Software

The PMAP tool is a one-dimensional plume model that predicts ash aggregation within an erupting volcanic plume. The tool was developed by D. W. Hoffman at Stanford, extending from the Plumeria model written by L. G. Mastin at USGS CVO. The code operates using Matlab. The purpose of this repository is to present the code used in the following publication, currently under review at Journal...

PopEquus is a website application that can be used to understand trade-offs and inform decisions in free-roaming horse (Equus caballus) population management. The application (https://rconnect.usgs.gov/popequus/) contains a predictive population modeling tool that can be used to simulate how different management actions drive changes in horse population size, while measuring management...

Results of 11 microsatellites for white-tailed deer collected in Maryland, New York, Ohio, Pennsylvania, and Virginia from 2014 to 2022 for genetic analysis. In this project we assessed genetic structure using different analyses, and evaluated the performance of assignment tests to correctly match deer to origin (defined as genetic cluster, state or physiographic province). This...

Code for simulating Spot-tailed earless lizard populations under habitat loss and road mortality threats in central Texas

The code herein uses a triple loop structure to simulate a spatially implicit stage structured matrix model for two species of western pond turtle with parametric uncertainty and temporal stochasticity.

The R package precompute is used to perform periodic computations to set up data for loading and rendering in Shiny applications. These computations typically take too long to conduct on the fly, which is why they are performed with some frequency using this package.

Predicting the effects of warming temperatures on the abundance and distribution of organisms under future climate scenarios often requires extrapolating species-environment correlations to thermal conditions not currently experienced by a species or to temperatures that exceed the range of observed data. For poikilotherms, incorporating species’ thermal physiology to inform...

This R script is reproduces a Bayesian belief network built within the propriety software program, Netica. The R- and Netica-based belief networks were used in Dunn and Schumann et al. (in press), which presents an approach for calculating imperilment of freshwater fishes.

This repository contains code that supports ongoing research in the southern Rocky Mountains in Colorado and northern New Mexico. This region hosted intracontinental magmatism that developed during a tectonic transition from shortening (Laramide orogeny, ca. 75 to 40 Ma) through extension and rifting. The code in this repository presents a novel approach that uses stochastic weighted...

raventools: A package to facilitate raven management in the western U.S. The raventools package centralizes several publicly available geospatial datasets that are essential to mapping and modeling for common raven (Corvus corax) management applications, including raven occurrence and density data, sensitive species distribution data, raven subsidy data, and Greater sage-grouse...

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.

RDAVT.r is an R Shiny-based app used to estimate immobile porosity, mobile porosity, and the mass transfer rate coefficient in dual-domain porosity media. The app allows for interactive fitting of the fluid versus bulk conductivity hysteresis curve from electrical tracer experiments using a semi-analytic graphical approach.