Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
Filter Total Items: 628
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.
Scenario Analysis of Management Alternatives for Free-roaming Horse Populations (Version 1.0.0)
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
ADOM: A Data Orchestration Manager
A Data Orchestration Manager (ADOM) is a user interface designed to enforce data management goals by entwining and extending the open-source file management tool rclone. The rclone tool provides data movement and management functionality in and between supported end-user-defined endpoints, also known as remotes. ADOM takes rclone a step further by wrapping rclone functionality into USGS-specific f
Modeling widespread declines in walleye recruitment following zebra mussel invasion in Minnesota lakes
Invasive zebra mussels (Dreissena polymorpha) alter lake ecosystems and can negatively affect first-year growth of walleye (Sander vitreus), potentially lowering walleye recruitment success. We quantified walleye recruitment responses to zebra mussel invasion in Minnesota lakes using data from 1,438 electrofishing surveys across 348 lakes collected between 1993 and 2019 to measure walleye recruit
Accounting for spatio-temporal variation in catchability in joint species distribution models
1: Estimating relative abundance is critical for informing conservation and management efforts and for making inferences about the effects of environmental change on populations. Freshwater fisheries span large geographic regions, occupy diverse habitats, and consist of varying species assemblages. Monitoring schemes used to sample these diverse populations often result in populations being sample