Ian Taylor

Support use of platoons by providing plots showing distribution of length-at-age

1

The biology plots for models with platoons show the growth curve associated with each platoon but there is no figure showing how these growth curves compare to each other. Also...

[Bug]: rho parameters not impacting semi-parametric (2D-AR) selectivity when multiple sigma values are used

5

### Describe the bug This issue was found in discussion with @rosana-ourens who successfully set up a model with semi-parametric selectivity where there were multiple sigma values to allow more...

revise RECR_DIST output to work better for models without 50/50 sex ratio at recruitment?

2

The 2nd dimension of the `recr_dist` array has length equal to the product of the number of growth patterns and number of sexes: https://github.com/nmfs-ost/ss3-source-code/blob/69cc71611cf790d520a53f7ee47fe6885fdeb8fe/SS_param.tpl#L157 However the RECRUITMENT_DIST output in Report.sso...

[Feature]: consider adding more stock-recruit functions

1

### Describe the solution you would like. Recent messages have suggested additional stock-recruit functions be considered (in addition to the 9 options currently in SS3 listed at https://nmfs-ost.github.io/ss3-doc/SS330_User_Manual_release.html#spawner-recruitment), including -...

The r4ss issue https://github.com/r4ss/r4ss/issues/460 "create a single function for running SS models for use in r4ss, SSMSE, and ss3sim" has been resolved thanks to PR https://github.com/r4ss/r4ss/pull/722 so the modified functions...

Add contributions by cohort to length comp fits

1

Google Code issue 87: Mark Maunder suggested this. It could be done in the style of the MFCL viewer plots. Would work best for models with relatively few age classes...

Functions for reading and plotting fully Bayesian output

1

Would be nice to not have to read MLE and add MCMC results but directly plot fully Bayesian output.

The yield curve plot depends on the table in Report.sso with keyword "SPR/YPR_Profile" but this output is only available for models with Hessian (as discussed at https://github.com/nmfs-stock-synthesis/stock-synthesis/issues/112). This plot is...

An email discussion has helped me realized that bad fits to discard observations with high precision are hard to see in the plot created by `SSplotDiscards()`. Adding either a new...

A sardine model with 2 seasons per year, spawning in season 2 and recruitment in season 1 revealed misalignment between horizontal position of point estimates and uncertainty intervals for multiple...