Ian Taylor

### Describe the solution you would like. As noted in https://github.com/nmfs-stock-synthesis/doc/issues/154, F_method 4 can replicate F_method 2 and 3 (although @chantelwetzel-noaa noted that further testing could be conducted). An additional...

smarter rules for when Bratio isn't available in derived quantities (e.g. prior to first catch year)?

4

This line of code seem to limit the Bratio values reported to DERIVED_QUANTITES to start after the first year with catch: https://github.com/nmfs-stock-synthesis/stock-synthesis/blob/main/SS_readdata_330.tpl#L3550-L3551 Thus, in the "Simple" model, where the start...

report forecast catch with and without 40:10 adjustment (or equivalent)

3

The 2021 lingcod south area assessment estimates current spawning biomass slightly below the B40% target leading to the additional impact of the 40:10 adjustment used in the harvest control rule...

Move r4ss into `nmfs-stock-synthesis` organization?

1

Moving the r4ss repo (and potentially ss3sim) into the `nmfs-stock-synthesis` organization (which didn't exist when the r4ss organization on github was created) could consolidate some of the overhead associated with...

Thanks to @roliveros-ramos and a team of folks at the Inter-American Tropical Tuna Commission, a new "empirical selectivity" output (`$empirical_selectivity` in the list returned by `SS_output()`) has been added in...

make HTML viewer meet Section 508 accessibility requirements

12

Assessment reports and auxiliary information posted to U.S. government websites as well as the Pacific Fishery Management Council website (and presumably other council sites too), need to meet Section 508...

add summary biomass to SSsummarize() and SSplotComparisons()

2

Comparing spawning output for models which have different maturity or fecundity relationships is problematic. Adding a comparison of summary biomass would help for these cases and may be useful in...

new function to calculate risk probabilities based on normal approximation

4

Table of values such as probability of relative spawning biomass falling below overfishing threshold in 2019, which I think would be calculated from "model" as pnorm(model$minbthresh, model$derived_quants["Bratio_2019","Value"], model$derived_quants["Bratio_2019","StdDev"]) Format of...

`SS_RunJitter()` automatically saves the `ParmTrace.sso` file from each jitter run (renamed to `ParmTrace1.sso`, `ParmTrace2.sso`, etc.). If the starter file is set to write parameter values to ParmTrace.sso (any option other...

add function, or expand SS_tune_comps(), to tune discard rates and mean body weight

4

The 2019 U.S. west coast Sablefish assessment says > Added variances for discard rates and mean body weights were set using values calculated iteratively using the RMSE of differences between...