Guidance on Clearance Rate, MUM, Prey Availability, KUP, KLP, and Mortality Rates

[Kévin Cazelles]

Dear Atlantis Community,

We are encountering similar challenges to those discussed in these threads:

• https://groups.google.com/g/atlantis-ecosystem-model/c/MPDRGuARQVM/m/G784Ky30mBEJ
• https://groups.google.com/g/atlantis-ecosystem-model/c/S3HvpmHc_eg/m/6ljiL2n1aoUJ

To improve the robustness of our parameter selection, we are carefully considering our values for clearance rate, MUM, prey availability, KUP, KLP, and mortality rates. We would greatly appreciate any pointers, references, even heuristics regarding the following questions:

1. Prey Availability: We have based our values on known diet compositions and best estimates of availability, refining them using the DietCheck.txt output (e.g., adjusting availability if the realized proportion is too high), as recommended in the manual (Part I, p. 147). Is this a valid approach?
2. Clearance Rate (CR), MUM, and Mortality Rates: We are currently setting flagfishrates = 0 and have not found clear references on how to derive these values. Are users basing their estimates on alternative metrics such as maximum growth rates, or relying mainly on reasonable guesses and exploratory simulations? Have we overlooked relevant guidelines?
3. K_UP and K_LOW: Do users typically derive these values from allometric relationships, or do most follow the manual’s recommendation (p. 154), where the lower and upper limits are 0.1% and ~40% of the predator size, respectively? Also, is it generally recommended to use UseHardFeedingWindow = 0 and UseBiLogisticFeedingWindow = 1?

Any general guidelines, publications, or relevant discussions would be greatly appreciated.

Best regards,

Kevin & Ying