Foothill yellow-legged frog assessment model

FYFAM: The Foothill Yellow-legged Frog Assessment Model


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 that turns red when the adult is ready to breed; egg masses are round dots; and the many thousands of tadpoles appear as very small wedges.

Why a river management model of frogs?

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: Railsback, S. F., B. C. Harvey, S. J. Kupferberg, M. M. Lang, S. McBain, and H. H. J. Welsh. 2016. Modeling potential river management conflicts between frogs and salmonids. Canadian Journal of Fisheries and Aquatic Sciences 73:773-84. A pre-publication version is here.

FYFAM is now used at sites throughout the foothill yellow-legged frog's range. It was examined as a example successful ecological management model in this review: Will et al. How to make socio-environmental modelling more useful to support policy and management? People and Nature doi:10.1002/pan3.10207.

Current Version of FYFAM

Versions 2.0.3 and 2.1.3 are updates of versions 2.0.2 and 2.1.2, which are described below. The new versions, released in April 2021, both include two changes: The equation for when adults become ready to breed was revised so users can skew breeding toward earlier or later dates, and scour mortality of both eggs and tadpoles was limited to velocities above a threshold. The NetLogo code, example input, and the documentation can be downloaded (ZIP format) here: Version 2.0.3 and Version 2.1.3.

Versions 2.0.2 and 2.1.2 were produced in January 2021. Version 2.0.2 simply updates the code of Version 2 so it is compatible with the current version of its NetLogo software platform. This version is simpler to install, but requires NetLogo version 6.2.0 or later. To use it (a) install the current version of NetLogo from here, and (b) download and unzip this zip file. The download includes the model file (a NetLogo code file), current model documentation (model description and software guide), and example input.

Version 2.1.2 is identical to V. 2.0.2 except that it allows habitat input to use variable spatial resolutions. This capability can be useful when input was generated by a hydrodynamic model with variable resolution, e.g., to represent uniform floodplain habitat more coarsely than the river channel. Version 2.1.2 is in this download file.

Version 2 of FYFAM includes two substantial changes in the model's formulation from the first version, plus numerous software improvements. The description of V. 2 (now superceded by V. 2.0.1) 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.

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 was developed in NetLogo version 6.0.x but should work in the most recent releases of NetLogo. The FYFAM software posted here since February, 2017, has software improvements that dramatically increase execution speed (by 20 times in our test case).

A large zip archive of code tests is available upon request.

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.