83 Works


Neil Terry & Frederick D. Day-Lewis
MoisturEC is an R-based GUI used to combine electrical conductivity (EC) data with point moisture measurements for an updated moisture estimate capitalizing on the accuracy of point moisture measurements and the spatial coverage of EC data.

An Open Source Spreadsheet for Calculation of Equivalent Freshwater Altitude in Brackish Water Mixing Zone of an Aquifer with Documentation on Appropriate Use

Eve L Kuniansky
This software release documents an open source spreadsheet that was developed by the USGS in 2007 and modified herein for general use for calculation of equivalent freshwater altitude at wells where the water quality data indicate the well is tapping brackish areas of an aquifer system. One example of this includes coastal wells in the diffusion/mixing or transition zone of the aquifer near the freshwater/saltwater interface. This correction for salinity allows for the inclusion of...

MT3D-USGS: Groundwater Solute Transport Simulator for MODFLOW

Matthew J. Tonkin, Vivek Bedekar, Eric D. Morway & Christian D. Langevin
MT3D-USGS is a USGS updated release of the groundwater solute transport code MT3DMS. MT3D-USGS includes new transport modeling capabilities to accommodate flow terms calculated by MODFLOW packages that were previously unsupported by MT3DMS and to provide greater flexibility in the simulation of solute transport and reactive solute transport.

HTCondor examples

Richard A Erickson
This file contains several examples for using HTCondor to scale scientific processing with cluster computing. These examples assume that one has a functioning HTCondor pool with the appropriate software installed and configured (e.g., Docker for the Docker examples; R or Python for R or Python examples). Installing these programs is beyond the scope of these examples, however, we do include the setups we used to setup a condor pool in the HTCondor_setup_Procedures_for_UMESC file.

Point-Source Load Estimation Tool (PSLoadEsT)

Lillian Gorman Sanisaca, Kenneth D. Skinner & Molly A. Maupin
The Point-Source Load Estimation Tool (PSLoadEsT) provides a user-friendly interface for generating reproducible load calculations for point source dischargers while managing common data challenges including duplicates, incompatible input tables, and incomplete or missing nutrient concentration or effluent flow data. Maintaining a consistent method across an entire study area is important when estimating loads to be used as calibration data for regional water-quality models. PSLoadEsT is written using the open-source programming language R and has an...

National Fish Habitat Partnership (NFHP) Data System

U.S. Geological Survey, Science Analytics And Synthesis Program

Online supporting information for "Improving geographically extensive acoustic survey designs for modeling species occurrence with imperfect detection and misidentification"

Rogelio M. Rodriguez, Wilson J Wright, Katharine M. Banner, Andrea R. Litt, Kathryn M Irvine & Thomas J. Rodhouse
R package developed to support study design for acoustic bat surveys with imperfect detection misidentification

Software Supplement to accompany "Estimating Species-Environment Relationships with Non-ignorable Sampling Designs"

Kathryn M Irvine, Thomas J. Rodhouse, Wilson J Wright & Anthony R. Olsen
R code to fit models with and without sample weights and simulation code

Highway-Runoff Database software support page

Gregory E Granato
The highway-runoff database (HRDB) was developed to serve as a data warehouse for current and future highway-runoff data sets. The database can be used by transportation agencies and researchers as a data warehouse to document information about a data set, monitoring site(s), highway-runoff data (including precipitation, runoff, and event mean concentrations). The HRDB application, which is the graphical-user interface and associated computer code, can be used to facilitate estimation of statistical properties of runoff coefficients,...

Creating Custom Bar Codes for Tracking Samples from the Field to the Laboratory

Justin L. Welty
This tool is being provided free to the public in support of field and laboratory specialists who would like to create custom bar codes in order to better maintain their field and laboratory samples.

Generalized Mortality Estimator (GenEst) - R code & GUI

Juniper Simonis, Manuela Huso, Daniel Dalthorp, Jeffrey M. Mintz, Lisa Madsen, Paul Rabie & Jared Studyvin
GenEst is a tool for estimating mortalities from efficiency, persistence, and carcass data.

Continuous Analog of a Binomial Distribution: d/p/q/r Family of Functions

Daniel Dalthorp
This R package provides a standard d/p/q/r suite of functions for a continuous binomial distribution as presented by: Ilienko, Andreii. 2013. Continuous counterparts of Poisson and binomial distributions and their properties. Annales Univ. Sci. Budapest, Sect. Comp. 39: 137-147. Several files are built into an R package and stored in two different formats: (1) .zip, which contains compiled binaries for installing on computers that use the Microsoft Windows operating system, and (2) .tar.gz, which includes...

Python Scripts for Bioinformatics, 2017

Damian M Menning & Sandra L Talbot
Bioinformatics software repository containing python scripts intended for search and download of genetic information obtained from GenBank NCBI genetics data resources in support of developing PCR primers, targeted genetic databases, genetic analyses, and data interpretation. Includes multiple functions to streamline this process. This repository represents an effort to strengthen the software community within the U.S. Geological Survey and follow the open source efforts promoted by the executive level of the federal government. The intent is...

MODFLOW-2005: USGS three-dimensional finite-difference groundwater model

Arlen W. Harbaugh, Christian D. Langevin, Joseph D. Hughes, Richard G. Niswonger & Leonard F Konikow
MODFLOW is a three-dimensional (3D) finite-difference groundwater model that was first published in 1984. It has a modular structure that allows it to be easily modified to adapt the code for a particular application. Many new capabilities have been added to the original model. MODFLOW 6 is presently the core MODFLOW version distributed by the USGS, but MODFLOW-2005 (the previous core version) is still actively maintained and supported. MODFLOW-2005 (Harbaugh, 2005) simulates steady and nonsteady...


Sorab Panday, Christian D. Langevin, Richard G. Niswonger, Motomu Ibaraki & Joseph D. Hughes
MODFLOW-USG is an unstructured grid version of MODFLOW for simulating groundwater flow and tightly coupled processes using a control volume finite-difference formulation. The current version of MODFLOW-USG is Version 1.3.00, released 01 December 2015. MODFLOW-USG (for UnStructured Grid) was developed to support a wide variety of structured and unstructured grid types, including nested grids and grids based on prismatic triangles, rectangles, hexagons, and other cell shapes. Flexibility in grid design can be used to focus...

TRIGRS version 2.1

Rex L Baum & Massimilliano Alvioli
The Transient Rainfall Infiltration and Grid-Based Regional Slope-Stability Model (TRIGRS) is a Fortran program designed for modeling the timing and distribution of shallow, rainfall-induced landslides. The program computes transient pore-pressure changes, and attendant changes in the factor of safety, due to rainfall infiltration. This release, 2.1.0a, includes bug fixes, new output formats, and various optimizations to improve performance of the TRIGRS serial code. These improvements have also been incorporated into a new parallel implementation of...

One Water Hydrologic Flow Model (MODFLOW-OWHM), version 2

Scott E. Boyce, Randall T Hanson, Ian Ferguson, Wesley Henson, Wolfgang Schmid, Thomas Reimann, Steffen M. Mehl & Marisa M. Earll

GSFLOW: coupled groundwater and surface-water flow model

Robert S. Regan, Richard G. Niswonger, Steven L. Markstrom, David E. Prudic & Paul M. Barlow
GSFLOW is a coupled Groundwater and Surface-water FLOW model based on the integration of the USGS Precipitation-Runoff Modeling System (PRMS) and the USGS Modular Groundwater Flow Model (MODFLOW). GSFLOW was developed to simulate coupled groundwater/surface-water flow in one or more watersheds by simultaneously simulating flow across the land surface, within subsurface saturated and unsaturated materials, and within streams and lakes. Climate data consisting of measured or estimated precipitation, air temperature, and solar radiation, as well...

Digital Shoreline Analysis System (DSAS) version 5.0

Emily Himmelstoss, Amy Farris, Rachel Henderson, Meredith Kratzmann, Ayhan Ergul, Ouya Zhang, Jessica Zichichi & Rob Thieler


Laura A DeCicco, Steven Corsi, Daniel L. Villeneuve, Brett R. Blackwell & Gerald T. Ankley
Evaluation of measured concentration data using the ToxCast high-throughput screening database or a user-defined set of concentration benchmarks.

Connecticut Streamflow and Sustainable Water Use Estimator (CTSSWUE Version 1.0) application software

Gregory E Granato
This software release provides the database application that runs the Connecticut Streamflow and Sustainable Water Use Estimator (CT SSWUE) computer program (version 1.0). The CT SSWUE was developed by the U.S. Geological Survey, in cooperation with the Connecticut Department of Energy and Environmental Protection, to provide a planning-level decision-support tool designed to help decision makers estimate daily mean streamflows and selected streamflow statistics that can be used to assess sustainable water use at ungaged sites...

Massachusetts Sustainable-Yield Estimator (MASYE) application software (version 2.0)

Gregory E Granato
This software release provides the database application that runs the Massachusetts Sustainable-Yield Estimator (MA SYE) computer program (version 2.0). The MA SYE was developed by the U.S. Geological Survey, in cooperation with the Massachusetts Department of Environmental Protection, to provide a planning-level decision-support tool designed to help decision makers estimate daily mean streamflows and selected streamflow statistics that can be used to assess sustainable water use at ungaged sites in Massachusetts. The MA SYE provides...

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