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The 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