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Habitat Risk Version 2 Software

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Abstract

The Habitat Risk Version 2 Software, hereafter “Habitat Risk V2”, leverages a previously published Bayesian hierarchical model framework 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 (Odocoileus virginianus) that tests positive for chronic wasting disease (CWD) in a small “study area” portion of the state. The three-part R scripts of Habitat Risk V2: 1) prepare the surveillance (testing) and geospatial (raster) data for model inclusion, 2) parameterize and estimate coefficient values for twenty five predetermined candidate model structures (Table 1), 3) select the model structure with the lowest Deviance Information Criterion (DIC) given the data, 4) gather diagnostic plots for the user to verify modeling assumptions have been met, and then 5) display the results of the best model in geographical and tabular context via an interactive user interface (UI). UI capabilities include interactive and downloadable maps of estimated risk (and associated error), a map of disease data overlaid onto spatial covariates, and detailed statistical information about the best model and the model selection process. The three R scripts must be run in sequence, as the data outputs of one become the data inputs of the next. The Habitat Risk V2 requires testing data in the state of interest to 1) contain locations of each deer in exact latitude/longitude coordinates, and 2) contain least one record that is CWD positive for each age/sex segment (adult male, adult female, yearling male, yearling female, fawn male, fawn female). The software will not work on datasets containing all CWD negative deer. We packaged Habitat Risk V2 using examples from Tennessee and New York. This packet does not furnish the real disease testing data necessary to run Habitat Risk V2. The Habitat Risk V2 software is adaptable for use in other areas with positive CWD samples. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the United States Government.

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The findings and conclusions in this material are those of the authors and do not necessarily represent the views of the U.S. Fish and Wildlife Service.

The Habitat Risk V2 Software is shared under a MIT license. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following considerations: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Sponsorship

Financial support comes from (1) Michigan Disease Initiative – Optimizing CWD Surveillance: Regional Synthesis of Demographic, Spatial, and Transmission-Risk Factors (2019); (2) Tennessee Wildlife Resources Agency - Modeling Risk of Infection for Individually Harvested Deer & Estimating Prevalence When Sampling is Limited (2020); (3) Michigan Disease Initiative - SOP4CWD Dashboard: A Web Application for Disease Visualization and Data-Driven Decisions (2020); (4) Multistate Conservation Grant Program - Surveillance Optimization Project for Chronic Wasting Disease: Streamlining a Web Application for Disease Visualization and Data-Driven Decisions (2021). This project was also funded by a Multistate Grant # F23AP00488-00, a program funded from the Wildlife and Sport Fish Restoration Program, and jointly managed by the U.S. Fish and Wildlife Service and the Association of Fish and Wildlife Agencies.

Date Issued

2023-08-18

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Keywords

Chronic Wasting Disease; CWD; Estimation of spatial risk of disease in wildlife species; Odocoileus virginianus; white tailed deer; wildlif disease; SOP4CWD

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https://cwhl.vet.cornell.edu/project/sop4cwd

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software

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Version History

Now showing 1 - 2 of 2
VersionDateSummary
2*
2023-08-18 16:53:50
Additional features and improved usability.
2021-08-19 22:53:22
* Selected version