BioenergeticHSC
User-friendly software for generating bioenergetics-based habitat suitability curves for drift-feeding fishes
Downloads
Click on the links below to download a folder containing the program, program manual, and demo input files. Open the program by unzipping the folder and clicking on the “BioenergeticHSC.app” icon (for mac OS) or the “BioenergeticHSC.exe” (for Windows). The Windows version has been tested on Windows 10 and Windows 7. It should theoretically work on Windows 8 but this is not certain. The “Resources” folder contains the user manual and demo input files.
Download for Mac OSX (requires OS X 10.11.6 or newer)
Link to source Python code on GitHub: https://github.com/JasonNeuswanger/BioenergeticHSC
Updates
2020-6-7 Overview paper on BioenergeticHSC is out as a pre-proof in Fisheries
2020-6-7 Updated manual (version 1.0) is now included with software download.
2020-5-15 Small bug in turn cost equation fixed.
2019-10-11 BioenergeticHSC v1.0.0 released.
2019-11-28 Updated draft of user manual posted, which includes more details on interpreting bioenergetic HSCs
Project Synopsis
Background and rationale
Determining environmental flow needs – the quantity and timing of flow necessary to protect aquatic life in streams and rivers – is a key challenge for natural resource management agencies. The most common approach for predicting the impacts of altered flows on fish are variants of the Physical Habitat Simulation Model (PHABSIM), which combines a hydraulic habitat simulation model with a biological model that predicts how habitat quality changes with velocity and depth. Habitat Suitability Curves (HSCs) are the most common biological model used in PHABSIM frameworks. HSCs are generally empirically derived microhabitat models, where the frequency of use of velocity and depth by the target fish species is compared to the ambient velocity and depth distribution available in the environment to generate a preference curve (use relative to availability) that is standardized to a maximum of 1.
While intuitive, this approach has been widely criticized. Primary concerns include: (1) territorial displacement of subordinate fish into lower quality habitat at high densities can make frequency-of-use (density) a poor metric of habitat quality; (2) HSCs are poorly transferable across locations; and (3) suitability metrics lack a clear biological interpretation. Despite these criticisms, few viable alternatives are available; consequently, frequency-based HSCs continue to be used.
We have attempted to address this issue using drift-foraging bioenergetic models that predict energy intake for fishes that occupy fixed focal points in the water column to forage on drifting invertebrates (e.g., salmon and trout; Hughes and Dill 1990, Hayes et al. 2007). Drift-foraging models represent habitat quality as the net rate of energy intake (NREI; equivalent to growth rate potential), estimated as gross energy intake less energy costs of swimming and maneuvering to intercept prey at a given focal velocity and depth. Because these models are inherently mechanistic rather than empirical, they should provide a more rigorous measure of habitat quality, with a clear biological interpretation (energy gain) that is transferable across locations.
Generating mechanistic bioenergetics-based HSCs is a complicated and time-consuming process, which represents a significant barrier to their wider use. Our motivation was to improve this situation by developing user-friendly software to allow simple and straightforward generation of bioenergetics-based habitat suitability curves.
Overview of software
BioenergeticHSC is an open source modelling tool designed to generate bioenergetics-based habitat suitability curves. Users supply data on invertebrate drift and specify initial parameters including fish size, temperature, and turbidity; then, the program uses a net energy intake model to produce a 2D surface of bioenergetics-based habitat suitability.
These HSCs can be exported and used the same as traditional habitat suitability curves with common instream flow modelling platforms, e.g., PHABSIM. There are several other functionalities of the software, including computation of net energy intake, habitat suitability and intermediate metrics (e.g., swimming costs) on user-supplied depth and velocity data. A comprehensive manual accompanies the program to give details and guidance.
Potential uses
1). Flow assessments:
(a) Standard HSC use. The modelling tool can be used to generate bioenergetic-based HSCs for use in standard habitat simulation applications, i.e., to determine how habitat availability changes across a range of flows.
(b) Using net energy intake rate (NREI) as a direct index of habitat quality. Rather than converting NREI to HSCs to use in a physical habitat simulation model, the modelling tool can be used to directly calculate NREI at individual sampling points in a channel using measured velocity and depth values (i.e., using imported transect data). This will allow the mean and variance (or frequency distribution) of NREI to be used directly as an index of habitat quality, rather than relying on conversion of NREI to a HSC as an intermediate step.
2). Assessing variation in habitat capacity within and among streams:
PHABSIM combines HSCs with a hydraulic model to generate weighted usable area (WUA) - a relative index of available habitat in a specific stream or reach across different flows. While differences in WUA among streams may serve as a very rough metric of differences in habitat quality, the strength of this inference is weak because traditional frequency-based HSCs do not account for differences in biological productivity; i.e. traditional frequency-based HSCs generated in different streams are all standardized to a maximum of 1 (regardless of differences in fish density among streams), so that any differences in algal, microbial, and invertebrate prey abundance (driven by underlying geology or nutrient chemistry) are removed. In contrast, predicted NREI values explicitly incorporate differences in prey abundance (invertebrate drift), so that NREI integrates the effect of both physical habitat quality and biological production at the base of the food chain. This means that NREI can be used as a direct index of relative habitat capacity among streams.
3). Assessing the sensitivity of habitat quality to parameter variation. The modelling tool can be used to predict the relative effects of changes in key parameters (e.g., fish length or prey abundance) on habitat suitability and flow requirements. This sort of sensitivity analysis could be useful for assessing the potential effects of a variety of environmental impacts, including climate change.
Additional Resources
BAckground Materials
We encourage users to familiarize themselves with the basics of drift-foraging theory to use this tool. Below are a few papers that give background on the approach used in this software.
Bioenergetics-based habitat suitability curves
Drift-foraging bioenergetics models
Spreadsheet tool to adjust existing HSCs
HSC right-shift tool for transforming HSCs based on average water column velocities at focal points to spatially-averaged HSCs. This is designed to address the potential bias in velocity HSCs due to fish exploiting lateral velocity gradients. This is described in detail in Naman et al. (In Press). North American Journal of Fisheries Management (download).
Appendix 1 - HSC Shift tool description
Disclaimer
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
For questions, contact: Sean Naman (seanaman@gmail.com) or Jordan Rosenfeld (jordan.rosenfeld@gov.bc.ca)