Software

This code can be used to rapidly create an annotated bibliography that will help users navigate and synthesize a large body of literature. Users can input a set of PDF or DOCX files that they have identified as relevant to their question as well as lists of relevant search terms. This code will convert the input documents into TXT files, trim the files to exclude extraneous text such as...

The purpose of this R software package is to easily download and process climate, anthropological, and environmental covariate data for specified areal units to use primarily in an integrated species distribution model. The package contains wrapper functions for the `geodata` R package and externally downloaded datasets.

The purpose of this R software package is to easily download and clean species data from the Global Biodiversity Information Facility (GBIF). This package relies on functions in the `rgif` package and contains wrappers to download and format data for the purposes of building an integrated species distribution model.

This geospatial tool is designed to calculate an estimated volume of mine waste using a polygon outline of the mine waste and elevation data obtained from remote sensing. The tool is developed to run as a toolbox in the ESRI ArcGIS Pro application. It calculates the volume using the geospatial data and a linear regression method described in the accompanying publication. This tool has...

Multi-species structured surveys following specific sampling design are powerful tools for understanding species’ distributions and trends, but are not equally well-suited for surveying all species. Combining data collected under different protocols or sampling designs has the potential to boost sample size, extend geographic and environmental coverage, and improve model estimates...

This code release provides the workflow and analysis code for a study that addresses the prevalence of PFAS on Federally protected lands in water and dragonfly larvae. This study quantifies the prevalence of PFAS in protected areas across the US, identifies ecologically relevant PFAS mixtures, and assesses the potential drivers of PFAS concentration in an effort to better understand...

The Digital Shoreline Analysis System (version 6) is a stand-alone desktop application that compliments a Geographic Information System (GIS). The DSAS software requires users to input a reference baseline and compilation of shoreline positions to generate measurement transects and shoreline intersections used to calculate rate-of-change statistics. DSAS provides an automated method for

MODFLOW 6 is an object-oriented program and framework developed to provide a platform for supporting multiple models and multiple types of models within the same simulation (Hughes and others, 2017; Langevin and others, 2024). This version of MODFLOW is labeled with a "6" because it is the sixth core version of MODFLOW to be released by the USGS (previous core versions were released in...

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

This product contains Jupyter Notebooks demonstrating how to retrieve, process, and analyze USGS analysis ready data (ARD) using Python. The purpose of these examples is to introduce novice Python users to real-life earth science data workflows. The examples include using the data retrieval package to pull NWIS data, pulling NOAA NOS CO-OPs water level data to visualize hurricane Helene...

Ursa is a python tool for the setup, management, and analysis of postfire debris-flow runout simulations. Ursa provides (1) a set of python functions that accomplish each phase of a hazard assessment workflow and (2) a Snakemake snakefile that uses the python functions to run the entire workflow. Ursa is intended as a flexible tool for a particular purpose. It is not intended as a...

This repository contains code and data used to analyze the influence of initial condition uncertainty on model simulations of ecosystem carbon dynamics in the U.S. state of California.