Description of Model Report
d_model_report.RmdThe following tables describe all elements contained within
obj$rep, which is generated after a model is run. Note that
when n_sexes > 1, the first dimension will always be
females and the second dimension will always be males. Similarly, when
n_pop > 1, populations are indexed in the order they are
defined.
Biological Processes
| Name | Description | Dimensions |
|---|---|---|
R0 |
Global mean or virgin recruitment for each population | n_pop |
rinit |
Global recruitment scalar for initialization for each population | n_pop |
rec_region_prop |
Recruitment regional apportionment proportions | n_pop × n_regions |
rec_seas_prop |
Recruitment seasonal apportionment proportions | n_pop × n_seas |
stray_rate |
Proportion of each population’s spawning biomass contributing to
non-natal regions (only relevant when n_pop > 1) |
n_pop × n_years |
sexratio |
Recruitment sex ratio (female proportion) | n_pop × n_regions × n_years × n_sexes |
h_trans |
Steepness parameter by population and region; ignored if mean recruitment is specified | n_pop × n_regions |
NAA |
Numbers-at-age (fished) | n_pop × n_regions × (n_years + 1) × n_seas × n_ages × n_sexes |
NAA0 |
Numbers-at-age (unfished) | n_pop × n_regions × (n_years + 1) × n_seas × n_ages × n_sexes |
NAA_bef |
Numbers-at-age before movement is applied | n_pop × n_regions × (n_years + 1) × n_seas × n_ages × n_sexes |
NAA_aft |
Numbers-at-age after movement is applied | n_pop × n_regions × (n_years + 1) × n_seas × n_ages × n_sexes |
ZAA |
Total instantaneous mortality | n_pop × n_regions × n_years × n_seas × n_ages × n_sexes |
natmort |
Instantaneous natural mortality | n_pop × n_regions × n_years × n_ages × n_sexes |
bias_ramp |
Vector of bias ramp correction values applied to recruitment deviations | n_est_rec_devs |
Movement |
Movement (transition) matrix | n_pop × n_regions × n_regions × (n_years + n_proj_yrs_devs) × n_seas × n_ages × n_sexes |
Mrate |
Instantaneous movement rate matrix (CTMC movement only;
NULL otherwise) |
n_pop × n_regions × n_regions × (n_years + n_proj_yrs_devs) × n_seas × n_ages × n_sexes |
sgl_seas_spawning_movement |
Spawning movement matrix applied during the spawning event when
n_seas == 1 and n_pop > 1
|
n_pop × n_regions × n_regions × n_years × n_ages × n_sexes |
Fishery Processes
| Name | Description | Dimensions |
|---|---|---|
init_F |
Initial fishing mortality applied to equilibrium age structure | n_regions × n_seas × n_fish_fleets |
ln_sigmaC |
Log-scale standard deviation for the region-aggregated catch likelihood | n_regions × n_years × n_seas × n_fish_fleets |
ln_sigmaC_pop |
Log-scale standard deviation for the population-specific catch likelihood | n_pop × n_regions × n_years × n_seas × n_fish_fleets |
Fmort |
Fishing mortality scalar | n_regions × n_years × n_seas × n_fish_fleets |
dmr |
Discard mortality rate | n_regions × n_years × n_seas × n_fish_fleets |
tot_FAA |
Total fishing mortality at age (retained + dead discards) | n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets |
ret_FAA |
Retained fishing mortality at age | n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets |
disc_FAA |
Dead discard fishing mortality at age | n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets |
CAA |
Retained catch-at-age | n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets |
DAA |
Dead discarded catch-at-age | n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_fish_fleets |
CAL |
Retained catch-at-length | n_pop × n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets |
DAL |
Dead discarded catch-at-length | n_pop × n_regions × n_years × n_seas × n_lens × n_sexes × n_fish_fleets |
PredCatch |
Predicted retained catch (population-specific; summed across populations for aggregated likelihood) | n_pop × n_regions × n_years × n_seas × n_fish_fleets |
PredDiscard |
Predicted discards (population-specific; summed across populations for aggregated likelihood) | n_pop × n_regions × n_years × n_seas × n_fish_fleets |
PredFishIdx |
Predicted fishery index (population-specific; summed across populations for aggregated likelihood) | n_pop × n_regions × n_years × n_seas × n_fish_fleets |
fish_sel |
Total fishery selectivity (age-based) | n_pop × n_regions × (n_years + n_proj_yrs_devs) × n_seas × n_ages × n_sexes × n_fish_fleets |
ret_sel |
Retention selectivity (age-based) | n_pop × n_regions × (n_years + n_proj_yrs_devs) × n_seas × n_ages × n_sexes × n_fish_fleets |
fish_q |
Fishery catchability | n_regions × n_years × n_fish_fleets |
Survey Processes
| Name | Description | Dimensions |
|---|---|---|
PredSrvIdx |
Predicted survey index (population-specific; summed across populations for aggregated likelihood) | n_pop × n_regions × n_years × n_seas × n_srv_fleets |
srv_sel |
Survey selectivity (age-based) | n_pop × n_regions × (n_years + n_proj_yrs_devs) × n_seas × n_ages × n_sexes × n_srv_fleets |
srv_q |
Survey catchability | n_regions × n_years × n_srv_fleets |
SrvIAA |
Survey index-at-age | n_pop × n_regions × n_years × n_seas × n_ages × n_sexes × n_srv_fleets |
SrvIAL |
Survey index-at-length | n_pop × n_regions × n_years × n_seas × n_lens × n_sexes × n_srv_fleets |
Note: Length-based selectivity arrays (fish_sel_l,
ret_sel_l, srv_sel_l) are only reported when
the corresponding fish_selex_type,
ret_selex_type, or srv_selex_type equals 1,
and share the same dimension structure as their age-based counterparts
but replacing n_ages with n_lens and without
the population and season dimensions (since length-based selectivity
does not vary across those dimensions directly — population and season
specificity enters only upon conversion to age via the size-age
transition matrix).
Tagging Processes
| Name | Description | Dimensions |
|---|---|---|
pred_conv_tag_fish_recap |
Predicted conventional tag recaptures | conv_tag_max_liberty × n_seas × n_conv_tag_cohorts × n_pop × n_regions × n_ages × n_sexes × n_fish_fleets |
conv_tag_fish_avail |
Number of tagged fish available for recapture at each time step | (conv_tag_max_liberty + 1) × n_seas × n_conv_tag_cohorts × n_pop × n_regions × n_ages × n_sexes |
conv_tag_fish_reporting |
Tag reporting rate by region, year, and fleet | n_regions × n_years × n_fish_fleets |
Parameter Deviations
| Name | Description | Dimensions |
|---|---|---|
ln_RecDevs |
Log-scale recruitment deviations by population, region, and year (including projection years) | n_pop × n_regions × (n_est_rec_devs + n_proj_yrs_devs) |
move_devs |
Movement deviations by population, region pair, year, age, and sex (including projection years) | n_pop × n_regions × (n_regions - 1) × (n_years + n_proj_yrs_devs) × n_ages × n_sexes |
ln_fishsel_devs |
Log-scale fishery selectivity deviations by region, year, bin, sex, and fleet | n_regions × (n_years + n_proj_yrs_devs) × n_bins × n_sexes × n_fish_fleets |
ln_srvsel_devs |
Log-scale survey selectivity deviations by region, year, bin, sex, and fleet | n_regions × (n_years + n_proj_yrs_devs) × n_bins × n_sexes × n_srv_fleets |
Likelihoods
Region-aggregated likelihoods combine contributions across all
populations; population-specific likelihoods (_pop_) are
only computed when the corresponding UseCatch_pop,
UseDiscard_pop, UseFishIdx_pop,
UseSrvIdx_pop, or composition _pop use-arrays
contain active observations.
| Name | Description | Dimensions |
|---|---|---|
Catch_nLL |
Negative log-likelihood for region-aggregated catch | n_regions × n_years × n_seas × n_fish_fleets |
Catch_pop_nLL |
Negative log-likelihood for population-specific catch | n_pop × n_regions × n_years × n_seas × n_fish_fleets |
Discard_nLL |
Negative log-likelihood for region-aggregated discards | n_regions × n_years × n_seas × n_fish_fleets |
Discard_pop_nLL |
Negative log-likelihood for population-specific discards | n_pop × n_regions × n_years × n_seas × n_fish_fleets |
FishIdx_nLL |
Negative log-likelihood for region-aggregated fishery index | n_regions × n_years × n_seas × n_fish_fleets |
FishIdx_pop_nLL |
Negative log-likelihood for population-specific fishery index | n_pop × n_regions × n_years × n_seas × n_fish_fleets |
SrvIdx_nLL |
Negative log-likelihood for region-aggregated survey index | n_regions × n_years × n_seas × n_srv_fleets |
SrvIdx_pop_nLL |
Negative log-likelihood for population-specific survey index | n_pop × n_regions × n_years × n_seas × n_srv_fleets |
FishAgeComps_nLL |
Negative log-likelihood for region-aggregated fishery age compositions | n_regions × n_years × n_seas × n_sexes × n_fish_fleets |
FishAgeComps_pop_nLL |
Negative log-likelihood for population-specific fishery age compositions | n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets |
FishLenComps_nLL |
Negative log-likelihood for region-aggregated fishery length compositions | n_regions × n_years × n_seas × n_sexes × n_fish_fleets |
FishLenComps_pop_nLL |
Negative log-likelihood for population-specific fishery length compositions | n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets |
FishAgeComps_discard_nLL |
Negative log-likelihood for region-aggregated discard age compositions | n_regions × n_years × n_seas × n_sexes × n_fish_fleets |
FishAgeComps_discard_pop_nLL |
Negative log-likelihood for population-specific discard age compositions | n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets |
FishLenComps_discard_nLL |
Negative log-likelihood for region-aggregated discard length compositions | n_regions × n_years × n_seas × n_sexes × n_fish_fleets |
FishLenComps_discard_pop_nLL |
Negative log-likelihood for population-specific discard length compositions | n_pop × n_regions × n_years × n_seas × n_sexes × n_fish_fleets |
SrvAgeComps_nLL |
Negative log-likelihood for region-aggregated survey age compositions | n_regions × n_years × n_seas × n_sexes × n_srv_fleets |
SrvAgeComps_pop_nLL |
Negative log-likelihood for population-specific survey age compositions | n_pop × n_regions × n_years × n_seas × n_sexes × n_srv_fleets |
SrvLenComps_nLL |
Negative log-likelihood for region-aggregated survey length compositions | n_regions × n_years × n_seas × n_sexes × n_srv_fleets |
SrvLenComps_pop_nLL |
Negative log-likelihood for population-specific survey length compositions | n_pop × n_regions × n_years × n_seas × n_sexes × n_srv_fleets |
M_nLL |
Negative log-likelihood (prior) for natural mortality | scalar |
Fmort_nLL |
Negative log-likelihood (penalty) for fishing mortality deviations | n_regions × n_years × n_seas × n_fish_fleets |
dmr_nLL |
Negative log-likelihood (penalty) for discard mortality rate deviations | n_regions × n_years × n_seas × n_fish_fleets |
Rec_nLL |
Negative log-likelihood (penalty) for recruitment deviations | n_pop × n_regions × n_est_rec_devs |
Init_Rec_nLL |
Negative log-likelihood (penalty) for initial age deviations | n_pop × n_regions × (n_ages - 2) |
conv_fish_tag_nLL |
Negative log-likelihood for conventional tag recaptures | conv_tag_max_liberty × n_seas × n_conv_tag_cohorts × n_regions × n_fish_fleets |
h_nLL |
Negative log-likelihood (prior) for steepness | scalar |
fish_q_nLL |
Negative log-likelihood (prior) for fishery catchability | scalar |
sel_nLL |
Negative log-likelihood (penalty/prior) for selectivity | scalar |
srv_q_nLL |
Negative log-likelihood (prior) for survey catchability | scalar |
Movement_nLL |
Negative log-likelihood (penalty/prior) for movement | scalar |
TagRep_nLL |
Negative log-likelihood (prior) for tag reporting rate | scalar |
rec_prop_nLL |
Negative log-likelihood (prior) for recruitment proportions | scalar |
jnLL |
Joint negative log-likelihood | scalar |
Derived Quantities (also reported via ADREPORT)
| Name | Description | Dimensions |
|---|---|---|
Total_Biom |
Total biomass | n_pop × n_regions × n_years |
SSB |
Spawning stock biomass by population and region | n_pop × n_regions × n_years |
eff_SSB |
Effective spawning stock biomass at each population’s natal region, including stray contributions from other populations | n_pop × n_years |
Dynamic_SSB0 |
Unfished spawning stock biomass by population and region | n_pop × n_regions × n_years |
Aggregated_SSB |
Spawning stock biomass summed across populations and regions | n_years |
Dynamic_Aggregated_SSB0 |
Unfished spawning stock biomass summed across populations and regions | n_years |
Rec |
Recruitment by population and region | n_pop × n_regions × n_years |
Note: All derived quantities are additionally reported in log space
via ADREPORT (e.g., log_SSB,
log_eff_SSB, log_Total_Biom, etc.) to
facilitate delta-method standard error estimation. A small constant
(1e-5) is added before log transformation to avoid numerical issues in
regions or populations with zero biomass.