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

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Code to Analyze Occupancy Data for Dixie Valley Toads, Anaxyrus williamsi in Churchill County, Nevada from 2018 to 2021

-R code to create and fit dynamic occupancy models to Dixie Valley Toad survey data in JAGS and produce useful summaries of model results. This script will perform the Gibbs Variable Selection (GVS) using the initial set of environmental covariates, and then fit the "final" model using only important environmental covariates. The dynamic occupancy model is adapted from the model published by Duart

OAF Tools - R package

This repository contains the source code for the oaftools package. The package creates visual tools to study aftershock behavior and the performance of the Operational Aftershock Forecasting system. The visual tools are: A global map, rendered by Leaflet to show the distribution of earthquakes with forecasts A local map, rendered by Leaflet to show the aftershock sequence and the aftershock zone

shinymgr: A framework for building, managing, and stitching Shiny modules into reproducible analyses and reports.

Shinymgr is an R package that provides a unifying framework for managing and deploying Shiny applications that consist of modules. Developers use the shinymgr framework to write modules and seamlessly combine them into Shiny apps, and users of these apps can execute reproducible analyses that can be incorporated into reports for rapid dissemination. The package includes 11 instructional tutorials


Scoops3D is software to analyze three-dimensional slope stability throughout a digital landscape.


Line-transect distance sampling (LTDS) surveys are commonly used to estimate abundance of animals or objects. In terrestrial LTDS surveys of gopher tortoise (Gopherus polyphemus) burrows, the presence of ground-level vegetation significantly decreases detection of burrows of all sizes, but no field or analytical methods exist to control for spatially heterogeneous vegetation obstruction as a sourc


The Hydrologic Analysis Package (HASP) can retrieve groundwater level and groundwater quality data, aggregate these data, plot them, and generate basic statistics. One of the benefits of HASP is its ability to aggregate two time-series of data into one record and generate statistics and graphics on hat record. By merging two data sets together, users can view and manipulate a much longer record o

Keys Carbonate Budget Calculations and Analysis

The code 'Keys Carbonate Budget Calculations', written in R (v.4.0.4;, uses benthic coral-reef survey data and fish survey data to calculate coral-reef carbonate budgets following the ReefBudget v2 methodology (; Perry and Lange, 2019). The carbonate budgets include estimates (means +/- standard errors) of gross carbonate product

Modflow 6.4.0 - Los Angeles Coastal Plain

MODFLOW 6 - LACP uses the MODFLOW 6.4.0 source code and modifies the Horizontal Flow Barrier (HFB) package to allow simulation of vertical hydraulic conductance (CV) by connection rather than by cell, an option available for previous versions of MODFLOW (USG). The MODFLOW 6 - LACP HFB package is used to simulate thin, vertical, and low-permeability geologic features (barriers) and acts to supplem

Code for analysis of polar bear maternal den abundance and distribution in four regions of northern Alaska and Canada within the Southern Beaufort Sea subpopulation boundary (1982-2015)

We have archived the derived data files and R/JAGS code for our analysis as a U.S. Geological Survey data release (link ). The code is divided into three R scripts: 1) pbdens_landdens_JWM.r contains R code for fitting hierarchical Bayesian models of polar bear maternal den abundance and distribution for the Southern Beaufort Sea (SBS) subpopulation, 1982-2015. This script requires the installation

Applying Simulated Treatments to Bat Populations Experiencing Severe White-nose Syndrome Mortality

We developed a model allowing for the application of treatment strategies to bat populations at risk of severe mortality from WNS. The model allows the bat population to exist within a network of hibernacula and updates survival, reproduction, movement, treatment applications, and treatment related disturbance annually. For simplicity, the effects of WNS are experienced across all hibernacula on t

grsg_lekdb: Compiling and standardizing greater sage-grouse lek databases, version 1.1.0

Greater sage-grouse (Centrocercus urophasianus) are landscape-scale sagebrush obligate species and an important gamebird and iconic species of the western United States. They occupy the sagebrush biome in western North America, extending east of the Sierra Nevada/Cascade Mountain ranges to the western regions of the Great Plains of the United States. Sage-grouse are one of the most closely monitor

USGS Model Catalog intake repository

This project contains the repository component of a modular catalog implementation.