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

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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

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 (

hydrolink - python package

The term hydrolink is being defined as the linkage of spatial data to a stream network. This is similar to the analogy of providing an address on a road network and provides locational context and position within a stream network. Hydrolinking data to a common stream network allows information to be centralized helping support landscape scale analyses and modeling efforts. Versions of the National

Joint Ecosystem Modeling (JEM) Restoration Runs R Library

restoration_runs is a library of R-language scripts used to summarize/post-process output of Joint Ecosystem Modeling (JEM; models used in Everglades restoration planning for projects such as the Lake Okeechobee System Operating Manual (LOSOM) and the Western Everglades Restoration Project (WERP). The scripts summarize model output and create graphs and maps for each model.

webmap---Interactive web maps using The National Map (TNM) services

The R package webmap creates interactive web maps using the JavaScript Leaflet library with base layers of The National Map (TNM). Map service endpoints are offered with no use restrictions and provide access to base geospatial information that describes the landscape of the United States and its territories. Base layers outside these areas are unavailable at higher spatial scales. This package is

Monosex control within integrated pest management

This repository contains code to simulate the use of YY-males and direct mortality such as harvest or pesticide applicaion as a control tools for different aquatic invasive species.

Simulations for assessing the suitability of YY-males as a control method across life histories

This repository contains code to simulate the use of YY-males as a control tool for different aquatic invasive species. The code uses the Meta-IPM Python package ( The code for this project assumes the reader is familiar with Jupyter Notebooks, enough Conda and Python to install the Meta-IPM package, and population ecology.

Habitat Risk Software

The Habitat Risk Software leverages a previously published Bayesian hierarchical model framework (Clayton and Kaldor 1987; Banderjee et al. 2004; Gelman et al. 2004; Evans et al. 2016) with opportunistic (hunter-harvest) wildlife surveillance disease testing data and publicly available geospatial (raster) data to estimate the geographical risk that a hunter will harvest a white-tailed deer (Odocoi