rgirardi/atlantisfmsy: Estimation of a functional group's Fmsy in Atlantis ecosystem model

An estimation of a functional group's Fmsy in Atlantis ecosystem model in R. It iteratively searchs for Fmsy of a specified functional group in a calibrated Atlantis model. The iterative simulations protocole was defined by Dr. Elisabeth Fulton (CSIRO) for the IndiSeas project (http://www.indiseas.org/, 03/01/2018). It is designed first to gradualy increase F for a particular functional group in the model up to the collapse of the stock. Then, it narrows down the value of Fmsy (in y-1) with a precision of two decimals. To do so, it copies/pastes all the files necessary to run the calibrated model into a seperate directory and then modifies the fishing mortality parameter (mFC) of the selected functinoal group in the harvest parameters file within this directory before each simulation. A new name is provided for the output files in the bach/shell file and finally the Atlantis model is run. It starts at F = 0 , with a step of F = 0.4, until reaching collapse (NEED TO BE MODIFY AS B = 0.1*B0). Then in the interval containing FMSY, reduce F-step by 50% progressively until a sufficiently smooth curve is obtained to enable estimation of FMSY at a precision of 10E-02.For each simulation allow a burn in time of at least 20 years (depends on the time that your model needs to stabilize), then run for another 30 years, and take average of the last 5 years to estimates the yield. See Atlantis website for more information on the ecosystem model (https://research.csiro.au/atlantis/, 03/01/2018).

install.packages("remotes")
remotes::install_github("rgirardi/atlantisfmsy")