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Software

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

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Python-based Subaerial Barrier Sediment Partitioning (pySBSP) model (ver. 1.0, February 2024)

The Python-based Subaerial Barrier Sediment Partitioning (pySBSP) model is a framework to simulate the morphological development of an idealized barrier coast in the cross-shore domain. It is based off the original framework of the same name, which is coded in in MATLAB. pySBSP consists of two scripts; one includes a basic graphical user interface (GUI) to simplify parameter input, while the other

MODFLOW 6: USGS Modular Hydrologic Model

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

Code to fit spatially explicit capture-recapture models to trapping data for western deer mice (Peromyscus sonoriensis) at Point Reyes National Seashore

This repository contains code to fit Spatially-Explicit Capture Recapture (SECR) Models to trapping data for Peromyscus sonoriensis (deer mice) at Point Reyes National Seashore and reproduce analyses in the following manuscript: Rose, J.P., Parsons, L.S., Kleeman, P.M., and Halstead, B.J. 2024. Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice) in Point

ListingAnalyst

ListingAnalyst is a program for viewing the main output file from MODFLOW-2005, MODFLOW-NWT, MODFLOW-LGR, MODFLOW-CFP, MODFLOW-OWHM, and MODFLOW 6.

Eelgrass Biomass Model

This code release contains R and JAGS code for estimating average eelgrass biomass at two lagoons (Izembek and Kinzarof) within the Izembek National Wildlife Refuge, Alaska, using data from point count surveys conducted by National Wildlife Refuge and U.S. Geological Survey (USGS) personnel. Biomass is estimated using a gamma hurdle model which models the probability of occurrence and eelgrass abu

Scripts to Analyze Altitude Selection in Migrating Pacific Flyway Geese

This code repo contains three scripts used in the associated manuscript to run the analyses (01_model_prob_flight.r; 02_model_altitude_selection.r) and the simulation used to make predictions (03_simulate_prob_fly_per_altitude.r). The analysis serves to evaluate conditions that affect 1) whether geese are in flight vs. resting on the water, 2) what altitude is selected by flying geese, and 3) what

Software for Bayesian Mapping of Regionally Grouped, Sparse, Univariate Earth Science Data (Program BMRGSU)

BMRGSU is software developed by the U.S. Geological Survey for Bayesian mapping of regionally-grouped, sparse, univariate, Earth-science data. This software implements an algorithm that smooths the estimated property across regions so that the deleterious effects of sparse data are mitigated. The algorithm can account for measurements that are censored, it can process multiple datasets with differ

Low Flow Period Seasonality Trend and Climate Linkages Across the United States Software Release version 1.0.0

This is scientific code released to support the paper Low Flow Period Seasonality Trend And Climate Linkages Across The United States.

RESTORE/TCEQswqmisESTUSAL, Source code for manipulation of data stemming from the Texas Commission on Environmental Quality Surface Water Quality Monitoring Program with emphasis on salinity change statistics for Texas coastal segments

The RESTORE/TCEQswqmisESTUSAL repository contains R language source code that can be used for digesting data retrieved from the Texas Commission on Environmental Quality Surface Water Quality Monitoring Program through their Surface Water Quality Data Viewer. The workflow described concerns data manipulations, base data filtering, and computations towards documenting long-term salinity change (par

pfdf 1.0.0

pfdf: A Python library to facilitate post-wildfire debris-flow hazard assessments and research. This release provides the core functionality needed to implement operational hazard assessments. This includes tools to: * Analyze watersheds * Delineate and filter stream segment networks * Compute earth-system variables for stream segments in a network * Assess debris-flow probabilities using the mo

Rayleigh Step-Selection Functions

This project aimed to find connections between step-selection functions (SSFs) and partial differential equation models of animal movement and, in doing so, improve the flexibility of SSFs. Please see the associated manuscript cited above for further details.

WiggleMatch: a spreadsheet for radiocarbon wiggle-matching

This spreadsheet enables statistical and visual wiggle-matching of sequential radiocarbon ages from a tree-ring chronology to the IntCal20 calibration curve. It will calculate and plot an optimal fit of the samples to the calibration curve and the user can then incrementally move the wiggle-match in time to see the effect in both goodness-of-fit statistics and visually on a graph. This is useful w