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Software

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

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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

Software for the program code AFCE (Aqueous-Flow-Concentration-Estimator) for estimation of ambient groundwater flow in bedrock open boreholes using concentrations of chlorinated volatile organic compounds from coupled straddle packer and passive sampling

Software program code for the AFCE (Aqueous Flow Concentration Estimator) that is used to estimate inflow of groundwater contaminants to a water column of an open borehole in a fractured-rock aquifer. It is particularly useful program for assessing ambient flow in low permeability open boreholes, which have no detectable flow as measured with conventional borehole flowmeter tools. The software is

Change-point models for identifying single behavioral transitions in wild animals

We present two change-point models for identifying singular changes in movement behavior: a location-based change-point model (LCPM) and a movement metric-based change-point model (MMCPM). This software includes R scripts to: 1) run both the LCPM and MMCPM on telemetry data in a Bayesian hierarchical framework using NIMBLE (mmcpm.R and lcpm.R), 2) generate realistic movement behavior parameters fo

Scale-dependent population drivers inform avian management in a declining saline lake ecosystem.

R code for data prep, processing, and population analysis associated with manuscript of same title.

Code to fit Integral Projection Models and simulate population reintroductions for San Francisco Gartersnakes, Thamnophis sirtalis tetrataenia

This repository contains code to fit Integral Projection Models and simulate population reintroductions for San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) This repository specifically contains code to reproduce analyses in: Rose, J.P., Kim, R., Schoenig, E.J., Lien, P.C., and Halstead, B.J. in-review. Comparing reintroduction strategies for the endangered San Francisco gartersnake (