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Software

An official USGS software project is code reviewed and approved at the bureau-level for distribution.

Filter Total Items: 597

SEIcarP

SEIcarP is an R package (R Core Team 2021) implementing the Spatially Explicit Invasive Carp (SEICarP; sometimes stylize as SEIcarP) population model for the Illinois River. This repository contains the SEIcarP model plus two additional packages required for the main model package to run. These are the SEIcarP Bighead Carp (BH) data (SEIcarPdataBHCP) and the SEIcarP Silver Carp (SV) data (SEIcarPd

CoSMoS-COAST: The Coastal, One-line, Assimilated, Simulation Tool of the Coastal Storm Modeling System

A software release of CoSMoS-COAST: The Coastal, One-line, Assimilated, Simulation Tool of the Coastal Storm Modeling System. The software (coded in Matlab) encapsulates a long-term shoreline change model that combines longshore and cross-shore transport and assimilates historical shoreline observations.

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

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

A hydrological modeling framework for lake water level drawdown management

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 for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California

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

Adaptive Topobathymetric Fusion Software Version 1.0

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.

Example application of MetaIPM to the Illinois River

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.

Indiana mussel metabolomics data analysis

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.

Calculations of BioLake climate data

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

Interpolating missing water quality data

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

Reproductive Success from Movement Data

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

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.