Guidance for decisions using the Vector Autoregressive Spatio-Temporal (VAST) package in stock, ecosystem, habitat and climate assessments

Fisheries scientists provide stock, ecosystem, habitat, and climate assessments to support interdisplinary fisheries management in the US and worldwide. These assessment activities have evolved different models, using different review standards, and are communicated using different vocabulary. Recent research shows that spatio-temporal models can estimate population density for multiple locations, times, and species, and that this is a "common currency" for addressing core goals in stock, ecosystem, habitat, and climate assessments. I therefore review the history and "design principles" for one spatio-temporal modelling package, the Vector Autoregressive Spatio-Temporal (VAST) package. I then provide guidance on fifteen major decisions that must be made by users of VAST, including: whether to use a univariate or multivariate model; when to include spatial and/or spatio-temporal variation; how many factors to use within a multivariate model; whether to include density or catchability covariates; and when to include a temporal correlation on model components. I finally demonstrate these decisions using three case studies. The first develops indices of abundance, distribution shift, and range expansion for arrowtooth flounder (Atheresthes stomias) in the Eastern Bering Sea, showing the range expansion for this species. The second involves "species ordination" of eight groundfishes in the Gulf of Alaska bottom trawl survey, which highlights the different spatial distribution of flathead sole (Hippoglossoides elassodon) relative to sablefish (Anoplopoma fimbria) and dover sole (Microstomus pacificus). The third involves a short-term forecast of the proportion of coastwide abundance for five groundfishes within three spatial strata in the US West Coast groundfish bottom trawl survey, and predicts large interannual variability (and high uncertainty) in the distribution of lingcod (Ophiodon elongatus). I conclude by recommending further research exploring the benefits and limitations of a "common currency" approach to stock, ecosystem, habitat, and climate assessments, and discuss extending this approach to optimal survey design and economic assessments.