W. David Walter, PhD (Former Employee)
Science and Products
Pennsylvania Cooperative Fish and Wildlife Research Unit
The Pennsylvania Cooperative Fish and Wildlife Research Unit, est. 1938, is a partnership among the Pennsylvania Game Commission, Pennsylvania Fish and Boat Commission, Pennsylvania State University, the U.S. Geological Survey, the U.S. Fish and Wildlife Service, and the Wildlife Management Institute.
Filter Total Items: 14
Predictive layers of trace elements in soil in the conterminous United States Predictive layers of trace elements in soil in the conterminous United States
This dataset provides posterior mean predicted rasters of the distribution of trace elements important to vertebrate health (cobalt, copper, iron, manganese, selenium, and zinc) in the soil across the conterminous United States. Rasters were generated using a Bayesian modeling framework implemented in R with the R-INLA framework (Integrated Nested Laplace Approximation) and the...
Data for Distance sampling accounting for density gradient and animal distribution Data for Distance sampling accounting for density gradient and animal distribution
There are 9 datasets. one distance sampling dataset, 4 resource selection datasets, and 4 outputs from bootstrapped resource selection models the use the estimated correction factor. The 4 resource selection datasets have data that can be used in a binomial generalized linear mixed effect model to create the correction factor. The distance sampling data set is used to estimate density...
White-tailed deer from culling efforts in Minnesota White-tailed deer from culling efforts in Minnesota
Dataset containing information for white-tailed deer samples from Minnesota. Samples were genotyped for 11 microsatellites markers and sequenced for a fragment of approx. 546 bp belonging to the mitochondrial control region. Marker OvirQ should not be used as it presents alleles inconsistent with reported pattern, with some alleles separated by only 1 base pair and inconsistent between...
Comparing datasets by surveillance method using spatial models Comparing datasets by surveillance method using spatial models
This software compares statistical methods to model habitat risk of CWD in white-tailed deer in Pennsylvania using Bayesian hierarchical models in R-INLA and compares these results with model output from WinBugs. The software also uses R-INLA with the Stochastic Partial Differential Approach (SPDE) to compare different surveillance methods to model CWD in relation to habitat features and...
Microsatellite genotypes and metadata for white-tailed deer samples from the Mid-Atlantic region of USA Microsatellite genotypes and metadata for white-tailed deer samples from the Mid-Atlantic region of USA
Dataset containing information for white-tailed deer samples from Ohio, Pennsylvania, Maryland, Virginia and New York, genotyped for 11 microsatellites markers. Marker OvirQ should not be used as it presents alleles inconsistent with reported pattern, with some alleles separated by only 1 base pair and inconsistent between runs. Projected coordinates representing sampling location are in...
Population genetic structure of white-tailed deer using microsatellites i the Mid-Atalntic region Population genetic structure of white-tailed deer using microsatellites i the Mid-Atalntic region
Results of 11 microsatellites for white-tailed deer collected in Maryland, New York, Ohio, Pennsylvania, and Virginia from 2014 to 2022 for genetic analysis. In this project we assessed genetic structure using different analyses, and evaluated the performance of assignment tests to correctly match deer to origin (defined as genetic cluster, state or physiographic province). This...
Chronic Wasting Disease Surveillance Optimization Software Version 2 Chronic Wasting Disease Surveillance Optimization Software Version 2
The Chronic Wasting Disease Surveillance Optimization Software Version 2 computes sampling recommendations to detect chronic wasting disease (CWD) in white-tailed deer (Odocoileus virginianus). Driven by a combinatorial optimization algorithm, the software maximizes the return-on-investment to the wildlife agency while keeping the overall surveillance program within budget. The software...
Change-point models for identifying single behavioral transitions in wild animals 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...
Input for Habitat Risk Software Input for Habitat Risk Software
Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy that was first detected in captive cervids in Colorado, United States (US) in 1967, but has since spread into free-ranging white-tailed deer (Odocoileus virginianus) populations across the US and Canada. In some areas, the disease is considered endemic in wild deer populations, and governmental wildlife agencies...
Habitat Risk Software 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...
Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels
R code to test for differences in DNA yield from of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed SNP panels. We calculated mean, median and standard deviation with package psych using the describe() function. Additionally, we generated boxplots using package ggplot2 where the quantity for each tissue sample is...
Evaluation of DNA yield from various sources for use in single nucleotide polymorphism panels Evaluation of DNA yield from various sources for use in single nucleotide polymorphism panels
Genetics studies are used by wildlife managers and researchers to gain inference into a population of a species of interest. To gain these insights, micro-satellites have been the primary method, however, there currently is a shift from micro-satellites to single nucleotide polymorphisms (SNPs). With the DNA requirements being different, an investigation into which samples can provide...
Filter Total Items: 56
Statewide agent-based model for management of chronic wasting disease in white-tailed deer: PAOvCWD Statewide agent-based model for management of chronic wasting disease in white-tailed deer: PAOvCWD
Chronic wasting disease (CWD) is an always-fatal disease infecting wild cervids globally. Ecologically and economically important, CWD presents a challenge for managing white-tailed deer (Odocoileus virginianus). We built an agent-based model to simulate CWD transmission and assess potential management actions that could slow disease spread: PAOvCWD. We developed PAOvCWD using contact...
Authors
Nathaniel H. Wehr, Christopher S. Rosenberry, David Stainbrook, Maureen Staats, Andrea L. Korman, W. David Walter
Generating geochemical and mineralogy distributions of soil in the conterminous United States using Bayesian hierarchical spatial models Generating geochemical and mineralogy distributions of soil in the conterminous United States using Bayesian hierarchical spatial models
Characterizing geochemical and mineralogical soil distributions across large spatial extents is essential for understanding mineral resources, ecosystem processes, and environmental risks. Rasters of soil geochemical distributions for the conterminous United States, however, are limited. We present a Bayesian modeling workflow and tool for generating predictive geochemical and mineralogy
Authors
Kristin J. Bondo, Tiffany M. Wolf, W. David Walter
Intraspecific contact among white-tailed deer: A literature review and chronic wasting disease case study Intraspecific contact among white-tailed deer: A literature review and chronic wasting disease case study
White-tailed deer (Odocoileus virginianus) are a valuable game mammal in the eastern United States necessitating detailed understanding of disease transmission. We conducted a literature review on intraspecific contact (i.e., interactions wherein disease transmission may occur) among deer. From 69 studies, we identified five themes underlying research on intraspecific deer contact...
Authors
Nathaniel H. Wehr, Kristin J. Bondo, Christopher S. Rosenberry, David Stainbrook, Bret D. Wallingford, W. David Walter
Viral outbreak dynamics and evolution in wildlife at the interface with humans Viral outbreak dynamics and evolution in wildlife at the interface with humans
In this study, we used a multi-faceted approach to understand patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and persistence in a wild white-tailed deer (Odocoileus virginianus) population. Serology data indicated transmission of SARS-CoV-2 and persistence during the seven-month sampling period. Traditional disease modelling based on deer-to-deer...
Authors
Rachael Marie Giglio, Aaron Westmoreland, Mark Q. Wilber, Grete WIlson-Henjum, Aung Nyein Chan, Billy Gardner, Wantida Horpiencharoen, Roderick B. Gagne, Avery M. Corondi, Alec Baker, Matthew A. Combs, Jefferey Chandler, Kezia R. Manlove, Kim M. Pepin, W. David Walter
Development of high-throughput genomic resources to inform white-tailed deer population and disease management Development of high-throughput genomic resources to inform white-tailed deer population and disease management
White-tailed deer (Odocoileus virginianus) are the most abundant and widespread cervid in North America. Genetic data are used as a tool to monitor populations and make management decisions for this game species. However, the development and use of genomic tools that can generate a set of markers suitable for longitudinal genomic data collection, whether for management purposes or to...
Authors
David Navarro, Emily K. Latch, Anaïs K. Tallon, Caitlin N. Ott-Conn, Randy W. DeYoung, Daniel P. Walsh, Peter T. Euclide, R.G. Chandika, Wes A. Larson, Arun S. Seetharam, Andrew J. Severin, Andrew J. Severin, James M. Reecy, Zhi-Liang Hu, Jay R. Cantrell, Michelle Carstensen, Joe N. Caudell, Charlie H. Killmaster, Mitch L. Lockwood, William T. McKinley, Andrew S. Norton, Krysten L. Schuler, Daniel J. Storm, Jason A. Sumners, W. David Walter, Julie A. Blanchong
Expanding national-scale wildlife disease surveillance systems with research networks Expanding national-scale wildlife disease surveillance systems with research networks
Efficient learning about disease dynamics in free-ranging wildlife systems can benefit from active surveillance that is standardized across different ecological contexts. For example, active surveillance that targets specific individuals and populations with standardized sampling across ecological contexts (landscape-scale targeted surveillance) is important for developing a mechanistic
Authors
Kim M. Pepin, Matthew A. Combs, Guillaume Bastille-Rousseau, M.E. Craft, Paul C. Cross, M.A. Diuk-Wasser, R.B. Gagne, Travis Gallo, Tyler Garwood, J.D. Heale, J. Hewitt, J. Hoy-Petersen, Jennifer L. Malmberg, Jennifer M. Mullinax, L. Plimpton, Lauren Smith, M.C. VanAcker, J.C. Chandler, W. David Walter, Grete WIlson-Henjum, George Wittemyer, Kezia R. Manlove
Evaluation of SARS-CoV-2 antibody detection methods for wild Cervidae Evaluation of SARS-CoV-2 antibody detection methods for wild Cervidae
Wildlife surveillance programs often use serological data to monitor exposure to pathogens. Diagnostic sensitivity and specificity of a serological assay quantify the true positive and negative rates of the diagnostic assay, respectively. However, an assay’s accuracy can be affected by wild animals’ pathogen exposure history and quality of the sample collected, requiring separate...
Authors
Joshua Hewitt, Grete Wilson-Henjum, Jeffrey C. Chandler, Aaron T. Phillips, Diego G. Diel, W. David Walter, Alec Baker, Jennifer Høy-Petersen, Guillaume Bastille-Rousseau, Tadao Kishimoto, George Wittemyer, Jeremy Alder, Sara Hathaway, Kezia R. Manlove, Travis Gallo, Jennifer Mullinax, Carson Coriell, Matthew Payne, Meggan E. Craft, Tyler J. Garwood, Tiffany M. Wolf, Maria A. Diuk-Wasser, Meredith C. VanAcker, Laura Dudley Plimpton, Mark Q. Wilber, Daniel Grove, Justin Koseiwska, Lisa I. Muller, Kim M. Pepin
Overview of North American isolates of chronic wasting disease used for strain research Overview of North American isolates of chronic wasting disease used for strain research
Chronic Wasting Disease (CWD) is a prion disease that affects Cervidae species, and is the only known prion disease transmitted among wildlife species. The key pathological feature is the conversion of the normal prion protein (PrPC) misfolding into abnormal forms (PrPSc), triggering the onset of CWD infections. The misfolding can generate distinct PrPSc conformations (strains) giving...
Authors
W. David Walter, Allen Jeffrey Herbst, Chia-Hua Lue, Jason C. Bartz, M. Camille Hopkins
Relatedness of white-tailed deer from culling efforts within chronic wasting disease management zones in Minnesota Relatedness of white-tailed deer from culling efforts within chronic wasting disease management zones in Minnesota
In white-tailed deer (Odocoileus virginianus), closely related females form social groups, avoiding other social groups. Consequently, females infected with chronic wasting disease (CWD) are more likely to infect social group members. Culling has been used to reduce CWD transmission in high-risk areas; however, its effectiveness in removing related individuals has not been assessed. We...
Authors
Alberto F. Fameli, Christopher S. Jennelle, Jessie Edson, Erik C. Hildebrand, Michelle Carstensen, W. David Walter
Neonatal antipredator tactics shape female movement patterns in large herbivores Neonatal antipredator tactics shape female movement patterns in large herbivores
Caring for newborn offspring hampers resource acquisition of mammalian females, curbing their ability to meet the high energy expenditure of early lactation. Newborns are particularly vulnerable, and large herbivores have evolved a continuum of neonatal anti-predator tactics, ranging from immobile hider to highly mobile follower offspring. How these tactics constrain female movements...
Authors
Kamal Atmeh, Christophe Bonenfant, Jean-Michel Gaillard, Mathieu Garel, A.J. Mark Hewison, Pascal Marchand, Nicolas Morellet, Pia Anderwald, Bayarbaatar Buuveibaatar, Jeffrey L. Beck, Matthew S. Becker, Floris M. van Beest, Jodi Berg, Ulrika A. Bergvall, Randall B. Boone, Mark S. Boyce, Simon Chamaill'e-Jammes, Yannick Chaval, Chimeddorj Buyanaa, David A Christianson, Simone Ciuti, Steeve D. Côté, Duane R. Diefenbach, Egil Droge, Johan T. Du Toit, Samantha P. Dwinnell, Julian Fennessy, Flurin Filli, Daniel Fortin, Emma E. Hart, Matthew Hayes, Mark Hebblewhite, Morten Heim, Ivar Herfindal, Marco Heurich, Christian von Hoermann, Katey Huggler, Craig Jackson, Andrew F. Jakes, Paul F. Jones, Petra Kaczensky, Matthew J. Kauffman, Petter Kjellander, Tayler N LaSharr, Leif Egil Loe, Roel May, Philip McLoughlin, Erling L. Meisingset, Evelyn Merrill, Kevin L. Monteith, Thomas Mueller, Atle Mysterud, Dejid Nandintsetseg, Kirk A. Olson, John Payne, Scott Pearson, Ashild Ønvik Pedersen, Dustin H. Ranglack, Adele K. Reinking, Thomas Rempfler, Clifford G Rice, Eivin Røskaft, Bernt-Erik Sæther, Sonia Saïd, Hugo Santacreu, Niels Martin Schmidt, Daan Smit, Jared A. Stabach, Martin-Hugues St-Laurent, Joëlle Taillon, W. David Walter, Kevin White, Guillaume Péron, Anne Loison
Comparison of butorphanol-azaperone-medetomidine and nalbuphine-medetomidine-azaperone in free-ranging elk (Cervus canadensis) in Pennsylvania, USA Comparison of butorphanol-azaperone-medetomidine and nalbuphine-medetomidine-azaperone in free-ranging elk (Cervus canadensis) in Pennsylvania, USA
Chemical immobilization is commonly used to capture and handle free-ranging elk (Cervus canadensis). Butorphanol-azaperone-medetomidine (BAM) and nalbuphine-medetomidine-azaperone (NalMed-A) are compounded drug combinations that are lower-scheduled in the US than drugs historically used for elk immobilizations. We compared BAM and NalMed-A for immobilization of free-ranging elk using...
Authors
Avery M. Corondi, Justin D. Brown, Jeremiah E. Banfield, W. David Walter
Predicting the odds of chronic wasting disease with Habitat Risk software Predicting the odds of chronic wasting disease with Habitat Risk software
Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy that was first detected in captive cervids in Colorado, United States (US) in 1967, but has since spread into free-ranging white-tailed deer (Odocoileus virginianus) across the US and Canada as well as to Scandinavia and South Korea. In some areas, the disease is considered endemic in wild deer populations, and...
Authors
W. David Walter, Brenda J. Hanley, Cara E. Them, Corey I. Mitchell, James Kelly, Daniel Grove, Nicholas Hollingshead, Rachel C. Abbott, Krysten L. Schuler
Home range and resource selection by American crow Home range and resource selection by American crow
This project contains 4 R Markdown scripts and requires a valid Movebank login is to access the data needed for these scripts. The purpose of this script is to import crow location data from movebank and group it by individual animal and season, run estimators of home range, and conducted integrated step selection function analysis.
Workflow to predict geochemical distributions of soil Workflow to predict geochemical distributions of soil
Mapping soil geochemistry across large spatial extents is essential for understanding mineral distributions and their environmental implications. However, rasters of soil geochemical distributions for the United States are limited. We present a Bayesian modeling framework for generating predictive geochemical distribution maps using integrated nested Laplace approximation in R (R-INLA).
Agent-based modeling of chronic wasting disease transmission among white-tailed deer and potential management responses Agent-based modeling of chronic wasting disease transmission among white-tailed deer and potential management responses
We provide the following R Markdown and NetLogo files corresponding to our application of agent-based models to assess management responses to chronic wasting disease among white-tailed deer in Pennsylvania, USA.
Contact rates for identifying interactions of white-tailed deer in a chronic wasting disease management area Contact rates for identifying interactions of white-tailed deer in a chronic wasting disease management area
Examinations of contact rates among white-tailed deer (Odocoileus virginianus; hereafter, deer) are important to applied management objectives given their societal value and disease transmission potential. This R script was used to curate the original GPS collar and capture data from Pennsylvania DMA2 in preparation for contact rates analysis.
Comparing datasets by surveillance method using spatial models Comparing datasets by surveillance method using spatial models
This software compares statistical methods to model habitat risk of CWD in white-tailed deer in Pennsylvania using Bayesian hierarchical models in R-INLA and compares these results with model output from WinBugs. The software also uses R-INLA with the Stochastic Partial Differential Approach (SPDE) to compare different surveillance methods to model CWD in relation to habitat features and...
Population genetic structure of white-tailed deer using microsatellites i the Mid-Atalntic region Population genetic structure of white-tailed deer using microsatellites i the Mid-Atalntic region
Results of 11 microsatellites for white-tailed deer collected in Maryland, New York, Ohio, Pennsylvania, and Virginia from 2014 to 2022 for genetic analysis. In this project we assessed genetic structure using different analyses, and evaluated the performance of assignment tests to correctly match deer to origin (defined as genetic cluster, state or physiographic province). This...
Chronic Wasting Disease Surveillance Optimization Software Version 2 Chronic Wasting Disease Surveillance Optimization Software Version 2
The Chronic Wasting Disease Surveillance Optimization Software Version 2 computes sampling recommendations to detect chronic wasting disease (CWD) in white-tailed deer (Odocoileus virginianus). Driven by a combinatorial optimization algorithm, the software maximizes the return-on-investment to the wildlife agency while keeping the overall surveillance program within budget. The software...
Change-point models for identifying single behavioral transitions in wild animals 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...
Habitat Risk Software 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...
Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels
R code to test for differences in DNA yield from of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed SNP panels. We calculated mean, median and standard deviation with package psych using the describe() function. Additionally, we generated boxplots using package ggplot2 where the quantity for each tissue sample is...
Workflow to acquire and process large spatial data and build complex models Workflow to acquire and process large spatial data and build complex models
This software involves R scripts to download and process large-scale spatial data defined by an extent input by the user. The code then resamples data to the desired resolution, downloads metadata from a public website on West Nile virus prevalence in mosquito pools, then extracts spatial layer data as covariates for each record. Also, this software involves R script to fit models of...
Spatial modeling of two mosquito vectors of West Nile virus using integrated nested Laplace approximation Spatial modeling of two mosquito vectors of West Nile virus using integrated nested Laplace approximation
This software involves R script to fit models of abundance of mosquito vectors (' Script_for_ECS22-0193_9_13_2215.R') to landscape and environmental covariates using INLA and SPDE. The dataset used for this analysis were originally provided by the Pennsylvania Department of Environmental Protection (DEP) with a confidentiality agreement. The majority of the data used in this study...
Science and Products
Pennsylvania Cooperative Fish and Wildlife Research Unit
The Pennsylvania Cooperative Fish and Wildlife Research Unit, est. 1938, is a partnership among the Pennsylvania Game Commission, Pennsylvania Fish and Boat Commission, Pennsylvania State University, the U.S. Geological Survey, the U.S. Fish and Wildlife Service, and the Wildlife Management Institute.
Filter Total Items: 14
Predictive layers of trace elements in soil in the conterminous United States Predictive layers of trace elements in soil in the conterminous United States
This dataset provides posterior mean predicted rasters of the distribution of trace elements important to vertebrate health (cobalt, copper, iron, manganese, selenium, and zinc) in the soil across the conterminous United States. Rasters were generated using a Bayesian modeling framework implemented in R with the R-INLA framework (Integrated Nested Laplace Approximation) and the...
Data for Distance sampling accounting for density gradient and animal distribution Data for Distance sampling accounting for density gradient and animal distribution
There are 9 datasets. one distance sampling dataset, 4 resource selection datasets, and 4 outputs from bootstrapped resource selection models the use the estimated correction factor. The 4 resource selection datasets have data that can be used in a binomial generalized linear mixed effect model to create the correction factor. The distance sampling data set is used to estimate density...
White-tailed deer from culling efforts in Minnesota White-tailed deer from culling efforts in Minnesota
Dataset containing information for white-tailed deer samples from Minnesota. Samples were genotyped for 11 microsatellites markers and sequenced for a fragment of approx. 546 bp belonging to the mitochondrial control region. Marker OvirQ should not be used as it presents alleles inconsistent with reported pattern, with some alleles separated by only 1 base pair and inconsistent between...
Comparing datasets by surveillance method using spatial models Comparing datasets by surveillance method using spatial models
This software compares statistical methods to model habitat risk of CWD in white-tailed deer in Pennsylvania using Bayesian hierarchical models in R-INLA and compares these results with model output from WinBugs. The software also uses R-INLA with the Stochastic Partial Differential Approach (SPDE) to compare different surveillance methods to model CWD in relation to habitat features and...
Microsatellite genotypes and metadata for white-tailed deer samples from the Mid-Atlantic region of USA Microsatellite genotypes and metadata for white-tailed deer samples from the Mid-Atlantic region of USA
Dataset containing information for white-tailed deer samples from Ohio, Pennsylvania, Maryland, Virginia and New York, genotyped for 11 microsatellites markers. Marker OvirQ should not be used as it presents alleles inconsistent with reported pattern, with some alleles separated by only 1 base pair and inconsistent between runs. Projected coordinates representing sampling location are in...
Population genetic structure of white-tailed deer using microsatellites i the Mid-Atalntic region Population genetic structure of white-tailed deer using microsatellites i the Mid-Atalntic region
Results of 11 microsatellites for white-tailed deer collected in Maryland, New York, Ohio, Pennsylvania, and Virginia from 2014 to 2022 for genetic analysis. In this project we assessed genetic structure using different analyses, and evaluated the performance of assignment tests to correctly match deer to origin (defined as genetic cluster, state or physiographic province). This...
Chronic Wasting Disease Surveillance Optimization Software Version 2 Chronic Wasting Disease Surveillance Optimization Software Version 2
The Chronic Wasting Disease Surveillance Optimization Software Version 2 computes sampling recommendations to detect chronic wasting disease (CWD) in white-tailed deer (Odocoileus virginianus). Driven by a combinatorial optimization algorithm, the software maximizes the return-on-investment to the wildlife agency while keeping the overall surveillance program within budget. The software...
Change-point models for identifying single behavioral transitions in wild animals 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...
Input for Habitat Risk Software Input for Habitat Risk Software
Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy that was first detected in captive cervids in Colorado, United States (US) in 1967, but has since spread into free-ranging white-tailed deer (Odocoileus virginianus) populations across the US and Canada. In some areas, the disease is considered endemic in wild deer populations, and governmental wildlife agencies...
Habitat Risk Software 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...
Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels
R code to test for differences in DNA yield from of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed SNP panels. We calculated mean, median and standard deviation with package psych using the describe() function. Additionally, we generated boxplots using package ggplot2 where the quantity for each tissue sample is...
Evaluation of DNA yield from various sources for use in single nucleotide polymorphism panels Evaluation of DNA yield from various sources for use in single nucleotide polymorphism panels
Genetics studies are used by wildlife managers and researchers to gain inference into a population of a species of interest. To gain these insights, micro-satellites have been the primary method, however, there currently is a shift from micro-satellites to single nucleotide polymorphisms (SNPs). With the DNA requirements being different, an investigation into which samples can provide...
Filter Total Items: 56
Statewide agent-based model for management of chronic wasting disease in white-tailed deer: PAOvCWD Statewide agent-based model for management of chronic wasting disease in white-tailed deer: PAOvCWD
Chronic wasting disease (CWD) is an always-fatal disease infecting wild cervids globally. Ecologically and economically important, CWD presents a challenge for managing white-tailed deer (Odocoileus virginianus). We built an agent-based model to simulate CWD transmission and assess potential management actions that could slow disease spread: PAOvCWD. We developed PAOvCWD using contact...
Authors
Nathaniel H. Wehr, Christopher S. Rosenberry, David Stainbrook, Maureen Staats, Andrea L. Korman, W. David Walter
Generating geochemical and mineralogy distributions of soil in the conterminous United States using Bayesian hierarchical spatial models Generating geochemical and mineralogy distributions of soil in the conterminous United States using Bayesian hierarchical spatial models
Characterizing geochemical and mineralogical soil distributions across large spatial extents is essential for understanding mineral resources, ecosystem processes, and environmental risks. Rasters of soil geochemical distributions for the conterminous United States, however, are limited. We present a Bayesian modeling workflow and tool for generating predictive geochemical and mineralogy
Authors
Kristin J. Bondo, Tiffany M. Wolf, W. David Walter
Intraspecific contact among white-tailed deer: A literature review and chronic wasting disease case study Intraspecific contact among white-tailed deer: A literature review and chronic wasting disease case study
White-tailed deer (Odocoileus virginianus) are a valuable game mammal in the eastern United States necessitating detailed understanding of disease transmission. We conducted a literature review on intraspecific contact (i.e., interactions wherein disease transmission may occur) among deer. From 69 studies, we identified five themes underlying research on intraspecific deer contact...
Authors
Nathaniel H. Wehr, Kristin J. Bondo, Christopher S. Rosenberry, David Stainbrook, Bret D. Wallingford, W. David Walter
Viral outbreak dynamics and evolution in wildlife at the interface with humans Viral outbreak dynamics and evolution in wildlife at the interface with humans
In this study, we used a multi-faceted approach to understand patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and persistence in a wild white-tailed deer (Odocoileus virginianus) population. Serology data indicated transmission of SARS-CoV-2 and persistence during the seven-month sampling period. Traditional disease modelling based on deer-to-deer...
Authors
Rachael Marie Giglio, Aaron Westmoreland, Mark Q. Wilber, Grete WIlson-Henjum, Aung Nyein Chan, Billy Gardner, Wantida Horpiencharoen, Roderick B. Gagne, Avery M. Corondi, Alec Baker, Matthew A. Combs, Jefferey Chandler, Kezia R. Manlove, Kim M. Pepin, W. David Walter
Development of high-throughput genomic resources to inform white-tailed deer population and disease management Development of high-throughput genomic resources to inform white-tailed deer population and disease management
White-tailed deer (Odocoileus virginianus) are the most abundant and widespread cervid in North America. Genetic data are used as a tool to monitor populations and make management decisions for this game species. However, the development and use of genomic tools that can generate a set of markers suitable for longitudinal genomic data collection, whether for management purposes or to...
Authors
David Navarro, Emily K. Latch, Anaïs K. Tallon, Caitlin N. Ott-Conn, Randy W. DeYoung, Daniel P. Walsh, Peter T. Euclide, R.G. Chandika, Wes A. Larson, Arun S. Seetharam, Andrew J. Severin, Andrew J. Severin, James M. Reecy, Zhi-Liang Hu, Jay R. Cantrell, Michelle Carstensen, Joe N. Caudell, Charlie H. Killmaster, Mitch L. Lockwood, William T. McKinley, Andrew S. Norton, Krysten L. Schuler, Daniel J. Storm, Jason A. Sumners, W. David Walter, Julie A. Blanchong
Expanding national-scale wildlife disease surveillance systems with research networks Expanding national-scale wildlife disease surveillance systems with research networks
Efficient learning about disease dynamics in free-ranging wildlife systems can benefit from active surveillance that is standardized across different ecological contexts. For example, active surveillance that targets specific individuals and populations with standardized sampling across ecological contexts (landscape-scale targeted surveillance) is important for developing a mechanistic
Authors
Kim M. Pepin, Matthew A. Combs, Guillaume Bastille-Rousseau, M.E. Craft, Paul C. Cross, M.A. Diuk-Wasser, R.B. Gagne, Travis Gallo, Tyler Garwood, J.D. Heale, J. Hewitt, J. Hoy-Petersen, Jennifer L. Malmberg, Jennifer M. Mullinax, L. Plimpton, Lauren Smith, M.C. VanAcker, J.C. Chandler, W. David Walter, Grete WIlson-Henjum, George Wittemyer, Kezia R. Manlove
Evaluation of SARS-CoV-2 antibody detection methods for wild Cervidae Evaluation of SARS-CoV-2 antibody detection methods for wild Cervidae
Wildlife surveillance programs often use serological data to monitor exposure to pathogens. Diagnostic sensitivity and specificity of a serological assay quantify the true positive and negative rates of the diagnostic assay, respectively. However, an assay’s accuracy can be affected by wild animals’ pathogen exposure history and quality of the sample collected, requiring separate...
Authors
Joshua Hewitt, Grete Wilson-Henjum, Jeffrey C. Chandler, Aaron T. Phillips, Diego G. Diel, W. David Walter, Alec Baker, Jennifer Høy-Petersen, Guillaume Bastille-Rousseau, Tadao Kishimoto, George Wittemyer, Jeremy Alder, Sara Hathaway, Kezia R. Manlove, Travis Gallo, Jennifer Mullinax, Carson Coriell, Matthew Payne, Meggan E. Craft, Tyler J. Garwood, Tiffany M. Wolf, Maria A. Diuk-Wasser, Meredith C. VanAcker, Laura Dudley Plimpton, Mark Q. Wilber, Daniel Grove, Justin Koseiwska, Lisa I. Muller, Kim M. Pepin
Overview of North American isolates of chronic wasting disease used for strain research Overview of North American isolates of chronic wasting disease used for strain research
Chronic Wasting Disease (CWD) is a prion disease that affects Cervidae species, and is the only known prion disease transmitted among wildlife species. The key pathological feature is the conversion of the normal prion protein (PrPC) misfolding into abnormal forms (PrPSc), triggering the onset of CWD infections. The misfolding can generate distinct PrPSc conformations (strains) giving...
Authors
W. David Walter, Allen Jeffrey Herbst, Chia-Hua Lue, Jason C. Bartz, M. Camille Hopkins
Relatedness of white-tailed deer from culling efforts within chronic wasting disease management zones in Minnesota Relatedness of white-tailed deer from culling efforts within chronic wasting disease management zones in Minnesota
In white-tailed deer (Odocoileus virginianus), closely related females form social groups, avoiding other social groups. Consequently, females infected with chronic wasting disease (CWD) are more likely to infect social group members. Culling has been used to reduce CWD transmission in high-risk areas; however, its effectiveness in removing related individuals has not been assessed. We...
Authors
Alberto F. Fameli, Christopher S. Jennelle, Jessie Edson, Erik C. Hildebrand, Michelle Carstensen, W. David Walter
Neonatal antipredator tactics shape female movement patterns in large herbivores Neonatal antipredator tactics shape female movement patterns in large herbivores
Caring for newborn offspring hampers resource acquisition of mammalian females, curbing their ability to meet the high energy expenditure of early lactation. Newborns are particularly vulnerable, and large herbivores have evolved a continuum of neonatal anti-predator tactics, ranging from immobile hider to highly mobile follower offspring. How these tactics constrain female movements...
Authors
Kamal Atmeh, Christophe Bonenfant, Jean-Michel Gaillard, Mathieu Garel, A.J. Mark Hewison, Pascal Marchand, Nicolas Morellet, Pia Anderwald, Bayarbaatar Buuveibaatar, Jeffrey L. Beck, Matthew S. Becker, Floris M. van Beest, Jodi Berg, Ulrika A. Bergvall, Randall B. Boone, Mark S. Boyce, Simon Chamaill'e-Jammes, Yannick Chaval, Chimeddorj Buyanaa, David A Christianson, Simone Ciuti, Steeve D. Côté, Duane R. Diefenbach, Egil Droge, Johan T. Du Toit, Samantha P. Dwinnell, Julian Fennessy, Flurin Filli, Daniel Fortin, Emma E. Hart, Matthew Hayes, Mark Hebblewhite, Morten Heim, Ivar Herfindal, Marco Heurich, Christian von Hoermann, Katey Huggler, Craig Jackson, Andrew F. Jakes, Paul F. Jones, Petra Kaczensky, Matthew J. Kauffman, Petter Kjellander, Tayler N LaSharr, Leif Egil Loe, Roel May, Philip McLoughlin, Erling L. Meisingset, Evelyn Merrill, Kevin L. Monteith, Thomas Mueller, Atle Mysterud, Dejid Nandintsetseg, Kirk A. Olson, John Payne, Scott Pearson, Ashild Ønvik Pedersen, Dustin H. Ranglack, Adele K. Reinking, Thomas Rempfler, Clifford G Rice, Eivin Røskaft, Bernt-Erik Sæther, Sonia Saïd, Hugo Santacreu, Niels Martin Schmidt, Daan Smit, Jared A. Stabach, Martin-Hugues St-Laurent, Joëlle Taillon, W. David Walter, Kevin White, Guillaume Péron, Anne Loison
Comparison of butorphanol-azaperone-medetomidine and nalbuphine-medetomidine-azaperone in free-ranging elk (Cervus canadensis) in Pennsylvania, USA Comparison of butorphanol-azaperone-medetomidine and nalbuphine-medetomidine-azaperone in free-ranging elk (Cervus canadensis) in Pennsylvania, USA
Chemical immobilization is commonly used to capture and handle free-ranging elk (Cervus canadensis). Butorphanol-azaperone-medetomidine (BAM) and nalbuphine-medetomidine-azaperone (NalMed-A) are compounded drug combinations that are lower-scheduled in the US than drugs historically used for elk immobilizations. We compared BAM and NalMed-A for immobilization of free-ranging elk using...
Authors
Avery M. Corondi, Justin D. Brown, Jeremiah E. Banfield, W. David Walter
Predicting the odds of chronic wasting disease with Habitat Risk software Predicting the odds of chronic wasting disease with Habitat Risk software
Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy that was first detected in captive cervids in Colorado, United States (US) in 1967, but has since spread into free-ranging white-tailed deer (Odocoileus virginianus) across the US and Canada as well as to Scandinavia and South Korea. In some areas, the disease is considered endemic in wild deer populations, and...
Authors
W. David Walter, Brenda J. Hanley, Cara E. Them, Corey I. Mitchell, James Kelly, Daniel Grove, Nicholas Hollingshead, Rachel C. Abbott, Krysten L. Schuler
Home range and resource selection by American crow Home range and resource selection by American crow
This project contains 4 R Markdown scripts and requires a valid Movebank login is to access the data needed for these scripts. The purpose of this script is to import crow location data from movebank and group it by individual animal and season, run estimators of home range, and conducted integrated step selection function analysis.
Workflow to predict geochemical distributions of soil Workflow to predict geochemical distributions of soil
Mapping soil geochemistry across large spatial extents is essential for understanding mineral distributions and their environmental implications. However, rasters of soil geochemical distributions for the United States are limited. We present a Bayesian modeling framework for generating predictive geochemical distribution maps using integrated nested Laplace approximation in R (R-INLA).
Agent-based modeling of chronic wasting disease transmission among white-tailed deer and potential management responses Agent-based modeling of chronic wasting disease transmission among white-tailed deer and potential management responses
We provide the following R Markdown and NetLogo files corresponding to our application of agent-based models to assess management responses to chronic wasting disease among white-tailed deer in Pennsylvania, USA.
Contact rates for identifying interactions of white-tailed deer in a chronic wasting disease management area Contact rates for identifying interactions of white-tailed deer in a chronic wasting disease management area
Examinations of contact rates among white-tailed deer (Odocoileus virginianus; hereafter, deer) are important to applied management objectives given their societal value and disease transmission potential. This R script was used to curate the original GPS collar and capture data from Pennsylvania DMA2 in preparation for contact rates analysis.
Comparing datasets by surveillance method using spatial models Comparing datasets by surveillance method using spatial models
This software compares statistical methods to model habitat risk of CWD in white-tailed deer in Pennsylvania using Bayesian hierarchical models in R-INLA and compares these results with model output from WinBugs. The software also uses R-INLA with the Stochastic Partial Differential Approach (SPDE) to compare different surveillance methods to model CWD in relation to habitat features and...
Population genetic structure of white-tailed deer using microsatellites i the Mid-Atalntic region Population genetic structure of white-tailed deer using microsatellites i the Mid-Atalntic region
Results of 11 microsatellites for white-tailed deer collected in Maryland, New York, Ohio, Pennsylvania, and Virginia from 2014 to 2022 for genetic analysis. In this project we assessed genetic structure using different analyses, and evaluated the performance of assignment tests to correctly match deer to origin (defined as genetic cluster, state or physiographic province). This...
Chronic Wasting Disease Surveillance Optimization Software Version 2 Chronic Wasting Disease Surveillance Optimization Software Version 2
The Chronic Wasting Disease Surveillance Optimization Software Version 2 computes sampling recommendations to detect chronic wasting disease (CWD) in white-tailed deer (Odocoileus virginianus). Driven by a combinatorial optimization algorithm, the software maximizes the return-on-investment to the wildlife agency while keeping the overall surveillance program within budget. The software...
Change-point models for identifying single behavioral transitions in wild animals 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...
Habitat Risk Software 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...
Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels
R code to test for differences in DNA yield from of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed SNP panels. We calculated mean, median and standard deviation with package psych using the describe() function. Additionally, we generated boxplots using package ggplot2 where the quantity for each tissue sample is...
Workflow to acquire and process large spatial data and build complex models Workflow to acquire and process large spatial data and build complex models
This software involves R scripts to download and process large-scale spatial data defined by an extent input by the user. The code then resamples data to the desired resolution, downloads metadata from a public website on West Nile virus prevalence in mosquito pools, then extracts spatial layer data as covariates for each record. Also, this software involves R script to fit models of...
Spatial modeling of two mosquito vectors of West Nile virus using integrated nested Laplace approximation Spatial modeling of two mosquito vectors of West Nile virus using integrated nested Laplace approximation
This software involves R script to fit models of abundance of mosquito vectors (' Script_for_ECS22-0193_9_13_2215.R') to landscape and environmental covariates using INLA and SPDE. The dataset used for this analysis were originally provided by the Pennsylvania Department of Environmental Protection (DEP) with a confidentiality agreement. The majority of the data used in this study...