ln_M

Factor vector of length equal to prod(dim(par$ln_M)). Each element is an integer estimation index when M_spec = "est_ln_M", or NA when M_spec = "fix".

$data$M_blocks

Integer array of dimensions [n_pop × n_regions × n_years × n_seas × n_ages × n_sexes] mapping each population-region-year-season-age-sex cell to its corresponding ln_M parameter index.