Software

Mapping soil geochemistry across large spatial extents is essential for understanding mineral distributions and their environmental implications. However, rasters of soil geochemical distributions for the United States are limited. We present a Bayesian modeling framework for generating predictive geochemical distribution maps using integrated nested Laplace approximation in R (R-INLA).

This repository contains all of the scripts to reproduce the analyses, figures, and tables associated with the manuscript Hoven et al. in prep. There is 1 Rmarkdown script that does the following: (1) format the data, (2) explores the data, and (3) goes through the analyses for each of the hypotheses (both linear models and path analysis).

American kestrels have been declining in North America for several decades for unknown causes despite extensive research. We examined long-term population trends at a continental scale to eliminate statistical artifacts of immigration and immigration, and were able to identify trends in specific vital rates that can better inform future management actions. Included in this repository is...

This software release consists of two tools for filtering and reformatting geochemical data from the associated data release of Granitto and others, 2025. They are provided as a Python toolbox for use in ArcGIS Pro, and scripts that can be used in the open-source software QGIS. Inputs to the ArcGIS tools should be stored in the file geodatabase or GeoPackage formats. The QGIS tools can...

DReAMER DReAMER: Depth Retrieval Algorithms for Mapping and Exploration of Rivers Description The software application made available through this repository is designed for mapping water depth in river channels from passive optical remotely sensed data. The program provides convenient access to a number of different methods for deriving bathymetric information from images and...

We provide the following R Markdown and NetLogo files corresponding to our application of agent-based models to assess management responses to chronic wasting disease among white-tailed deer in Pennsylvania, USA.

This software release contains 4 files with R scripts organized according to the objective (e.g., format the data, model fitting, etc.). The overall objective of the project was to: analyzed ten years of capture-mark-recapture data spanning 2000 − 2014 for a population of Espadarana prosoblepon in El Copé, Panama, encompassing a period before and after a Batrachochytrium dendrobatidis...

This code release provides the workflow and analysis for our propose approach to (i) learn the effect of environmental covariates on detection probabilities from CR data and (ii) transfer these detection functions to CPUE models for improved inference.

This release introduces the pwfdf-api package. The package provides Python and command-line interfaces to search, query, and download hazard assessments from the PWFDF collection. This initial release introduces the four main commands: assessments: List PWFDF assessments that match search criteria browse: Open PWFDF search results in a web browser download: Download PWFDF assessments to...

Github repository that contains python code workflows for generating 3-dimensional images of topography, hydrography, and other remote sensing data with Blender, an open-source visualization software.

Code for R Shiny application to visualize and download sea otter population survey data in Alaska. The Sea Otter Survey Data Visualization Tool was developed by the U.S. Geological Survey (USGS) to facilitate visualizing and downloading sea otter population survey data in an interactive mapping application. Numerous survey efforts have occurred over the years. Sea otter survey data can...

This software contains five R Markdown files and two R script files that comprise an analysis to 1. develop freshwater fish and mussel models using survey occurrence data, land use data, stream flow data, and stream temperature data within the Northeast United states, 2. predict the impacts of climate change on vulnerable groups of freshwater fish and mussel species, and 3. asses the...