An Introduction to Logistic Regression Analysis and Reporting M
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Arxiv:1910.08883V3 [Stat.ML] 2 Apr 2021 in Real Data [8,9]
Nonpar MANOVA via Independence Testing Sambit Panda1;2, Cencheng Shen3, Ronan Perry1, Jelle Zorn4, Antoine Lutz4, Carey E. Priebe5 and Joshua T. Vogelstein1;2;6∗ Abstract. The k-sample testing problem tests whether or not k groups of data points are sampled from the same distri- bution. Multivariate analysis of variance (Manova) is currently the gold standard for k-sample testing but makes strong, often inappropriate, parametric assumptions. Moreover, independence testing and k-sample testing are tightly related, and there are many nonparametric multivariate independence tests with strong theoretical and em- pirical properties, including distance correlation (Dcorr) and Hilbert-Schmidt-Independence-Criterion (Hsic). We prove that universally consistent independence tests achieve universally consistent k-sample testing, and that k- sample statistics like Energy and Maximum Mean Discrepancy (MMD) are exactly equivalent to Dcorr. Empirically evaluating these tests for k-sample-scenarios demonstrates that these nonparametric independence tests typically outperform Manova, even for Gaussian distributed settings. Finally, we extend these non-parametric k-sample- testing procedures to perform multiway and multilevel tests. Thus, we illustrate the existence of many theoretically motivated and empirically performant k-sample-tests. A Python package with all independence and k-sample tests called hyppo is available from https://hyppo.neurodata.io/. 1 Introduction A fundamental problem in statistics is the k-sample testing problem. Consider the p p two-sample problem: we obtain two datasets ui 2 R for i = 1; : : : ; n and vj 2 R for j = 1; : : : ; m. Assume each ui is sampled independently and identically (i.i.d.) from FU and that each vj is sampled i.i.d. -
Logistic Regression, Dependencies, Non-Linear Data and Model Reduction
COMP6237 – Logistic Regression, Dependencies, Non-linear Data and Model Reduction Markus Brede [email protected] Lecture slides available here: http://users.ecs.soton.ac.uk/mb8/stats/datamining.html (Thanks to Jason Noble and Cosma Shalizi whose lecture materials I used to prepare) COMP6237: Logistic Regression ● Outline: – Introduction – Basic ideas of logistic regression – Logistic regression using R – Some underlying maths and MLE – The multinomial case – How to deal with non-linear data ● Model reduction and AIC – How to deal with dependent data – Summary – Problems Introduction ● Previous lecture: Linear regression – tried to predict a continuous variable from variation in another continuous variable (E.g. basketball ability from height) ● Here: Logistic regression – Try to predict results of a binary (or categorical) outcome variable Y from a predictor variable X – This is a classification problem: classify X as belonging to one of two classes – Occurs quite often in science … e.g. medical trials (will a patient live or die dependent on medication?) Dependent variable Y Predictor Variables X The Oscars Example ● A fictional data set that looks at what it takes for a movie to win an Oscar ● Outcome variable: Oscar win, yes or no? ● Predictor variables: – Box office takings in millions of dollars – Budget in millions of dollars – Country of origin: US, UK, Europe, India, other – Critical reception (scores 0 … 100) – Length of film in minutes – This (fictitious) data set is available here: https://www.southampton.ac.uk/~mb1a10/stats/filmData.txt Predicting Oscar Success ● Let's start simple and look at only one of the predictor variables ● Do big box office takings make Oscar success more likely? ● Could use same techniques as below to look at budget size, film length, etc. -
On the Meaning and Use of Kurtosis
Psychological Methods Copyright 1997 by the American Psychological Association, Inc. 1997, Vol. 2, No. 3,292-307 1082-989X/97/$3.00 On the Meaning and Use of Kurtosis Lawrence T. DeCarlo Fordham University For symmetric unimodal distributions, positive kurtosis indicates heavy tails and peakedness relative to the normal distribution, whereas negative kurtosis indicates light tails and flatness. Many textbooks, however, describe or illustrate kurtosis incompletely or incorrectly. In this article, kurtosis is illustrated with well-known distributions, and aspects of its interpretation and misinterpretation are discussed. The role of kurtosis in testing univariate and multivariate normality; as a measure of departures from normality; in issues of robustness, outliers, and bimodality; in generalized tests and estimators, as well as limitations of and alternatives to the kurtosis measure [32, are discussed. It is typically noted in introductory statistics standard deviation. The normal distribution has a kur- courses that distributions can be characterized in tosis of 3, and 132 - 3 is often used so that the refer- terms of central tendency, variability, and shape. With ence normal distribution has a kurtosis of zero (132 - respect to shape, virtually every textbook defines and 3 is sometimes denoted as Y2)- A sample counterpart illustrates skewness. On the other hand, another as- to 132 can be obtained by replacing the population pect of shape, which is kurtosis, is either not discussed moments with the sample moments, which gives or, worse yet, is often described or illustrated incor- rectly. Kurtosis is also frequently not reported in re- ~(X i -- S)4/n search articles, in spite of the fact that virtually every b2 (•(X i - ~')2/n)2' statistical package provides a measure of kurtosis. -
Univariate and Multivariate Skewness and Kurtosis 1
Running head: UNIVARIATE AND MULTIVARIATE SKEWNESS AND KURTOSIS 1 Univariate and Multivariate Skewness and Kurtosis for Measuring Nonnormality: Prevalence, Influence and Estimation Meghan K. Cain, Zhiyong Zhang, and Ke-Hai Yuan University of Notre Dame Author Note This research is supported by a grant from the U.S. Department of Education (R305D140037). However, the contents of the paper do not necessarily represent the policy of the Department of Education, and you should not assume endorsement by the Federal Government. Correspondence concerning this article can be addressed to Meghan Cain ([email protected]), Ke-Hai Yuan ([email protected]), or Zhiyong Zhang ([email protected]), Department of Psychology, University of Notre Dame, 118 Haggar Hall, Notre Dame, IN 46556. UNIVARIATE AND MULTIVARIATE SKEWNESS AND KURTOSIS 2 Abstract Nonnormality of univariate data has been extensively examined previously (Blanca et al., 2013; Micceri, 1989). However, less is known of the potential nonnormality of multivariate data although multivariate analysis is commonly used in psychological and educational research. Using univariate and multivariate skewness and kurtosis as measures of nonnormality, this study examined 1,567 univariate distriubtions and 254 multivariate distributions collected from authors of articles published in Psychological Science and the American Education Research Journal. We found that 74% of univariate distributions and 68% multivariate distributions deviated from normal distributions. In a simulation study using typical values of skewness and kurtosis that we collected, we found that the resulting type I error rates were 17% in a t-test and 30% in a factor analysis under some conditions. Hence, we argue that it is time to routinely report skewness and kurtosis along with other summary statistics such as means and variances. -
Multivariate Chemometrics As a Strategy to Predict the Allergenic Nature of Food Proteins
S S symmetry Article Multivariate Chemometrics as a Strategy to Predict the Allergenic Nature of Food Proteins Miroslava Nedyalkova 1 and Vasil Simeonov 2,* 1 Department of Inorganic Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier Blvd., 1164 Sofia, Bulgaria; [email protected]fia.bg 2 Department of Analytical Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier Blvd., 1164 Sofia, Bulgaria * Correspondence: [email protected]fia.bg Received: 3 September 2020; Accepted: 21 September 2020; Published: 29 September 2020 Abstract: The purpose of the present study is to develop a simple method for the classification of food proteins with respect to their allerginicity. The methods applied to solve the problem are well-known multivariate statistical approaches (hierarchical and non-hierarchical cluster analysis, two-way clustering, principal components and factor analysis) being a substantial part of modern exploratory data analysis (chemometrics). The methods were applied to a data set consisting of 18 food proteins (allergenic and non-allergenic). The results obtained convincingly showed that a successful separation of the two types of food proteins could be easily achieved with the selection of simple and accessible physicochemical and structural descriptors. The results from the present study could be of significant importance for distinguishing allergenic from non-allergenic food proteins without engaging complicated software methods and resources. The present study corresponds entirely to the concept of the journal and of the Special issue for searching of advanced chemometric strategies in solving structural problems of biomolecules. Keywords: food proteins; allergenicity; multivariate statistics; structural and physicochemical descriptors; classification 1. -
Logistic Regression Maths and Statistics Help Centre
Logistic regression Maths and Statistics Help Centre Many statistical tests require the dependent (response) variable to be continuous so a different set of tests are needed when the dependent variable is categorical. One of the most commonly used tests for categorical variables is the Chi-squared test which looks at whether or not there is a relationship between two categorical variables but this doesn’t make an allowance for the potential influence of other explanatory variables on that relationship. For continuous outcome variables, Multiple regression can be used for a) controlling for other explanatory variables when assessing relationships between a dependent variable and several independent variables b) predicting outcomes of a dependent variable using a linear combination of explanatory (independent) variables The maths: For multiple regression a model of the following form can be used to predict the value of a response variable y using the values of a number of explanatory variables: y 0 1x1 2 x2 ..... q xq 0 Constant/ intercept , 1 q co efficients for q explanatory variables x1 xq The regression process finds the co-efficients which minimise the squared differences between the observed and expected values of y (the residuals). As the outcome of logistic regression is binary, y needs to be transformed so that the regression process can be used. The logit transformation gives the following: p ln 0 1x1 2 x2 ..... q xq 1 p p p probabilty of event occuring e.g. person dies following heart attack, odds ratio 1- p If probabilities of the event of interest happening for individuals are needed, the logistic regression equation exp x x .... -
Generalized Linear Models
CHAPTER 6 Generalized linear models 6.1 Introduction Generalized linear modeling is a framework for statistical analysis that includes linear and logistic regression as special cases. Linear regression directly predicts continuous data y from a linear predictor Xβ = β0 + X1β1 + + Xkβk.Logistic regression predicts Pr(y =1)forbinarydatafromalinearpredictorwithaninverse-··· logit transformation. A generalized linear model involves: 1. A data vector y =(y1,...,yn) 2. Predictors X and coefficients β,formingalinearpredictorXβ 1 3. A link function g,yieldingavectoroftransformeddataˆy = g− (Xβ)thatare used to model the data 4. A data distribution, p(y yˆ) | 5. Possibly other parameters, such as variances, overdispersions, and cutpoints, involved in the predictors, link function, and data distribution. The options in a generalized linear model are the transformation g and the data distribution p. In linear regression,thetransformationistheidentity(thatis,g(u) u)and • the data distribution is normal, with standard deviation σ estimated from≡ data. 1 1 In logistic regression,thetransformationistheinverse-logit,g− (u)=logit− (u) • (see Figure 5.2a on page 80) and the data distribution is defined by the proba- bility for binary data: Pr(y =1)=y ˆ. This chapter discusses several other classes of generalized linear model, which we list here for convenience: The Poisson model (Section 6.2) is used for count data; that is, where each • data point yi can equal 0, 1, 2, ....Theusualtransformationg used here is the logarithmic, so that g(u)=exp(u)transformsacontinuouslinearpredictorXiβ to a positivey ˆi.ThedatadistributionisPoisson. It is usually a good idea to add a parameter to this model to capture overdis- persion,thatis,variationinthedatabeyondwhatwouldbepredictedfromthe Poisson distribution alone. -
In the Term Multivariate Analysis Has Been Defined Variously by Different Authors and Has No Single Definition
Newsom Psy 522/622 Multiple Regression and Multivariate Quantitative Methods, Winter 2021 1 Multivariate Analyses The term "multivariate" in the term multivariate analysis has been defined variously by different authors and has no single definition. Most statistics books on multivariate statistics define multivariate statistics as tests that involve multiple dependent (or response) variables together (Pituch & Stevens, 2105; Tabachnick & Fidell, 2013; Tatsuoka, 1988). But common usage by some researchers and authors also include analysis with multiple independent variables, such as multiple regression, in their definition of multivariate statistics (e.g., Huberty, 1994). Some analyses, such as principal components analysis or canonical correlation, really have no independent or dependent variable as such, but could be conceived of as analyses of multiple responses. A more strict statistical definition would define multivariate analysis in terms of two or more random variables and their multivariate distributions (e.g., Timm, 2002), in which joint distributions must be considered to understand the statistical tests. I suspect the statistical definition is what underlies the selection of analyses that are included in most multivariate statistics books. Multivariate statistics texts nearly always focus on continuous dependent variables, but continuous variables would not be required to consider an analysis multivariate. Huberty (1994) describes the goals of multivariate statistical tests as including prediction (of continuous outcomes or -
An Introduction to Logistic Regression: from Basic Concepts to Interpretation with Particular Attention to Nursing Domain
J Korean Acad Nurs Vol.43 No.2, 154 -164 J Korean Acad Nurs Vol.43 No.2 April 2013 http://dx.doi.org/10.4040/jkan.2013.43.2.154 An Introduction to Logistic Regression: From Basic Concepts to Interpretation with Particular Attention to Nursing Domain Park, Hyeoun-Ae College of Nursing and System Biomedical Informatics National Core Research Center, Seoul National University, Seoul, Korea Purpose: The purpose of this article is twofold: 1) introducing logistic regression (LR), a multivariable method for modeling the relationship between multiple independent variables and a categorical dependent variable, and 2) examining use and reporting of LR in the nursing literature. Methods: Text books on LR and research articles employing LR as main statistical analysis were reviewed. Twenty-three articles published between 2010 and 2011 in the Journal of Korean Academy of Nursing were analyzed for proper use and reporting of LR models. Results: Logistic regression from basic concepts such as odds, odds ratio, logit transformation and logistic curve, assumption, fitting, reporting and interpreting to cautions were presented. Substantial short- comings were found in both use of LR and reporting of results. For many studies, sample size was not sufficiently large to call into question the accuracy of the regression model. Additionally, only one study reported validation analysis. Conclusion: Nurs- ing researchers need to pay greater attention to guidelines concerning the use and reporting of LR models. Key words: Logit function, Maximum likelihood estimation, Odds, Odds ratio, Wald test INTRODUCTION The model serves two purposes: (1) it can predict the value of the depen- dent variable for new values of the independent variables, and (2) it can Multivariable methods of statistical analysis commonly appear in help describe the relative contribution of each independent variable to general health science literature (Bagley, White, & Golomb, 2001). -
Nonparametric Multivariate Kurtosis and Tailweight Measures
Nonparametric Multivariate Kurtosis and Tailweight Measures Jin Wang1 Northern Arizona University and Robert Serfling2 University of Texas at Dallas November 2004 – final preprint version, to appear in Journal of Nonparametric Statistics, 2005 1Department of Mathematics and Statistics, Northern Arizona University, Flagstaff, Arizona 86011-5717, USA. Email: [email protected]. 2Department of Mathematical Sciences, University of Texas at Dallas, Richardson, Texas 75083- 0688, USA. Email: [email protected]. Website: www.utdallas.edu/∼serfling. Support by NSF Grant DMS-0103698 is gratefully acknowledged. Abstract For nonparametric exploration or description of a distribution, the treatment of location, spread, symmetry and skewness is followed by characterization of kurtosis. Classical moment- based kurtosis measures the dispersion of a distribution about its “shoulders”. Here we con- sider quantile-based kurtosis measures. These are robust, are defined more widely, and dis- criminate better among shapes. A univariate quantile-based kurtosis measure of Groeneveld and Meeden (1984) is extended to the multivariate case by representing it as a transform of a dispersion functional. A family of such kurtosis measures defined for a given distribution and taken together comprises a real-valued “kurtosis functional”, which has intuitive appeal as a convenient two-dimensional curve for description of the kurtosis of the distribution. Several multivariate distributions in any dimension may thus be compared with respect to their kurtosis in a single two-dimensional plot. Important properties of the new multivariate kurtosis measures are established. For example, for elliptically symmetric distributions, this measure determines the distribution within affine equivalence. Related tailweight measures, influence curves, and asymptotic behavior of sample versions are also discussed. -
Variance Partitioning in Multilevel Logistic Models That Exhibit Overdispersion
J. R. Statist. Soc. A (2005) 168, Part 3, pp. 599–613 Variance partitioning in multilevel logistic models that exhibit overdispersion W. J. Browne, University of Nottingham, UK S. V. Subramanian, Harvard School of Public Health, Boston, USA K. Jones University of Bristol, UK and H. Goldstein Institute of Education, London, UK [Received July 2002. Final revision September 2004] Summary. A common application of multilevel models is to apportion the variance in the response according to the different levels of the data.Whereas partitioning variances is straight- forward in models with a continuous response variable with a normal error distribution at each level, the extension of this partitioning to models with binary responses or to proportions or counts is less obvious. We describe methodology due to Goldstein and co-workers for appor- tioning variance that is attributable to higher levels in multilevel binomial logistic models. This partitioning they referred to as the variance partition coefficient. We consider extending the vari- ance partition coefficient concept to data sets when the response is a proportion and where the binomial assumption may not be appropriate owing to overdispersion in the response variable. Using the literacy data from the 1991 Indian census we estimate simple and complex variance partition coefficients at multiple levels of geography in models with significant overdispersion and thereby establish the relative importance of different geographic levels that influence edu- cational disparities in India. Keywords: Contextual variation; Illiteracy; India; Multilevel modelling; Multiple spatial levels; Overdispersion; Variance partition coefficient 1. Introduction Multilevel regression models (Goldstein, 2003; Bryk and Raudenbush, 1992) are increasingly being applied in many areas of quantitative research. -
Randomization Does Not Justify Logistic Regression
Statistical Science 2008, Vol. 23, No. 2, 237–249 DOI: 10.1214/08-STS262 c Institute of Mathematical Statistics, 2008 Randomization Does Not Justify Logistic Regression David A. Freedman Abstract. The logit model is often used to analyze experimental data. However, randomization does not justify the model, so the usual esti- mators can be inconsistent. A consistent estimator is proposed. Ney- man’s non-parametric setup is used as a benchmark. In this setup, each subject has two potential responses, one if treated and the other if untreated; only one of the two responses can be observed. Beside the mathematics, there are simulation results, a brief review of the literature, and some recommendations for practice. Key words and phrases: Models, randomization, logistic regression, logit, average predicted probability. 1. INTRODUCTION nπT subjects at random and assign them to the treatment condition. The remaining nπ subjects The logit model is often fitted to experimental C are assigned to a control condition, where π = 1 data. As explained below, randomization does not C π . According to Neyman (1923), each subject has− justify the assumptions behind the model. Thus, the T two responses: Y T if assigned to treatment, and Y C conventional estimator of log odds is difficult to in- i i if assigned to control. The responses are 1 or 0, terpret; an alternative will be suggested. Neyman’s where 1 is “success” and 0 is “failure.” Responses setup is used to define parameters and prove re- are fixed, that is, not random. sults. (Grammatical niceties apart, the terms “logit If i is assigned to treatment (T ), then Y T is ob- model” and “logistic regression” are used interchange- i served.