In recent years, increased use of formal harvest strategies in fisheries management has expanded demand for formal stock assessments of exploited fish stocks. In Australia, even the notoriously low-bar harvest strategy inherent in the SAFS system (Status of Australian Fish Stocks) has been responsible for a large increase in the number of formal stock assessments.
Fortunately, several stock assessment software packages, such as Stock Synthesis (Methot and Wetzel, 2013), are flexible and can be used for assessments ranging from relatively data-poor (age-structured production models) to more sophisticated spatially structured multi-fleet age-structured integrated assessments. Unfortunately, resources to assist assessment scientists understand how such software works remain relatively limited.
An attempt is underway to produce a book that provides an initial explanation of some of the more important processes involved in conducting a model-based stock assessment. It starts from the simplest models, age-structured production models using annual harvest rates. These are iteratively modified to include nulti-fleet models using instantaneous fishing mortality rates and including age-composition and size-composition data. How to characterize uncertainty is described, along with numerous other process such as implementing likelihood profiles, and in some examples, translations to RTMB versions are described.
The objective is to provide a freely available, downloadable, book, plus a series of R packages, that will enable assessment scientists to explore these subjects at their own pace (Haddon, 2026, 2026a, 2026b, 2026d, 2026e).