SAES-422 Multistate Research Activity Accomplishments Report

Sections

Status: Approved

Basic Information

Participants

1. Nora M. Bello, USDA Agricultural Research Service, nora.bello@usda.gov 2. Bruce A. Craig, Purdue University, bacraig@purdue.edu 3. Bryan T. Vinyard, USDA Agricultural Research Service (retired), bryan.vinyard@gmail.com 4. Quentin D. Read, USDA Agricultural Research Service, quentin.read@usda.gov 5. Conor G. Fair, University of Georgia, cfair13@uga.edu 6. Jennifer Clarke, UNL, jclarke3@unl.edu 7. Raúl E. Macchiavelli, University of Puerto Rico, raul.macchiavelli@upr.edu 8. John R. Stevens, Utah State University, john.r.stevens@usu.edu 9. Carla L. Goad, Oklahoma State University, carla.goad@okstate.edu 10. Reka Howard, University of Nebraska - Lincoln, rekahoward@unl.edu 11. Xin Dai, Utah State University, xin.dai@usu.edu 12. Robert J. Tempelman, Michigan State University tempelma@msu.edu 13. Daniel Runcie, University of California Davis, deruncie@ucdavis.edu 14. Philip Dixon, Iowa State University (retired), pdixon@iastate.edu 15. Jarad Niemi, Iowa State University, niemi@iastate.edu 16. Samuel B. Fernandes, University of Arkansas, samuelbf@uark.edu 17. Alexander E. Lipka, University of Illinois at Urbana-Champaign, alipka@illinois.edu 18. Edzard van Santen, University of Florida (retired), evsanten@ufl.edu 19. Josefina Lacasa, Kansas State University, lacasa@ksu.edu 20. Larry Madden, The Ohio State University (retired), madden1@osu.edu 21. Clark Kogan, Washington State University, clark.kogan@wsu.edu 22. Susan Durham, Utah State University (retired), sldurham61@gmail.com 23. Neil Paton, Cargill, neil_paton@cargill.com 24. Guilherme Rosa, University of Wisconsin-Madison, grosa@wisc.edu 25. Kathleen Yeater, USDA Agricultural Research Service (retired), kyeater@kyroconsulting.com

NCCC-170_2025_Minutes.docx

Accomplishments

Accomplishments:

 1) Outputs: Workshops, short courses

A total of 24 workshops and short courses were delivered by members of NCCC170 during this period. Audiences ranged from academic trainees (i.e. graduate students and post-docs) to peer statisticians and professionals in allied disciplines, including academic faculty and research scientists in government and industry. Delivery venues spanned domestic and international settings, ranging from Maine, Rhode Island, North and South Carolina, Texas, Kansas, Mississippi, Arkansas, Georgia, Louisiana and Illinois in the US, to Colombia and India abroad. The complete list of workshops and short courses is provided below for illustration purposes. Member co/instructors are highlighted in bold.

  1. Short Course: “Advanced Quantitative Genetics”, taught at the Hunan Agricultural University, Changsha, China. Instructor: Guilherme Rosa. August 12-16, 2024.

 

  1. Short Course: “Generalized Linear Mixed Models: Concepts and Applications”, hosted at the National Meeting of Mathematics and Statistics (Encuentro Nacional de Matemáticas y Estadística), University of Tolima, Ibagué, Colombia. Instructor: Raúl E. Macchiavelli. September 5-6, 2024.
  2. Workshop: “How to Specify a Statistical Model?”, hosted by the USDA Agricultural Research Service – Northeast Area, Orono, Maine. Instructors: Nora Bello & Bryan Vinyard. October 3-4, 2024.
  3. Workshop: “How to Specify a Statistical Model?”, hosted by the USDA Agricultural Research Service – Northeast Area, Kingston, Rhode Island. Instructors: Nora Bello & Bryan Vinyard. October 8-9, 2024.
  4. Short Course: “Big Data and Digital Tools Applied to Livestock Production”, hosted by the Sao Paulo School of Advanced Science on Precision Livestock Farming, Jaboticabal - Brazil. Instructor: Guilherme Rosa. Oct 15 - 19, 2024.
  5. Training Course: “Data Analysis in R”, sponsored by the University of Georgia College of Agriculture and Environmental Sciences, Athens, Griffin and Tifton, Georgia. Instructors: Conor Fair & Xuelin Luo. November 4-15, 2024.
  6. Training Course: “Regression and Classification Applied to Precision Agriculture”, taught at Aarhus University, Aarhus - Denmark, Instructor: Guilherme Rosa. Nov 06-08, 2024.
  7. Workshop: “Do It Right: Conducting a Systematic Review with Meta-Analysis”, hosted by the American Society of Agronomy at its ASA-CSSA-SSSA International Annual Meeting, San Antonio, Texas. Instructors: Bruce A Craig with Brouder, S, Cai, C, Barford, C, and Volenec J. November 10, 2024.
  8. Workshop: “Analysis of Complex Data Using SAS”, sponsored by the American Society of Agronomy at its ASA-CSSA-SSSA International Annual Meeting, San Antonio, Texas. Instructors: Edzard van Santen, Simon Riley, Brandon Smith. November 10, 2024.
  9. Workshop: “Writing the Materials and Methods section of a manuscript, the dos and don’ts”, sponsored by the American Society of Agronomy at its ASA-CSSA-SSSA International Annual Meeting, San Antonio, Texas. Instructors: Edzard van Santen, Simon Riley, Lynn Sollenberger, Michael Casler. November 11, 2024.
  10. Workshop: “A crash course in Bayesian mixed models with brms (parts 2 and 3)”, hosted by the USDA Agricultural Research Service – Southeast Area, Raleigh, North Carolina. Instructor: Quentin Read. November 21-22, 2024, Raleigh, North Carolina.
  11. Workshops: “Mixed models in R for SAS users”, “Machine learning demystified”, hosted by the USDA Agricultural Research Service – Southeast Area, Florence, South Carolina. Instructor: Quentin Read. December 5-6, 2024.

 

  1. Training Course: “Introduction to Mixed Models in Quantitative Genetics”, delivered at the University of Surrey, Guildford - UK. Instructor: Guilherme Rosa. December 11-12, 2024.
  2. Training Workshop on Genomic Selection for Dryland Crops, sponsored by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India. Instructors: Reka Howard, Bruce Walsh, Nelson Lubanga, Vamsi Manthena. February 3-7, 2025
  3. Workshops: “Mixed models in R for SAS users”, “Power analysis tutorial”, “Machine learning demystified”, hosted by the USDA Agricultural Research Service – Southeast Area, Starkville & Oxford, Mississippi. Instructor: Quentin Read. March 4-6, 2025.
  4. Workshop: “Data analysis in R”, sponsored by the Ecological Society of America (ESA) Southeastern Branch at its annual meeting, Baton Rouge, Louisiana. Instructor: Conor Fair. March 11, 2025.
  5. Short Course: “Big Data and Digital Tools Applied to Livestock Production”, taught at the Chungnam National University (CNU), Daejeon - South Korea. Instructor: Guilherme Rosa. March 24-28, 2025.
  6. Workshop: “Fundamentals of Linear Mixed Models for Designed Experiments”, sponsored by the Institute for Digital Agriculture and Advanced Analytics, Kansas State University, Manhattan, Kansas. Instructor: Josefina Lacasa. March 26-31, 2025.
  7. Training Course: “Data Analysis in R”, sponsored by the University of Georgia College of Agriculture and Environmental Sciences, Griffin, Georgia. Instructor: Connor Fair. April 28-29, 2025.
  8. Workshops: “R Boot Camp”, “Machine learning demystified”, “Multiomics”, hosted by USDA Agricultural Research Service – Southeast Area and the University of Arkansas for Medical Sciences, Little Rock, Arkansas. Instructor: Quentin Read. June 2-3, 2025.
  9. Short Course: “Quantitative Genetics”, hosted by the Bruce Weir Summer Institute in Statistical Genetics (SISG), Georgia Tech, Atlanta - GA. Instructor: Guilherme Rosa. June 2-4, 2025.
  10. Short Course: “Mixed Models in Quantitative Genetics”, hosted by the Bruce Weir Summer Institute in Statistical Genetics (SISG), Georgia Tech, Atlanta - GA. Instructor: Guilherme Rosa. June 4-6, 2025.
  11. Workshop: “Polymorphisms and Association Tests” taught in the context of “Introduction to Computational Genomics Course”, sponsored by the Institute for Genomic Biology at University of Illinois – Urbana-Champaign, Illinois. Instructor: Alex Lipka. June 23, 2025.
  12. Training Course: “Data Analytics and Digital Tools Applied to Animal Husbandry”, delivered at the University of Surrey, Guildford - UK. Instructor: Guilherme Rosa. June 24-26, 2025.

 

2) Presentations

A total of 44 presentations, at least 22 of them by invitation, were delivered by members of NCCC170 during this period to a varied professional audience consisting of both statisticians and domain scientists. Delivery venues were both domestic and international. A selected subset is listed below for illustrative purposes.

  1. Bello, NM and W. Stroup; co-authors: J. Lacasa, J. Piaskowski, R. Howard, P. Dixon, C. Fair, Q. Read, BA Craig, C. Kogan, S. Durham, R. Macchiavelli, D. Palmer. Invited talk: “Best Practices for GLMM Implementation: Hard-won lessons and Ongoing struggles – Setting the Stage” and “… Wrap up”. Conference on Applied Statistics in Agriculture and Natural Resources, Gainesville, Florida (virtual attendance). May 13-15, 2025.
  2. Craig, BA. Invited talk: “Is three a crowd?  Development of a triple-system estimator for the U.S. Census of Agriculture”, University of Minnesota, May 15-16, 2025.
  3. Read, Q. Invited talk: “Experimental design matters!” USDA Agricultural Research Service Feed & Food Safety Research Unit seminar series, New Orleans, LA (virtual). May 28, 2025.
  4. Fair, CG. Piaskowski J, Macchiavelli R, Lacasa J, Craig BA, and Stroup W. “Best practices for GLMMs with zero-inflation – unique challenges for repeated-measures data and fitting covariates in binary process”. NCCC-170 Annual Meeting, Moscow, ID.
  5. Clarke, J. Invited talk: “Plant Phenomics and AI/ML”. PHENET Annual Meeting 2025, NOVA University of Science and Technology, Lisbon, Portugal, May 20-22, 2025.
  6. Macchiavelli, R., F. Henao. Invited talk: “Zero-inflated Poisson regression models with censored data”. XXVIII Meeting of the Biostatistics Argentinean Region of the International Biometric Society. Buenos Aires, Argentina. October 8-10, 2024.
  7. Stevens, J.R. and Lister M. “Improving Interpretability in Machine Learning Using Confidence Intervals in ALE Plots”. Annual meeting of NCCC-170 Research Advances in Agricultural Statistics, Moscow ID, June 5, 2025.
  8. Poudel, B., Howard, R, Bello, N. Stroup, W. “Allowing Negative Variance Component Estimates in REML: Inferential Consequences for Fixed Effects and Type I Error Control”. Conference on Applied Statistics in Agriculture and Natural Resources, Gainesville, FL, May 14
  9. Tempelman, R.J. 2024. “Assessing different cross-validation schemes for predicting novel traits using sensor data: an application to dry matter intake and residual feed intake using milk spectral data”.  Webinar provided for the 8th Data Scientist Meeting of the European Union HoliCow Project, September 9, 2024.
  10. Runcie, D.E. “How to find beneficial alleles for climate adaptation in crop gene banks”. University of Minnesota, September 12, 2024.
  11. Dixon, P. “Using an extension of fragmentary data analysis methods to predict sex from fragmented skeletons”.  NCCC-170 Annual meeting, Moscow, ID, June 5, 2025
  12. Niemi, J. “Bayesian methodology for disease severity forecasting”. Medical College of Wisconsin, May 2, 2025
  13. Fernandes, S.B. “Can We Better Utilize the Data We Have?” National Association For Plant Breeding. Rethink, Reinvent, Revolutionize: Innovation for Change. St Louis, MO – USA. 2024.
  14. Lipka AE. “Applying omnigenic model theory and mixed random forests to leverage genetic diversity in exotic germplasm,” National Association for Plant Breeding (NAPB) Annual Meeting, Kona, HI. May 20, 2025.
  15. Lacasa, J., and Rudnick, D. “Leveraging TAPS extension efforts for research purposes – opportunities, and challenges”. NCCC-170 Annual meeting, June 2025.
  16. Rosa, G.J.M. “Use of AI to Improve Livestock Disease Surveillance”. AI Hackathon for Livestock Data. University of Surrey, UK. December 10th, 2024.

 

3) Books and Book Chapters

  • Amaral, T. B., Rosa, G. J. M., Visoli, M. C. and Dias, F. M. G. N. “Data science applied to beef cattle production”. In: Agricultura de Precisão: Um Novo Olhar na Era digital. Bassoi, L. H. et al. (Eds.) Sao Carlos, SP, Brazil: Cubo Multimídia, 2024. ISBN 978-65-86819-38-0.

 

4) Other Project Related Activities: awards, grants 

Members of NCCC170 served as principal investigators, co-principal investigators or collaborators for 17 interdisciplinary competitive grant awards active during the funding period and totaling over $ 26 million. Funding sources included federal agencies such as the US Department of Agriculture (USDA), as well as state agencies and private organizations. Grant awards are listed below; member co/authors are highlighted in bold.

 

Grants:

  1. Clarke, J. USDA AFRI. NIFA AG2PI Collaborative: Continuing to Seed the Future of Agriculture Genome to Phenome Research, $1,920,000, 09/01/22 – 08/31/24. Role: co-Principal Investigator and Lead Site PI
  2. Clarke, J. USDA AFRI, ODF: National Agricultural Producers Data Cooperative: Expansion through Strategic Development, $958,410, 09/15/24–09/14/2026. Role: Principal Investigator
  3. Clarke, J. USDA AFRI, Clarke, J. ODF: National Ag Producer Data Cooperative: Strategic Development of a National Framework, $960,000, 09/01/23–08/31/2025. Role: Principal Investigator
  4. Clarke, J. USDA ARS Multistate Hatch, Tuinstra, M. NC1212: Exploring the Plant Phenome in Controlled and Field Environments, $250,000, 10/01/22– 09/30/25. Role: Participant
  5. Niemi, J. USDA NIFA (#2020-68012-31824) Consortium for Cultivating Human and Naturally reGenerative Enterprises (C-CHANGE). $10,000,000, 10/01/2020 - 09/31/2025 Role: Co-PI
  6. Fernandes, S.B. Integrating genomic prediction with crop modeling to develop climate-resilient cultivars. Foundation for Food & Agriculture Research, $448,491, 01/01/2025 - 12/31/2027. Role: Principal Investigator
  7. Macchiavelli, R. Puerto Rico Environmental Quality Board (PREQB). “Development of an integrated platform for monitoring and forecasting Harmful Algal Blooms at San José Lagoon and documenting the history of PFAS pollution in selected watersheds of Puerto Rico”. Role: Collaborator. Timeline: 2023-2026. $2,450,000.
  8. Rosa, G. J. M., Lourenco, D., Rowan, T., Brito, L., Gondro, C., Huang, J., and Valle de Souza, S. USDA IDEAS: “Integrating Enviromics, Genomics, and Machine Learning for Precision Breeding of Resilient Beef Cattle”. Role: Principal Investigator. Timeline: 05/2023-04/2027. $1,000,000.
  9. Rosa, G. J. M., Tempelman, R. J. and Knapp, J. R. USDA-AFRI : “47th ADSA Discover Conference: Dairy Cow and Farm Resilience: Mitigating Stress Impacts to Welfare, Health, and Profitability”. Roles: Principal Investigators. Timeline: 1-12/2025, $30,000.
  10. Rosa, G. J. M., Weigel, K. A., Peñagaricano, F., Dórea, J. R. R., White, H. M., and Cabrera, V. E. USDA-AFRI: “The Resilient Cow: Next-Generation Selection Strategies using High-Frequency Phenotypes to Achieve Predictable Performance under Unpredictable Conditions”. Role: Principal Investigator. Timeline: 03/2023-02/2027, $650,000.
  11. Brito, L., Rosa, G. J. M. et al. USDA-AFRI DSFAS: “Integrating Multiomics and High-Throughput Phenotypic Datasets Through Machine Learning to Improve Animal Resilience and Welfare”. Role: co-Principal Investigator. Timeline: 05/2022-05/2026, $650,000.
  12. Rosa, G. J. M. “Development of an Efficient Computer Vision System to Monitor Beef Cattle Growth in Feedlots”, HATCH-CALS. Role: Principal investigator. Timeline: 10/2022-09/2026, $140,632.
  13. Steibel, J. P., Brown-Brandl, T., Rosa, G. J. M., et al. USDA-FACT CIN: “A Coordinated Innovation Network for Advancing Computer Vision in Precision Livestock Farming”. Role: co-Principal Investigator. Timeline: 09/2021-08/2026, $1,000,000.
  14. Penagaricano, F., H. C. Mantovani, H.M. White, K.A. Weigel, J.E.P. Santos, K.C. Jeong, J.E. Koltes, J.A.D.R.N. Appuhamy, M.J. Vandehaar, R.J. Tempelman, R.L. Baldwin and P. VanRaden. Integrating genomic ,nutritional, and microbial strategies to mitigate enteric methane emissions from dairy cattle. Foundation for Food and Agricultural Research and Council for Dairy Cattle Breeding. 01/01/2023-12/31/2025. $3,200,000
  15. De Guzman, C., Srivastava, V.; Fernandes, S. B. USDA-NIFA-AFRI: Breeding for Rice Yield and Grain Quality Under High Night Temperature Conditions Using Conventional Breeding, Genomics and Gene Editing Approach. $585,650, 04/01/24 – 03/31/28. Role: co-Principal Investigator
  16. Eicher-Miller, R Bailey, BA Craig, A Abbott, J Tooze, B Mayfiled, and B Connolly. USDA-NIFA: Maximizing the impact of nutrition education to meet the dietary quality and food security needs of children and parents. $969,996 09/01/2022 – 08/31/2027. Role: Co-Investigator
  17. S Brouder, J Volenec, S Murrell, BA Craig, C Cai, C Barford, M Ruark, W Berg, G Bossaer, DS Brandt, B Erickson, J Scott, N Thompson, J Zhu, DN Walker. USDA-NIFA, FACT: An Innovative Cyber-Framework Integrating Public/Private Data for Evidence-Based Recommendations. $1,000,000 08/01/2019 – 07/31/2025. Role: Co-Investigator

 

Also listed below are honors and professional awards conferred to members of the NCCC170 during the reporting period.

  1. Guilherme Rosa: Vilas Distinguished Achievement Professorship, University of Wisconsin-Madison, 2024.
  2. Guilherme Rosa: Chair, 47th American Dairy Science Association (ADSA) Discover Conference “Dairy Cow and Farm Resilience: Mitigating Stress Impacts to Welfare, Health, and Profitability”, Itasca, IL. May 5-8, 2025. https://www.adsa.org/Meetings/47th-Discover-Conference.

 

5) Milestones: Implementation and dissemination efforts. Benchmarking.

  1. Lacasa J. , J. Piaskowski, R. Howard, N.M. Bello, W. Stroup, S. Durham, Q. Read, D. Palmer, C. Fair, BA Craig, R. Macchiavelli, C. Kogan, P. Dixon. Ongoing joint research effort to benchmark and articulate “Best Practices for Implementation of Generalized Linear Mixed Models”. July 2024-June 2025.
  2. Edzard van Sante, Philip Dixon, Reka Howard, Neil Paton, Julia Piaskowski, Kathleen Yeater, Guilherme Rosa, Hans-Peter Piepho, Simon Riley, Carlos Messina, Andrea Arias. Planning committee and local host (van Santen) for the 2025 Conference on Applied Statistics in Agriculture and Natural Resources, held in Gainesville, Florida on May 11-15, 2025. https://conference.ifas.ufl.edu/appliedstats/index.php
  3. Julia Piaskowski & W. Price; Idaho Ag Stats - instructional blog posts, tutorials and workshops. https://agstats.io/post/
  4. CRAN Task View: Agricultural Sciences, launched and co-maintained by Julia Piaskowki: https://cran.r-project.org/web/views/Agriculture.html
  5. CRAN Task View: Mixed, Multilevel and Hierarchical Models in R, launched and co-maintained by Julia Piaskowki: https://cran.r-project.org/web/views/MixedModels.html
  6. YouTube channel (https://www.youtube.com/jaradniemi): >6,900 subscribers, >1.39 million views. Jarad Niemi

Impacts

Publications

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