Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
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Media Metadata Editor Media Metadata Editor
This Python-based toolbox reads media (photo, audio, video) file locations, creates a metadata template CSV file, and uses the metadata template CSV file to embed metadata into the media files themselves. Created to function exclusively in ArcGIS Pro, the toolbox provides a GUI (graphical user interface) interface to complete functions without the need for Python coding or scripting...
EnergyStorageUQ R and JAGS code EnergyStorageUQ R and JAGS code
The EnergyStorageUQ repository of R and JAGS code provides JAGS models and an R workflow for analyzing energy storage capacity of gas reservoirs using material balance methods embedded in statistical models. The code contains tools for a workflow that includes fitting models, making predictions with uncertainty through Monte Carlo simulation, and visualizing the resulting material...
Code to evaluate the effect of the 2021 Dixie Fire on the occurrence of foothill yellow-legged frogs (Rana boylii) in northeastern California in 2022 Code to evaluate the effect of the 2021 Dixie Fire on the occurrence of foothill yellow-legged frogs (Rana boylii) in northeastern California in 2022
This repository contains code to fit a static occupancy model to time-to-detection data for foothill yellow-legged frogs (Rana boylii). This repository specifically contains code to reproduce analyses in: Halstead, B.J., Kleeman, P.M., and Rose, J.P., 2024, Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence: Journal of Fish and...
Jackson Bison Population Projections Jackson Bison Population Projections
The aim of this software is to perform the simulations that evaluate the alternatives associated with the National Elk Refuge Bison and Elk Management Plan. In particular, it produces results associated with bison population dynamics, harvest, and conflict potential. For additional detail on the methodology and case study, please refer to: Cook, J.D., McEachran, M.C., Cotterill, G.G...
mlms---Multilevel Monitoring System (MLMS) data storage and processing for the U.S. Geological Survey Idaho National Laboratory Project Office mlms---Multilevel Monitoring System (MLMS) data storage and processing for the U.S. Geological Survey Idaho National Laboratory Project Office
Package used to store and process data from the Multilevel Monitoring System (MLMS) used in wells within the U.S. Geological Survey (USGS) aquifer-monitoring network at the Idaho National Laboratory (INL) in Idaho. Supported by the U.S. Department of Energy (DOE), the USGS collected discrete measurements of hydraulic head at various depths from wells in the eastern Snake River Plain...
Supporting material for Challenges and opportunities for data integration to improve estimation of migratory connectivity Supporting material for Challenges and opportunities for data integration to improve estimation of migratory connectivity
This is supporting code for the paper "Challenges and opportunities for data integration to improve estimation of migratory connectivity" by Jeffrey A. Hostetler, Emily B. Cohen, Christen M. Bossu, Amy L. Scarpignato, Kristen Ruegg, Andrea Contina, Clark S. Rushing, and Michael T. Hallworth in Methods in Ecology and Evolution. It allows the reader to run the simulations and case studies...
R scripts for the analysis of a predatory fish invasion on a riverine food web R scripts for the analysis of a predatory fish invasion on a riverine food web
Catfishes are opportunistic feeders that are among the world's worst invasive species. Flathead catfish Pylodictus olivaris -- a large predatory catfish -- were first detected in the Susquehanna River, Pennsylvania, USA in 2002. Since then, they established a viable and rapidly growing population that is expanding its range throughout the river system. Although the predatory effects of...
hyRefactor: Tools for Manipulating the NHDPlus Network in Preparation for Hydrologic Modeling hyRefactor: Tools for Manipulating the NHDPlus Network in Preparation for Hydrologic Modeling
This software was used to make derivatives of the features in the NHDPlusV2 geospatial dataset for use in hydrologic model applications. It is not intended for users to deploy/use and may produce unexpected results outside the workflow and environment in which it was implemented. For users seeking to deploy a version of this software, please see https://github.com/noaa-owp/hydrofab. The...
Code release for simulated tag-return study for monitoring invasive fish removals Code release for simulated tag-return study for monitoring invasive fish removals
This repository is a code release to create and analyze simulated datasets to represent a tag-return study for the purposes of estimating annual removal rates of an invasive fish. The simulated scenarios cover ranges of parameters such as the number of fish tagged per year, magnitude of annual harvest rate, length of simulated study, probability of tag retention, probability of tag...
HyMED Hydrologic Model Evaluation for Drought HyMED Hydrologic Model Evaluation for Drought
This package facilitates the analysis and evaluation of hydrologic model streamflow output during periods of drought. This package calculates the Cohen's Kappa, Spearman correlation coefficient, ratio of standard deviation, percent bias, normalized mean absolute error (NMAE) in the annual time series of drought duration, NMAE in the annual times series of the distance the minimum...
Code for Distance sampling accounting for density gradient and animal distribution Code for Distance sampling accounting for density gradient and animal distribution
Code to estimate animal density from line transect surveys where auxiliary data are available to model the distribution of animals near the survey line and the distribution of animals across the study area.
occstanhm: Hierarchical occupancy models with correlated error structure occstanhm: Hierarchical occupancy models with correlated error structure
This repository contains a R package with 2-level and 3-level occupancy models. The package also contains a set of tutorials designed to help users understand how to use and code occupancy models in Stan. The models include a statistical hierarchy that allows for multi-species modeling and estimating correlations among species. The models may also be used as a more general "random-effect...