Map natural mortality parameters to a block structure

Builds the M_blocks index array and the ln_M factor map. Each combination of blocks takes a sequential integer, and every cell in a block shares one ln_M.

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 with $data, $par and $map.

M_spec

"est_ln_M" estimates ln_M across the blocks, "fix" maps every parameter to NA.

M_popblk_spec_vals

List of integer vectors assigning population indices to blocks, e.g. list(1, 2) or list(1:2).

M_regionblk_spec_vals

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

M_yearblk_spec_vals

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

M_seasblk_spec_vals

List of integer vectors assigning season indices to blocks, e.g. list(1, 2).

M_ageblk_spec_vals

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

M_sexblk_spec_vals

List of integer vectors assigning sex indices to blocks, list(1:2) for one shared rate or list(1, 2) for sex-specific mortality.

Value

input_list with $map$ln_M, a factor vector of length prod(dim(par$ln_M)) holding estimation indices or NA, and $data$M_blocks, an integer array [n_pop × n_regions × n_years × n_seas × n_ages × n_sexes] giving each cell's ln_M index.