[Feature]: Might want to add mature_num and mature_bio for time-series plots

[e-perl-NOAA]

Describe the feature request.

Might be good to add mature_num and mature_bio as an option for r4ss time-series plots.

Stock Synthesis issue #502
Stock Synthesis branch associated with issue
Adding mature_bio and mature_num to time-series report PR

Describe alternatives you have considered

Not including them, others would have to create their own plots that include mature_bio and mature_num.

Statistical validity, if applicable

No response

Describe if this is needed for a management application

No response

Additional context

No response

Code of Conduct

• I agree to follow this project's Code of Conduct

[e-perl-NOAA]

Rick sees no need to add these plots into r4ss.

[chantelwetzel-noaa]

This new output would have really come in handy for sablefish since there were multiple questions about the proportion of the population mature vs. immature given the recent high recruitments. I think adding a very basic time series plot of the proportion mature in numbers and biomass could be quite useful for these types of situations. @iantaylor-NOAA what do you think? I will note that this would also be a very simple plot for users to create themselves if desired.

[iantaylor-NOAA]

That is makes sense to me.
I think for models with a fecundity relationship where spawning biomass != mature biomass it might be useful to have a time series plot of mature_bio and then for all models it could be good to have a plot of the proportion mature (mature_bio / Bio_all). Getting proportion mature by numbers may require calculating total numbers in the population. @chantelwetzel-noaa, do we really need that separately from the proportion mature by biomass?

[Rick-Methot-NOAA]

seems easier to do %mature by numbers in SS3. Would be easy to pair that calc with the recently added calc of sex ratio.

[chantelwetzel-noaa]

I think we could also collapse the numbers-at-age matrix across ages since that is already outputted to calculate the percent mature in numbers. I think providing this in terms of numbers can be more useful to understand the magnitude of recent recruitments to the population as a whole. For sablefish, the proportion in terms of numbers showed the potential impact on maturing and growing young recruits since looking at this in terms of biomass loses some of the signal given the difference in mass between old and young fish.

[iantaylor-NOAA]

@Rick-Methot-NOAA, I think it makes sense to add the calculations for mature fraction in both numbers and biomass inside of SS3 and report as additional TIME_SERIES columns. I just realized that the mature biomass is female only so would need to be compared to female-only total biomass, which is also not currently output, rather than Bio_all. If it's in TIME_SERIES, that means these proportions would be by area in spatial models, which I think is fine.

We could sum across the numbers at age table in r4ss but would also need to aggregate across morphs and birth seasons and other dimensions that are reported in NUMBERS_AT_AGE but not TIME_SERIES, so I'm happy to skip that complexity.

[Rick-Methot-NOAA]

There is no SS3 concept of %mature for males. Maturity is defined only for females.

[iantaylor-NOAA]

Ignoring male maturity makes sense, but now I'm wondering if it's better to think about %mature as fem. mature / fem. total or if it's better to think about %mature as fem. mature / fem.+male total.

In cases where the fraction female gets reduced due to differences in growth and/or selectivity, it might be useful to see what a small proportion of the total of both sexes are mature females. That second approach (relative to total for both sexes) would probably be the only way you could calculate %mature for models with hermaphroditism.

[Rick-Methot-NOAA]

the hermaphroditism calculations already assume all males are mature and there is an option to define SSB as mature females plus all males.

For hermaphroditism, males "move" from the male container to the female container (or vice versa). So the %males is dynamic over time as fishing affects the population.
For maturity in SS3, a defined fraction of the females are mature and rest are immature.
in the CASAL model, maturity is implemented the way that SS3 does herm. So, there is an immature container and some fish move from immature to mature. That is logical except for environmental influence on maturity could change annually causing some fish to regress to immature.

[Rick-Methot-NOAA]

Here is the code that calcs sexratio on-the-fly for the biology-at-age-in-endyear table

https://vscode.dev/github/nmfs-stock-synthesis/stock-synthesis/blob/main/SS_write_report.tpl#L3688-L3689

so it would be easy to create another table formatted just like the current numbers-at-age table and output %female to that table.

[iantaylor-NOAA]

@chantelwetzel-noaa, could you share the sablefish model files so I could explore some options for plotting %mature? If you want to try out some plots, all the better.