Stock Synthesis models and scripts used for testing
All SS3 models are in the "models" subfolder. All testing scripts and specifications files used by the SS3 development team are in the ".github" subfolder.
It is always helpful to have more examples of Stock Synthesis models! Please open a pull request in the ss3-user-examples repository to share your own models publicly.
This repository houses models used for testing Stock Synthesis. These are often based on stock assessment models, but may not be the final model version or may have been altered for testing purposes. In addition, the data in the model files should not be used as data sources, as the data may have been altered for testing purposes.
Regression tests are the primary way that Stock Synthesis is tested. Regression tests are conducted automatically using Github actions. Each time, the set of models in ss3-test-models are run and then key model quantities are checked to determine if they have changed or remained the same relative to a reference run.
Most of these models have at least 1 unique feature. The table below includes some key ones, as well as the approximate time it takes to run the model with estimation.
| Model | Features | Approx. Run Times |
|---|---|---|
| BigSkate_2019 | Uses F method 3 (hybrid), cessation growth model, catchability time blocks, catchability priors, Mirrored and DN selectivity, discard data, conditional age at length data, Input var. adjustments | 0 hours, 5 minutes, 43 seconds |
| Empirical_Wtatage_Age_Selex | Empirical Weight at age model, with empirical (as random walk) age selectivity | 0 hours, 1 minutes, 18 seconds |
| growth_morphs | Uses 5 platoons, 1 growth pattern | 0 hours, 4 minutes, 38 seconds |
| growth_timevary | Time-varying growth using time blocks, Fmethod 1 | 0 hours, 0 minutes, 54 seconds |
| Hake_2018 | Empirical weight at age model, Dirichlet Multinomial comps weighting, time varying selectivity using annual deviations | 0 hours, 1 minutes, 5 seconds |
| Hake_2019_semi-parametric_selex | Empirical Weight at age model, with semiparametric (2DAR) selectivity | 0 hours, 1 minutes, 7 seconds |
| KelpGreenling2015 | Maturity option 6 (read length-maturity), Mirrored selectivity, input variance adjustment | 0 hours, 4 minutes, 59 seconds |
| Sablefish2015 | Cubic spline selectivity with male offset, DN length selectivity, special recdev survey | 0 hours, 13 minutes, 9 seconds |
| Simple | Uses sd reporting and mean size-at-age data | 0 hours, 1 minutes, 43 seconds |
| Simple_Lorenzen_tv_trend | Lorenzen natural morality, lambdas, extra stddev input (M-at-age), tv trends on selectivity (-1,-2,-3) | 0 hours, 2 minutes, 2 seconds |
| Simple_NoCPUE | No index of abundance | 0 hours, 1 minutes, 35 seconds |
| Simple_with_Discard | Uses discards | 0 hours, 2 minutes, 7 seconds |
| Simple_with_DM_sizefreq | Generalized size-composition (sizefreq) data in the same units as the length-composition data (2 cm bins), 2 areas with identical fisheries and surveys in both areas, 2 seasons of unequal durations with all catch in season 1, fleet 7 as a depletion survery, Dirichlet Multinomial (D-M) for fleets 1, 2, 3, and 4 and all use the same shared parameter. Note that fleet 3 has no composition data so D-M is irrelevant and fleet 5 has composition data but does not have D-M so it provides a comparison to fleet 2. | 0 hours, 7 minutes, 42 seconds |
| Spinydogfish_2011 | Stock Recruitment option 7 (survival 3 parameter), fecundity option 4 | 0 hours, 4 minutes, 48 seconds |
| tagging_mirrored_sel | Time varying growth using annual deviations, Tagging data and movement parameters, selectivity, environmental variable data | 0 hours, 2 minutes, 49 seconds |
| three_area_nomove | Spatial model with areas, no movement | 0 hours, 3 minutes, 32 seconds |
| two_morph_seas_areas | 2 area model with movement, 2 growth patterns, 2 seasons, uses generalized size comp | 0 hours, 3 minutes, 35 seconds |
| vermillion_snapper | Uses F method 2 (estimated parameters) | 0 hours, 3 minutes, 42 seconds |
| vermillion_snapper_F4 | Uses F method 4 | 0 hours, 2 minutes, 52 seconds |
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