Dr. Tim Miller and I are developing the Woods Hole Assessment Model (WHAM), an R + TMB package to run state-space age-structured stock assessment models. 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.

• Designed to include environmental effects on population processes (recruitment, M)
• Random effects with 2D autocorrelation (recruitment, numbers at age, selectivity, M)

Miller TJ and Stock BC. 2020. The Woods Hole Assessment Model (WHAM). Version 1.0. https://timjmiller.github.io/wham.