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ss3sim: An R Package for Fisheries Stock Assessment Simulation with Stock Synthesis

Figure 2

Illustration of input and output folder and file structure for an ss3sim simulation.

Folders are shown in blue, input files in orange, and output files in grey. All input and output files are in plain text format. OM refers to operating model and EM to estimation model. Case files (orange files at bottom left) combine cases (e.g. M0 for a given natural mortality trajectory) with species or life-history OMs and EMs (e.g. cod-like or sardine-like). Alternatively, a user can skip setting up case files and specify the simulation cases directly in R code (see the vignette).

Figure 2

doi: https://doi.org/10.1371/journal.pone.0092725.g002