Software

R code to evaluate the effects of wastewater reuse on smallmouth bass (Micropterus dolomieu) relative abundance in the Shenandoah River Watershed, USA

This model was written in python3 which can simulate water level fluctuations under different drawdown operation rules. We submitted the manuscript about this model to the Journal of Environmental Management. The model file was saved in directory “models/WDLake”, and you can reproduce the results by running the jupyter notebooks in “notebooks/”.

Code to fit a Multiple Population Viability Analysis (MPVA) to time series of Foothill yellow-legged frog (Rana boylii) egg mass counts. Rose, J.P., and Halstead, B.J., 2023, Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California: U.S. Geological Survey software release, https://doi.org/10.5066/P9QWX2GR. This code

Software release for a topobathymetric DEM fusion approach. The operation, theory, and processes used in this software release can be used to fuse two topobathymetric digital elevation models (DEMs), creating seamless transitions around the two datasets' seamlines. This software heavily utilizes the arcpy python module, installation of ArcGIS Pro and a valid spatial analyst license is required.

This repository contains an example application of the `Meta-IPM` Python package (https://doi.org/10.5066/P9PW673G). The specific application focuses on the Illinois River using existing public data.

This repository contains code to cluster a sample of Mussels based up their metabolic levels via Non-Metric Multidimensional Scaling (NMDS) and distance based-Redundancy Analysis (db-RDA). Mussel sample is broken down and examined by catch location, sex, and species. The code for this project assumes the reader is familiar with R and clustering techniques.

Climate data allow people to examine species distributions and possible distributions. This script takes ERA5-Land climate estimates (https://www.ecmwf.int/en/forecasts/datasets/reanalysis-datasets/era5) for precipitation and lake temperature and processes them to create summary climate layers for use with biological organisms in lakes. This code could be modified to use a different subset of year

This repository contains analysis codes to interpolate missing data from the Upper Mississippi River LTRM dataset.

This software release includes code to conduct analyses presented in the manuscript titled: A hierarchical modeling framework for estimating individual- and population-level reproductive success from movement data

SeaLog is a robust data-logging application designed to collect at-sea data of marine birds and mammals. This software was developed collaboratively with the U.S. Geological Survey, the National Park Service, the U.S. Fish and Wildlife Service, and ABR, Inc. SeaLog is Windows 10 compatible, is highly customizable, and provides user designed maps to allow visual feedback of observations.

PopEquus is a predictive modeling tool to support decisions related to the management of free-roaming horse populations. It permits the simulation and comparison of how management alternatives influence horse population size and metrics associated with management. This repository uses R scripts with predictive functions from the PopEquus model to simulate how management alternatives (e.g., removin