Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
Filter Total Items: 863
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...
Code for Fomites could determine severity of SARS-CoV-2 outbreaks in low-density white-tailed deer Odocoileus virginianus populations Code for Fomites could determine severity of SARS-CoV-2 outbreaks in low-density white-tailed deer Odocoileus virginianus populations
This software release contains 1 RMarkdown file (Indirect_SARS_analysis.RMD) and necessary input data and functions that support the analysis presented in referenced manuscript (IP-166277). This RMarkdown file that steps through the estimation of parameters that allow: Compile estimated and derived parameters for both indirect and direct transmission pathways for SARS-CoV-2 in white...
R workflow for the analysis of fish tissue mercury concentrations following the invasion of zebra mussels in Minnesota Lakes R workflow for the analysis of fish tissue mercury concentrations following the invasion of zebra mussels in Minnesota Lakes
Aquatic invasive species can influence mercury methylation and bioaccumulation in lake ecosystems by altering chemical and biological pathways and dynamics. Invasive zebra mussels Dreissena polymorpha, which have invaded lakes and rivers throughout North America, may amplify mercury bioavailability by disrupting food webs and altering biogeochemical processes. This potential...
Code for similar population dynamics before and after a chytridiomycosis outbreak in a tropical riparian amphibian species. Code for similar population dynamics before and after a chytridiomycosis outbreak in a tropical riparian amphibian species.
This software release contains 4 files with R scripts organized according to the objective (e.g., format the data, model fitting, etc.). The overall objective of the project was to: analyzed ten years of capture-mark-recapture data spanning 2000−2014 for a population of Espadarana prosoblepon in El Copé, Panama, encompassing a period before and after a Batrachochytrium dendrobatidis (Bd)...
Piping plover adult breeding dispersal and annual survival in the northern Great Plains, USA, model code Piping plover adult breeding dispersal and annual survival in the northern Great Plains, USA, model code
The affiliated manuscript examines adult survival and breeding dispersal for piping plovers at two spatial scales and examines covariates that influence them. This product includes the R and JAGS model code to run the models in the manuscript with the data from the affiliated data release.