Software

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...

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...

This software script is designed to generate a first infrastructure line polyline vector that delineates the seaward-most extent of impervious infrastructure, including parking lots, buildings, and roads. The software requires two inputs which include A) a raster representing the coverage of impervious surface B) a polyline baseline located seaward of and running parallel to the first

These Python scripts calculate Fe-Mg diffusion timescales in orthopyroxene crystals for use in studies of pre-eruption processes. The model is based on a centered space, forward time implicit finite difference solution to the diffusion equation with with a compositionally depended diffusivity. The model includes an initial condition optimization step and a Monte Carlo approach to...

The code in this repository generates and analyzes directed acyclic graphs (DAGs) representing hypotheses about variables affecting the occurrence and surface availability of Plethodon salamanders in northern California; formats data from field surveys and GIS for analysis; and analyzes multi-scale occupancy models, including model selection, to evaluate the model and variables with the...

Welcome to the README for the Bull Trout Population Dynamics Simulation Tool. This tool can be used directly in an R console (including IDEs such as RStudio) or it can be used via the web and an R Shiny interface (https://rconnect.usgs.gov/BullTroutPopulationDynamicsSimulationTool/).

shakingstats is a Python package for calculating earthquake statistics from continuous seismic amplitudes. It calculates the time-varying amplitude completeness (A_C) and amplitude-based b‑value (b_A​) by fitting the joint distribution of seismic noise and earthquake shaking. It also provides an implementation of the b-positive (β+) method for comparison to catalog-based statistics.

An R shiny application to organize and streamline the process of regression model development using time series data. An interactive browser interface allows users to evaluate potential variables, compare models, and output summary documents compiling descriptive graphs and statistics for archival purposes. The application allows for the processing of left-censored response variables...