Brief Summary of Minutes of Annual Meeting

Annual meeting held at the National Laboratory for Agriculture and the Environment on the campus of Iowa State University, Ames, Iowa, July 8-9, 2010. Joint meeting with SCC-013 (USSES) Official Members Present: Ted Bailey (IA), John Boyer (KS, Admin), Bruce Craig (IN), Susan Durham (UT), Ed Gbur (AR), Mark Hinds (Pioneer Hi-Bred), Ken Koehler (IA), Kevin McCarter (LA), David Meek (USDA-ARS), George Milliken (KS), Margaret Nemeth (Monsanto), Rob Tempelman (MI), Mark West (USDA-ARS) Official Members Absent: Rich Alldredge (WA), Bert Bishop (OH), German Bollero (IL), Don Bullock (IL), Mary Christman (FL), Paul Cornelius (KY), Sara Duke (USDA-ARS), George Fernandez (NV), Larry Madden (OH), Bahram Momen (MD), Cuirong Ren (SD), Dan Schmoldt (UDSA-CREES, Admin.), Bahman Shafii (ID), Linda Young (FL), Hao Zhang (IN), Jun Zhu (WI) Other NCCC-170 Participants Present: Matt Kramer (USDA-ARS), John Stevens (UT), Kathy Yeater (USDA-ARS) SCC-013 Members and Visitors: Philip Dixon, Brian Fergen, Andy Mauromoustakos, Fernando Miguez, Ben Mullinix, Dan Nettleton, Long Qu, Julia Sharp, Man-Yu Yum 2009 Officers: Ed Gbur, Chair; Kathy Yeater, Program Chair; David Meek and Ted Bailey, Local Arrangements Chairs; Susan Durham, Secretary NCCC-170 Website: http://www.uark.edu/misc/ncr170/ Technical program: The meeting began at 8:30 am on Thursday, July 8, 2010, with opening remarks by Jerry Hatfield (NLAE Director), Wendy Wintersteen (Dean of the College), and Ken Koehler (Chair of the ISU Statistics Department). The technical program consisted of the following presentations. David Meek -- Graphics for paired observations John Stevens -- Recent statistical tools for Next-Gen Sequencing data Long Qu -- A hierarchical semi-parametric model for incorporating inter-gene information for analysis of gene expression profiling data Andy Mauromoustakos -- New analytics and features in upcoming JMP Version 9 Ben Mullinix -- Analysis of the Uniform Peanut Performance Tests using mixed models Julia Sharp -- Testing for co-directional interactions in two-factor factorial experiments using union-intersection and intersection-union methods Fernando Miguez -- BioCro: An R package for crop simulation and statistics Business meeting: The business meeting began at 9:00 am on Friday, July 9, 2010. Ed Gbur presided. Kathy Yeater, Kevin McCarter (SCC-013 program chair), Ted Bailey and David Meek were thanked for organizing a productive and enjoyable meeting. The following items were discussed: (1) The 2011 meeting will be held at Purdue and hosted by Bruce Craig. The date was set for July 7-8. John Stevens will serve as program chair. Rob Tempelman volunteered to host the 2012 meeting at Michigan State. (2) The group reviewed and discussed specific goals for the next three years and impact statements. The annual report and impact statement are due shortly after the annual meeting. Participants need to send Ed (egbur@uark.edu) accountings of all activities (workshops, papers, presentations, teaching related, etc.) from October 1, 2009 to September 30, 2010 (or since last year's report) that are related to or inspired by their participation in NCCC-170 as soon as possible. (3) Mary Christman, Kevin McCarter and Walt Stroup will present a workshop on generalized linear mixed models and will participate in a related symposium organized by Kathy Yeater at the ASA-CSSA-SSSA annual meeting in Long Beach in November. Workshops have been offered several times at the Animal and Dairy Science Societies annual meetings. Tentative plans are to do so again. Approaching other professional societies to offer workshops was discussed. The possible use of a webinar format was also mentioned. (4) Following the discussion at last year's annual meeting, the American Society of Agronomy was contacted and agreed to publish a book on generalized linear mixed models written by project members and participants. The project members involved in the writing are Mary Christman, Susan Durham, Ed Gbur, Matt Kramer, Kevin McCarter, Walt Stroup, Mark West and Linda Young. The manuscript is due to the publishers by October 1, 2010. Ed gave a brief progress report. Six of the seven chapters have been through at least one draft and revision. Outside reviewers have been lined up. George Milliken asked about the possibility of sharing the material with group members. Kathy Yeater volunteered to set up a Sharepoint web site. Ed will check with the Agronomy Society to see if this would be permissible under the contract. (5) The current project is scheduled to end in September, 2011. The renewal process must be completed this Fall. Projects must make a special request to keep the same number. Otherwise a new number will be assigned. Current members will not automatically be rolled over into the new project. Everyone must submit a new Appendix E form. John Boyer agreed to continue to serve as our Administrative Advisor. Deadlines are as follows. September 15 -- Initial request due. Includes issues, justification, administrative advisor, and request to retain same project number. October 15 -- Objectives due. November 15 -- New Appendix E for everyone (no automatic rollover). Enough forms must be filed to demonstrate sufficient interest. December 1 -- Complete proposal due. The current project proposal was reviewed and changes, additions and deletions for the new project were discussed. The meeting adjourned at approximately 10:35 a.m. A group photograph for the project web site was taken immediately afterward.

Statisticians who consult and do research in an Agricultural Experiment Station environment enable land grant institutions to perform their agricultural research missions more effectively and efficiently than would otherwise be possible. However, most stations have at most one or two professional statisticians who are not, and can not be expected to be, experts in every area of statistics. This multi-state committee brings together statisticians to work cooperatively to determine the best current approaches to common statistical problems and to help guide future directions of sound statistical practice. In addition to group outputs such as workshops, it serves as a resource for its members and a sounding board for new ideas in their applied statistical research. As a result, all members are able to provide more effective assistance to agricultural researchers addressing national research priorities than they would without NCCC-170. Outputs: Workshops: George Milliken presented a half day work shop entitled "Mixed models analysis using SAS" at the 11th Scientific Conference of Sub-Saharan Africa Network of the International Biometric Society in August, 2009 at Kabarak University, Nakuru, Kenya. Larry Madden presented a half-day workshop entitled "Regression Analysis with SAS" at the Annual Meeting of the American Phytopathological Society in Portland OR in August 2009. Rob Tempelman presented a half-day workshop entitled "Mixed model analysis of research data" for the Center for Statistical Consulting and Training at Michigan State University (www.cstat.msu.edu) in December, 2009. Rob Tempelman presented workshop lectures at the 10th International Microarray Workshop (http://ag.arizona.edu/microarray/workshopJan2010.html) on experimental design, data normalization and statistical inference in January, 2010. Linda Young presented workshops entitled "Applied linear and generalized linear mixed models" to the San Diego Chapter of the American Statistical Association and the El Paso Chapter of the American Statistical Association in April, 2010. The workshops were one and two days, respectively. Linda Young presented a two day workshop on applied linear mixed models for researchers at the University of Florida's Agricultural Experiment Station in May, 2010. Linda Young presented a two day workshop on applied generalized linear mixed models for researchers at the University of Floridas Agricultural Experiment Station in May, 2010. Presentations: Kathy Yeater. "Design and analysis of augmented designs in screening trials" at 3rd Curators Workshop for USDA-ARS germplasm curators and their collaborators in February, 2010 in Atlanta (Invited). John Stevens. "Statistical issues in the normalization of multi-species microarray data" at the Brigham Young University Statistics Department Seminar in October, 2009 and to the BYU-Idaho Mathematics Department Seminar in November, 2009. (Invited) Kevin McCarter. "Using semi-parametric models to account for spatial variability in developing variable rate treatment prescriptions for applications in precision agriculture" at the International Conference on Statistics, Probability, Operations Research, Computer Science, and Allied Areas. in January, 2010 at Andhra University, Visakhapatnam, India. (Invited) Julia Sharp and P.D. Gerard. "Testing for co-directional interactions using union-intersection and intersection union tests" at the International Indian Statistical Association Joint Statistical Meeting in January, 2010 at Andhra University, Visakhapatnam, India. (Invited) Rob Tempelman. "Addressing scope of inference for global genetic evaluation of livestock" at the 47th Annual Meeting of the Brazilian Society of Animal Science in July, 2010 in Salvador, Brazil. (Invited) C.A. Gotway, Linda Young, K.K. Lopiano, G. Kearney and C. DuClos. "Models for assessing uncertainty in local regression" at GeoMED in November, 2009 in Charleston, SC. (Invited) Linda Young, C.A. Gotway, X. Xu, G. Kearney and M. Hyman. "Assessing the association between public health and environmental factors" at the Annual Meeting of the Society for Risk Analysis in December, 2009 in Baltimore. (Invited) Linda Young, C.A. Gotway, K.K. Lopiano, G. and C. DuClos. "Relating public health to environmental factors: Assessing uncertainty in the presence of predicted environmental factors" at the Fields Workshop on Modeling Indirectly and Imprecisely Observed Data in December, 2009 in London, Ontario. (Invited keynote address) Linda Young, C.A. Gotway and K.K. Lopiano. "Challenges associated with integrating data from multiple scales to assess relationships" at Accuracy 2010 in July, 2010 in Leicester, UK. (Invited) Linda Young, D. Abreu, P. Arroway, A.C. Lamas and K.K. Lopiano. "Precise estimates of the number of farms in the United States" in August, 2010 at the Joint Statistical Meetings in Vancouver. (Invited) Kevin McCarter and E. Burris. "Accounting for spatial correlation using radial smoothers In statistical models used for developing variable-rate treatment prescriptions" at the 10th International Conference on Precision Agriculture in July, 2010 in Denver. Kathy Yeater, M. Anders and S. Brooks. "Resolving disease severity in 4ice within a multi-year, multi-cropping system experiment" at the Biometry Symposium entitled "Design and analysis of complex cropping system experiments" held in conjunction with the ASA-CSSA-SSSA International Meetings in November, 2009 in Pittsburgh. D. Boykin, M. Camp, L. Johnson, Matt Kramer, David Meek, D. Palmquist, B. Vinyard, and Mark West. "Generalized mixed model estimation using PROC GLIMMIX, Part 1: Results when data and models match" at the Conference on Applied Statistics in Agriculture in April, 2010 in Manhattan, KS. Mark West, B. Vinyard, D. Palmquist, David Meek, Matt Kramer, L. Johnson, M. Camp and D. Boykin. "Generalized mixed model estimation using PROC GLIMMIX, Part 2: Results under model misspecification" at the Conference on Applied Statistics in Agriculture in April, 2010 in Manhattan, KS. David Meek. "Modern statistical graphics that provide insight" at the Biometry Symposium entitled "Design and analysis of complex cropping system experiments" held in conjunction with the ASA-CSSA-SSSA International Meetings in November, 2009 in Pittsburgh. John Stevens. "Statistical issues in the normalization of multi-species microarray data" at the Mathematical Association of America Intermountain Section Meeting in March, 2010. A.A. Masud and John Stevens. "A comparison of weighted p-value and multi-stage analyses in multiple hypothesis testing" at the Conference on Applied Statistics in Agriculture in April, 2010 in Manhattan, KS. John Stevens and G.N. Nicholas. "Assessing and accounting for dependence in gene expression summaries" at the ICSA Applied Statistics Symposium in June, 2010. Larry Madden. "What is meta-analysis and how is it used for evidence synthesis" at the Annual Meeting of the American Phytopathological Society in August, 2009 in Portland, OR. Larry Madden. "Analysis of temporal observations in epidemics when there is no definable functional relationship between the variable and time: An argument for the use of radial smoothing" at the International Epidemiology Workshop in June 2009 at Cornell University. Matthew Kramer, S.C. Chen, S.K. Gebauer and D.J. Baer. "Estimating the subject by treatment interaction in non-replicated crossover diet studies" at the Joint Statistical Meetings in August, 2010 in Vancouver. Mark West. "Fitting mixed models with spatial data" at the Northern Plains Agricultural Research Laboratory in Sidney, MT in April, 2010. Mark West. "Fitting linear models to experimental data" at the Center for Grain and Animal Health Research in Manhattan, KS in April, 2010. N.M. Bello, Rob Tempelman and J.P. Stieibel. "A hierarchical bivariate generalized linear mixed model for inferring upon heterogeneous covariances: Application in dairy production systems" at the Conference on Applied Statistics in Agriculture in April, 2010 in Manhattan, KS. W. Yang and Rob Tempelman. "A Bayesian antedependence model to account for linkage disequilibrum in whole genome selection" at the 9th World Congress on Genetics Applied to Livestock Production in Leipzig, Germany in August, 2010. G.R. Olbricht, Bruce Craig and R.W. Doerge. "Modeling DNA methylation tiling array data" at the Conference on Applied Statistics in Agriculture in April, 2010 in Manhattan, KS. John Aleong. "The generalized linear mixed model with spatial-temporal data" at the Joint Statistics Meetings in August, 2010 in Vancouver. Other project related activities: David Meek is the incoming Chair of the A11 Section (Biometry) of the American Society of Agronomy. George Milliken taught a class on design of experiments, mixed models and analysis of messy data in February, 2009 for the African Centre for Crop Improvement, University of KwaZulu-Natal, Pietermaritzburg, South Africa. John Stevens received funding from the Utah Agricultural Experiment Station to continue a project entitled "Probe-Level Statistical Models for Differential Expression of Genes in Bovine NT Studies." This is in association with the W-1112 Multi-State Research Project Reproductive Performance in Domestic Ruminants. July 2010 - June 2011. Rob Tempelman was Chair and Organizer of "Statistical methods: Linear and nonlinear models" section at the 9th World Congress on Genetics Applied to Livestock Production in August, 2010 in Leipzig, Germany. Specific goals for the next three years: (1) Publish a monograph/book targeted to agricultural scientists on transitioning from general linear models to generalized linear models. (2) Complete the revision of the mixed model workshop to include generalized linear mixed models and the use of new software. (3) Offer the mixed model workshop upon request from subject matter groups. (4) Educate project members in statistical issues and methodology related to statistical problems in which large number of variables are collected on relatively few experimental units. Application areas include biotechnology, precision agriculture and chemometrics.

Aston K.I., Li G.P., Hicks B.A., Sessions B.R., Davis A.P., Rickords L.F., Stevens J.R.,and White K.L. (2010). Abnormal levels of transcript abundance of developmentally important genes in various stages of preimplantation bovine somatic cell nuclear transfer embryos. Cellular Reprogramming 2(1):23-32. Bangarwa, S.K., J.K. Norsworthy and E.E. Gbur (2009). Cover crop and herbicide combinations for weed control in polyethylene-mulched bell pepper. Hort Technology 19: 405-410. Bathke, A. C., O. Schabenberger, R.D. Tobias and L.V. Madden (2009). Greenhouse-Geisser adjustment and the ANOVA-type statistic: Cousins or twins? The American Statistician 63: 239-246. Bello, N.M., J.P. Steibel and R.J. Tempelman (2010). A hierarchical Bayesian approach to mixed effects modeling of random and residual variance-covariance matrices in bivariate mixed effects models. Biometrical Journal 52: 297-313. Brazil, S.M., C.D. Steelman, A.L. Szalanski and E.E. Gbur (2009). Detection of Cochlosoma anatis (Kotlan) in Musca domestica L. (Diptera: Muscidae) collected from commercial turkey farms in Arkansas. Journal of Agricultural and Urban Entomology 24(4): 217-225. Burris, E., D. Burns, K.S. McCarter, C. Overstreet and M. Wolcott (2010). Evaluation of the effects of Telone II (fumigation) on nitrogen management and yield in Louisiana delta cotton. Precision Agriculture 11: 239-257. Caesar, TC, S.E. Wright, U.M. Sainju, R.L. Kolberg and M.S. West (2010). Impacts of long-term no-tillage and conventional tillage management of spring wheat-lentil cropping systems in dryland Eastern Montana, USA, on fungi associated to soil aggregation. World Congress of Soil Science. Dominigue MJ, Kramer M, Feldlaufer MF (2010). Sexual dimorphism of arrestment and gregariousness in the bed bug (Cimex lectularius) in response to cuticular extracts from nymphal exuviae. Physiological Entomology. 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A meta-analytic review of corridor effectiveness. Conservation Biology 24(3):660-668. Greene SN, Ramos-Vara JA, Craig BA, Hooser SB, Anderson C, Fourez LM, Johnson BM, Stewart JC and Knapp DW (2009). Effects of cyclooxygenase inhibitor treatment on the renal toxicity of cisplatin in rats. Cancer Chemotherapy and Pharmacology 10.1007/s00280-009-1061-2. Hammack, l., J.L. Pikul and M.S. West (2010). Phenology and abundance of bean leaf beetle (Coleoptera: Chrysomelidae) in eastern South Dakota on alfalfa and soybean relative to tillage, fertilization and yield. Environmental Entomology. In press. Kabara, E., C.C. Kloss, M. Wilson, R.J. Tempelman, S. Sreevatsan, H. Janagama, and P.M. Coussens (2010). A large-scale study of differential gene expression in monocyte derived macrophages infected with several strains of Mycobacterium avium subspecies paratuberculosis. Briefings in Functional Genomics 9: 220-237. Kramer M, Weldon PJ and Carroll JF (2009). Canonical discriminant analysis for constructing composite scores for concurrently measured behaviours. Animal Behaviour 77: 763-768. Kramer M, Feldlaufer MF and Chauhan KR (2010). Mosquito biting behavior: Statistical power and sources of variation in toxicity and repellent bioassays. Journal of Medical Entomology 47: 199-204. Lopiano, K.K., C.A. Gotway and L.J. Young (2010). A comparison of errors in variables methods for use in regression models with spatially misaligned data. Statistical Methods in Medical Research. OnlineFirst as Doi:10.1177/0962280210370266. Madden, L.V. and P.A. Paul (2009). Assessing heterogeneity in the relationship between wheat yield and Fusarium head blight intensity using random-coefficient mixed models. Phytopathology 99: 850-860. Malone, R., D. Jaynes, L. Ma, T. Nolan, D. Meek and D. Karlen (2010). Soil-test N recommendations augmented with PEST optimized RZWQM simulations. Journal of Environmental Quality. In press. McCarter, K. and E. Burris (2010). Accounting for spatial correlation using radial smoothers In statistical models used for developing variable-rate treatment prescriptions. Proceedings of the 10th International Conference on Precision Agriculture. McDonald, M., K.R. Brye, D.M. Miller and E.E. Gbur (2009). Broiler litter application history and soil depth effects on arsenic adsorption in soil. Soil Science 174: 661-675. Miller, M.M., C.M. Murrieta, K.E. Bennett, M.A. Stuart and M.S. West (2010). Comparison of hamster anesthetics and their effect on mosquito blood feeding. Journal of Entomological Science. In press. Milliken, G., J. Willers, K. McCarter and J. Jenkins (2009). Designing experiments to evaluate the effectiveness of precision agricultural practices on research fields: Part 1 Concepts for their formulation. Operational Research, Business and Economics, 1109-2858 (Print) 1866-1505 (Online). Norman, R.J., C.E. Wilson, N.A. Slaton, B.R. Griggs, J.T. Bushong and E.E. Gbur (2009). Nitrogen fertilizer sources and timing before flooding dry-seeded, delayed-flood rice. Soil Science Society of America Journal 73: 2184-2190. Njuho, P.M. and G.A. Milliken (2009). Analysis of linear models with two factors having both fixed and random levels. Communications in StatisticsTheory and Methods 38: 23482365. Olbricht GR, Sardesai N, Gelvin SB, Craig BA and Doerge RW (2010). Statistical methods for affymetrix tiling array data. Proceedings of the 2009 Kansas State University Conference on Applied Statistics in Agriculture, Manhattan, KS. Shappell, N.W., K.H. Elder and M.S. West (2010). Estrogenicity and nutrient concentration of surface waters surrounding a large confinement dairy operation using best management practices for land application of animal wastes. Environmental Science and Technology. In press. Shivrain, V.K., N.R. Burgos, R.C. Scott, E.E. Gbur, L.E. Estorninos and M.R. McClelland (2010). Diversity of weedy red rice (Oryza sativa L.) in Arkansas, U.S.A. in relation to weed management. Crop Protection 29: 721-730. Singer, J., K. Kohler, K, Moore and D. Meek (2009). Living mulch forage yield and botanical composition in a corn-soybean-forage rotation. Agronomy Journal 101:1249-1257. Stevens J.R., Bell J.L., Aston K.I. and White K.L. (2010). A comparison of probe-level and probeset models for small-sample gene expression data. BMC Bioinformatics 11:281. Suwonsichon, S., E. Chambers, IV, D.H. Chambers and G.A. Milliken (2009). Effects of oral rinsing on the perception of residual cooling and burn in highly mentholated toothpaste. Journal of Sensory Studies 24: 290-300. Yang, W. and R.J. Tempelman (2010). A Bayesian antedependence model to account for linkage disequilibrum in whole genome selection. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production. Leipzig, Germany. Yocum, G.D., J.P. Rinehart, M.S. West and W.P. Kemp (2010). Interrupted incubation and short-term storage of the alfalfa pollinator, Megachile rotundata (Hymenoptera: Megachilidae): A potential tool for synchronizing bees with bloom. Journal of Economic Entomology. In press. Young, L.J., C.A. Gotway, J. Yang, G. Kearney and C. DuClos (2009). Linking health and environmental data in geographical analysis: Its so much more than centroids. Spatial and Spatio-temporal Epidemiology 1: 73-84. Young, L.J. and C.B. Fisher (2010). Advancing the science of EPA guidelines for sponsor-financed topical insect repellent efficacy studies. Regulatory Toxicology and Pharmacology 56: 51-53. Young, L.J., C.A. Gotway and K.K. Lopiano (2010). Challenges associated with integrating data from multiple scales to assess relationships. Proceedings of the 9th International Symposium on Spatial Accuracy Assessment in Natural Resources and Environmental Sciences, Leicester, UK. Young, L.J., C.A. Gotway, K.K. Lopiano. G. Kearney and C. DuClos (2010). Assessing the association between environmental exposures and human health. 19th International Conference on Computational Statistics. Paris, France.