Life Sciences Commons^™

The Power Of Structured Designs And Mixed Models In A Real World Experiment, J. C. Galland, G. A. Milliken, D. R. Hyatt, M. Hornback, K. Cudjoe

Conference on Applied Statistics in Agriculture

Justifications usually given for adopting an automated system pertain to a reduction in labor and an improvement in quality control. A manufacturer of a prototype instrument that automated some of the steps for culturing bacteria wanted to compare the automated system to the manual system. The manufacturer wanted to compare the two systems in 1) Total time needed to isolate the target bacteria, 2) Ability to isolate the target bacteria, 3) Amount of interference from background (non-target) bacterial growth, and 1) Extent of cross (sample to sample) contamination.

This paper presents the experimental design used to make these comparisons and …

Investigating Power Of Analysis Of Covariance Methods, James R. Schwenke, J. Mark Donovan

Conference on Applied Statistics in Agriculture

Analysis of covariance is a well-utilized statistical methodology. The procedure involves a series of statistical tests to first construct a most significant analysis model to characterize the effect of the covariate on response. Pairwise comparisons among treatments are then based on the finalized model.

For traditional Normal error assumptions, each step of the process is based on exact statistical tests. However, the series of statistical tests defines a conditional probability scheme with possible multiplicity issues. The question then becomes if the analysis of covariance methodology considered in entirety is able to maintain a nominal level of significance with good power. …

Starting Values For Proc Mixed With Repeated Measures Data, J. C. Recknor, W. W. Stroup

Conference on Applied Statistics in Agriculture

A major advantage of PROC MIXED for repeated measures data is that one could choose from many different correlated error models. However, MIXED uses default starting values that may cause difficulty obtaining REML estimates of the covariance parameters for several of the models available. This can take the form of excessively long run times or even failure to converge. We have written a program to obtain initial covariance parameter estimates that result in greatly improved performance of the REML algorithm. We will use two covariance models frequently of interest in animal health experiments, the first-order ante-dependence model [ANTE(l)] and the …

Analysis Of Genotype-By-Environment Interaction With Ammi Models Using Sas Proc Mixed, Raul E. Macchiavelli, James S. Beaver

Conference on Applied Statistics in Agriculture

Genotype-by-environment (GE) interaction can be analyzed using different approaches. Among these, the additive main effects and multiplicative interaction model yields useful interpretations and can be applied successfully to plant breeding programs. In this paper we review fitting strategies for this model and show how to combine the capabilities of the Mixed and IML procedures in SAS to fit this model. This permits straightforward use of likelihood-based inference in standard and non standard situations like complex experimental designs. The proposed procedures were applied to data from red mottled bean variety trials conducted in the Dominican Republic and Puerto Rico in 9 …

The Analysis Of Count Data In A One-Way Layout, Yuhua Wang, Dallas E. Johnson, Linda J . Young

Conference on Applied Statistics in Agriculture

An efficient score statistic for testing the equality of the means of several groups of count data in the presence of a common dispersion parameter is introduced and a new approximation to its distribution is given. The performance of the efficient score statistic using this approximation, the original efficient score statistic approximated by X ² (t -1), the likelihood ratio statistic and four more ANOVA methods based on raw data or transformed data are compared in terms of size and power by using Monte Carlo simulations. The efficient score statistic with its new approximation is recommended. An application is given.

Hydrological Normalization Of Nutrient Deliveries From Agricultural Catchments, Per Stalnacke, Anders Grimvall

Conference on Applied Statistics in Agriculture

Nutrient deliveries from agricultural catchments are strongly influenced by natural fluctuations in water discharge. Hydrological normalization of such data may therefore facilitate estimation of human impact on the environment. In the present study, we compared conventional statistical normalization techniques with a recently proposed, semi-parametric regression technique, which can accommodate time-dependent relationships between nutrient deliveries and water discharge. Case studies of agricultural catchments in Sweden and Norway demonstrated that all of the tested normalization techniques were able to remove a substantial fraction of the interannual variation in nitrogen deliveries, whereas normalization of phosphorus loads was problematic. Semi-parametric regression models were found …

A Computationally Efficient Method For Determining Significance In Interval Mapping Of Quantitative Trait Loci, Dan Nettleton

Conference on Applied Statistics in Agriculture

This paper provides a brief introduction to the mapping of quantitative trait loci (QTL). An example on mapping QTL for root thickness in rice is presented to illustrate popular statistical methods used in QTL mapping. Interval mapping is used in conjunction with permutation testing techniques to detect significant associations between genetic positions and quantitative traits while controlling overall type I error rate. A review of a recent technique that can greatly reduce the computational expense of permutation testing in QTL mapping is discussed. Theory is provided for an extension of recent results that may lead to more powerful methods of …

An Improved Estimator For Assessing The Measure Of Agreement With A Gold Standard, Brent D. Burch, Ian R. Harris, Roy T. St. Laurent

Conference on Applied Statistics in Agriculture

St. Laurent (1998, Biometrics 54, 537-545) developed a measure of agreement for method comparison studies in which an approximate method of measurement is compared to a gold standard method of measurement. The measure of agreement proposed was shown to be related to a population intraclass correlation coefficient. This paper develops a family of estimators for the measure of agreement based on pivotal quantities. A blend of two particular members of the family is suggested as an estimator itself. In general, this estimator outperforms the maximum likelihood estimator in terms of bias and mean-squared error.

Nonlinear Models For Multi-Factor Plant Nutrition Experiments, R. D. Landes, W. W. Stroup, E. T. Paparozzi, M. E. Conley

Conference on Applied Statistics in Agriculture

Plant scientists are interested in measuring plant response to quantitative treatment factors, e.g. amount of nutrient applied. Response surface methods are often used for experiments with multiple quantitative factors. However, in many plant nutrition studies, second-order response surface models result in unacceptable lack of fit. This paper explores multi-factor nonlinear models as an alternative. We have developed multi-factor extensions of Mitscherlich and Gompertz models, and fit them to data from experiments conducted at the University of Nebraska-Lincoln Horticulture department. These data are typical of experiments for which conventional response surface models perform poorly. We propose design selection strategies to facilitate …

Using Isotonic Regression To Improve Estimation In Factorial Experiments With Ordered Factor Levels, Matt Strand, Jim Higgins

Conference on Applied Statistics in Agriculture

In many designed experiments in agriculture and the life sciences, a researcher can anticipate the direction that responses will take when treatments are varied. For example, in a 2-way factorial, a researcher may know that increasing the levels of nitrogen and phosphorus will increase yields of a crop. Classical analysis of variance does not take into account a known ordering among population means. However, it can be shown that by restricting the estimates of means to have the same ordering as the anticipated ordering of population means, a reduction in mean-squared errors of estimators will likely occur, often by more …

Characterizing The Statistical Distribution Of Organic Carbon And Extractable Phosphorus At A Regional Scale, John J. Brejda, David W. Meek, Douglas L. Karlen

Conference on Applied Statistics in Agriculture

Greater awareness of potential environmental problems has created the need to monitor total organic carbon (TOC) and extractable phosphorus (P) concentrations at a regional scale. The probability distribution of these soil properties can have a significant effect on the power of statistical tests and the quality of inferences applied to these properties. The objectives of this study were to: (1) evaluate the probability distribution of TOC and extractable P at the regional scale in three Major Land Resource Areas (MLRA), and (2) identify appropriate transformations that will result in a normal distribution. Both TOC and extractable P were non-normally distributed …

Analysis Of Nuclei Fluorescence Histograms Using Non-Linear Functions Or Wavelets, Susanne Aref, Maria Kocherginsky, Carrie A. Northcott, Lane A. Rayburn

Conference on Applied Statistics in Agriculture

Histograms based on 5,000 nuclei from cells (Chinese hamster ovary cells, bone marrow cells) are used to determine the coefficient of variation (CV) of observations surrounding the highest peak. The cells are subjected to various treatments, for example exposure to herbicides. By eyeballing the histogram, an interval under the highest peak is determined. The CV calculated from the histogram on the eyeballed interval is the response variable in an ANOVA. To avoid the subjectivity of eyeballing the histogram, non-linear functions such as the Gaussian density function can be used to model the histogram. The CV may then be determined from …

On Using Proc Mixed For Longitudinal Data, Walter W. Stroup

Conference on Applied Statistics in Agriculture

PROC MIXED has become a standard tool for analyzing repeated measures data. Its popularity results from a wide choice of correlated error models compared to other software, e.g. PROC GLM. However, PROC MIXED's versatility comes at a price. Users must take care. Problems may result from MIXED defaults. These include: questionable criteria for selecting correlated error models; starting values that may impede REML estimation of covariance components; and biased standard errors and test statistics. Problems may be induced by inadequate design. This paper is a survey of current knowledge about mixed model methods for repeated measures. Examples are presented using …

Modeling The Fate Of Toxic Chemicals In Soils, Anabayan Kessavalou, Anne M. Parkhurst

Conference on Applied Statistics in Agriculture

Studies on the fate of toxic chemicals in soils are often reported with a minimum of descriptive statistics. Use of modeling techniques to describe the kinetics of chemical degradation provides a better understanding of the fate of chemicals in soil systems. When modeling nonlinear systems, assumptions made about the error term greatly influence the parameter estimation. Inappropriate use of linearization and failure to account for autocorrelated errors may result in inaccurate models. Information is also needed about the effects of the magnitude of autocorrelation on parameter estimation. The exponential decay function was chosen to fit the data obtained from a …

Estimating The Likelihood Of Yellow Starthistle Occurrence Using An Empirically Derived Nonlinear Regression Model, Bahman Shafii, William J. Price, Lawrence W. Lass, Donn C. Thill

Conference on Applied Statistics in Agriculture

Yellow starthistle is a noxious weed common in the semiarid climate of Central Idaho and other western states. Early detection of yellow starthistle and predicting its infestation potential have important scientific and managerial implications. Weed detection and delineation are often carried out by visual observation or survey techniques. However, such methods may be ineffective in detecting sparse infestations. The distribution of yellow starthistle over a large region may be affected by various exogenous variables such as elevation, slope and aspect. These landscape variables can be used to develop prediction models to estimate the potential invasion of yellow starthistle into new …

Statistics In The New Millennium: Some Personal Views, Bryan F.J. Manly

Conference on Applied Statistics in Agriculture

In this paper I discuss three topics that I believe are relevant to the subject of statistics in the new millennium: (a) the impact of computers, and the state of computer-intensive methods as far as practical applications of statistics are concerned; (b) methods for the analysis of the extremely large data sets that are now becoming available; and (c) the use of statistics by scientists in general. For the first topic I suggest that the main advantage of computer-intensive methods is that they can under certain circumstances give simple and believable answers to questions when other methods fail. However, I …

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

Conference on Applied Statistics in Agriculture

These proceedings contain papers presented in the eleventh annual Kansas State University Conference on Applied Statistics in Agriculture, held in Manhattan, Kansas, April 25-27, 1999.

Effects Of Diet Processing Method On Growth Performance Of Segregated Early-Weaned Pigs (1999), J T. Sawyer, J C. Woodworth, P R. O'Quinn, Jim L. Nelssen, Michael D. Tokach, Robert D. Goodband, Steven S. Dritz

Kansas Agricultural Experiment Station Research Reports

A 28-d growth trial was conducted to evaluate the effects ofdifferent diet processing methods on growth perfornlance of segregated early-weaned pigs. From d 0 to 14, pigs were fed diets processed by one of four different methods: meal, universal pellet cooker CUPC), expanded, or pelleted. Pigs fed pelleted or UPC diets had improved ADO and F/G, and pigs fed meal diets had the poorest ADO and F/G. From d 14 to 28, pigs were fed one of six diets consisting of complex meal and expanded diets and two (least cost and complex) UPC and pelleted diets. From d 14 to …

Examination Of Stocking Density And Marketing Strategies In A Commercial Production Environment (1999), Michael D. Tokach, Robert D. Goodband, Jim L. Nelssen, Steven S. Dritz

Kansas Agricultural Experiment Station Research Reports

The influence of stocking density (7.4 or 6.6 sq ft per pig) and marketing strategy (0, 1, or 2 sorts before closeout) was examined in a commercial production environment. No interaction between stocking density and marketing strategy was observed. Higher stocking density had no negative effects on growth performance or carcass characteristics. The major advantage of one or two sorts was a reduction in sort loss of $.27/cwt carcass ($.52/pig) compared to no sorts. No differences were found between one and two sorts under the packer matrix used in this study.; Swine Day, Manhattan, KS, November 18, 1999

Margins Of Safety Can Be Lowered For Supplemental Copper, Zinc, Iron, And Manganese In Finishing Diets Without Affecting Growth Performance (1999), Michael D. Tokach, Robert D. Goodband, Jim L. Nelssen, Steven S. Dritz

Kansas Agricultural Experiment Station Research Reports

Finishing pig diets are commonly supplemented with copper, zinc, iron, and manganese with large margins of safety compared to those suggested by NRC requirements. In this study, pigs were fed a control diet that provided these minerals supplemented at concentrations similar to current KSU recommendations, diets containing 50 and 25% of the recommendation, or a combination of 50% of the recommendations until 145 lb and no added trace minerals from 145 lb until market. The trial used pigs from 100 lb until market weight at 265 lb. No differences in growth perfonnance or carcass characteristics were observed as a result …

Influence Of Dietary Supplementation Of Modified Tall Oil, Chromium Nicotinate, And L-Carnitine On Pork Chop Display Color Stability, Warner-Bratzler Shear, And Sensory Panel Traits (1999), A T. Waylan, P R. O'Quinn, J C. Woodworth, K Q. Owen, John A. Unruh, Robert D. Goodband, Jim L. Nelssen, Michael D. Tokach

Kansas Agricultural Experiment Station Research Reports

Eighty crossbred (PIC) gilts were used to determine the influence of feeding modified tall oil (MTO, 0 or .5% of diet), chromium nicotinate (0 or 50 ppb), and L-carnitine (0 or 50 ppm) on display color stability, Warner-Bratzler shear, and sensory panel traits of pork chops. Dietary additions of MTO, chromium nicotinate, and L-camitine to growing and finishing swine diets had minimal effects on quality characteristics and display color stability of pork chops. Therefore, producers probably can take advantage of any production or carcass cutability improvement from these feed supplements without affecting muscle quality of pork chops.; Swine Day, Manhattan, …

Manure Composition From Kansas Swine Lagoons (1999), G L. Keeler, Joel M. Derouchey, Robert D. Goodband, Jim L. Nelssen, Michael D. Tokach, Steven S. Dritz

Kansas Agricultural Experiment Station Research Reports

Analysis of 41 manure samples from Kansas swine lagoons revealed that nutrient concentrations were higher than previously reported values from the Nebraska Cooperative Extension Service and the Midwest Planning Service. In addition, high standard deviations indicated that considerable variation exists in composition of waste in swine lagoons. Although means from some lagoons were lower, most producers had manure that analyzed higher than previously published values from other sources. These data reveal the imnportance of individual analysis of lagoons for proper application to cropland to maximize yield and environmental stewardship. Additional research needs to be completed to provide a more detailed …

Effects Of Modified Tall Oil And Creatine Monohydrate On Growth Performance, Carcass Characteristics, And Meat Quality Of Growing-Finishing Barrows (1999), P R. O'Quinn, B S. Andrews, J C. Woodworth, Robert D. Goodband, John A. Unruh, Jim L. Nelssen, Michael D. Tokach

Kansas Agricultural Experiment Station Research Reports

A trial was conducted to evaluate the effects of modified tall oil (MTO; .50% of the diet) and creatine monohydrate (CMH; 25 g/pig/day for 10 days prior to slaughter) on performance, carcass characteristics, and meat quality of finishing barrows. Feeding MTO improved ADG and F/G during the growing phase and improved F/G over the entire trial and during the 10 day CMH loading period. Feeding MTO reduced backfat, but neither CMH nor MTO affected other carcass characteristics or meat quality measures at 24 h postmortem. These data suggest that MTO improves performance and reduces backfat with little effect on meat …

Influence Of Added Zinc From Zinc Sulfate On Weanling Pig Growth Performance And Plasma Zinc Concentration (1999), J C. Woodworth, P R. O'Quinn, J T. Sawyer, Michael D. Tokach, Jim L. Nelssen, Robert D. Goodband

Kansas Agricultural Experiment Station Research Reports

A total of288 weanling pigs (13.4lb and 18 d of age) was used in a 27 d growth assay to determine the effects of adding Zn from ZnS04 or ZnO on growth performance. Pigs were allotted to one of eight dietary treatments consisting of a control diet; diets containing one of six concentrations of Zn from ZnS04 (SOD, 1,000, 1,500,2,000,2,500, or 3,000 ppm); and a diet containing 3,000 ppm of Zn from ZnO. Increasing Zn from ZnS04 linearly improved ADO and FlO from d 9 to 19; however, adding ZnS04 to the diet decreased ADO from d 19 to 33. …

Effects Of Spray-Dried Animal Plasma Source On Weanling Pig Performance (1999), M U. Steidinger, P R. O'Quinn, J C. Woodworth, Robert D. Goodband, Michael D. Tokach, Jim L. Nelssen, Steven S. Dritz

Kansas Agricultural Experiment Station Research Reports

Three studies were conducted to evaluate the effects of different spray-dried animal plasma (SDAP) sources on weanling pig performance. For this study, different sources of SDAP were obtained from each of the four largest marketers. In each experiment, a different lot of each of the four plasma sources was used. Pigs were fed either a control diet or one of four diets containing different plasma sources added at 5.0 % of the total diet. The results of these experiments suggest that larger differences occur between lots or batches of SDAP then between sources of SDAP, when weanling pig performance is …

Interactive Effects Of Modified Tall Oil And Fat Source On Growth Performance And Carcass Characteristics Of Finishing Barrows And Gilts (1999), J C. Woodworth, P R. O'Quinn, A T. Waylan, J T. Sawyer, Robert D. Goodband, John A. Unruh, Jim L. Nelssen, Michael D. Tokach

Kansas Agricultural Experiment Station Research Reports

A total of 144 pigs (initially 90 lb) was used to determine the interactive effects of fat source: none (NF), 6% choice white grease (CWG), or 6% poultry fat (PF); modified tall oil (MTO, 0 or .5%); and sex (barrows or gilts) on growth performance and carcass characteristics. Regardless of fat source, MTO improved belly firmness but did not influence growth performance. Gilts were leaner, had increased loin muscle area, and had softer bellies compared to barrows. Added fat decreased ADFI and improved F/G. Pigs fed PF had the best F/G, but the fattest carcasses and softest loins and bellies.; …

Effects Of Chromium Picolinate On Reproduction And Farrowing Performance Of Parity One Sows (1999), Michael D. Tokach, Robert D. Goodband, Jim L. Nelssen, Steven S. Dritz

Kansas Agricultural Experiment Station Research Reports

We examined the influence ofchromium picolinate fed to gilts during the growing phase from 50 Ib through their first farrowing on reproductive and farrowing performance. No differences were detected in first service farrowing rate or total or live born litter size. These datafail to support a positive influence of chromium picolinate fed during development and gestation on reproductive and farrowing performance ofparity 1 sows.; Swine Day, Manhattan, KS, November 18, 1999

Influence Of Dietary Supplementation Of Modified Tall Oil And Vitamin E On Pork Chop Quality, Display Color Stability, Warner-Bratzler Shear, And Sensory Panel Traits (1999), A T. Waylan, P R. O'Quinn, J C. Woodworth, S I. Koo, John A. Unruh, Robert D. Goodband, Jim L. Nelssen, Michael D. Tokach

Kansas Agricultural Experiment Station Research Reports

Seventy-two crossbred (PIC) barrows were used to determine the influence of feeding modified tall oil (MTO, 0 or .5% of diet) and vitamin E (0, 10, or 50 IU/lb of feed) on display color stability, Warner-Bratzler shear, and sensory panel traits of pork chops. Feeding MTO in combination with high levels of vitamin E to pigs during both the growing and finishing phases improved display color stability and delayed lipid oxidation of the pork loin chops without affecting tenderness and sensory evaluations. Therefore, feeding swine MTO (.5%) with high levels of vitamin E (50 IU/lb of feed) can increase the …

Effects Of Modified Tall Oil And Vitamin E On Growth Performance And Carcass Characteristics Of Growing-Finishing Barrows (1999), P R. O'Quinn, A T. Waylan, J C. Woodworth, S I. Koo, Jim L. Nelssen, John A. Unruh, Robert D. Goodband, Michael D. Tokach

Kansas Agricultural Experiment Station Research Reports

A trial was conducted to investigate the interactive effects of modified tall oil (MTO) and vitamin E on growth performance and carcass characteristics of growing-finishing barrows. Feeding MTO resulted in increased ADG and improved F/G during the growing phase; otherwise dietary treatment did not affect growth performance during the rest of the trial or overall. Feeding MTO also decreased backfat thickness and increased belly firmness. Increasing vitamin E in diets containing MTO decreased drip loss percentage of the loin. These results indicate that MTO may function as a growth promoter; reduce backfat; and in conjunction with vitamin E, itnprove some …

Economics Of Adding Fat And Increasing Lysine:Calorie Ratio In Diets For Growing-Finishing Gilts (1999), M De La Llata, Michael R. Langemeier, Michael D. Tokach, Robert D. Goodband, Jim L. Nelssen, Steven S. Dritz

Kansas Agricultural Experiment Station Research Reports

A total of 1,200 gilts was used to evaluate the economics ofadding fat and increasing lysine:calorie ratio in diets for growing-finishing pigs. Diets were fed in four phases and consisted of a 2 x 4 factorial arrangement with two levels of fat (0 and 6%) and four increasing lysine:calorie ratios. Eight economic scenarios combining com, soybean meal, fat, and hog prices with two packer grading systems were created. Stochastic dominance analysis was performed on 64 alternatives (8 treatments x 8 scenarios). The third "and fourth (higher) lysine: calorie ratios increased income over feed cost when fat was added to the …