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    Casal2 User Manual for Age-Based Models

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    Document Number:
    Casal2 Development Team
    Submitted By:
    Mr Nathan Walker (New Zealand)
    Approved By:
    Mr Nathan Walker (New Zealand)
    NIWA Technical Report, 139 (2022): ISSN 1174-2631. User manual for age-based models with Casal2 v22.06 (2022-06-07)

    Casal2 is an open-source integrated statistical catch-at-age assessment tool for modelling the population dynamics of marine populations. Casal2 is designed for quantitative assessments of marine populations, including fish, invertebrates, marine mammals and seabirds.

    Casal2 implements generalised age (Casal2 for age-based models) or length structured (Casal2 for length-based models) population models that allows for a great deal of choice in specifying the population dynamics, parameters and those parameters that should be estimated, and the model outputs. Casal2 is designed for flexibility. It allows implementation of age or length structured models from single species or stocks, to multiple species or stocks, using user-defined categories such as area, sex, and maturity stage. The categories are are generic, are not predefined, and are easily specified. Casal2 models can be used for a single population with a single anthropogenic event (i.e., a single fish stock with a single fishery), or for multiple species and populations, areas, and/or anthropogenic or exploitation methods, and including predator-prey interactions.

    In Casal2 the processes and observations that occur over each year are defined by the user. Processes include recruitment, natural mortality, and anthropogenic mortality. Observations used to fit the models can be from many different sources, including removals-at-size or -age (e.g., a fishery), research survey or other biomass indices, and mark-recapture data. Model parameters can be estimated using penalised maximum likelihood or Bayesian methods.

    As well as the point estimates of the parameters, Casal2 can calculate the likelihood or posterior distribution profiles for estimated parameters, and can generate Bayesian posterior distributions using Markov chain Monte Carlo methods. Casal2 can project the population status into the future using both deterministic or stochastic population dynamics. Casal2 can also simulate observations from a given model for both actual or potential observations.

    The Casal2 user manual has been split into two separate manuals one for the age-based functionality and the other for the length based functionality. These two manuals contain a great deal over common components but differ in processes and observations.