Ian Taylor

It would be useful to easily compare time series of total catch for models that either have different catch inputs or differences in internally estimated discards. This idea inspired by...

add note to caption for figures representing data excluded from the likelihood (lambda = 0)

2

It's useful to see fits to data that aren't included in the likelihood, but it's not clear from the plots which might have lambda = 0. It should be straightforward...

add support for tuning hyper-parameter sigma_s when using semi-parametric (2D-AR) selectivity

5

Except below from [Xu et al. (2018)](https://cdnsciencepub.com/doi/10.1139/cjfas-2017-0446) describes a tuning algorithm for the hyper-parameter sigma_s used with semi-parametric selectivity (which has a label like "sigmasel_Fishery" in SS). A table similar...

The r4ss package has just revised the column names used in the functions to read SS3 input files (see https://github.com/r4ss/r4ss/releases/tag/v1.50.0). ss3sim uses the old names in many places (e.g. 15...

@AgurtzaneUrtizberea and @GiancarloMCorrea noted that the SS_writedat function rounds values to 6 significant digits. That happens in the custom https://github.com/r4ss/r4ss/blob/main/R/write_fwf4.r function written by @yukio-takeuchi (which was inspired by https://github.com/r-gregmisc/gdata/blob/main/R/write.fwf.R (currently...

The `run-extra-tests-for-code-coverage` github action to test the code against a larger set of test models and check code coverage consistently takes 4-5 hours to run: https://github.com/r4ss/r4ss/actions/workflows/r4ss-extra-tests.yml which @e-perl-NOAA noted slows...

Add summary biomass to SS_summarize()

1

PR is also intended to test trigger of doc-and-style workflow.

[Feature]: add figures to illustrate time-varying stock-recruit quantities (when present)

1

### Describe the feature request. Discussion of new alpha-beta parameterization of Beverton-Holt being added to SS3 (see issue https://github.com/nmfs-ost/ss3-source-code/issues/191 and draft pull-request https://github.com/nmfs-ost/ss3-source-code/pull/442), includes note that "If biology is time-varying,...

### Describe the feature request. The following really informative four-panel figure was shared during a recent DFO review meeting and I think should serve as inspiration for a new default...

get_ss3_exe() function failing for some users due to SSL error unrelated to r4ss

4

Thanks to @MOshima-PIFSC for pointing out that an issue that only NOAA folks (as far as I know) have been having for a few weeks with R on Windows not...