Software

This repo contains the source code for the Streamflow Rank Estimation (SRE) model, which is a deep learning model designed to estimate streamflow using timelapse imagery. The model is built using PyTorch and can be run on any system with or without a GPU. This model has been integrated into the USGS Flow Photo Explorer, a cloud-based machine learning platform for training the model and...

R Code to run shortnose sturgeon population estimates for Higgs et al. 2025 The purpose of this software is to estimate the abundance of overwintering shortnose sturgeon using acoustic telemetry and side-scan sonar data. The code is based on work conducted on the Hudson River, New York, but could be readily adapted to other applications with a similar study design.

ezMCDA is a user-friendly software to conduct Multicriteria Decision Analysis (MCDA) while considering uncertainty and nonlinear utility functions.

The purpose of this software is to develop predictions about future changes in the social and economic benefits provided by bison and elk and their management on the National Elk Refuge. The effects are estimated as a function of changing wildlife populations under different management alternatives. For additional detail on the methodology and case study, please refer to: McEachran, M.C...

The aim of this software is to perform the simulations that evaluate the alternatives associated with the National Elk Refuge Bison and Elk Management Plan. In particular, it produces results associated with bison population dynamics, harvest, and conflict potential. For additional detail on the methodology and case study, please refer to: Cook, J.D., McEachran, M.C., Cotterill, G.G...

This is supporting code for the paper "Challenges and opportunities for data integration to improve estimation of migratory connectivity" by Jeffrey A. Hostetler, Emily B. Cohen, Christen M. Bossu, Amy L. Scarpignato, Kristen Ruegg, Andrea Contina, Clark S. Rushing, and Michael T. Hallworth in Methods in Ecology and Evolution. It allows the reader to run the simulations and case studies...

R Code to Run Composition Sampling for Cook et al. 2023 The aim of this software is to perform composition sampling on simulated disease observation data. Composition sampling is a valuable approach for statistical inference in data limited systems. This software implements composition sampling on simulated chronic wasting disease surveillance data in white-tailed deer in Michigan, U.S...

The aim of this software is to share results from Prosser et al. (2024) by allowing users to explore different spatial layers over each week of the year via an interactive mapping interface. This web application serves as a decision support tool for decision makers related to transmission risk during the ongoing highly pathogenic avian influenza outbreak. This software provides a user...

Code and associated files hosted on USGS GitLab which support the USGS Chesapeake Bay Studies Data Catalog Application available at https://rconnect.usgs.gov/ChesapeakeBayDataCatalog/.

Source code to run Shiny app of North American bat SARS2 risk model during winter fieldwork

Python code generated for the purpose of summarizing a defined set of discrete/categorical and/or continuous raster layers within zones that may be overlapping. Many widely used GIS tools to summarize raster layers within zones are not capable of handling overlapping zones. This code also allows for the computations to be completed over a number of separate raster layers at once and...

To assist decision makers in risk assessments, two sets of indices have been developed to rank terrestrial vertebrates for their utility in biomonitoring and susceptibility.