Life Sciences Commons^™

Another Look At Clark's Adit-Silver Series, David W. Meek

Conference on Applied Statistics in Agriculture

The empirical semivariogram for Clark's adit-silver series has been the subject of several publications. Its use in the literature along with some other discussed considerations makes this series a suitable selection for a classroom or workshop semivariogram modeling exercise. My emphasis in this exercise is on estimating the scale of fluctuation (8). Alternative unbounded, bounded asymptotic, and bounded transitional models are developed via weighted least-squares estimation for both regular and integral semivariogram parameterizations (ISV). Results are compared with Clark's recommendation along with some other traditional models, nonparametric models, and ad hoc numerical methods. When a given model fits well using …

An Uncertainty Analysis Procedure For Spatially Joint Simulations Of Multiple Attributes, Shoufan Fang, Guangxing Wang, George Z. Gertner, Alan Anderson

Conference on Applied Statistics in Agriculture

In this study, an uncertainty analysis procedure for joint sequential simulation of multiple attributes of spatially explicit models was developed based on regression analysis. This procedure utilizes information obtained from joint sequential simulation to establish the relationship between model uncertainty and variation of model inputs. Using this procedure, model variance can be partitioned by model input parameters on a pixel by pixel basis. In the partitioning, the correlation of neighboring pixels is accounted for. With traditional uncertainty analysis methods, this is not possible. In a case study, spatial variation of soil erodibility from a joint sequential simulation of soil properties …

Comparison Of Sas Proc Nlin And Nlmixed For Parameter Estimation In Pet Model, Y. Xie, A. M. Parkhurst, T. L. Mader, J. B. Gaughan

Conference on Applied Statistics in Agriculture

Cattle body temperatures were measured under semi-controlled hot cyclic chamber temperatures. The four-parameter nonlinear PET model, is used to estimate body temperature in cattle challenged by heat stress. For each steer, the parameters can be estimated by the Nlin procedure and the sensitivity of each animal can be studied. It is also desirable to generalize the results by using the Nlmixed procedure to combine both the fixed and random effects. When comparing the results from the two procedures, we found heterogeneity among animals and/or days caused convergence problems for proc Nlmixed. Simulation studies were used to study how deviations from …

Developing System For Auditing The Database Of Agricultural Trial, Olga Susana Filippini De Delfino, Ana Aguua, Hugo Delfino

Conference on Applied Statistics in Agriculture

Many steps are involved in getting data from an experimental unit of an agricultural trial into a final report. Each step may introduce a great variety of errors. Building quality into systems is much more productive than building checks onto the end. Poor quality database have effects on final study results in terms of estimation, significance testing and power; but auditing agricultural trial is a complex process designed to ensure that it will provide a reliable answer to the question being posed. By introducing digit errors into database in a tomato assay, with small sample size, we demonstrate that simple …

Assessing Refinements In Modeling Sinusoidal Conditions Used To Drive Cattle Body Temperatures, Sheng Feng, Anne Parkhurst, Kent Eskridge, Daryl Travnicek, Donald Spiers, G. L. Hahn, Terry Mader

Conference on Applied Statistics in Agriculture

A model, termed the PET model, is used to estimate body temperature in cattle challenged by hot cyclic chamber temperatures. The model is based on Newton's law of cooling, driven by an estimated sinusoidal function. In practice, it is often difficult to maintain hot sinusoidal fluctuations in chamber temperatures. However, it is possible to model cyclic chamber temperatures using a discrete Fourier series. By increasing the precision in estimating the cyclic temperature driving function, we can more precisely estimate the parameters in the PET model. Simulation studies were performed to investigate the effect of under- and over-parameterization on accuracy of …

Predicting Soybean Weight Per Pod, Timothy P. Keller, Michael Schmidt, Catherine Schmidt

Conference on Applied Statistics in Agriculture

The National Agricultural Statistics Service (NASS) makes predictions of soybean yield at both the state and national level. Experience indicates that the key to improving yield predictions is improving the prediction of soybean weight pod. Towards this end, NASS has entered into a three year cooperative agreement with the Department of Plant, Soil and General Agriculture at Southern lllinois University at Carbondale (SID-C) to investigate predictive models for soybean weight per pod based on a measurement of pod width and a count of the number of seeds per pod. Aside from the scientific issues involved in this effort, the practical …

Development Of Experiments For The Harvesting And Storing Of Vidalia Sweet Onions, Ben G. Mullinix, Bryan W. Maw, Reid L. Torrance

Conference on Applied Statistics in Agriculture

Sweet onions brought in nearly $70 million in 1998. Sweet onions have a soft bulb which makes them susceptible to injury if handled too roughly. Once injured, invasion by pathogens tends to render the bulbs unusable except for quick sale. They were harvested by hand until about ten years ago when efforts were begun to develop a mechanical harvester. Also, at that time, work was underway to develop a way of storing part of the crop so as to extend the market window beyond the traditional 6-8 weeks. Low temperature and low oxygen atmosphere conditions proved to be the most …

Are Spatial Models Needed With Adequately Blocked Field Trials?, Reid D. Landes, Kent M. Eskridge, P. Stephen Baenziger, David B. Marx

Conference on Applied Statistics in Agriculture

The use of nearest neighbors and spatial models (SPAT) to analyze field trial data has become commonplace in recent years. These two types of analyses improve precision compared to ANOVA when trials are poorly blocked, but results are less clear in well-blocked trials. We examined data from wheat trials containing 60 cultivars, conducted at five locations, where each location was set up as an alpha lattice design. We compared the relative efficiency of detecting cultivar differences for spatial models and nearest neighbors analyses (NNA) to ANOVA, fit of the models, and correlations of ranked cultivars. Though the SPAT and NNA …

An Analysis Of Daily Peak Stream Discharge Using A Non-Gaussian Time Series Model, S. Perera

Conference on Applied Statistics in Agriculture

Daily peak stream discharge data, collected over time, are typically characterized by a few large peaks separated by runs of small values, where peaks correspond to the occurrence of storms. Furthermore, the peak discharge on the first day of a storm has little or no relationship to the previous day's discharge. These characteristics are not present in standard Gaussian time series models in which a zig-zag behavior not conducive to runs of small values is observed and the present value always depends on the previous value. However, they can be successfully captured with non-Gaussian time series models.

Daily peak stream …

Using Proc Nlmixed To Analyze A Time Of Weed Removal Study, Erin E. Blankenship, Sean Evans, Walter W. Stroup, Stevan Z. Knezevic

Conference on Applied Statistics in Agriculture

Many studies in weed science involve fitting a nonlinear model to experimental data. Examples of such studies include dose-response experiments and studies to determine the critical period of weed control. The experiments typically use block designs and often have additional complexity such as split-plot features. However, nonlinear models are typically fit using software such as SAS PROC NLIN that are limited to a single error term and whose ability to account for blocking is either awkward or lacking entirely. For example, Seefeldt et al. (1995) only proceeded in fitting the nonlinear model after establishing that the block effect was negligible. …

Model Building In Multi-Factor Plant Nutrition Experiments, L. M. Olson, W. W. Stroup, E. T. Paparozzi, M. E. Conley

Conference on Applied Statistics in Agriculture

Often, the goal of plant science experiments is to model plant response as a function of quantitative treatment factors, such as the amount of nutrient applied. As the number of factors increases, modeling the response becomes increasingly challenging, especially since the resources available for such experiments are usually severely limited. Typical methods of analysis, notably second-order response surface regression, often fail to accurately explain the data. Alternatives such as non-linear models and segmented regression have been used successfully with two-factor experiments (Landes, et. aI, 1999). This paper extends previous work to three-and-more factor experiments. Models are assessed to explain the …

Designing Microarrays, B. A. Craig, O. Vitek, M. A. Black, M. Tanurdzic, R. W. Doerge

Conference on Applied Statistics in Agriculture

Microarrays allow the simultaneous assessment of expression levels for thousands of genes across various treatment conditions and time. It has been shown that in these experiments expression levels can also be affected by factors in the printing of the slide, in the hybridization process, and in the post-hybridization process. Recently, variations of the incomplete block design were proposed as a way to avoid confounding the expression levels of interest with several of these nuisance factors. In this paper, we propose additional design procedures to remove factors that contribute to the spatial variability on a slide. This approach requires the use …

Calculation Of The Minimum Number Of Replicate Spots Required For Detection Of Significant Gene Expression Fold Change In Microarra Y Experiments, Michael A. Black, R. W. Doerge

Conference on Applied Statistics in Agriculture

Calculations for the number of per gene replicate spots in microarray experiments are presented for the purpose of obtaining estimates of the sampling variability present in microarray data, and for determining the minimum number of replicate spots required to achieve a high probability of detecting a significant fold change in gene expression. Our approach is based on data from control microarrays, and employs standard statistical estimation techniques. We have demonstrated the usefulness of our framework by analyzing two experimental data sets containing control array data. The minimum number of replicate spots required on a treatment array were calculated to achieve …

Statistical Issues In The Analysis Of Microbial Communities In Soil, J. D. Wilbur, C. H. Nakatsu, S. M. Brouder, J. K. Ghosh, R. W. Doerge

Conference on Applied Statistics in Agriculture

Corn and soybean production dominates the agricultural systems of the mid-western United States. Studies have found that when a single crop species is grown continually, without the rotation of other crops, yield decline occurs. At present, this phenomenon, remains poorly understood, but there are possible links to microbial community dynamics in the associated rhizosphere soil. In this study, corn plants were grown in disturbed and undisturbed soils with a 24 year history of growth as a mono culture crop or two crops grown in annual rotation. Characteristic profiles of the microbial communities were obtained by denaturing gradient gel electrophoresis of …

Another Look At New Gma Orthogonal Arrays, Yingfu Li, Timothy Wittig

Conference on Applied Statistics in Agriculture

Non-regular factorial designs have not been advocated until last decade clue to their complex aliasing structure. However, some researchers recently found that the complex aliasing structure of non-regular factorial designs is a challenge as well as an opportunity. Li, Deng, and Tang (2000) studied nonl-regular designs and generated a collection of non-equivalent orthogonal arrays using a generalized miniumm aberration criterion, proposed by Deng and Tang (1999). Some new orthogonal arrays they found cannot be embedded into Hadamard matrices. In this paper, we study these orthogonal arrays from the angle of projection. We show that these new GMA orthogonal arrays are …

A Comparison Of Some Methods To Analyze Repeated Measures Ordinal Categorical Data, Yaobing Sui, Walter W. Stroup

Conference on Applied Statistics in Agriculture

Recent advances in statistical software made possible by the rapid development of computer technology in the past decade have made many new procedures available to data analysts. We focus in this paper on methods for ordinal categorical data with repeated measures that can be implemented using SAS. These procedures are illustrated using data from an animal health experiment. The responses, measured as severity of symptoms on an ordinal scale, are recorded for test animals over time. The experiment was designed to estimate treatment and time effects on the severity of symptoms. The data were analyzed with various approaches using PROC …

Assessing The Performance Of Closed-Form Approximations To The Reml Estimator Of Heritability, Brent D. Burch, Ian R. Harris

Conference on Applied Statistics in Agriculture

For many researchers the restricted maximum likelihood (REML) method of estimation is the procedure of choice for estimating heritability. In most applications the REML estimate can only be obtained via an iterative method. In some cases the algorithm used to compute the REML estimate may be slow or fail to converge. These predicaments have provided the motivation to develop closed-form approximations to the REML estimator of heritability in mixed linear models having two variance components. These estimators are compared to the REML estimator by considering their large and small sample properties. We provide guidance on how to select the closed-form …

Comparing Binomial Bootstrap And Bayesian Estimation Methods In Assessing The Agreement Between Classified Images And Ground Truth Data., Bahman Shafii, William J. Price

Conference on Applied Statistics in Agriculture

The degree of agreement between classification and ground truth in remotely sensed data is often quantified with an error matrix and summarized using agreement measures such as Cohen's kappa. In the case of ground truth however, the kappa statistic can be shown to be a transformation of the marginal proportions commonly referred to as omissional and commissional error rates. A more meaningful statistical interpretation of remote sensing results and less ambiguous conclusions can be obtained via direct utilization of these measures. Several estimation techniques have been suggested for these marginal proportions. In this study, we will develop the exact binomial, …

Papadakis Nearest Neighbor Analysis Of Yield In Agricultural Experiments, Radha G. Mohanty

Conference on Applied Statistics in Agriculture

Papadakis analysis, originally proposed by Papadakis in 1937 belongs to a larger class of methodologies called the nearest neighbor analysis which is primarily based on the fact that plots in close proximity ("neighbors") are exposed to similar environmental conditions and therefore, for a given plot, information from its neighboring plots could be used for adjustment of its response for spatial variability. The basic theory behind the application of Papadakis methodology to field trials is relatively simple. It is based on an analysis of covariance where the covariate is an index of fertility environment), and the response is some observable trait …

Enumeration Of Mixed Linear Models And A Sas Macro For Computation Of Confidence Intervals For Variance Components, Ann Hess, Hari Iyer

Conference on Applied Statistics in Agriculture

It is well known that there is a one-to-one correspondence between fixed effects ANOVA models involving both crossed and nested factors, and combinatorial objects called "posets". The enumeration of nonisomorphic posets is an interesting and nontrivial combinatorial problem for which answers are available for posets of order 14 or less, i.e. for fixed effects ANOVA models with 14 or fewer factors. Such an enumeration problem does not appear to have been considered for mixed effects models. In this paper we study this problem and obtain a list of nonisomorphic mixed effects models involving five or fewer factors. For instance, it …

A Statistical Model Using Reference Evapotranspiration And Weather Data To Predict The Economic Optimal Irrigation Level For Corn Production In The Texas Panhandle, W. Arden Colette, Clay Robinson, Lal Khan Almas

Conference on Applied Statistics in Agriculture

Corn yield and evapotranspiration (ET) data obtained from weighing lysimeters is accumulated from nine experiments over six years and used to estimate a response function. The quadratic response function of corn yield as a function of water use by the plants indicates that yield increases at a decreasing rate as ET increases. Extending the analysis to water application data by commercial producers in a thirteen county area in the Texas Panhandle provides a response function of yield as a function of water application to meet ET needs. The best estimate of the relationship is a quadratic function. The response function …

Simulation Study Of Spatial-Poisson Data Assessing Inclusion Of Spatial Correlation And Non-Normality In The Analysis, Rebecca A. Hensberry, David B. Marx, Daryl Travnicek, Stephen Kachman

Conference on Applied Statistics in Agriculture

Spatial correlation and non-normality in agricultural, geological, or environmental settings can have a significant effect on the accuracy of the results obtained in the statistical analyses. Generalized linear mixed models, spatial models, and generalized linear models were compared in order to assess how critical the inclusion of non-normality and spatial correlation is to the analysis. Spatially correlated data with a Poisson distribution were generated in a completely randomized design (CRD) with 2 treatments and 18 repetitions. Four analyses: spatial Poisson, non-spatial Poisson, spatial normal, and non-spatial normal, were conducted on the simulated data to compare their power functions. The degree …

From Farms To Pharmaceuticals: Multiple Comparisons Enters The 21st Century, Peter H. Westfall

Conference on Applied Statistics in Agriculture

The subject of multiple comparisons has early roots in statistical methods that were applied in agricultural sciences, often using simple methods with questionable properties popularized by no less than R.A. Fisher. More recently, problems of multiple comparisons have surfaced in the pharmaceutical sciences. In the extremely competitive and highly regulated pharmaceutical environment, it has become essential to take multiple comparisons more seriously, and to use more sophisticated methods. In this paper I describe the need for considering multiple comparisons, with special reference to the recent shift in approach to multiple comparisons in the pharmaceutical industry. I also offer speculations about …

Editor's Preface, Table Of Contents, And List Of Attendees, George A. Milliken

Conference on Applied Statistics in Agriculture

These proceedings contain papers presented in the thirteenth annual Kansas State University Conference on Applied Statistics in Agriculture, held in Manhattan, Kansas, April 29-May 1, 2001.

Kansas Fertilizer Research 2000, Ray E. Lamond

Kansas Agricultural Experiment Station Research Reports

No abstract provided.

Roundup 2001

Kansas Agricultural Experiment Station Research Reports

Roundup is the major beef cattle education and outreach event sponsored by the Agricultural Research Center-Hays. The purpose is to communicate timely, applicable research information to producers and extension personnel. The research program of the Agricultural Research Center-Hays is dedicated to serving the people of Kansas by developing new knowledge and technology to stabilize and sustain long-term production of food and fiber in a manner consistent with conservation of natural resources, protection of the environment, and assurance of food safety. Primary emphasis is on production efficiency through optimization of inputs in order to increase profit margins for producers in the …

2001 Agricultural Research Southeast Agricultural Research Center, Kansas State University. Agricultural Experiment Station And Cooperative Extension Service

Kansas Agricultural Experiment Station Research Reports

No abstract provided.

Relationships Among Beef Carcass Quality And Cutability Indicators, T.E. Lawrence, D.A. King, T.H. Montgomery, Michael E. Dikeman

Kansas Agricultural Experiment Station Research Reports

We evaluated beef carcass data (12th rib fat thickness, hot carcass weight, ribeye area, percentage of kidney-pelvic-heart fat, USDA yield grade, and USDA quality grade) from 60,625 A-maturity steer and heifer carcasses. Data were analyzed to evaluate changes in quality grade with increasing fat thickness, changes in cutability indicators across quality grades, and the association of hot carcass weight with ribeye area. Percentage of USDA Standard and Select carcasses decreased, while Low Choice and Premium Choice increased as fat thickness increased. Percentage of Low Choice remained steady for fat thickness of 0.56 - 0.60 in. and higher. Percentage of yield …

Carcass Merit Project: Development Of Epds And Genetic Marker Validation, E.J. Pollak, R.D. Green, J. Taylor, S. Davis, T. Holm, S. Koontz, C. Gill, Daniel W. Moser, E.A. Westcott, Michael E. Dikeman

Kansas Agricultural Experiment Station Research Reports

Carcass and Warner-Bratzler shear force data on strip loin steaks have been obtained on over 4,200 cattle from contemporary progeny groups from the most widely used sires in 15 beef cattle breed associations (16 breeds). Trained sensory panel evaluations have been conducted on over 1,500 strip loin steaks from a sample of contemporary progeny groups from sires included in the QTL (quantitative trait loci) validation component of the project. One breed association has published Warner-Bratzler shear force Expected Progeny Differences (EPDs) for 57 sires of two breeds. DNA analyses and screening have been completed for 11 QTL on eight sires …

The Effects Of Quality Grade, Postmortem Aging, And Blade Tenderization On Warner-Bratzler Shear Force And Cookery Traits Of Biceps Femoris Steaks, B.S. Andrews, John A. Unruh

Kansas Agricultural Experiment Station Research Reports

We used 108 top sirloin butts to determine the influence of quality grades, postmortem aging periods, and blade tenderization passes on percentages of thawing and cooking losses and Warner-Bratzler shear (WBS) force of biceps femoris muscles. Top sirloin butts that qualified for either USDA Select (SEL, n=36), USDA Choice (CHO, n=36), or Certified Angus Beef™ Program (CAB, n=36), were aged for 14 or 21 days and blade tenderized zero (0X), one (1X), or two (2X) times. Steaks with higher quality grades (CHO and CAB) aged for 21 days had lower thawing losses than steaks aged 14 days and than SEL …