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

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Inferring pathogen presence when sample misclassification and partial observation occur

This software contains four separate R scripts and one Matlab script that comprise an analysis to estimate the posterior probability of pathogen presence when sample misclassification and partial observations occur. We develop a Bayesian hierarchal framework that accommodates false negative, false positive, and uncertain detections and apply this framework to a case study of the fungal pathogen Ps

Code for Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses

Code will be submitted to the Dryad repository upon acceptance of the manuscript. These R code are used for simulations and case studies. Simulations include data for generating age-period survival data. We have provided code for each of the 10 models that were fit using NIMBLE, where each model has four R scripts including: 1) A script to execute and run all the additional R scripts for each simu

Code for Rapid prototyping for quantifying belief weights of competing hypotheses about emergent diseases

Code submitted to Journal of Environmental Management and ScienceBase for running Bayesian hierarchical models on a dataset that was collected using expert elicitation of a panel of 15 experts on the etiology of stony coral tissue loss disease and its impacts on coral reefs. The code is for a rapid prototyping method for quantifying belief weights for competing hypotheses about the etiology of dis

Toolbox for River Velocimetry using Images from Aircraft (TRiVIA)

# TRiVIA Toolbox for River Velocimetry using Images from Aircraft: TRiVIA ## Description The Toolbox for River Velocimetry using Images from Aircraft, or TRiVIA for short, is an application to facilitate estimation of surface flow velocities in river channels from various types of remotely sensed data acquired with a nadir-viewing geometry (i.e., looking straight down). Spatially distributed info

gravmagsubs: Gravitational and magnetic attraction of 3-D vertical rectangular prisms

gravmagsubs is a software package for the R language that provides tools for forward modeling gravity and magnetic anomalies from 3-D right rectangular prisms. The gravity anomaly is defined as the vertical component of gravitational acceleration, while the magnetic anomaly includes the effects of both induced and remanent magnetization. The package can model the total anomaly from a collection

Agisoft Metashape/Photoscan Automated Image Alignment and Error Reduction version 2.0

This repository contains python scripts which automate image alignment and sparse point cloud error reduction in the Agisoft Metashape/Photoscan structure from motion photogrammetry software package using the Agisoft Metashape Python API. The current version of the script (version 2.0) approximates the workflow described in U.S. Geological Survey Open-File Report 2021-1039 (Over et al., 2021). The

GageStats Services

The Gage Statistic (GageStats) Services were developed to provide gage characteristics and streamflow statistics to support the StreamStats application via RESTful principles. The StreamStats application uses GageStats Services to display the gages and related gage pages. These services provide U.S. Geological Survey developed and published gage characteristics such as drainage area or mean basin

USGS Model Catalog Tools and Metadata

Tools and metadata for the USGS Model Catalog.


The U.S. Geological Survey (USGS) developed an R package called dataRetrieval to help simplify the process of discovering and retrieving water quality sample data, streamflow, groundwater, and other data available from Federal hydrologic web services such as National Water Information Systems (NWIS), the EPA Water Quality Exchange (WQX) System, and the National Hydrologic Dataset via the Hydro-Ne

QFASA Robustness to Assumption Violations: Computer Code

Quantitative fatty acid signature analysis (QFASA; Iverson et al. 2004) has become a common method of estimating diet composition, especially for marine mammals, but the performance of the method has received limited investigation. Bromaghin et al. (In press) used computer simulation to compare the bias of several QFASA estimators and developed recommendations regarding estimator selection. Simula

MODFLOW 6: USGS Modular Hydrologic Model

MODFLOW is a popular open-source groundwater flow model distributed by the U.S. Geological Survey. 

MODFLOW One-Water Hydrologic Flow Model (MF-OWHM)

The MODFLOW One-Water Hydrologic Flow Model (MF-OWHM) is an integrated hydrologic model designed for the analysis of conjunctive-use management.