Citation: Brown, C.J., Taylor, W., Wabnitz, C.C.C. et al. Dependency of Queensland and the Great Barrier Reef’s tropical fisheries on reef-associated fish. Sci Rep 10, 17801 (2020). https://doi.org/10.1038/s41598-020-74652-2

Open-access

Code from the paper, specifically the code for figure 5. Uses stan to fit a Pella-Tomlinson surplus production model to CPUE series. Then estimates the probability of overfishing, given a sudden productivity decline (ostensibly caused by coral habitat loss, as per processes described in Brown et al. 2019)

The stan code is optimized for computational efficiency. See notes therein. The optimization does make interpreting the model a bit more difficult, but it speeds up the MCMC chains considerably.

Figure 5 Probability present day catch exceeds estimated MSY reference point given different assumed % reductions in the intrinsic growth rate (r).

Spreadsheets from Qfish with the fish data in them

Creates dataframes to input to the next script that does model fitting

Loops over all species to fit the models, then calculates risk of overfishing.

The model fitting in stan!

Handy Rmd script that creates supplemental tables of model parameter estimates.