Software

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.

This release adds functionality for building debris-flow likelihood lookup tables, and uploading the results to the National Weather Service (NWS) FTP endpoint. The release: * Adds the `authenticate nws` command, which collects authentication credentials for uploading to the NWS FTP endpoint * Updates the `run` command to compute debris-flow likelihood lookup tables, and save the results...

Effective future fire planning and decision-making in Alaska requires accessible, interpretable, and locally relevant climate data to anticipate fire danger. To meet this need, we utilized an existing dataset of projected fire danger metrics from the Canadian Forest Fire Danger Rating System (Young et al. 2025). This dataset contains daily projections from 1980 through 2099 for key...

R code and Stan models to simulate sample data set, perform parameter estimation, project future scenarios, and produce plots for accompanying publication examining the integrated dynamics of waterfowl and hunter populations through harvest.

This software was developed using the statistical program R (R Core Team 2024) to compile multiple wildlife tracking datasets that contain locations of animals recorded through time. The software is organized through a series of scripts that run hierarchically through script sourcing. To demonstrate how the software works, we simulated four wildlife tracking datasets, each representing...