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

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Chronic Wasting Disease Modeling for Bridger Teton National Forest Structured Decision Making (cwd-btnf-sdm-v2)

This software release contains the code necessary to run the chronic wasting disease (CWD) and elk habitat selection models used to support the U.S. Forest Service decision on whether to continue to permit supplemental feeding of elk on USFS land. The models allow for four different management alternatives: continued feeding, emergency feeding, phase-out after three years, or no feeding. The CWD m

Optimal harvest of a theoretical population under system change

This code solves optimal harvest policies under different scenarios of system change, represented as changes in demographic parameters over time. This document contains code to solve policies using backwards iteration stochastic dynamic programming, project populations forward to simulate the policies, and generate figures.

R Code Supporting the Manuscript: Using Stochastic Point Pattern Analysis to Track Regional Orientations of Magmatism During the Transition to Cenozoic Extension and Rio Grande Rifting, Southern Rocky Mountains

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 bootstrap sim

SAS: Software Application for SMASH (Spectral Mixture Analysis for Surveillance of Harmful Algal Blooms)

The Software Application for SMASH (Spectral Mixture Analysis for Surveillance of Harmful Algal Blooms), or SAS for short, is an application to facilitate mapping of potentially harmful algal blooms in reservoirs, rivers, and lakes from remotely sensed data. More specifically, SAS is designed to exploit the detailed observations of reflectance available within a hyperspectral image to infer which

HOPS: Hyperparameter optimization and predictor selection

We developed the hyperparameter optimization and predictor selection (HOPS) software to optimize hyperparameters and predictor selection while limiting correlation among the selected predictors for machine learning models. Including correlated predictors in machine learning models can distort model estimation and prediction and introduce bias in predictor importance estimates. The HOPS software ex

Bayesian Hierarchical Model of Whimbrel Survival

This model combines resighting data from Whimbrels breeding at Kanuti National Wildlife Refuge with known-fate data and pseudo-resighting history from Whimbrels breeding at the Colville River Delta ('colv'). All Whimbrels in the study (n = 76) were marked with a USGS metal band and a uniquely coded engraved leg flag. In addition, 15 Whimbrels at Kanuti were equipped with surgically implanted satel

Code for: Small enzootic survival costs mask the potential for long-term population size suppression

This repository contains all of the scripts to reproduce the analyses, figures, and tables associated with the manuscript Glorioso et al. in review. The scripts are organized into folders, and the folders are numbered in the order in which they should be executed. Briefly, there are six folders that do the following: (1) format the data, (2) fit the model, (3) run the population projections, (4) r

Planetary Geologic Mapping Python Toolbox for ArcGIS

A collection of ArcGIS python toolboxes and plugins used by the Planetary Geologic Mapping program. They are designed to work with ArcPro 2.0 and ArcMap 10.0 or higher.

DSWE_GEE v1.0.0

Code for implementation of the Dynamic Surface Water Extent algorithm in Google Earth Engine. Multiple scripts allow the creation of single-scene or composited Dynamic Surface Water Extent (DSWE) images from Landsat and MODIS data. All code is written for use in the JavaScript API.

whitetailedSIRS: A package to project SARS-CoV-2 outbreak dynamics in white-tailed deer

This software release contains several R scripts that generate epidemic projections of SARS-CoV-2 in white tailed deer populations using a Susceptible-Infected-Recovered-Susceptible (SIRS) modeling framework. We provide a workflow of vignettes used in Rosenblatt et al. In Prep and Cook et al. In Prep. Users are able to specify transmission parameters for human-deer and deer-deer transmission to qu

Hunter and prey linked population models

Herein we present a simulation model to predict future prey and hunter populations in a stochastic population simulation model. In the simulation script the two populations (prey and hunters) are linked through feed back functions, where the hunters can affect the prey abundance through harvest rate and harvest success functions, and the prey affects hunter population retention and recruitment. Th

The US Inland Creel and Angler Survey Catalog (CreelCat) Application and CreelCatch R Package

The US Inland Creel and Angler Survey Catalog (CreelCat) application contains a web viewer which allows users to interact with the data included in the CreelCat data release. This includes the ability to view and download the data, explore data availability, develop custom summarizations, and create visualizations including maps and plots. In addition to the web application, a custom R package, Cr