Software

This document serves as an open code book detailing application of a multi-scale occupancy model to bat acoustic data collected according to the North American Bat Monitoring Program (NABat) sampling design. In this document, we detail a complete analysis of acoustic data collected on Hoary bats in Montana between 2020 and 2022, including: examples of data cleaning and preparation for analysis, mo

The purpose of this document is to demonstrate how data collected by the Pacific Northwest Bat Hub, a member of the North American Bat Monitoring Program (NABat), may be used to make inferences about species occurrence. As motivation, we consider occurrence data collected on Silver-haired bats (Lasionycteris noctivagans, LANO) in Oregon and Washington in 2019. In particular, we are interested in t

Code release for a statistical framework that provides a solution to overcome institutionally siloed monitoring activities in order to inform species conservation across large landscapes. Stan code and documentation to provide access and adaptation for other wildlife disease applications.

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

RETRACTED see https://doi.org/10.5066/P9R7XWO1

This is a repository with R code for CWD simulation models and interactive Shiny applications. Currently there are deterministic and stochastic models that are intended to model hunting scenarios for a 5 to 10 year time horizon. The models are sex and age structured with direct and indirect transmission.

This package is designed to estimate, summarize, and visualize wildlife aggregation metrics using location information like GPS collar data. The motivation for the development of this package began with two research efforts studying the aggregation and density of elk on the National Elk Refuge, Wyoming (Janousek et al.2021; and Graves et al. 2021). The primary goal of the WildAgg package is to pro

The Risk of Contact Tool (RoCT) is an R-based implementation of the Risk of Contact model described in O'Brien et al. (2014). It uses a variety of spatial inputs (including telemetry point data, a core herd home range (CHHR) polygon, a habitat raster model, and a set of active domestic sheep allotments) together with estimates of bighorn sheep foray behavior to estimate the probability and rate of

R code to fit models with and without sample weights and simulation code

R package developed to support study design for acoustic bat surveys with imperfect detection misidentification

Code for implementing the Zero-Augmented Beta Model with Errors (ZABE) , simulation study code, and code for assessing trade-offs in study design via simulations.