Ian Taylor

[Feature]: provide input with units of spawning output

3

### Describe the feature request. Stock Synthesis is ignorant of the units of spawning output (if different from biomass) because it depends on the units you choose for the fecundity...

A comment on draft assessment report noted that this titles on these figures are misleading:  The titles are based on the fact that the upper panel uses sex-specific data...

Next CRAN submission

4

Timing could align with next release of Stock Synthesis or a major change in r4ss. Checklist update from previous submission discussed in #206, where example models, tests, and vignette are...

[Feature]: develop `sample_ss3()` wrapper for {adnuts}

2

### Describe the feature request. As suggested by @Cole-Monnahan-NOAA in discussion at https://github.com/Cole-Monnahan-NOAA/adnuts/issues/34, it would be useful to have a `sample_ss3()` which would automate the process of adding the informative...

@inheritParams is what tidyverse seems to use. This same issue is on {ss3sim} (originally having come from `nmfs-stock-synthesis/workflows`) of https://github.com/ss3sim/ss3sim/issues/408 Use `@inheritParams` instead of [template folder](https://github.com/ss3sim/ss3sim/tree/f5e133dc897154c1bccc56380858a70264f8faff/man/roxygen/templates) for roxygen of arguments...

treatment of excluded index observations in plot comparing all indices?

1

@EJDick-NOAA noted that an index with all observations excluded via negative fleet number was not appearing in the plot comparing all indices created by `SS_plots()`. The current logic (in https://github.com/r4ss/r4ss/blob/main/R/SSplotIndices.R#L631-L632)...

fixes composition plotting error #770

1

As discussed in #770 there was a bug in the read of the comp data specification table for the format used in 3.30.21. This should fix it.

### Describe the feature request. Current code has a separate parameter for each fleet: https://github.com/r4ss/r4ss/blob/3ea969763a3c3df13249c8a7d6026fca2aa56510/R/tune_comps.R#L449-L451 but it would be useful to let the user specify a vector of `ParmSelect` values...

add contour plot or other representation of matrix of M at age

2

Models that contain both time-varying mortality parameters and non-constant M at age would benefit from a contour plot or other representation that shows M as a function of both time...

[Feature]: add index comparison figure that is rescaled by catchability

1

### Describe the feature request. It should be possible to create something like the figure below from the 2013 cowcod assessment (@EJDick-NOAA and MacCall 2014): https://www.pcouncil.org/documents/2014/08/status-and-productivity-of-cowcod-sebastes-levis-in-the-southern-california-bight-2013-august-20-2014.pdf/#page=151. Relates to #67 which...