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

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R code for calculating imperilment of freshwater fish with a Bayesian belief network

This R script is reproduces a Bayesian belief network built within the propriety software program, Netica. The R- and Netica-based belief networks were used in Dunn and Schumann et al. (in press), which presents an approach for calculating imperilment of freshwater fishes.


The goal of algaeClassify is to facilitate the analysis of taxonomic and functional trait data for phytoplankton.

Population Viability Model for Spot-tailed earless lizard

Code for simulating Spot-tailed earless lizard populations under habitat loss and road mortality threats in central Texas

Predicting fish responses to climate change using a joint species, spatially dependent physiologically guided abundance model

Predicting the effects of warming temperatures on the abundance and distribution of organisms under future climate scenarios often requires extrapolating species-environment correlations to thermal conditions not currently experienced by a species or to temperatures that exceed the range of observed data. For poikilotherms, incorporating species’ thermal physiology to inform extrapolations under

Population genetic structure of white-tailed deer using microsatellites i the Mid-Atalntic region

Results of 11 microsatellites for white-tailed deer collected in Maryland, New York, Ohio, Pennsylvania, and Virginia from 2014 to 2022 for genetic analysis. In this project we assessed genetic structure using different analyses, and evaluated the performance of assignment tests to correctly match deer to origin (defined as genetic cluster, state or physiographic province). This repository include


Estimating High Resolution Multi-Cropped Irrigated Land Use Using a Pesticide Use Reporting Database in California Estimating the amount of water needed for agriculture is vital for food and water security. These estimates rely on maps of crop type and acreage that have limited ground-truthing or represent multiple years or regional cropping patterns. In regions where crops change frequently or m

Numerical model of coastal Erosion by Waves and Transgressive Scarps (NEWTS)

The Numerical model of coastal Erosion by Waves and Transgressive Scarps (NEWTS) model is a framework to simulate the erosion of a closed-basin coastline through time by fetch-dependent erosion or uniform erosion. The model is written in MATLAB and the MATLAB Image Processing Toolbox and a MEX compiler are required.

Chronic Wasting Disease Surveillance Optimization Software Version 2

The Chronic Wasting Disease Surveillance Optimization Software Version 2 computes sampling recommendations to detect chronic wasting disease (CWD) in white-tailed deer (Odocoileus virginianus). Driven by a combinatorial optimization algorithm, the software maximizes the return-on-investment to the wildlife agency while keeping the overall surveillance program within budget. The software pinpoints

Chronic Wasting Disease Modeling for Bridger Teton National Forest Structured Decision Making (cwd-btnf-sdm-v2)

This software release contains the code necessary to run the chronic wasting disease (CWD) and elk habitat selection models used to support the U.S. Forest Service decision on whether to continue to permit supplemental feeding of elk on USFS land. The models allow for four different management alternatives: continued feeding, emergency feeding, phase-out after three years, or no feeding. The CWD m

Optimal harvest of a theoretical population under system change

This code solves optimal harvest policies under different scenarios of system change, represented as changes in demographic parameters over time. This document contains code to solve policies using backwards iteration stochastic dynamic programming, project populations forward to simulate the policies, and generate figures.

R Code Supporting the Manuscript: Using Stochastic Point Pattern Analysis to Track Regional Orientations of Magmatism During the Transition to Cenozoic Extension and Rio Grande Rifting, Southern Rocky Mountains

This repository contains code that supports ongoing research in the southern Rocky Mountains in Colorado and northern New Mexico. This region hosted intracontinental magmatism that developed during a tectonic transition from shortening (Laramide orogeny, ca. 75 to 40 Ma) through extension and rifting. The code in this repository presents a novel approach that uses stochastic weighted bootstrap sim

SAS: Software Application for SMASH (Spectral Mixture Analysis for Surveillance of Harmful Algal Blooms)

The Software Application for SMASH (Spectral Mixture Analysis for Surveillance of Harmful Algal Blooms), or SAS for short, is an application to facilitate mapping of potentially harmful algal blooms in reservoirs, rivers, and lakes from remotely sensed data. More specifically, SAS is designed to exploit the detailed observations of reflectance available within a hyperspectral image to infer which