Software

This software contains five R Markdown files and two R script files that comprise an analysis to 1. develop freshwater fish and mussel models using survey occurrence data, land use data, stream flow data, and stream temperature data within the Northeast United states, 2. predict the impacts of climate change on vulnerable groups of freshwater fish and mussel species, and 3. asses the...

This code automates the extraction of publicly available PDF documents from the Bureau of Land Management's National NEPA Register website based on a list of NEPA project numbers provided in a CSV file. It is designed to support scientific analysis of environmental planning documents. It was developed for internal and partner use to simplify large-scale text analysis efforts.

Code for implementation of the Dynamic Surface Water Extent (DSWE) algorithm in Google Earth Engine. Multiple scripts allow for the generation of single-scene or composited (monthly) DSWE images from Landsat and MODIS imagery. All code is written for use in the Google Earth Engine JavaScript API.

The mmlCHICOTla repository contains R, Mermaid, and Perl language source code that can be used for construction multiple methods of machine learning (MML) of water levels in the Chicot aquifer system, southwestern Louisiana. The source code is written in R (primary and extensive), Mermaid (workflow diagrams), and Perl (minor utility for simple implementation of parallel processing on...

The covCHICOTla repository contains primarily R and limited Mermaid, Perl, and Python language source code that collectively can be used for the construction of many tables of monthly groundwater levels (response variable) and predictor variables (covariates) intended to be inputs to statistical modeling of water levels in the Chicot aquifer system, southwestern Louisiana. The source...

This "software technical note" (`TECHNOTE.md`) provides extensive details involving the construction of typical well-depth grids from research-grade statistical study of the Chicot aquifer system. The README also within this directory is designed and intended to parallel the documentation of individual covariate construction as part of the primal feature of the **covCHICOTla** software...

The spread of non-native dreissenid mussels across North America has resulted in significant ecological and economic damage. Management efforts implementing early detection efforts (including watercraft inspections) may help reduce potential spread and new introductions, but optimizing effective deployment of these efforts in a resource-constrained environment is challenging. Raymond et...

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

Ecological restoration is essential to meeting global biodiversity conservation goals. Given limited conservation budgets, deciding where to restore habitat is a key challenge for the coming decade. We developed a modeling approach to maximize conservation benefit/restoration cost ratios to optimize restoration. We illustrate this approach using a case study for highly threatened...

The qualitative review document titled "QualitativeReviewWSAF_ForRECOVERReview_2025May5_FINAL.pdf" provides the motivation and background for developing this Shiny Application. The document provides a review of the Wet Season Aquatic Fauna (WSAF) MAP Agreement’s monitoring design using a qualitative statistical review framework that emphasizes connecting desired measurable objectives...

This software release consists of R shiny code for a site prioritization tool for invasive species management: https://rconnect.usgs.gov/site-prioritization-tool/

NLDI Flowtools is a Python package for basin delineation and flow path tracing from any point within CONUS. It can return either the full upstream drainage basin or just the portion within the local NHD catchment (i.e., splitcatchment). The flow path tracing tool follows terrain downhill until it intersects the nearest NHD stream line, returning both the traced path and the intersected...