Compute Movement Process Error Log-Likelihood (Positive Scale)
Get_move_PE_loglik.RdCalculates the positive log-likelihood contribution for movement
process error deviations under multiple IID structural assumptions.
Deviations are penalized as \(N(0, \sigma^2)\) where \(\sigma\)
is drawn from PE_pars according to the selected model structure.
Only origin-destination pairs that are adjacent (non-zero in
adjacency_collapsed) contribute to the likelihood.
Usage
Get_move_PE_loglik(
PE_model,
PE_pars,
move_devs,
map_move_devs,
do_recruits_move,
adjacency_collapsed,
move_type
)Arguments
- PE_model
Integer specifying the movement process error structure. All models are IID; they differ in which dimensions share a common standard deviation. Models 1–5 are single-population (fix
pop = 1); models 6–10 estimate separate parameters per population:1 – IID across years (single \(\sigma\) per origin region)
2 – IID across ages (single \(\sigma\) per origin region and age)
3 – IID across years and ages
4 – IID across years, ages, and sexes
5 – IID across years, seasons, ages, and sexes
6 – IID across populations and years
7 – IID across populations and ages
8 – IID across populations, years, and ages
9 – IID across populations, years, ages, and sexes
10 – IID across populations, years, seasons, ages, and sexes
- PE_pars
Array of movement process error parameters (log standard deviations) dimensioned
[pop, from_region, seas, age, sex]. Exponentiated internally to obtain \(\sigma\). Which dimensions are active depends onPE_model; unused dimensions should be fixed at a constant (e.g., index 1) via the parameter map.- move_devs
Movement deviation array dimensioned
[pop, from_region, to_region, year, seas, age, sex].- map_move_devs
Integer array dimensioned
[pop, from_region, to_region, year, seas, age, sex]mapping deviations to unique estimated parameters. Shared deviations carry the same integer value; dimensions are extracted from this array to determine loop bounds.- do_recruits_move
Integer (0/1). If
0andn_ages >= 2, age-1 recruits are excluded from the likelihood (loop starts at age 2). If1, all ages including recruits are penalized.- adjacency_collapsed
Square
[n_regions x n_regions]matrix of allowable movement connections among regions, excluding self-retention (diagonal entries should be 0). Origin-destination pairs with a value of 0 are skipped and contribute nothing to the likelihood.- move_type
Integer specifying the movement formulation:
0 = Unstructured multinomial logit movement
1 = CTMC-based movement
Currently used for dispatch context; likelihood computation is identical across movement types within this function.