Important SS3 Set-up Decisions

Model dimensions to figure out before adding data

Areas

flowchart TB
    accTitle: Number of areas
    A["How many areas should I have?"] --> B["Do I have lots of data"]
    B -- Yes --> C["Is there limited movement"]
    C -- Yes --> D["Is there evidence of significant spatial 
                    differences in growth or relative stock size?"]
    D -- Yes --> E("Use more than one area")
    B -- No --> F("Use one area")
    C -- No --> F
    D -- No --> F
    linkStyle 1,2,3,4,5,6 stroke-width:2px,color:black
    style F fill:#5EB6D9,stroke:#fff,color:#fff
    style E fill:#5EB6D9,stroke:#fff,color:#fff

Seasons

flowchart TB
    A["How many seasons should I have?"] --> B["Is it a short-lived, 
                                                fast growing species?"]
    B -- Yes --> C["Am I using length data?"]
    C --Yes --> D("Use multiple seasons")
    C -- No --> E("Use one season")
    B -- No --> F["Is fishing during a short season that 
                  precedes the survey or spawning?"]
    F -- Yes --> D
    F -- No --> E
    linkStyle 1,2,3,4,5,6 stroke-width:2px,color:black
    style D fill:#5EB6D9,stroke:#fff,color:#fff
    style E fill:#5EB6D9,stroke:#fff,color:#fff

Empirical weight-at-age (EWWA) vs. parametric growth

flowchart TB
    A["Should I use EWAA or parametric growth?"] --> B["Do I have lots of age data"]
    B -- Yes --> C["Is there evidence of variability 
                  in weight-at-age"]
    C -- Yes --> D("Use EWWA")
    B -- No --> E("Use parametric growth")
    C -- No --> E
    linkStyle 1,2,3,4 stroke-width:2px,color:black
    style D fill:#5EB6D9,stroke:#fff,color:#fff
    style E fill:#5EB6D9,stroke:#fff,color:#fff

Fleets

flowchart TB
    A["How many fleets should I have?"] --> B["Are there significant differences in size
                                              composition of the catch of different subsets
                                              of the fishery?"]
    B --Yes --> C("Multiple fleets")
    B -- No --> D["Is there some management reason to 
                  model the catch separately?"]
    D -- Yes --> C
    D -- No --> E("Group all catch as one fleet")
    linkStyle 1,2,3,4 stroke-width:2px,color:black
    style C fill:#5EB6D9,stroke:#fff,color:#fff
    style E fill:#5EB6D9,stroke:#fff,color:#fff

One sex or two

flowchart TB
    A["Should I have one sex or two"] --> B["Am I modeling growth?"]
    B -- Yes --> C["Is the species sexually dimorphic?"]
    C -- Yes --> D("Use two sexes")
    A --> E["Do I have sex-specific composition data?"]
    E -- Yes --> D
    B -- No --> F("Combine females and males into one sex")
    C -- No --> F
    E -- No --> F
    linkStyle 1,2,3,4,5,6,7 stroke-width:2px,color:black
    style D fill:#5EB6D9,stroke:#fff,color:#fff
    style F fill:#5EB6D9,stroke:#fff,color:#fff

Number of population age bins

Data age bins should cover the majority of the observed ages (i.e. not too large that a fraction is in the maximum age/plus group).

The first age is always 0, but recruitment can occur at age 1.

flowchart TB
    A["Can population age bins go 
      higher than data age bins?"] --> B["Is growth asymptotic within
                                                observed ages?"]
    B -- No --> C["Is unfished equilibrium estimated to 
                  have older fish than has been observed?"]                                    
    B -- Yes --> D("Population age bins can go 
                   higher than data age bins")
    C -- Yes --> D
    C -- No --> E("Population age bins can't go 
                  higher than data age bins")
    linkStyle 1,2,3,4 stroke-width:2px,color:black
    style D fill:#5EB6D9,stroke:#fff,color:#fff
    style E fill:#5EB6D9,stroke:#fff,color:#fff

In models with growth, the plus group should be old enough so that fish nearly achieve \(L_{inf}\) by the time they are in the plus group.