Software

This code set is an R workflow for phenological date matching to provide an open-source solution for projects with limited funding to allow users to calculate Normalized Difference Vegetation Index (NDVI) from sentinel-2 imagery dates specified by a user supplied date raster (phenology raster) for mapping and forecasting geographic distributions of invasive plant species at large spatial...

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...

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.

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

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...

This is repository contains all publicly-released code and data supporting the Southern Rocky Mountains boreal toad decision support tool, which was developed as a part of a North Central Climate Adaptation Science Center-funded project entitled “A framework for guiding management decisions for amphibians in an uncertain future”, by Dr. Amanda M. Kissel (USGS), Dr. Erin Muths (USGS), Mae...

This software release contains the code for modeling and analysis of bat fatality data at a sample of wind energy facilities in the Upper Midwest United States. The model estimates total bat fatalities at each turbine across multiple wind energy facilities, years, and species of bats based on post-construction monitoring data with imperfect detection.

This repository contains the code for modeling and analysis of bat fatality data at a sample of wind turbine facilities across the United States. The software is written in R and includes hierarchical Bayesian n-mixture models implemented in JAGS to predict bat fatalities across wind facilities retrospectively from 2001-2024 and under future potential wind development build-out scenarios...

The North American Bat Monitoring Program: R Data Connection Package can be used to extract and upload data to the NABat Monitoring Program through the GQL API. This software is written as a wrapper around the NABat GQL API. Documentation for the database and API can be found at https://sciencebase.usgs.gov/. This code includes the ability to reformat NABat data, upload NABat data...

Wildlife conservation and management increasingly considers genetic information to plan, understand, and evaluate implemented population interventions. These actions commonly include conservation translocation and population reductions through removals. Change in genetic variation in response to management actions can be unintuitive due to the influence of multiple interacting drivers of...

Invasive species are a major cause of biodiversity loss and are notoriously expensive and challenging to manage. We developed a decision-analytic framework for evaluating invasive species removal strategies, given objectives of maximizing eradication probability and minimizing costs. The framework uses an existing estimation model for spatially referenced removal data – one of the most...

The North American Bat Monitoring Program: R Data Connection Package can be used to extract and upload data to the NABat Monitoring Program through the GQL API. This software is written as a wrapper around the NABat GQL API. Documentation for the database and API can be found at https://sciencebase.usgs.gov/. This code includes the ability to reformat NABat data, upload NABat data...