index.qmd

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# Tutorial goals

The following outline shows the goals of different sections of the
tutorial. See table of contents (left) for specific section details and
practical considerations.

## Basic running of examples

1.  Introduction to the jjm model (Link
    [here](https://github.com/SPRFMO/jjm))
    a.  Running the model from start to finish
    b.  Data input (ALK excel files)
    c.  Data input into JJM
    d.  Model setting, Model equations, Parameters (refer to technical
        annex)
    e.  Running the 2021 assessment
    f.  Updating input data
    g.  Updating control file
    h.  Single-stock vs two-stock models

## Outputs and Diagnostics

1.  Understanding the Outputs
    a.  Ascii files (difference between standard ADMB output and
        specialized ones for JJM)
    b.  JJM outputs (standard)
    c.  Pulling out important quantities from the jjm object (e.g. MSY
        table)
    d.  Making plots from JJM (custom)
    e.  Stock status under different regimes
2.  Generating new plots for diagnostic purposes
3.  Retrospective analysis

## Sensitivity analyses and model comparisons

1.  Sensitivities in data -- e.g. include/drop data
    a.  Replacing CPUE indices
    b.  Replacing age composition data
2.  Sensitivities in model settings
    a.  Changing individual parameters
3.  Comparing model runs
    a.  Current diagnostics available
    b.  Making custom diagnostics
4.  Alternative uncertainty estimates