Look into {calibrar}

[kellijohnson-NOAA]

I was recently notified of a publication coauthored by Isaac Kaplan regarding Atlantis and thought it might be good to look at {calibrar} to get a sense of the data and the outputs from Atlantis. {calibrar} is an R package that is meant to help calibrate Atlantis models by matching ecosystem dynamics to input values. It would be awesome if there ended up being some overlap between the packages. But, at the very least it will probably help us learn the structure of the output. Everything for the study in this manuscript is public, including the results of the Atlantis run.

[e-perl-NOAA]

Relevant links to the Atlantis packages and repos:

• {atlantis2ls} - Atlantis tools (2ls) to couple Atlantis with calibrar
• Atlantis_Calibration GitHub repo - provides scripts to calibrate the Atlantis ecosystem model using the calibrar R package
• {calibrar}

Obviously, because I know nothing about any of this, I talked with Fernando (what I've named my Gemini & Copilot). I definitely can't translate that conversation over here effectively as I barely understand it, however I have shared the conversation with both of you @Bai-Li-NOAA and @kellijohnson-NOAA. My TLDR is that it seems like you basically need to create a function of the entire ecosystemom process and then you can pass that through calibrar. Also there are some formatting differences. The way the Atlantis_Calibration repo dealt with that in this function did not seem the very efficient to me and so Fernando also gave some suggestions about a function to do that in a cleaner, more automated way.