Books:

• 1. Hooten, M.B. and T.J. Hefley. (2019) Bringing Bayesian Models to Life. Chapman and Hall/CRC [R code] [errata].

Journal publications:

• 2024

  1. Pereyra, V.M., T.J., Hefley, P.V. Prasad, I. Ciampitti (accepted) Soybean seed yield, protein, and oil concentration for a modern and old genotype under varying row spacing. Heliyon

  2. Rieber, C.J., T.J., Hefley, D.A. Haukos. (accepted) Treed Gaussian processes for animal movement modeling. Ecology and Evolution.

  3. Palermo, F., J.A. Fernandez, J.E. Habben, J.R. Schussler, T. Masek, B. Weers, J. Bing,  T. Hefley, P.V. Prasad I. Ciampitti (in press) Optimization of carbon and nitrogen partitioning in DP202216 maize hybrids Field Crops Research.

  4. Massigoge, I., R. Baral, S. Cominelli, E. Denson, P García Helguera, C. Guareschi, L. Machado Simao, J. Peraza Rud, C. Pires, J. Dille, R Lollato, D. Min, A. Patrignani, D.. Ruiz Diaz, T. Hefley, S. Lira, P.V. Prasad, C. Rice, J. Hatfield, I. Ciampitti (in press) Exploring alternative crop rotations to continuous winter wheat for agricultural intensification in the US central Great Plains. Agricultural Systems.

  5. Silber, K.M., T.J. Hefley, H.N Castro-Miller, Z.J. Ratajczak, W.A. Boyle (in press) ​​The long shadow of woody encroachment: an integrated approach to modeling grassland songbird habitat. Ecological Applications.

• 2023

  1. Enders, L., T.J. Hefley  (2023) Modeling host-microbiome interactions to improve mechanistic understanding of aphid vectored plant pathogens. Frontiers in Ecology and Evolution 11:1251165.

  2. Oh, G., S.Aravamuthan, T.F. Ma, J.F.M. Reyes, A. Ballmann, T.J. Hefley, I. McGahan, R. Russell, D. Walsh, J. Zhu. (2023) Model-based surveillance system design under practical constraints with application to white-nose syndrome. Environmental and Ecological Statistics 30:649−667.

  3. Igwe, K., S. Vaishali, T.J. Hefley (2023) Evaluating the impact of future seasonal climate extremes on crop evapotranspiration of maize in western Kansas using a machine learning approach. Land 12:1500.

  4. Veenstra, R., T. Hefley, D. Berning, C. Messina, L. Haag, P.V. Prasad, I. Ciampitti. (2023) Predicting corn tiller development in restrictive environments can be achieved to enhance defensive management decision tools for producers. Frontiers in Plant Science 14:1223961.

  5. Haley, O.C., Y. Zhao, T.J. Hefley, L. Britton, L. Nwadike, C. Rivard, M. Bhullar. (2023) Developing a decision-making tool for agricultural surface water decontamination using ultraviolet-C light. Journal of Food Protection 86:100129.

  6. Massigoge, I., A. Carcedo, A., Lingenfelser, T. Hefley, P.V. Prasad, D. Berning, S. Lira, C. Messina, I. Ciampitti (2023) Maize planting date and maturity in the US central great plains: exploring windows for maximizing yields. European Journal of Agronomy 149:126905.

  7. Cook, J.D., D.M. Williams, D.P. Walsh., T.J. Hefley (2023) Bayesian forecasting of disease spread with little or no local data. Scientific Reports 13:8137.

  8. Mohankumar, N.M., T.J. Hefley, K. Silber, W.A. Boyle (2023) Data fusion of distance sampling and capture-recapture data. Spatial Statistics 55:100756. 

  9. Fletcher, R.J., M.G. Betts, E.I. Damschen, T.J. Hefley, J.N. Hightower, T. Smith, M.J. Fortin, N.M. Haddad. (2023) Addressing the problem of scale that emerges with habitat fragmentation. Global Ecology and Biogeography 32:828−841.

  10. Freeman, N.E., M., Gustafson, T.J. Hefley, W.A. Boyle. (2023) Riding out the storm: depleted fat stores and elevated haematocrit in a small-bodied endotherm exposed to severe weather. Conservation Physiology 11:coad11.

  11. Almeida, L.F.A, A.A. Correndo, J. Ross, M. Litch, S. Casteel, M. Singh, S. Naeve, R. Vann, H. Kendel, L. Lindsey, S. Conley, J. Kleinjan, P. Kovacs, D. Berning , T. Hefley, I. Ciampitti (2023) Soybean yield response to nitrogen (N) and sulfur fertilization in the United States: contribution of soil N and N fixation processes. European Journal of Agronomy 145:126791.

  12. Lacasa, J., D. Makowski, T.J. Hefley, J. Fernandez, E. van Versendaal, G. Lemaire, I. Ciampitti. (2023) Comparison of statistical methods to fit critical nitrogen dilution curves. European Journal of Agronomy 145:126770.

  13. Silber, K.M., N.M. Mohankumar, T.J. Hefley, W.A. Boyle (2023) ​​Emigration and survival correlate with different precipitation metrics throughout a grassland songbird’s annual cycle. Journal of Wildlife Management 97:e22371.

  14. Post van der Burg, M., MacDonald, G., Glassberg, T.J. Hefley (2023) ​​Point-scale habitat and weather patterns influence the distribution of regal fritillaries in the central United States. Ecosphere 14:e4429.

  15. Veenstra, R., C. Messina, D. Berning, L. Haag, P. Carter, T.J Hefley, P.V. Prasad. (2023) Tiller biomass in low plant-density corn enhances transient C sink without direct harvest index detriment. Field Crops Research 292: 108804.

  16. Veenstra, R., C. Messina, D. Berning, L. Haag, P. Carter, T. Hefley, V. Prasad I., Ciampitti. (2023) Corn yield components can be stabilized via tillering in sub-optimal plant densities. Frontiers in Plant Science 13:1047268.

• 2022

  1. Vaishali S., T. Wiederstein, J. Aguilar, T.J. Hefley, I. Ciampitti, A. Sharda, K. Igwe. (2022). Evaluating spatial and temporal variations in sub-field level crop water demands. Frontiers in Agronomy 4:983244.

  2. Niederwerder M.C., and T.J. Hefley. (2022) Assessing the diagnostic sensitivity of biological samples for detecting African swine fever virus infection after natural consumption in feed and liquid. Transboundary and Emerging Diseases 69:2727− 2734 [pdf] [R code]

  3. Mohankumar, N.M., and T.J. Hefley. (2022) Using machine learning to identify nontraditional spatial dependence in occupancy data. Ecology 103:e03563 [pdf]

• 2021

  1. Rossini, P., I.A. Ciampitti, T.J. Hefley, A. Patrignani. (2021) A soil moisture-based framework for guiding the number and location of soil moisture sensors in agricultural fields. Vadose Zone Journal 20:e20159 [pdf]

  2. Grider, J., R.E. Russell, A.E. Ballmann, T.J. Hefley. (2021) Long-term Pseudogymnoascus destructans surveillance data reveal factors contributing to pathogen presence. Ecosphere 12:e03808. [pdf]

  3. Veenstra, R.L., C. Messina, D. Berning, L. Haag, P. Carter, T. Hefley, V. Prasad I. Ciampitti. (2021) Effect of tillers on corn yield: Exploring trait plasticity potential in unpredictable environments. Crop Science 61:3660−3674. [pdf]

  4. Correndo, A.A., T.J. Hefley, D. Holzworth, D., I.A. Ciampitti. (2021) Revisiting linear regression to test agreement in continuous predicted-observed datasets. Agricultural Systems Journal 192:103194 [pdf]

  5. Lacasa, J., T.J. Hefley, F. Curin, M.E Otegui, I.A. Ciampitti. (2021) A practical guide to estimating the light extinction coefficient with nonlinear models – an example in maize. Plant Methods 17:60.[pdf]

  6. Walker, N.B., T.J. Hefley, A.E. Ballmann, R.E. Russell, D.P. Walsh. (2021) Recovering individual-level spatial inference from aggregated binary data. Spatial Statistics 44:100514. [pdf]

• 2020

  1. Mainali K.P., T.J. Hefley, L. Ries, W. Fagan. (2020) Matching expert range maps with species distribution model predictions. Conservation Biology 34:1292−1304. [pdf]

  2. Munaro L.B., T.J. Hefley, E. DeWolf, S. Haley, A.K. Fritz, G. Zhang, L.A. Haag, A.J Schlegel, J.T. Edwards, D. Marburger, P. Alderman, S.M. Jones-Diamond, J. Johnson, J.E. Lingenfelser, S.H. Unêda-Trevisoli, R.P. Lollato. (2020) Exploring long-term variety performance trials to improve genotype, management, and environment recommendations: a case-study for winter wheat. Field Crops Research. 255:107843. [pdf]

  3. McDonough, K.R., S.L., Hutchinson, J. Liang, T.J. Hefley, S. Hutchinson (2020) Spatial configurations of land cover influence flood regulation. Journal of Water Resources Planning and Management 146:04020082. [pdf]

  4. Khalaf, L., A. Timm, W. Chuang, L. Enders, T. Hefley, C. Smith. (2020) Spatio-temporal modeling of Aceria tosichella biotype occurrence and distribution. PLOS ONE 15: e0233507. [pdf]

  5. Walker, N.B., T.J. Hefley, D.P. Walsh. (2020) Bias correction of bounded location error in binary data. Biometrics 76: 530−539.  [pdf]

• 2019

  1. Stoian, A., J. Zimmerman, J. Ji, T. Hefley, S. Dee, D. Diel, R. Rowland, M. Niederwerder. (2019) Half-life of African swine fever virus in animal feed ingredients exposed to transoceanic environmental conditions. Emerging Infectious Diseases 25: 2261−2263. [pdf]

  2. Fletcher, R., T. Hefley, E.  Robertson, B. Zuckerberg, R. McCleery, R. Dorazio. (2019) A practical guide for combining data to model species distributions. Ecology 100:e02710. [pdf]

  3. Niederwerder M., A. Stoian, R. Rowland, S. Dritz, V. Petrovan, L. Constance, J. Gebhardt, M. Olcha, C. Jones, J. Woodworth, Y. Fang, J. Liang, T. Hefley. (2019) Infectious dose of African swine fever virus when consumed naturally in liquid or feed. Emerging Infectious Diseases 25:891−897. [pdf] [R code]

  4. Schmid, R. T.J. Hefley, R. Lollato, B. McCornack. (2019) Landscape effects on Hessian fly, Mayetiola destructor (Diptera: Cecidomyiidae), distribution within six Kansas commercial wheat fields.  Agriculture, Ecosystems and Environment 274:52-61. [pdf] [R code]

• 2018

  1. Enders, L.S., T.J. Hefley, J.J. Girvin, J.R. Whitworth, C.M. Smith. (2018) Spatio-temporal distribution and environmental drivers of Barley yellow dwarf virus and vector abundance in Kansas. Phytopathology 108:1196-1205. [pdf] [R code]

  2. Hooten, M.B., H.R. Scharf, T.J. Hefley, A.T. Pearse, M.D. Weegman. (2018) Animal movement models for migratory individuals and groups. Methods in Ecology and Evolution 9:1692-1705. [pdf]

• 2017

  1. Hefley, T.J., B.M. Brost, M.B. Hooten (2017) Bias correction of bounded location errors in presence­-only data. Methods in Ecology and Evolution 8:1566-1573. [pdf] [R code S1 & S3]

  2. Hefley, T.J., M.B. Hooten, R.E. Russell, D.P. Walsh, J.A., Powell. (2017) When mechanism matters: Bayesian forecasting using models of ecological diffusion. Ecology Letters 20:640-650. [pdf] [R code S1 & S2]

  3. Hefley, T.J., M.B. Hooten, E.M. Hanks, R.E. Russell, D.P. Walsh (2017) Dynamic spatio-temporal models for spatial data. Spatial Statistics 20: 206-220. [pdf] [R code]

  4. Hefley, T.J., K.M. Broms, B.M. Brost, F.E. Buderman, S. Kay, H.R. Scharf, J.R. Tipton, P.J., Williams, M.B. Hooten. (2017) The basis function approach for modeling autocorrelation in ecological data. Ecology 98:632-646. [pdf] [R code S3, S4, & S5]

  5. Williams, P.J., M.B. Hooten, J.N Womble, G.G Esslinger, M.R. Bower, T.J. Hefley. (2017) An integrated data model to estimate spatio-temporal occupancy, abundance, and colonization dynamics. Ecology 98:328-336. [pdf]

  6. Hefley, T.J., M.B. Hooten, E.M. Hanks, R.E. Russell, D.P. Walsh. (2017) The Bayesian group lasso for confounded spatial data. Journal of Agricultural, Biological, and Environmental Statistics 22:42-59. [pdf] [R code]

• 2016

  1. Hefley, T.J., M.B. Hooten, J.M. Drake, R.E. Russell, D.P. Walsh. (2016) When can the cause of a population decline be determined? Ecology Letters 19:1353-1362. [pdf] [data] [R code]

  2. Hefley, T.J., M.B. Hooten. (2016) Hierarchical species distribution models. Current Landscape Ecology Reports 1:87-97. [pdf]

• 2015

  1. Baasch, D.M., T.J. Hefley, S.D. Cahis. (2015) A comparison of breeding population estimators using nest and brood monitoring data. Ecology and Evolution 5:4197-4209 [pdf] [spreadsheet]

  2. Hefley, T.J., D.M. Baasch, A.J. Tyre, E.E. Blankenship. (2015) Use of opportunistic sightings and expert knowledge to predict and compare whooping crane stopover habitat. Conservation Biology 29:1337-1346. [pdf] [data] [R code]

  3. Hefley, T.J., M.B. Hooten. (2015) On the existence of maximum likelihood estimates for presence-only data. Methods in Ecology and Evolution 6:648-655. [pdf] [data] [R code S2 & S3]

• 2014

  1. Hefley, T.J., D.M. Baasch, A.J. Tyre, E.E. Blankenship. (2014) Correction of location errors for presence-only species distribution models. Methods in Ecology and Evolution 5:207-214. [pdf] [data] [R code]

  2. Nemec, K., J. Chan, C. Hoffman, T. Spanbauer, J. Hamm, C. Allen, T. Hefley, D. Pan, P. Shrestha. (2014) Assessing resilience in stressed watersheds. Ecology and Society 19(1):34. [pdf]

• 2013

  1. Hefley, T.J., A.J. Tyre, D.M. Baasch, E.E. Blankenship. (2013) Non-detection sampling bias in marked presence-only data. Ecology and Evolution 3:5225-5236. [pdf] [Rcode]

  2. Hefley, T.J., A.J. Tyre, E.E. Blankenship. (2013) Statistical indicators and state-space population models predict extinction in a population of bobwhite quail. Theoretical Ecology 6:319-331. [pdf]

  3. Hefley, T.J., A.J. Tyre, E.E. Blankenship. (2013) Fitting population growth models in the presence of measurement and detection error. Ecological Modelling 263:244-250. [pdf] 

  4. Hefley, T.J., S.E. Hygnstrom, J.M. Gilsdorf, G.M. Clements, M.J. Clements, A.J. Tyre, D.M. Baasch, K.C. VerCauteren. (2013) Effects of deer density and cropland conversion on mass of white-tailed deer. Journal of Fish and Wildlife Management 4:20-32. [pdf] [data] [R code]

• 2009 - 2012

  1. Hefley, T.J., A.J. Tyre. (2011)  Favorable team scores under the team-based learning paradigm: a statistical artifact? Review of Undergraduate Research in Agricultural and Life Sciences 6(1). [pdf]  

  2. Lavelle, M.J., K.C. VerCauteren, T.J. Hefley, G.E. Phillips, S.E Hygnstrom, D.B. Long, J.W. Fischer, S.R. Swafford, T.A. Campbell. (2011) Evaluation of fences for containing feral swine under simulated depopulation conditions. Journal of Wildlife Management 75:1200-1208. [pdf]

  3. Thiele, J., T. Hefley, L. Beck-Johnson, E. Mathews. (2009) Early season mosquito population dynamics in Lancaster County, Nebraska and implications for West Nile Virus. Review of  Undergraduate Research in Agricultural and Life Sciences 4(3). [pdf]  

Dissertation: 

• 1. Hefley, T.J. (2014). New statistical methods for analysis of historical data from wildlife populations. University of Nebraska-Lincoln. [pdf]

Reports: 

• 1. Pearse, A.T., D.A. Brandt, W.C. Harrell, K.L. Metzger, D.M. Baasch, and T.J. Hefley. (2015) Whooping crane stopover site use intensity within the Great Plains. U.S. Geological Survey Open-File Report 2015-1166. [pdf]

  2. Smith, C.B., D.M. Baasch, and T.J. Hefley. (2012) Forage fish abundance and the influence of river flow−management implications for the endangered least tern. Technical report published by Executive Director’s office of the Platte River Recovery Implementation Program. [pdf]   

  3. Hefley, T.J., S.E. Hygnstrom, J.M. Gilsdorf, G.M. Clements, M.J. Clements, A.J. Tyre, D.M. Baasch, and K.C. VerCauteren. (2010) Analysis of deer hunting harvest data from DeSoto National Wildlife Refuge, 1990-2009. Final Report presented to DeSoto National Wildlife Refuge. [pdf]

Book chapters:

1. Birge, H., Shulski, M., Trump, B., Ernakovich, J., Hefley, T., Huntington, O., Jardine, C., Klasa, K., Lines, Laurie-Ann, Linkov, I., Garcia, J., Meek, C., Torpy, K., Watson, A. “An Information-Based Resilience Framework for the Changing Arctic.” Cybersecurity and Resilience in the Arctic, edited by B. Trump, K. Hossain, I. Linkov, vol. 58, IOS Press, 2020, pp. 427–443. NATO Science for Peace and Security Series - D: Information and Communication Security. [pdf]

Data packages: 

• 1. Enders, L.S., T.J. Hefley, J.J. Girvin, J.R. Whitworth, C.M. Smith. (2018). Data for: Spatio-temporal distribution and environmental drivers of Barley yellow dwarf virus and vector abundance in Kansas. https://doi.org/10.5061/dryad.mk69rg6 [data]

  2. Hefley, T.J., B.M. Brost, M.B. Hooten (2017) Data for: Bias correction of bounded location errors in presence­-only data. http://datadryad.org/resource/doi:10.5061/dryad.82qd0. [data] 

  3. Hefley, T.J., D.M. Baasch, A.J. Tyre, E.E. Blankenship. (2015) Data for: Use of opportunistic sightings and expert knowledge to predict and compare whooping crane stopover habitat. http://datadryad.org/resource/doi:10.5061/dryad.t6859. [data]

  4. Hefley, T.J., D.M. Baasch, A.J. Tyre, E.E. Blankenship. (2014) Data for: Correction of location errors for species distribution models. http://datadryad.org/resource/doi:10.5061/dryad.h81s5. [data]

  5. Hefley, T.J., S.E. Hygnstrom, J.M. Gilsdorf, G.M. Clements, M.J. Clements, A.J. Tyre, D.M. Baasch, and K.C. VerCauteren. (2013) Data for: Effects of deer density and cropland conversion on mass of white-tailed deer. http://datadryad.org/resource/doi:10.5061/dryad.hn45t [data]

Preprints:

• 1. Edelsparre, A. H., T.J. Hefley, M.A. Rodriguez, M.J Fitzpatrick, M.B. Sokolowski. Scaling up: understanding movement from individual differences to population-level dispersal. https://www.biorxiv.org/content/10.1101/2021.01.04.425125v1.full.pdf

  2. Hefley, T.J., R.E. Russell, A.E. Ballmann, H. Zhang. When and where: estimating the time and location of introduction for exotic pests and pathogens. https://arxiv.org/abs/2006.16982

  3. Hefley, T.J., W.A. Boyle, N.M. Mohankumar. Accounting for location uncertainty in distance sampling data. https://arxiv.org/abs/2005.14316

  4. Hefley, T.J., H. Zhang, B.R. Gray, K.L., Bouska. Model selection for ecological community data using tree shrinkage priors. https://arxiv.org/abs/2005.14303.