A review of stock assessment packages in the United States

Stock assessments provide scientific advice in support of fisheries decision making. Ideally, assessments involve fitting population dynamics models to fishery and monitoring data to provide estimates of time-trajectories of biomass and fishing mortality in absolute terms and relative to biological reference points such as BMSY and FMSY, along with measures of uncertainty. Some stock assessments are conducted using software developed for a specific stock or group of stocks. However, increasingly, stock assessments are being conducted using packages developed for application to several taxa and across multiple regions. We review the range of packages used to conduct assessments of fish and invertebrate stocks in the United States because these assessments tend to have common goals, and need to provide similar outputs for decision making. Sixteen packages are considered, five based on surplus production models, one based on a delay-difference model, and the remainder based on age-structured models. Most of the packages are freely available for use by analysts in the US and around the world, have been evaluated using simulations, and can form the basis for forecasts. The packages differ in their ease of use and the types of data inputs they can use. This paper highlights the benefits of stock assessment packages in terms of allowing analysts to explore many assessment configurations and facilitating the peer-review of assessments. It also highlights the disadvantages associated with the use of packages for conducting assessments. Packages with the most options and greatest flexibility are the most difficult to use, and see the greatest development of auxiliary tools to facilitate their use.