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Compute Movement Process Error Log-Likelihood (Positive Scale)

Source: R/model_priors_penalties.R
Get_move_PE_loglik.Rd

The log likelihood of move_devs, a field over origin-destination pair, population, year, season, age and sex (see do_move_re_mapping). Each process error block of pairs is one separable Gaussian density, dseparable with a factor per dim built from that dim's first level in the block: dautoreg where the dim is "ar1", dmvnorm with the unstructured correlation where the dim is "us", and a standard normal otherwise. The sd in PE_pars is the conditional one, as ln_sigmaNAA is for the numbers-at-age state, so for each "ar1" dim the field is scaled by that sd divided by sqrt(1 - rho^2), which gives the marginal sd. With no correlation on any dim, each cell is penalized on its own, and a cell left NA in map_move_devs is skipped – this is how a dsem takes over a single series. With a correlation, a block is evaluated as a whole: skipped when every cell is NA, refused when only some are. Returns zero when the dsem holds the density (move_dsem = 1) or no deviation is estimated.

Usage

Get_move_PE_loglik(
  move_year_re,
  move_age_re,
  move_pop_re,
  move_seas_re,
  move_sex_re,
  PE_pars,
  move_pop_corr_pars,
  move_seas_corr_pars,
  move_sex_corr_pars,
  move_devs,
  map_move_devs,
  move_pairs,
  move_pe_block,
  move_pop_block,
  move_year_block,
  move_seas_block,
  move_age_block,
  move_sex_block,
  move_dsem
)

Arguments

move_year_re, move_age_re

Integer codes, 0 none, 1 iid, 2 ar1.

move_pop_re, move_seas_re, move_sex_re

Integer codes, 0 none, 1 iid or blocks, 2 unstructured.

PE_pars

Array [n_regions x n_regions_to x 3] of log conditional sd, unconstrained age correlation and unconstrained year correlation, shared within each process error block.

move_pop_corr_pars, move_seas_corr_pars, move_sex_corr_pars

Unconstrained parameters of the unstructured correlations, read under "us".

move_devs

Array [n_pop x n_regions x n_regions_to x n_years x n_seas x n_ages x n_sexes] of movement deviations.

map_move_devs

Integer mirror of the deviation map, NA where a cell is fixed or a dsem holds it.

move_pairs

Integer matrix, one row per pair, giving its origin and destination.

move_pe_block

Process error block of every pair.

move_pop_block, move_year_block, move_seas_block, move_age_block, move_sex_block

Block of every level of the dim, NA where inactive.

move_dsem

Integer flag; 1 when the dsem holds the density.

Value

Scalar log likelihood (positive scale).