--- title: "Description of Model Report" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{d_model_report} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- ```{r, include = FALSE} knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ``` The following tables describes all elements contained within `obj$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. ## 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` |