Review alterations from updated CalCurr and SS3 work #61
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HAP: incorporated the changes I made in order to get the updated CalCurr Atlantis files to run with with updated SS3.
HAP: the OG function did now work for me, so I used a function based on script in the ReactiveAtlantis package
HAP: I incorporated code changes I needed to get the updated CalCurr Atlantis files to run with the updated SS3 model.
I incorporated the changes I needed to make in order to get the updated CalCurr Atlantis files to run with the updated SS3.
I incorporated the changes I needed to make in order to get the updated CalCurr Atlantis files to run with the updated SS3.
These are the atlantisom example scripts I developed based on the previous scripts. Basically, I did some reorganizing and added more comments to provide additional information and guidance. Also, I have a version of the script with 2 fleets (1 fishery and 1 survey) and a version of the script with 6 fleets (3 fisheries and 3 surveys).
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thank you @hollyannperryman! I appreciate this contribution; I plan to review in the next couple days |
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Hei!
This is my first time forking and doing a pull request so I hope I am doing this correctly :)
Over the last couple of months, I have done a bit of work with atlantisom to get the updated CalCurr files to run with the updated SS3 model. I was able to get an updated dat files to run through SS3 but I did have to make some changes to these atlantisom functions. Additionally, I swapped out one of the functions (calc_biomass_age) for a function based on ReactiveAtlantis functions (calc_bio_age).
I also included the two script files I developed so you can see how I was using atlantisom. I was going to add RData for these, but the files are a bit too large. Let me know if you want access to these RData files and I can find another means to send them to you.
I will be starting a new position, so I will not be doing much with atlantisom for the time being, but I am going to try to keep up and support the CalCurr work in my spare time.
Thanks! Hope these alterations prove to be useful for the wider group!
-Holly