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.
| Name | Description |
|---|---|
R0 |
Global mean or virgin recruitment parameter |
Rec_trans_prop |
Recruitment apportionment parameters, length of n_regions |
h_trans |
Steepness parameter by region; not used if mean recruitment is specified |
NAA |
Numbers-at-age array:
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_ages × n_sexes
|
init_F |
Initial fishing mortality applied to equilibrium age structure |
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_ages × n_sexes × n_fish_fleets
|
fish_sel_l |
Fishery length-selectivity:
n_regions × n_years × n_lens × n_sexes × n_fish_fleets
|
fish_q |
Fishery catchability:
n_regions × n_years × n_fish_fleets
|
PredSrvIdx |
Predicted survey index:
n_regions × n_years × n_srv_fleets
|
srv_sel |
Survey age-selectivity:
n_regions × n_years × n_ages × n_srv_fleets × n_sexes
|
srv_sel_l |
Survey length-selectivity:
n_regions × n_years × 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
|
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
|
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 |
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 |
fish_q_nLL |
Negative log-likelihood for fishery catchability |
sel_nLL |
Negative log-likelihood for selectivity |
srv_q_nLL |
Negative log-likelihood for survey catchability |
Movement_nLL |
Negative log-likelihood for movement |
TagRep_nLL |
Negative log-likelihood for tag reporting |
jnLL |
Joint negative log-likelihood |
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
|