The Woods Hole Assessment Model (WHAM) is a state-space age-structured stock assessment model that can include environmental effects on population processes. WHAM can be configured to estimate a range of assessment models: a traditional statistical catch-at-age (SCAA) model with recruitments as fixed effects, SCAA with recruitments as random effects, or a "full state-space" model with abundance at all ages treated as random effects. WHAM is a generalization of the R and TMB code from Miller et al. (2016), Miller and Hyun (2018), and Miller et al. (2018). WHAM also has many similarities of input data sources with ASAP (Legault and Restrepo 1999) and provides functions to generate a WHAM input file from an ASAP3 dat file. Many of the plotting functions for input data, results, and diagnostics are modified from ASAP code written by Chris Legault and Liz Brooks.
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