Tutorials and Vignettes for Stock Assessment
These code vignettes will walk you through how to set up and use some commonly used fish stock assessment models. All of these tools can be found in NOAA Fisheries Integrated Toolbox.
Stock Synthesis (SS3)
Stock Synthesis (SS3) is an age-structured population dynamics model that is used to assess the impact of fisheries on fish and shellfish stocks while taking into account the influence of environmental factors. Tutorials are available on the SS3 website.
Woods Hole Assessment Model (WHAM)
The Woods Hole Assessment Model (WHAM) is a general state-space age-structured stock assessment framework designed to include environmental effects on population processes. The state-space framework is attractive because it can estimate observation and process error, as well as naturally propagate random effect parameters in stock projections. WHAM can be configured to estimate a range of assessment models including statistical catch-at-age (SCAA) model with recruitments as fixed effects, SCAA with recruitments as random effects, and “full state-space model”, abundance at all ages are random effects.