9_4_Figures_Assessment.Rmd

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## Model Results Figures

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<!-- ***********History of modeling approaches FIGURES******************* --> 
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<!-- ****************STAR PANEL Recommendations FIGURES******************** --> 
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<!-- ****************Model description section FIGURES********************* --> 
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<!-- *********************BASE MODEL FIGURES******************************* -->
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<!-- ***********MODEL 1 BASE MODEL FIGURES********************************* --> 

### Growth and Selectivity

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\noindent
\begin{minipage}{\linewidth}% to keep image and caption on one page
\makebox[\linewidth]{%        to center the image
  \includegraphics[keepaspectratio=true,width=6in]{r4ss/plots_mod1/bio3_sizeatage_plus_WT_and_MAT.png}}
\captionof{figure}{Estimated length-at-age for female and male Big Skate (top left panel). }\label{fig:growth}%
\begin{centering}
Shaded areas indicate 95\% intervals for distribution of lengths at each age. Values represent beginning-of-year growth.  Weight (thick line) and maturity (thin line) are shown in the top-right and lower-left panels as a function of length and age, respectively, where the values-at-age are calculated by mapping the length-based relationships through the estimated distribution of length at each age.
\end{centering}
\end{minipage}

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<!-- ![Estimated length-at-age for female and male `r spp` (top left panel). Shaded areas indicate 95% intervals for distribution of lengths at each age. Values represent beginning-of-year growth. Weight (thick line) and maturity (thin line) are shown in the top-right and lower-left panels as a function of length and age, respectively, where the values-at-age are calculated by mapping the length-based relationships through the estimated distribution of length at each age.\label{fig:growth}](r4ss/plots_mod1/bio3_sizeatage_plus_WT_and_MAT.png) -->


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![Estimates of natural morality and catchability of the WCGBT Survey with normal approximations to their uncertainty compared to their prior distributions. \label{fig:fit_to_priors}](Figures/fit_to_priors.png)

![Selectivity at length for all of the fleets in the base model. Female selectivity is shown in the solid lines and males in the dashed lines. \label{fig:sel01_multiple_fleets_length1}](r4ss/plots_mod1/sel01_multiple_fleets_length1.png)

![Selectivity at age derived from the combination of selectivity-at-length (shown above) and the estimated distribution of length at each age for all of the fleets in the base model. Female selectivity is shown in the solid lines and males in the dashed lines. \label{fig:sel02_multiple_fleets_age2}](r4ss/plots_mod1/sel02_multiple_fleets_age2.png)

![Female fishery selectivity and retention in 2018 with associated derived quantities. \label{fig:sel09_len_flt1sex1}](r4ss/plots_mod1/sel09_len_flt1sex1.png)

![Time-varying retention for the fishery (left) with the time-series of asymptotic retention rates (right). \label{fig:retention}](Figures/retention.png)



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### Fits to the Data

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\noindent
\begin{minipage}{\linewidth}% to keep image and caption on one page
\makebox[\linewidth]{%        to center the image
  \includegraphics[keepaspectratio=true,width=6in]{r4ss/plots_mod1/index2_cpuefit_WCGBT Survey.png}}
\captionof{figure}{Fit to index data for WCGBT Survey.}\label{fig:index2_cpuefit_WCGBTS}%
\begin{centering}
Lines indicate 95\% uncertainty interval around index values. Thicker lines indicate input uncertainty before addition of estimated additional uncertainty parameter. The blue line indicates the model estimate.
\end{centering}
\end{minipage}

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<!-- ![Fit to index data for WCGBT Survey. Lines indicate 95% uncertainty interval around index values. Thicker lines indicate input uncertainty before addition of estimated additional uncertainty parameter. The blue line indicates the model estimate.\label{fig:index2_cpuefit_WCGBTS}](r4ss/plots_mod1/index2_cpuefit_WCGBT Survey.png) -->

![Fit to index data for Triennial Survey. Lines indicate 95% uncertainty interval around index values. Thicker lines indicate input uncertainty before addition of estimated additional uncertainty parameter. The blue line indicates the model estimate with a change between 1992 and 1995 associated with the estimated change in catchability.\label{fig:index2_cpuefit_Triennial}](r4ss/plots_mod1/index2_cpuefit_Triennial Survey.png)



![Fits to length composition data, aggregated across time by fleet. \label{fig:comp_lenfit_aggregated_across_time}](r4ss/plots_mod1/comp_lenfit__aggregated_across_time.png)

![Pearson residuals for length composition data for all years and fleets, with females in red and males in blue. Closed bubbles are positive residuals (observed > expected) and open bubbles are negative residuals (observed < expected). \label{fig:comp_lenfit__multi-fleet_comparison}](r4ss/plots_mod1/comp_lenfit__multi-fleet_comparison.png)

![Pearson residuals for the fit to conditional age-at-length data from the fishery. Closed bubbles are positive residuals (observed > expected) and open bubbles are negative residuals (observed < expected). \label{fig:age_fit_fishery}](r4ss/plots_mod1/comp_condAALfit_residsflt1mkt2.png)

![Pearson residuals for the fit to conditional age-at-length data from the WCGBT Survey. Closed bubbles are positive residuals (observed > expected) and open bubbles are negative residuals (observed < expected). \label{fig:age_fit_WCGBTS}](r4ss/plots_mod1/comp_condAALfit_residsflt5mkt0.png)

<!-- ***********Implied fits to the sex ratios ************************** --> 

![Observed sex ratios (points) from the fishery length composition data with 75% intervals (vertical lines) calculated as a Jeffreys interval based on the adjusted input sample size. The model expectation is shown in the blue line.\label{fig:sexratio_len_flt1mkt2}](r4ss/plots_mod1/sexratio_len_flt1mkt2.png)

![Observed sex ratios (points) from the WCGBT Survey length composition data with 75% intervals (vertical lines) calculated as a Jeffreys interval based on the adjusted input sample size. The model expectation is shown in the blue line.\label{fig:sexratio_len_flt5mkt0}](r4ss/plots_mod1/sexratio_len_flt5mkt0.png)

<!-- ***********Fits to the discards and mean body weight *************** --> 
![Fit to the discard fraction estimates. Points are model estimates with 95% uncertainty intervals. The model estimate is shown in the blue lines.\label{fig:discard_fitFishery}](r4ss/plots_mod1/discard_fitFishery.png)

![Fit to the mean weight of the discards. Points are model estimates with 95% uncertainty intervals. The model estimate is shown in the blue lines.\label{fig:bodywt_fit_fltFishery}](r4ss/plots_mod1/bodywt_fit_fltFishery.png)

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<!-- ****************Time series FIGURES******************* -->
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### Time Series Figures

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\begin{figure}[!h]
\begin{centering}
\includegraphics{r4ss/plots_mod1/ts7_Spawning_biomass_(mt)_with_95_asymptotic_intervals_intervals.png}
\caption{Estimated spawning biomass (mt) with approximate 95\% asymptotic intervals.}\label{fig:ts7_Spawning_biomass_(mt)_with_95_asymptotic_intervals_intervals}
\end{centering}
\end{figure}

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<!-- ![Estimated spawning biomass (mt) with approximate 95% asymptotic intervals. \label{fig:ts7_Spawning_biomass_(mt)_with_95_asymptotic_intervals_intervals}](r4ss/plots_mod1/ts7_Spawning_biomass_(mt)_with_95_asymptotic_intervals_intervals.png) -->


![Estimated %unfished with approximate 95% asymptotic intervals. \label{fig:ts9_unfished_with_95_asymptotic_intervals_intervals}](r4ss/plots_mod1/ts9_unfished_with_95_asymptotic_intervals_intervals.png)


<!-- ![Estimated time-series of recruitment deviations for `r spp` with 95% intervals. \label{fig:recdevs2_withbars}](r4ss/plots_mod1/recdevs2_withbars.png) -->


![Estimated time-series of recruitment for `r spp`. \label{fig:ts11_Age-0_recruits_(1000s)_with_95_asymptotic_intervals}](r4ss/plots_mod1/ts11_Age-0_recruits_(1000s)_with_95_asymptotic_intervals.png)


![Estimated recruitment and the assumed stock-recruit relationship. \label{fig:SR_curve2}](r4ss/plots_mod1/SR_curve2.png)

<!-- removing total catch figure which is redundant with new figure added earlier -->
<!-- ![Estimated total catch including discards estimated within the model. The historical discards shown in green have been scaled to account for an assumed 50% discard mortality but the discards in the recent period show both live and dead discards. \label{fig:catch_total_plot}](r4ss/plots_mod1/catch5 total catch (including discards) stacked.png) -->

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<!-- ****************Uncertainty and Sensitivity FIGURES******************* -->
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### Sensitivity Analyses and Retrospectives

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\noindent
\begin{minipage}{\linewidth}% to keep image and caption on one page
\makebox[\linewidth]{%        to center the image
  \includegraphics[keepaspectratio=true,width=6in]{Figures/sens.sel_and_Q_compare1_spawnbio.png}}
\captionof{figure}{Time series of spawning biomass (mt) estimated in sensitivity analyses related to selectivity and catchability.}\label{fig:Sensitivity_sel_and_Q}%
\begin{centering}.
\end{centering}
\end{minipage}

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<!-- ![Time series of spawning biomass (mt) estimated in sensitivity analyses related to selectivity and catchability. \label{fig:Sensitivity_sel_and_Q}](Figures/sens.sel_and_Q_compare1_spawnbio.png) -->

![Time series of spawning biomass (mt) estimated in sensitivity analyses related to biology. \label{fig:Sensitivity_bio}](Figures/sens.bio_compare1_spawnbio.png)

![Comparison of the estimated growth curves from the sensitivities analyses. The increase at age 20 in the von Bertalanffy and Richards growth models is an adjustment to account for average size in the plus group based on an assumed exponential decay of the numbers at age beyond age 20.\label{fig:growth_curve_comparison}](Figures/growth_curve_comparison.png)

![Time series of spawning biomass (mt) estimated in sensitivity analyses related to data weighting and recruitment. \label{fig:Sensitivity_misc}](Figures/sens.misc_compare1_spawnbio.png)

![Fit to the WCGBT Survey estimated in the sensitivity analyses related to data weighting and recruitment. \label{fig:Sensitivity_misc2}](Figures/sens.misc_compare11_indices_flt5.png)


![Time series of spawning biomass (mt) estimated in sensitivity analyses related to historic catch and discards. \label{fig:Sensitivity_catch}](Figures/sens.catch_compare1_spawnbio.png)

![Fit to the WCGBT Survey estimated in the sensitivity analyses related to historic catch and discards. \label{fig:Sensitivity_catch2}](Figures/sens.catch_compare11_indices_flt5.png)

![Catch by category for the sensitivity analysis where multipliers on historical discards were estimated. The estimated time series including the multipliers is shown in the solid green line and the input values in the base model are shown in the dashed green line. \label{fig:catch_multiplier_catch_comparison}](Figures/catch_multiplier_catch_comparison.png)

![Comparison of the instantaneous rate of fishing mortality for fully selected ages for the base model and the sensitivity analyses where historic catch was adjusted either by the estimated multipliers or to match the time series of F for Petrale Sole. The Petrale Sole time series is shown for comparison, where the F for Petrale divided by 2.54 to match the estimated Big Skate F.  The 1950--1994 period in which the Big Skate F was fit to the Petrale F is shaded in gray. \label{fig:F_comparison}](Figures/F_comparison.png)

![Comparison of total mortality for the base model and the sensitivity analyses where historic catch was adjusted either by the estimated multipliers or to match the time series of F for Petrale Sole. Total mortality shown here includes discards with the discard rate applied. \label{fig:adjusted_historic_catch_comparison}](Figures/adjusted_historic_catch_comparison.png)

![Time series of fraction unfished with approximate 95% asymptotic intervals estimated for the base model and the sensitivity analyses where historic catch was adjusted either by the estimated multipliers or to match the time series of F for Petrale Sole. \label{fig:Sensitivity_catch3}](Figures/sens.catchB_compare4_Bratio_uncertainty.png)




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<!-- *****************Retrospective analysis FIGURES*********************** -->
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<!-- ***********MODEL 1 Retrospective analysis FIGURE********************** --> 


![Time series of spawning biomass (mt) with approximate 95% asymptotic intervals estimated in retrospective analyses in which the final 5 years of data are successively removed from the model.\label{fig:retro}](Figures/retro_compare2_spawnbio_uncertainty.png)

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<!-- ******************Likelihood profile FIGURES************************** --> 
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### Likelihood Profiles

<!-- ***********R0 Likelihood profile FIGURES****************************** --> 

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\noindent
\begin{minipage}{\linewidth}% to keep image and caption on one page
\makebox[\linewidth]{%        to center the image
  \includegraphics[keepaspectratio=true,width=6in]{Figures/profile_logR0.png}}
\captionof{figure}{Likelihood profile over the log of equilibrium recruitment ($R_0$).}\label{fig:profile_logR0}%
\begin{centering}.
\end{centering}
\end{minipage}

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<!-- ![Likelihood profile over the log of equilibrium recruitment ($R_0$).\label{fig:profile_logR0}](Figures/profile_logR0.png) -->

![Time series of spawning biomass (mt) estimated for the models included in the profile over the log of equilibrium recruitment ($R_0$).\label{fig:profile_R0_compare1_spawnbio}](Figures/profile_R0_compare1_spawnbio.png)



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<!-- ***********q Likelihood profile FIGURES****************************** --> 

![Likelihood profile over the catchability of the WCGBT survey ($q$) without the addition of the prior likelihood for q (the prior on natural mortality remains).\label{fig:profile_logQ_noprior}](Figures/profile_Q_noprior.png)

![Likelihood profile over the catchability of the WCGBT survey ($q$) including the prior likelihood contribution.\label{fig:profile_logQ}](Figures/profile_Q.png)

![Time series of spawning biomass (mt) estimated for the models included in the profile over the catchability of the WCGBT Survey ($q$).\label{fig:profile_Q_compare1_spawnbio}](Figures/profile_Q_compare1_spawnbio.png)


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<!-- ***********h Likelihood profile FIGURES******************************* -->

![Likelihood profile over stock-recruit steepness ($h$). \label{fig:profile_h}](Figures/profile_h.png)

![Time series of spawning biomass (mt) estimated for the models included in the profile over stock-recruit steepness ($h$). \label{fig:profile_h_compare1_spawnbio}](Figures/profile_h_compare1_spawnbio.png)


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<!-- ***********M Likelihood profile FIGURES******************************* -->

![Likelihood profile over natural mortality ($M$). \label{fig:profile_M}](Figures/profile_M.png)

![Time series of spawning biomass (mt) estimated for the models included in the profile over natural mortality ($M$). \label{fig:profile_M_compare1_spawnbio}](Figures/profile_M_compare1_spawnbio.png)

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### Reference Points and Forecasts

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<!-- *********************REFERENCE POINTS FIGURES************************* --> 
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<!-- ***********MODEL 1 REFERENCE POINTS FIGURES*************************** --> 

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\begin{figure}[!h]
\begin{centering}
\includegraphics{Figures/yield2_yield_curve_with_refpoints.png}
\caption{Equilibrium yield curve for the base case model. Values are based on the fishery selectivity and with steepness fixed at 0.4.}\label{fig:yield1_yield_curve}
\end{centering}
\end{figure}


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<!-- *************************FORECAST FIGURES***************************** --> 
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