Figure S1. Stock Status Relative to Blim (Solid Lines), and 95% Confidence Intervals (Dashed

Figure S1. Stock status relative to Blim (solid lines), and 95% confidence intervals (dashed lines), for the northern cod (Gadus morhua) S2 (better catch) model formulation. Two y-axis scales are used and the solid vertical line indicates where the change occurs.

Figure S2. Stock status relative to Blim (solid lines), and 95% confidence intervals (dashed lines), for the northern cod (Gadus morhua) S3 (dome q) model formulation. Two y-axis scales are used and the solid vertical line indicates where the change occurs.

Figure S3. Stock status relative to Blim (solid lines), and 95% confidence intervals (dashed lines), for the northern cod (Gadus morhua) S4 (no change in inshore/offshore distribution) model formulation. Two y-axis scales are used and the solid vertical line indicates where the change occurs.

Figure S4. A comparison of stock status relative to Blim for the four northern cod (Gadus morhua) model formulations: base, S2 (better catch), S3 (dome q), and S4 (no change in inshore/offshore distribution). Two y-axis scales are used and the solid vertical line indicates where the change occurs.

Figure S5. Comparisons of base and S4 model results (solid lines), for (a) SSB, (b) recruits per spawner, (c) F, and (d) M. Mortality rates are stock size-weighted averages for ages 5-12. Dashed lines indicate 95% confidence intervals. Two y-axis scales are used in (a) and the solid vertical line indicates where the change occurs.

Figure S6. Comparisons of base and S2 model (i.e. better catch) results (solid lines), for (a) SSB, (b) recruits per spawner, (c) F, and (d) M. Mortality rates are stock size-weighted averages for ages 5-12. Dashed lines indicate 95% confidence intervals. Two y-axis scales are used in (a) and the solid vertical line indicates where the change occurs.

Figure S7. Comparisons of base and S3 model (i.e. dome q) results (solid lines), for (a) SSB, (b) recruits per spawner, (c) F, and (d) M. Mortality rates are stock size-weighted averages for ages 5-12. Dashed lines indicate 95% confidence intervals. Two y-axis scales are used in (a) and the solid vertical line indicates where the change occurs.

Figure S8. Illustration of the S2 model (i.e. better catch) estimates of M.

Figure S9. Illustration of the S3 model (i.e. dome q) estimates of M.

Figure S10. Illustration of the S4 model (i.e. no change in inshore/offshore distribution) estimates of M.

Figure S11. Observed (red lines) and base model predicted (black lines) catch proportions at age. Each panel shows results for an age which is listed in the top strip. The y-axis scale varies for each panel.

Figure S12. DFO RV survey standardized residuals from the base model. These residuals are the log observed survey catch minus the estimate and divided by the survey estimated standard deviation. From top to bottom the panels show residuals versus year, cohort, age, and predicted value. The dashed line in the top panel indicates the average residual each year and the plotting symbols indicate age.

Figure S13. Matrix plot of base model DFO RV standardized log residuals. Red +’s are positive, black ×’s are negative, and grey ×’s are residuals when indices are zero. The sizes of plotting symbols are proportional to the absolute value of the residuals. Blanks indicate missing values.

Figure S14. Observed (circles) versus base model predicted (lines) Smith Sound acoustic biomass estimates. Vertical grey line segments indicate 95% confidence intervals based on survey standard errors.

Figure S15. Observed (red lines) and base model predicted (black lines) Smith Sound trawl catches for age compositions. Each panel shows results for an age which is listed in the top strip. The y-axis scale varies for each panel.

Figure S16. Observed (circles) and base model predicted (lines) number of reported tag recaptures. Each panel shows results for a release experiment (year and experiment number) which is listed at the right-hand size. The y-axis scale varies for each panel.

Figure S21. Five year S2 model (better catch) projections of stock status. Dashed lines indicate 95% confidence intervals for projections based on status quo model predicted catch. Panel (a): Projections for status quo catch (heavy solid line) and a 50% increase or decrease in catch (thin solid lines). Circles indicate status quo CV’s. The grey horizontal dashed line indicates a CV = 30% and projections with CV’s > 30% should be interpreted with more caution. Panel (b): Projections of SSB (heavy solid line) and the percent change in SSB from 2012 (grey line) for status quo catch. The grey horizontal dashed line indicates a 50% increase.

Figure S22. Five year S3 model (dome q) projections of stock status. Dashed lines indicate 95% confidence intervals for projections based on status quo model predicted catch. Panel (a): Projections for status quo catch (heavy solid line) and a 50% increase or decrease in catch (thin solid lines). Circles indicate status quo CV’s. The grey horizontal dashed line indicates a CV = 30% and projections with CV’s > 30% should be interpreted with more caution. Panel (b): Projections of SSB (heavy solid line) and the percent change in SSB from 2012 (grey line) for status quo catch. The grey horizontal dashed line indicates a 50% increase.

Figure S23. Five year S4 model (no change in inshore/offshore distribution) projections of stock status. Dashed lines indicate 95% confidence intervals for projections based on status quo model predicted catch. Panel (a): Projections for status quo catch (heavy solid line) and a 50% increase or decrease in catch (thin solid lines). Circles indicate status quo CV’s. The grey horizontal dashed line indicates a CV = 30% and projections with CV’s > 30% should be interpreted with more caution. Panel (b): Projections of SSB (heavy solid line) and the percent change in SSB from 2012 (grey line) for status quo catch. The grey horizontal dashed line indicates a 50% increase.

Figure S24. Comparisons of four northern cod (Gadus morhua) projections of stock status based on status quo model predicted catch. The models are: base, S2 (better catch), S3 (dome q), and S4 (no change in inshore/offshore distribution.

Figure S25. Base model self-test simulation results for (a) SSB, (b) average F, (c) percent bias in SSB, and (d) percent bias in average F. Percent bias is based on the difference between the simulation average, or percentiles, and the true values, divided by true values. Dashed lines indicate 5th and 95th percentiles of simulation results. The number of converged simulations was 1141.

Figure S26. Base model self-test simulation results for some model parameters. Simulations results are plotted as kernel densities using the vioplot R package (Adler, 2005). Values used to generate simulation data are indicated by X’s.

References

Adler, D. 2005. vioplot: Violin plot. R package version 0.2. http://wsopuppenkiste.wiso.uni goettingen.de/~dadler