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BookDOI

Design and Analysis of Experiments with R

17 Dec 2014-

TL;DR: In this paper, the authors present an example of a two-factor Factorial Plan in R with fixed and random factors for estimating variance components of two-Factor Factorial Plans.

AbstractIntroduction Statistics and Data Collection Beginnings of Statistically Planned Experiments Definitions and Preliminaries Purposes of Experimental Design Types of Experimental Designs Planning Experiments Performing the Experiments Use of R Software Completely Randomized Designs with One Factor Introduction Replication and Randomization A Historical Example Linear Model for Completely Randomized Design (CRD) Verifying Assumptions of the Linear Model Analysis Strategies When Assumptions Are Violated Determining the Number of Replicates Comparison of Treatments after the F-Test Factorial Designs Introduction Classical One at a Time versus Factorial Plans Interpreting Interactions Creating a Two-Factor Factorial Plan in R Analysis of a Two-Factor Factorial in R Factorial Designs with Multiple Factors-Completely Randomized Factorial Design (CRFD) Two-Level Factorials Verifying Assumptions of the Model Randomized Block Designs Introduction Creating a Randomized Complete Block (RCB) Design in R Model for RCB An Example of a RCB Determining the Number of Blocks Factorial Designs in Blocks Generalized Complete Block Design Two Block Factors Latin Square Design (LSD) Designs to Study Variances Introduction Random Sampling Experiments (RSE) One-Factor Sampling Designs Estimating Variance Components Two-Factor Sampling Designs-Factorial RSE Nested SE Staggered Nested SE Designs with Fixed and Random Factors Graphical Methods to Check Model Assumptions Fractional Factorial Designs Introduction to Completely Randomized Fractional Factorial (CRFF) Half Fractions of 2k Designs Quarter and Higher Fractions of 2k Designs Criteria for Choosing Generators for 2k-p Designs Augmenting Fractional Factorials Plackett-Burman (PB) Screening Designs Mixed-Level Fractional Factorials Orthogonal Array (OA) Definitive Screening Designs Incomplete and Confounded Block Designs Introduction Balanced Incomplete Block (BIB) Designs Analysis of Incomplete Block Designs Partially Balanced Incomplete Block (PBIB) Designs-Balanced Treatment Incomplete Block (BTIB) Row Column Designs Confounded 2k and 2k-p Designs Confounding 3 Level and p Level Factorial Designs Blocking Mixed-Level Factorials and OAs Partially CBF Split-Plot Designs Introduction Split-Plot Experiments with CRD in Whole Plots (CRSP) RCB in Whole Plots (RBSP) Analysis Unreplicated 2k Split-Plot Designs 2k-p Fractional Factorials in Split Plots (FFSP) Sample Size and Power Issues for Split-Plot Designs Crossover and Repeated Measures Designs Introduction Crossover Designs (COD) Simple AB, BA Crossover Designs for Two Treatments Crossover Designs for Multiple Treatments Repeated Measures Designs Univariate Analysis of Repeated Measures Design Response Surface Designs Introduction Fundamentals of Response Surface Methodology Standard Designs for Second-Order Models Creating Standard Response Surface Designs in R Non-Standard Response Surface Designs Fitting the Response Surface Model with R Determining Optimum Operating Conditions Blocked Response Surface (BRS) Designs Response Surface Split-Plot (RSSP) Designs Mixture Experiments Introduction Models and Designs for Mixture Experiments Creating Mixture Designs in R Analysis of Mixture Experiment Constrained Mixture Experiments Blocking Mixture Experiments Mixture Experiments with Process Variables Mixture Experiments in Split-Plot Arrangements Robust Parameter Design Experiments Introduction Noise Sources of Functional Variation Product Array Parameter Design Experiments Analysis of Product Array Experiments Single Array Parameter Design Experiments Joint Modeling of Mean and Dispersion Effects Experimental Strategies for Increasing Knowledge Introduction Sequential Experimentation One-Step Screening and Optimization An Example of Sequential Experimentation Evolutionary Operation Concluding Remarks Appendix: Brief Introduction to R Answers to Selected Exercises Bibliography Index A Review and Exercises appear at the end of each chapter.

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Citations
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Journal ArticleDOI
TL;DR: A methodological description of nutritional metabolomics is provided that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance as well as points of reflections to harmonize this field.
Abstract: The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance (funded by the European Joint Programming Initiative "A Healthy Diet for a Healthy Life" (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but rather to present a pragmatic guidance on metabolomic methodologies, providing readers with useful "tips and tricks" along the analytical workflow.

96 citations

Book
07 Jun 2016
TL;DR: This survey provides an overview of online evaluation techniques for information retrieval, and shows how online evaluation is used for controlled experiments, segmenting them into experiment designs that allow absolute or relative quality assessments.
Abstract: Online evaluation is one of the most common approaches to measure the effectiveness of an information retrieval system. It involves fielding the information retrieval system to real users, and observing these users' interactions in-situ while they engage with the system. This allows actual users with real world information needs to play an important part in assessing retrieval quality. As such, online evaluation complements the common alternative offline evaluation approaches which may provide more easily interpretable outcomes, yet are often less realistic when measuring of quality and actual user experience.In this survey, we provide an overview of online evaluation techniques for information retrieval. We show how online evaluation is used for controlled experiments, segmenting them into experiment designs that allow absolute or relative quality assessments. Our presentation of different metrics further partitions online evaluation based on different sized experimental units commonly of interest: documents, lists and sessions. Additionally, we include an extensive discussion of recent work on data re-use, and experiment estimation based on historical data.A substantial part of this work focuses on practical issues: How to run evaluations in practice, how to select experimental parameters, how to take into account ethical considerations inherent in online evaluations, and limitations that experimenters should be aware of. While most published work on online experimentation today is at large scale in systems with millions of users, we also emphasize that the same techniques can be applied at small scale. To this end, we emphasize recent work that makes it easier to use at smaller scales and encourage studying real-world information seeking in a wide range of scenarios. Finally, we present a summary of the most recent work in the area, and describe open problems, as well as postulating future directions.

88 citations


Cites methods from "Design and Analysis of Experiments ..."

  • ...An experiment design specifies how data will be collected to test a given hypothesis [Lawson, 2014]....

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Journal ArticleDOI
TL;DR: The benefits of experimental designs over alternative research approaches for the social sciences, advantages and disadvantages of different types of experiments, review existing experimental studies specific to tourism and hospitality, and offer guidance to researchers who wish to conduct such studies are discussed.
Abstract: Well-designed and executed experiments prove cause-and-effect relationships. The ability to draw causal conclusions is critical to knowledge development in any field of research. In this article, we discuss the benefits of experimental designs over alternative research approaches for the social sciences, discuss advantages and disadvantages of different types of experiments, review existing experimental studies specific to tourism and hospitality, and offer guidance to researchers who wish to conduct such studies. Properly executed experiments using actual behaviour of real stakeholders as a dependent variable lead to conclusions with high external validity. Our discussion of practical implementation issues culminates in a checklist for researchers. The article launches the Annals of Tourism Research Curated Collection on experimental research in tourism and hospitality.

79 citations

Journal ArticleDOI
TL;DR: Mixexp as discussed by the authors provides functions for creating mixture designs composed of extreme vertices and edge and face centroids in constrained mixture regions where components are subject to upper, lower and linear constraints.
Abstract: This article discusses the design and analysis of mixture experiments with R and illustrates the use of the recent package mixexp. This package provides functions for creating mixture designs composed of extreme vertices and edge and face centroids in constrained mixture regions where components are subject to upper, lower and linear constraints. These designs cannot be created by other R packages. mixexp also provides functions for graphical display of models fit to data from mixture experiments that cannot be created with other R packages.

32 citations


Cites background or methods from "Design and Analysis of Experiments ..."

  • ...This data set is stored in the data frame MPV which is part of the daewr package (Lawson 2015b) that contains the data frames and functions from the book Design and Analysis of Experiments with R (Lawson 2015a)....

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  • ...Lawson and Erjavec (2001) describe an experiment where an extreme vertices design was used to study the fixed carbon resulting from a coke briquette composed of a mixture of x1 = calcinate, x2 = tar free solids, and x3 = tar solids, and baked at a constant temperature....

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Book
Stanley E. Lazic1
08 Dec 2016
TL;DR: In this paper, the authors present a practical guide for lab-based biomedical researchers to design experiments that are reproducible, with low bias, high precision, and widely applicable results.
Abstract: Specifically intended for lab-based biomedical researchers, this practical guide shows how to design experiments that are reproducible, with low bias, high precision, and widely applicable results. With specific examples from research using both cell cultures and model organisms, it explores key ideas in experimental design, assesses common designs, and shows how to plan a successful experiment. It demonstrates how to control biological and technical factors that can introduce bias or add noise, and covers rarely discussed topics such as graphical data exploration, choosing outcome variables, data quality control checks, and data pre-processing. It also shows how to use R for analysis, and is designed for those with no prior experience. An accompanying website (https://stanlazic.github.io/EDLB.html) includes all R code, data sets, and the labstats R package. This is an ideal guide for anyone conducting lab-based biological research, from students to principle investigators working in either academia or industry.

31 citations