Description of Model Report
d_model_report.RmdThe following tables describes 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.
Biological Processes
| Name | Description | Dimensions |
|---|---|---|
R0 |
Global mean or virgin recruitment parameter | scalar |
Rec_trans_prop |
Recruitment apportionment parameters | n_regions |
sexratio |
Recruitment sex ratio | n_regions × n_years × n_sexes |
h_trans |
Steepness parameter by region; ignored if mean recruitment specified | n_regions |
NAA |
Numbers-at-age | n_regions × n_years × n_ages × n_sexes |
NAA0 |
Unfished Numbers-at-age | n_regions × n_years × n_ages × n_sexes |
ZAA |
Total instantaneous mortality | n_regions × n_years × n_ages × n_sexes |
natmort |
Instantaneous natural mortality | n_regions × n_years × n_ages × n_sexes |
bias_ramp |
Vector of bias ramp values | n_years |
Movement |
Movement array | n_regions × n_regions × (n_years + n_proj_yrs_devs) × n_ages × n_sexes |
Fishery Processes
| Name | Description | Dimensions |
|---|---|---|
init_F |
Initial fishing mortality applied to equilibrium age structure | n_regions × n_ages × n_sexes |
ln_sigmaC |
Log standard deviation of regional catches | n_regions × n_years × n_fish_fleets |
ln_sigmaC_agg |
Log standard deviation for aggregated catch | n_years × n_fish_fleets |
Fmort |
Fishing mortality rate | n_regions × n_years × n_fish_fleets |
FAA |
Fishing mortality at age | n_regions × n_years × n_ages × n_sexes × n_fish_fleets |
CAA |
Catch-at-age | n_regions × n_years × n_ages × n_sexes × n_fish_fleets |
CAL |
Catch-at-length | n_regions × n_years × n_lens × n_fish_fleets |
PredCatch |
Predicted catch | n_regions × n_years × n_fish_fleets |
PredFishIdx |
Predicted fishery index | n_regions × n_years × n_fish_fleets |
fish_sel |
Fishery age-selectivity | n_regions × (n_years + n_proj_yrs_devs) × n_ages × n_sexes × n_fish_fleets |
fish_sel_l |
Fishery length-selectivity | n_regions × (n_years + n_proj_yrs_devs) × n_lens × 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 | n_regions × n_years × n_srv_fleets |
srv_sel |
Survey age-selectivity | n_regions × (n_years + n_proj_yrs_devs) × n_ages × n_srv_fleets × n_sexes |
srv_sel_l |
Survey length-selectivity | n_regions × (n_years + n_proj_yrs_devs) × n_lens × n_srv_fleets × n_sexes |
srv_q |
Survey catchability | n_regions × n_years × n_srv_fleets |
SrvIAA |
Survey index-at-age | n_regions × n_years × n_ages × n_sexes × n_srv_fleets |
SrvIAL |
Survey index-at-length | n_regions × n_years × n_lens × n_sexes × n_srv_fleets |
Tagging Processes
| Name | Description | Dimensions |
|---|---|---|
Pred_Tag_Recap |
Predicted tag recaptures | n_tag_liberty × n_years × n_regions × n_ages × n_sexes |
Tags_Avail |
Available tags | (n_tag_liberty + 1) × n_years × n_regions × n_ages × n_sexes |
Tag_Reporting |
Tag reporting rate | n_regions × n_years |
Likelihoods
| Name | Description | Dimensions |
|---|---|---|
Catch_nLL |
Negative log-likelihood for catch | n_regions × n_years × n_fish_fleets |
FishIdx_nLL |
Negative log-likelihood for fishery index | n_regions × n_years × n_fish_fleets |
SrvIdx_nLL |
Negative log-likelihood for survey index | n_regions × n_years × n_srv_fleets |
FishAgeComps_nLL |
Negative log-likelihood for fish age composition | n_regions × n_years × n_sexes × n_fish_fleets |
SrvAgeComps_nLL |
Negative log-likelihood for survey age composition | n_regions × n_years × n_sexes × n_srv_fleets |
FishLenComps_nLL |
Negative log-likelihood for fish length composition | n_regions × n_years × n_sexes × n_fish_fleets |
SrvLenComps_nLL |
Negative log-likelihood for survey length composition | n_regions × n_years × n_sexes × n_srv_fleets |
M_nLL |
Negative log-likelihood for natural mortality | scalar |
Fmort_nLL |
Negative log-likelihood for fishing mortality | n_regions × n_years × n_fish_fleets |
Rec_nLL |
Negative log-likelihood for recruitment | n_regions × n_years |
Init_Rec_nLL |
Negative log-likelihood for initial recruitment | n_regions × (n_ages - 2) |
Tag_nLL |
Negative log-likelihood for tag recapture | n_tag_liberty × n_years × n_regions × n_ages × n_sexes |
h_nLL |
Negative log-likelihood for steepness | scalar |
fish_q_nLL |
Negative log-likelihood for fishery catchability | scalar |
sel_nLL |
Negative log-likelihood for selectivity | scalar |
srv_q_nLL |
Negative log-likelihood for survey catchability | scalar |
Movement_nLL |
Negative log-likelihood for movement | scalar |
TagRep_nLL |
Negative log-likelihood for tag reporting | scalar |
Rec_prop_nLL |
Negative log-likelihood for recruitment proportions | scalar |
jnLL |
Joint negative log-likelihood | scalar |
Parameter Deviations
| Name | Description | Dimensions |
|---|---|---|
ln_RecDevs |
Log recruitment deviations by region and year (including projected years). | n_regions × (n_years + n_proj_yrs_devs) |
logit_move_devs |
Logit-scale movement deviations among regions, by year, age, and sex. | n_regions × (n_regions - 1) × (n_years + n_proj_yrs_devs) × n_ages × n_sexes |
ln_fishsel_devs |
Log-scale deviations in fishery selectivity-at-length or age, by fleet. | n_regions × (n_years + n_proj_yrs_devs) × bins × n_sexes × n_fish_fleets |
ln_srvsel_devs |
Log-scale deviations in survey selectivity-at-length or age, by fleet. | n_regions × (n_years + n_proj_yrs_devs) × bins × n_sexes × n_srv_fleets |
Derived Quantities
| Name | Description | Dimensions |
|---|---|---|
Total_Biom |
Total biomass | n_regions × n_years |
SSB |
Spawning stock biomass | n_regions × n_years |
Aggregated_SSB |
Aggregated spawning stock biomass | n_years |
Dynamic_SSB0 |
Unfished spawning stock biomass | n_regions × n_years |
Dynamic_Aggregated_SSB0 |
Unfished aggregated spawning stock biomass | n_years |
Rec |
Recruitment | n_regions × n_years |