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FYFAM: The Foothill Yellow-legged Frog Assessment Model

Why a river management model of frogs?

Animation of a FYFAM simulation
FYFAM is implemented in NetLogo, which provides a power graphical user interface and tools for designing, executing, and observing simulation experiments. This is an animation of the model at our South Fork Trinity River (California) site. Submerged habitat is shaded by depth (blue) or velocity (yellow-red). Breeding adults have a frog shape; egg masses are round dots; and the many thousands of tadpoles appear as very small wedges.

The foothill yellow-legged frog (Rana boylii) is unique and important because it breeds in rivers and streams, not still water. In spring, adult breeders place eggs along channel margins in habitat that, for eggs to survive and hatch into tadpoles, must neither be dried out as flows decrease after the rainy season ends nor be washed away by late-season flow events. Tadpoles are also subject to being either stranded or washed away by sudden changes in flow. Lower temperatures increase the time it takes eggs and tadpoles to develop. Therefore, breeding success depends very much on flow and temperature regimes.

What is FYFAM designed for?

Our Foothill Yellow-legged Frog Assessment Model (FYFAM) is designed as a tool for evaluating and comparing flow and temperature regimes for their effect on frog breeding success. In much of California's breeding habitat, flows and temperatures are controlled by upstream reservoirs; and potentially also affected by land and water management actions. FYFAM can predict how changes in flow and temperature, from sub-hourly to seasonal scales, can affect the success and timing of frog breeding, incubation, and tadpole development.

The model is driven by two-dimensional hydrodynamic modeling (done separately using any hydrodynamic model) mapped onto a square grid space, with a user-chosen spatial resolution (grid cell size). To date we have modeled sites using 1-meter and 1-foot resolution. The time step is determined by the flow and temperature input: daily input produces one-day time steps; hourly input would produce one-hour time steps; or the user can insert short-term events such as sub-daily recreational flow pulses into a daily simulation.

Our first publication using FYFAM describes its first version and applies the model to the question of how river management to enhance salmonid populations could affect frog breeding success. This paper is appearing inthe Canadian Journal of Fisheries and Aquatic Sciences; a pre-publication version is here.

Current Version of FYFAM

Version 2 of FYFAM includes two substantial changes in the model's formulation from the first version, plus numerous software improvements. A complete description of the model and its software is here.

Note: Prior to 12 March 2018, Version 2 had a software error that miscalculated output of median metamorphosis date. The software released 7 May 2018 fixes a small programming issue that could raise an unnecessary error statement when applying the model to a new study site. The most recent update, the version dated 29 October 2018, makes minor improvements to file output.

The most recent update of Version 2 of FYFAM can be downloaded here. The download is a zip file that contains the model software (a NetLogo file), the current model documentation and user guide, example input and parameter files, the "time" extension to NetLogo, and the software license. Users must install NetLogo, which is free. FYFAM currently requires NetLogo version 6.0.x (the most recent release of NetLogo, as of 2018). The FYFAM software posted here since February, 2017, has software improvements that dramatically increase execution speed (by 20 times in our test case).

Version 2 of FYFAM for version 5.3 of NetLogo can be downloaded here.

A large zip archive of code tests can be downloaded here.

Please feel free to use FYFAM, and contact Steve Railsback or Bret Harvey to ask for assistance and let us know about your application.

FYFAM's development was sponsored by USDA Forest Service, Pacific Southwest Research Station. The software is copyrighted but users are free to modify it.