Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
Filter Total Items: 867
Ecoflows body size analysis Ecoflows body size analysis
The code repository has been produced by the CONUS Ecological Flows project and contains scripts to run an analysis of fish body size relationships with flow regimes, functional traits, and land-use. This code can be run with the input dataset found from Woods (2025).
multi-species frog occupancy multi-species frog occupancy
Anurans (frogs and toads) were surveyed using aural call surveys across the upper Midwest, United States from 2003 to 2008, and again in 2024. This code analyzes these data (from the associated data releases) using a multi-species occupancy model with imperfect detection, species traits, and species associations. It tests for relationships between covariates, occupancy, and detection...
King Rail (Rallus elegans) occupancy trends in the Arkansas Delta King Rail (Rallus elegans) occupancy trends in the Arkansas Delta
This code cleans and analyzes historical King Rail (Rallus elegans) occurrence data in the Arkansas Delta to generate a multi-season spatial occupancy model. The data itself is publicly-available from Arkansas Game & Fish Commission.
Track Segmentation: Stops and Movements Track Segmentation: Stops and Movements
This R script inputs animal tracking data and segments the time series for each individual animal into sequential periods of stops and movements. The algorithm identifies stops based on two influential user-defined thresholds: 1) a distance threshold (hereafter 'Dist') that defines the upper limit of spatial displacement permissible while occupying a stop, and 2) a duration threshold...
neic-supershear-analysis neic-supershear-analysis
NEIC Supershear Analysis This software evalutes potential supershear ruptures by attempting to detect a Rayleigh Mach wave. It follows the work of Valle and Dunham (2012): Vallée, M., and E. M. Dunham (2012), Observation of far-field Mach waves generated by the 2001 Kokoxili supershear earthquake, Geophys. Res. Lett., 39, L05311, doi:10.1029/2011GL050725. Long-period observations of...
Simulation code for Surprise Inlet landslides v1.0.0 Simulation code for Surprise Inlet landslides v1.0.0
This repository contains the code needed to reproduce the D-Claw simulation presented in Karasözen and others (2025). D-Claw is numerical software package for simulating granular-fluid flows (George and others, 2025; George & Iverson, 2014; Iverson & George, 2014). This code simulates a landslide generated tsunami scenario in which one of the Surprise Inlet landslides described by...
Analysis code for evaluation of the acute toxicity of 4-Nitro-3-(trifluoromethyl)phenol (TFM) to Burbot (Lota lota) Analysis code for evaluation of the acute toxicity of 4-Nitro-3-(trifluoromethyl)phenol (TFM) to Burbot (Lota lota)
Analysis code to evaluate Burbot tolerance to lampricide TFM, which is used in tributaries of the Great Lakes to control larval Sea Lamprey. A lab test of toxicity of this non-target species was conducted. This code examines the length and weight of test animals, visualizes water quality measures taken during the tests, and fits a dose response curve.
Example application of MetaIPM to the upper Mississippi River Example application of MetaIPM to the upper Mississippi 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 upper Mississippi River using existing public data. The code for this project assumes the reader is familiar with Jupyter Notebooks, enough Conda and Python to install the `Meta-IPM` package, and population ecology. The example also...
Code to evaluate the effect of weather on the demography of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite National Park Code to evaluate the effect of weather on the demography of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite National Park
This repository contains code to fit open population models to capture-mark-recapture data for Sierra Nevada yellow-legged frogs (Rana sierrae). This repository specifically contains code to reproduce analyses in: Halstead, B.J., Kleeman, P.M., Rose, J.P., and Fellers, G.M. 2025. Climate-induced extirpation of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite...
ModelMuse: A Graphical User Interface for Groundwater Models ModelMuse: A Graphical User Interface for Groundwater Models
ModelMuse is a graphical user interface (GUI) for the U.S. Geological Survey (USGS) models MODFLOW 6, MODFLOW–2005, MODFLOW-LGR, MODFLOW-LGR2, MODFLOW-NWT, MODFLOW-CFP, MODFLOW-OWHM versions 1 and 2, MODPATH, ZONEBUDGET, PHAST, SUTRA 2.2, SUTRA 3.0, SUTRA 4.0, MT3D-USGS, and WellFootprint and the non-USGS programs MT3DMS and PEST.
R scripts to run model of bird density and habitat associations R scripts to run model of bird density and habitat associations
The script (habitat_density_model.r) in this code repository filters data, sets up model input, and runs an N-mixture model with two components of detection (availability and perceptibility) to estimate bird density from point-count data. This analysis was developed to evaluate covariates of population density for three species of boreal birds: Lesser Yellowlegs, Olive-sided Flycatcher...
Prioritizing catchments for native freshwater mussel conservation in the Northeastern United States Prioritizing catchments for native freshwater mussel conservation in the Northeastern United States
This software contains two separate R Markdown files that comprise an analysis to: 1.) Build and test MaxEnt models predicting the distribution of twelve species of native freshwater mussels in the Six North-Eastern most U.S. states. We generate models with beta multipliers 1-15 and identify optimal models using the dismo package, maxent.jar, and ENMeval. 2.) Using the species...