Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
Filter Total Items: 820
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.
Streamflow Rank Estimation (SRE) Model Streamflow Rank Estimation (SRE) Model
This repo contains the source code for the Streamflow Rank Estimation (SRE) model, which is a deep learning model designed to estimate streamflow using timelapse imagery. The model is built using PyTorch and can be run on any system with or without a GPU. This model has been integrated into the USGS Flow Photo Explorer, a cloud-based machine learning platform for training the model and...
STACS STACS
STACS: Software Tool for Approximating Channel Shapes Description The software application made available through this repository provides an integrated end-to-end workflow for modeling the geometry of river channel cross sections. This standalone program is called the Software Tool for Approximating Channel Shapes, or STACS for short, and provides convenient access to a flexible...
Agisoft Metashape Bounding Box Helper Tool Agisoft Metashape Bounding Box Helper Tool
The Bounding Box Helper written by Connor Jenkins in support of Selena Johnson's diver-based Structure-from-Motion processing workflow for precise application of bounding box dimensions between related chunks in Agisoft Metashape for extraction of identical data areas. The Bounding Box Helper is designed for two primary uses: to facilitate precise manipulation of bounding box dimensions...
Grazing Management Tool Grazing Management Tool
Science-based grazing management is crucial to preserving and improving rangeland productivity and sagebrush ecosystem health. By adjusting the timing, duration, frequency, and intensity of grazing, managers can contribute to ecosystem services such as fuel reduction and invasive annual grass control. They can also utilize rotational grazing to minimize or mitigate impacts on sensitive...