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A directional measure for marginal homogeneity in square contingency tables with ordered categories 一类有序列联表中边际齐性的方向性测度
Pub Date : 2019-06-01 DOI: 10.2478/bile-2019-0001
Kiyotaka Iki, Hiroshi Nakano, S. Tomizawa
Summary For square contingency tables with ordered categories, Iki, Tahata and Tomizawa (2012) considered a measure to represent the degree of departure from marginal homogeneity. However, the maximum value of this measure cannot distinguish two kinds of marginal inhomogeneity. The present paper proposes a measure which can distinguish two kinds of marginal inhomogeneity. In particular, the proposed measure is useful for representing the degree of departure from marginal homogeneity when the marginal cumulative logistic model holds.
对于有序类别的方形列联表,Iki, Tahata和Tomizawa(2012)考虑了一种度量来表示偏离边际同质性的程度。然而,该测度的最大值不能区分两种边际不均匀性。本文提出了一种能够区分两种边际不均匀性的测度。特别是,当边际累积逻辑模型成立时,所提出的度量对于表示偏离边际同质性的程度是有用的。
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引用次数: 0
Gene selection ensembles and classifier ensembles for medical diagnosis 用于医学诊断的基因选择集成和分类集成
Pub Date : 2019-04-12 DOI: 10.2478/bile-2019-0007
M. Ćwiklińska-Jurkowska
Summary The usefulness of combining methods is examined using the example of microarray cancer data sets, where expression levels of huge numbers of genes are reported. Problems of discrimination into two groups are examined on three data sets relating to the expression of huge numbers of genes. For the three examined microarray data sets, the cross-validation errors evaluated on the remaining half of the whole data set, not used earlier for the selection of genes, were used as measures of classifier performance. Common single procedures for the selection of genes—Prediction Analysis of Microarrays (PAM) and Significance Analysis of Microarrays (SAM)—were compared with the fusion of eight selection procedures, or of a smaller subset of five of them, excluding SAM or PAM. Merging five or eight selection methods gave similar results. Based on the misclassification rates for the three examined microarray data sets, for any examined ensemble of classifiers, the combining of gene selection methods was not superior to single PAM or SAM selection for two of the examined data sets. Additionally, the procedure of heterogeneous combining of five base classifiers—k-nearest neighbors, SVM linear and SVM radial with parameter c=1, shrunken centroids regularized classifier (SCRDA) and nearest mean classifier—proved to significantly outperform resampling classifiers such as bagging decision trees. Heterogeneously combined classifiers also outperformed double bagging for some ranges of gene numbers and data sets, but merging is generally not superior to random forests. The preliminary step of combining gene rankings was generally not essential for the performance for either heterogeneously or homogeneously combined classifiers.
通过微阵列癌症数据集的例子来检验组合方法的有效性,其中报告了大量基因的表达水平。在与大量基因表达有关的三个数据集上,对两组的歧视问题进行了检查。对于三个被检查的微阵列数据集,在整个数据集的剩余一半上评估的交叉验证误差(之前未用于基因选择)被用作分类器性能的度量。将常见的基因选择单一程序——微阵列预测分析(PAM)和微阵列显著性分析(SAM)——与八种选择程序的融合或其中五种较小子集的融合进行比较,不包括SAM或PAM。合并五种或八种选择方法得到了类似的结果。根据三个被检测的微阵列数据集的误分类率,对于任何被检测的分类器集合,基因选择方法的组合并不优于两个被检测数据集的单个PAM或SAM选择。此外,5种基本分类器(k近邻分类器、参数c=1的支持向量机线性分类器和支持向量机径向分类器、萎缩质心正则化分类器(SCRDA)和最接近均值分类器)的异质组合过程被证明显著优于bagging决策树等重采样分类器。在某些基因数量和数据集的范围内,异构组合分类器也优于双套袋,但合并通常并不优于随机森林。对于异质或同质组合分类器的性能来说,组合基因排序的初步步骤通常不是必需的。
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引用次数: 0
On a new approach to the analysis of variance for experiments with orthogonal block structure. 正交块结构试验方差分析的新方法。
Pub Date : 2018-12-01 DOI: 10.2478/bile-2018-0011
T. Caliński, I. Siatkowski
Summary The main estimation and hypothesis testing procedures are presented for experiments conducted in nested block designs of a certain type. It is shown that, under appropriate randomization, these experiments have the convenient orthogonal block structure. Due to this property, the analysis of experimental data can be performed in a comparatively simple way. Certain simplifying procedures are indicated. The main advantage of the presented methodology concerns the analysis of variance and related hypothesis testing procedures. Under the adopted approach one can perform these analytical methods directly, not by combining the results from analyses based on stratum submodels. The application of the presented theory is illustrated by three examples of real experiments in relevant nested block designs. The present paper is the second in the planned series concerning the analysis of experiments with orthogonal block structure.
摘要介绍了在某类型嵌套块设计中进行的实验的主要估计和假设检验程序。结果表明,在适当的随机化条件下,这些实验具有方便的正交块结构。由于这一特性,可以比较简单地对实验数据进行分析。指出了某些简化程序。所提出的方法的主要优点在于方差分析和相关的假设检验程序。在采用的方法下,可以直接执行这些分析方法,而不是将基于地层子模型的分析结果结合起来。通过三个相关嵌套块设计的实际实验实例说明了该理论的应用。本论文是计划进行的正交砌块结构试验分析系列中的第二篇。
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引用次数: 5
AMMI and GGE Biplot for genotype × environment interaction: a medoid–based hierarchical cluster analysis approach for high–dimensional data 基因型与环境相互作用的AMMI和GGE双图:一种基于媒介的高维数据分层聚类分析方法
Pub Date : 2018-12-01 DOI: 10.2478/bile-2018-0008
Anderson Cristiano Neisse, Jhessica L. Kirch, Kuang Hongyu
Summary The presence of genotype-environment interaction (GEI) influences production making the selection of cultivars in a complex process. The two most used methods to analyze GEI and evaluate genotypes are AMMI and GGE Biplot, being used for the analysis of multi environment trials data (MET). Despite their different approaches, both models complement each other in order to strengthen decision making. However, both models are based on biplots, consequently, biplot-based interpretation doesn’t scale well beyond two-dimensional plots, which happens whenever the first two components don’t capture enough variation. This paper proposes an approach to such cases based on cluster analysis combined with the concept of medoids. It also applies AMMI and GGE Biplot to the adjusted data in order to compare both models. The data is provided by the International Maize and Wheat Improvement Center (CIMMYT) and comes from the 14th Semi-Arid Wheat Yield Trial (SAWYT), an experiment concerning 50 genotypes of spring bread wheat (Triticum aestivum) germplasm adapted to low rainfall. It was performed in 36 environments across 14 countries. The analysis provided 25 genotypes clusters and 6 environments clusters. Both models were equivalent for the data’s evaluation, permitting increased reliability in the selection of superior cultivars and test environments.
基因型-环境互作(GEI)的存在影响着产量,使得品种选择是一个复杂的过程。分析GEI和评估基因型最常用的两种方法是AMMI和GGE Biplot,用于分析多环境试验数据(MET)。尽管它们的方法不同,但这两种模型相辅相成,以加强决策。然而,这两个模型都基于双标图,因此,基于双标图的解释不能很好地扩展到二维标图之外,每当前两个分量没有捕捉到足够的变化时,就会发生这种情况。本文提出了一种基于聚类分析并结合媒介概念的方法。并对调整后的数据应用AMMI和GGE双标图进行比较。该数据由国际玉米小麦改良中心(CIMMYT)提供,来自第14届半干旱小麦产量试验(SAWYT),该试验涉及适应低降雨的50个基因型春面包小麦(Triticum aestivum)种质。它在14个国家的36个环境中进行。分析得到25个基因型聚类和6个环境聚类。这两种模型对数据的评估是相同的,从而提高了选择优良品种和试验环境的可靠性。
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引用次数: 41
An overview of statistical methods to detect and understand genotype-by-environment interaction and QTL-by-environment interaction 基因型与环境相互作用和qtl与环境相互作用的统计检测方法综述
Pub Date : 2018-12-01 DOI: 10.2478/bile-2018-0009
P. Rodrigues
Summary Genotype-by-environment interaction (GEI) is frequently encountered in multi-environment trials, and represents differential responses of genotypes across environments. With the development of molecular markers and mapping techniques, researchers can go one step further and analyse the whole genome to detect specific locations of genes which influence a quantitative trait such as yield. Such a location is called a quantitative trait locus (QTL), and when these QTLs have different expression across environments we talk about QTL-by-environment interaction (QEI), which is the basis of GEI. Good understanding of these interactions enables researchers to select better genotypes across different environmental conditions, and consequently to improve crops in developed and developing countries. In this paper we present an overview of statistical methods and models commonly used to detect and to understand GEI and QEI, ranging from the simple joint regression model to complex eco-physiological genotype-to-phenotype simulation models.
基因型-环境相互作用(GEI)是多环境试验中经常遇到的问题,它代表了基因型在不同环境下的差异反应。随着分子标记和定位技术的发展,研究人员可以进一步分析整个基因组,以检测影响产量等数量性状的基因的特定位置。这样的位置被称为数量性状位点(QTL),当这些QTL在不同的环境中有不同的表达时,我们谈论QTL-by-environment interaction (QEI),这是GEI的基础。对这些相互作用的良好理解使科学家能够在不同的环境条件下选择更好的基因型,从而改善发达国家和发展中国家的作物。本文综述了用于检测和理解GEI和QEI的统计方法和模型,从简单的联合回归模型到复杂的生态生理基因型-表型模拟模型。
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引用次数: 9
Adapting Hellwig’s method for selecting concomitant variables under a certain growth curve model 在一定的增长曲线模型下,采用Hellwig的方法选择伴随变量
Pub Date : 2018-12-01 DOI: 10.2478/bile-2018-0010
M. Wesołowska-Janczarek, M. Różańska-Boczula
Summary This paper presents an application of Hellwig’s method for selecting concomitant variables under a growth curve model, where the values of the concomitant variables change over time and are the same for all experimental units. The authors present a simple adaptation of the growth curve model to the multiple regression model for which Hellwig’s method applies. The theoretical considerations are applied to the selection of significant concomitant variables for raspberry fruiting.
本文介绍了Hellwig方法在生长曲线模型下选择伴随变量的应用,其中伴随变量的值随时间而变化,并且对所有实验单元都是相同的。作者提出了一个简单的适应增长曲线模型的多元回归模型,其中Hellwig的方法适用。理论考虑应用于树莓果实显著伴随变量的选择。
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引用次数: 0
Linear Markovian models for lag exposure assessment 滞后暴露评估的线性马尔可夫模型
Pub Date : 2018-12-01 DOI: 10.2478/bile-2018-0012
Alessandro Magrini
Summary Linear regression with temporally delayed covariates (distributed-lag linear regression) is a standard approach to lag exposure assessment, but it is limited to a single biomarker of interest and cannot provide insights on the relationships holding among the pathogen exposures, thus precluding the assessment of causal effects in a general context. In this paper, to overcome these limitations, distributed-lag linear regression is applied to Markovian structural causal models. Dynamic causal effects are defined as a function of regression coefficients at different time lags. The proposed methodology is illustrated using a simple lag exposure assessment problem.
具有时间延迟协变量的线性回归(分布滞后线性回归)是滞后暴露评估的标准方法,但它仅限于感兴趣的单一生物标志物,不能提供对病原体暴露之间关系的见解,因此排除了在一般情况下的因果效应评估。为了克服这些局限性,本文将分布滞后线性回归应用于马尔可夫结构因果模型。动态因果效应被定义为不同时间滞后的回归系数的函数。提出的方法是用一个简单的滞后暴露评估问题说明。
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引用次数: 3
Determining the change point for the error in the Macrophyte Index for Rivers 确定河流大型植物指数误差的变化点
Pub Date : 2018-12-01 DOI: 10.2478/bile-2018-0015
Anna Budka
Summary The consequences of the growing demand for water include a significant deterioration in its quality and a drastic decline in biodiversity, which is a serious threat to the hydrological and biocenotic balance of freshwater ecosystems. A good indicator of aquatic environment quality is macrophytes. Studies on macrophytes are one of the primary elements in the ecological status assessment of surface waters, in accordance with the guidelines of the Water Framework Directive. In Poland, research on the ecological status of rivers with regard to macrophytes has been carried out since 2008, using the Macrophyte Index for Rivers (MIR), which takes into account the number and coverage of macrophyte taxa. An analysis of numbers of species that need to be indicated at a site for valid assessment of the ecosystem was conducted on the basis of studies on macrophytes from 2008–2013, at 60 sites in small lowland rivers with a sandy substrate, of which 20 sites were selected on the most diverse watercourses: the least clean (quality class V), moderate (quality class III), and the cleanest (quality class I). The results of the botanical studies served to assess the completeness of the samples (the number of species recorded at a site) used to evaluate the ecological status of a river. The proposed analyses enabled estimation of the approximate number of species required to determine the MIR for rivers in each quality class.
对水日益增长的需求的后果包括水的质量严重恶化和生物多样性急剧下降,这是对淡水生态系统的水文和生物群落平衡的严重威胁。水生环境质量的一个很好的指标是大型植物。根据《水框架指令》的指导方针,对大型植物的研究是地表水生态状况评估的主要内容之一。在波兰,自2008年以来,利用河流大型植物指数(MIR)开展了关于大型植物的河流生态状况的研究,该指数考虑了大型植物分类群的数量和覆盖范围。基于2008年至2013年对大型植物的研究,对一个地点需要显示的物种数量进行了分析,以有效评估生态系统,在60个具有沙质底质的低地小河流地点,其中20个地点选择在最多样化的水道上:最不干净(质量等级V),中等(质量等级III)和最干净(质量等级I)。植物学研究的结果用于评估样本的完整性(在一个地点记录的物种数量),用于评估河流的生态状况。拟议的分析能够估计出确定每一水质等级的河流的MIR所需的物种的大致数量。
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引用次数: 1
Use of classification and regression trees (CART) for analyzing determinants of winter wheat yield variation among fields in Poland 使用分类和回归树(CART)分析波兰冬小麦田间产量变化的决定因素
Pub Date : 2018-12-01 DOI: 10.2478/bile-2018-0013
M. Iwańska, A. Oleksy, M. Dacko, B. Skowera, T. Oleksiak, E. Wójcik-Gront
Summary Wheat is one of the modern world’s staple food sources. Its production requires good environmental conditions, which are not always available. However, agricultural practices may mitigate the effects of unfavorable weather or poor-quality soils. The influence of environmental and crop management variables on yield can be evaluated only based on representative long-term data collected on farms through well-prepared surveys.The authors of this work analyzed variation in winter wheat yield among 3868 fields in western and eastern Poland for 12 years, as dependent on both soil/weather and crop management factors, using the classification and regression tree (CART) method. The most important crop management deficiencies which may cause low wheat yields are insufficient use of fungicides, phosphorus deficiency, non-optimal date of sowing, poor quality of seeds, failure to apply herbicides, lack of crop rotation, and use of cultivars of unknown origin not suitable for the region. Environmental variables of great importance for the obtaining of high yields include large farm size (10 ha or larger) and good-quality soils with stable pH. This study makes it possible to propose strategies supporting more effective winter wheat production based on the identification of characteristics that are crucial for wheat cultivation in a given region.
小麦是现代世界的主要食物来源之一。它的生产需要良好的环境条件,而这些条件并不总是可用的。然而,农业实践可以减轻不利天气或劣质土壤的影响。环境和作物管理变量对产量的影响只能根据通过精心准备的调查在农场收集的有代表性的长期数据来评估。本文作者利用分类回归树(CART)方法,分析了波兰西部和东部3868块田12年来冬小麦产量的变化,分析了土壤/天气和作物管理因素对冬小麦产量的影响。可能导致小麦低产量的最重要的作物管理缺陷是杀菌剂使用不足、缺磷、非最佳播种日期、种子质量差、未施用除草剂、缺乏作物轮作以及使用不适合该地区的来源不明的品种。对获得高产非常重要的环境变量包括大型农场(10公顷或更大)和具有稳定ph值的优质土壤。这项研究使得在确定对特定地区小麦种植至关重要的特征的基础上提出支持更有效冬小麦生产的策略成为可能。
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引用次数: 6
Entropy as a measure of dependency for categorized data 熵是对分类数据依赖性的度量
Pub Date : 2018-12-01 DOI: 10.2478/bile-2018-0014
E. Skotarczak, A. Dobek, K. Moliński
Summary Data arranged in a two-way contingency table can be obtained as a result of many experiments in the life sciences. In some cases the categorized trait is in fact conditioned by an unobservable continuous variable, called liability. It may be interesting to know the relationship between the Pearson correlation coefficient of these two continuous variables and the entropy function measuring the corresponding relation for categorized data. After many simulation trials, a linear regression was estimated between the Pearson correlation coefficient and the normalized mutual information (both on a logarithmic scale). It was observed that the regression coefficients obtained do not depend either on the number of observations classified on a categorical scale or on the continuous random distribution used for the latent variable, but they are influenced by the number of columns in the contingency table. In this paper a known measure of dependency for such data, based on the entropy concept, is applied.
用双向列联表排列的数据是生命科学中许多实验的结果。在某些情况下,分类特征实际上是由一个不可观察的连续变量(称为负债)决定的。了解这两个连续变量的Pearson相关系数与度量分类数据对应关系的熵函数之间的关系可能会很有趣。经过多次模拟试验,估计Pearson相关系数和归一化互信息(均在对数尺度上)之间存在线性回归。观察到,得到的回归系数既不取决于分类尺度上分类的观测值的数量,也不取决于用于潜在变量的连续随机分布,但它们受列联表中列数的影响。在本文中,基于熵的概念,对这类数据应用了一种已知的依赖性度量。
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引用次数: 4
期刊
Biometrical Letters
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