Extract simulation outputs into SPoRC estimation model format
Source:R/sim_self_test.R
simulation_data_to_SPoRC.RdSubsets and reshapes the biological, tagging, fishery and survey arrays of a
simulation environment to years 1:y and replicate sim, giving a
list ready for Setup_Mod_Biologicals,
Setup_Mod_Catch_and_F, Setup_Mod_SrvIdx_and_Comps
and Setup_Mod_Tagging. The Use* flags are derived from the
extracted observations, 1 where a value is present and positive.
Arguments
- sim_env
Simulation environment or list, from
Simulate_Pop_StaticorSetup_sim_env, holding the operating model arrays.- y
Integer. Last year to include; years
1:yare kept.- sim
Integer. Simulation replicate to extract.
Value
Named list, every array with y in its year dim. The
biological elements are WAA [n_pop x n_regions x y x n_seas x
n_ages x n_sexes], WAA_fish and WAA_srv with a trailing fleet
dim, MatAA, SizeAgeTrans, AgeingError [y x n_ages x
n_obs_ages], whose columns are the observed ages the model ages are read
onto, and AgeingError_fish and AgeingError_srv, NULL when
the fleets share one matrix. LenBinMap is the map onto the length bins
the length compositions are recorded on, NULL when those are the
model's bins, and goes to Setup_Mod_Biologicals with the rest,
as does CAAL_LenBinMap, the model bins each age-at-length row covers.
The tagging elements are
use_conv_fish_tagging, conv_tag_release_indicator,
obs_conv_tag_fish_recap, conv_tagged_fish,
conv_tagged_fish_attr and n_tag_cohorts.
Each fishery and survey data source contributes its observations, its
observation error or input sample sizes, and its use flag: ObsCatch
with ln_sigmaC and UseCatch, ObsDiscard with
ln_sigmaD and UseDiscard, ObsFishIdx and
ObsSrvIdx with their _SE and use arrays, and the four
composition streams (fishery and survey age and length) with their
ISS_* and Use* arrays. Each has a _pop counterpart, and
the fishery compositions also have _discard and _discard_pop
ones. The length composition elements and their input sample sizes are
NULL when no size-age transition matrix is present.
The at-age data sources, ObsCatchAA, ObsDiscardAA and
ObsSrvIdxAA and their _pop counterparts, come with their
_SE arrays and the operating model's own use flags, since a normal
likelihood can draw a value at or below zero. Each is NULL when the
operating model draws none of it.
Details
Population-specific arrays are extracted when sim_env holds them, with
their own flags derived the same way. The length composition outputs and
SizeAgeTrans are NULL when the environment holds no size-age
transition matrix, and the tagging outputs are NULL under
use_conv_fish_tagging = 0; otherwise only cohorts released in
1:y are kept.