LINEAR REGRESSION for BINARY OUTCOMES 1 Logistic Or
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Generalized Linear Models (Glms)
San Jos´eState University Math 261A: Regression Theory & Methods Generalized Linear Models (GLMs) Dr. Guangliang Chen This lecture is based on the following textbook sections: • Chapter 13: 13.1 – 13.3 Outline of this presentation: • What is a GLM? • Logistic regression • Poisson regression Generalized Linear Models (GLMs) What is a GLM? In ordinary linear regression, we assume that the response is a linear function of the regressors plus Gaussian noise: 0 2 y = β0 + β1x1 + ··· + βkxk + ∼ N(x β, σ ) | {z } |{z} linear form x0β N(0,σ2) noise The model can be reformulate in terms of • distribution of the response: y | x ∼ N(µ, σ2), and • dependence of the mean on the predictors: µ = E(y | x) = x0β Dr. Guangliang Chen | Mathematics & Statistics, San Jos´e State University3/24 Generalized Linear Models (GLMs) beta=(1,2) 5 4 3 β0 + β1x b y 2 y 1 0 −1 0.0 0.2 0.4 0.6 0.8 1.0 x x Dr. Guangliang Chen | Mathematics & Statistics, San Jos´e State University4/24 Generalized Linear Models (GLMs) Generalized linear models (GLM) extend linear regression by allowing the response variable to have • a general distribution (with mean µ = E(y | x)) and • a mean that depends on the predictors through a link function g: That is, g(µ) = β0x or equivalently, µ = g−1(β0x) Dr. Guangliang Chen | Mathematics & Statistics, San Jos´e State University5/24 Generalized Linear Models (GLMs) In GLM, the response is typically assumed to have a distribution in the exponential family, which is a large class of probability distributions that have pdfs of the form f(x | θ) = a(x)b(θ) exp(c(θ) · T (x)), including • Normal - ordinary linear regression • Bernoulli - Logistic regression, modeling binary data • Binomial - Multinomial logistic regression, modeling general cate- gorical data • Poisson - Poisson regression, modeling count data • Exponential, Gamma - survival analysis Dr. -
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. -
The Hexadecimal Number System and Memory Addressing
C5537_App C_1107_03/16/2005 APPENDIX C The Hexadecimal Number System and Memory Addressing nderstanding the number system and the coding system that computers use to U store data and communicate with each other is fundamental to understanding how computers work. Early attempts to invent an electronic computing device met with disappointing results as long as inventors tried to use the decimal number sys- tem, with the digits 0–9. Then John Atanasoff proposed using a coding system that expressed everything in terms of different sequences of only two numerals: one repre- sented by the presence of a charge and one represented by the absence of a charge. The numbering system that can be supported by the expression of only two numerals is called base 2, or binary; it was invented by Ada Lovelace many years before, using the numerals 0 and 1. Under Atanasoff’s design, all numbers and other characters would be converted to this binary number system, and all storage, comparisons, and arithmetic would be done using it. Even today, this is one of the basic principles of computers. Every character or number entered into a computer is first converted into a series of 0s and 1s. Many coding schemes and techniques have been invented to manipulate these 0s and 1s, called bits for binary digits. The most widespread binary coding scheme for microcomputers, which is recog- nized as the microcomputer standard, is called ASCII (American Standard Code for Information Interchange). (Appendix B lists the binary code for the basic 127- character set.) In ASCII, each character is assigned an 8-bit code called a byte. -
Understanding Linear and Logistic Regression Analyses
EDUCATION • ÉDUCATION METHODOLOGY Understanding linear and logistic regression analyses Andrew Worster, MD, MSc;*† Jerome Fan, MD;* Afisi Ismaila, MSc† SEE RELATED ARTICLE PAGE 105 egression analysis, also termed regression modeling, come). For example, a researcher could evaluate the poten- Ris an increasingly common statistical method used to tial for injury severity score (ISS) to predict ED length-of- describe and quantify the relation between a clinical out- stay by first producing a scatter plot of ISS graphed against come of interest and one or more other variables. In this ED length-of-stay to determine whether an apparent linear issue of CJEM, Cummings and Mayes used linear and lo- relation exists, and then by deriving the best fit straight line gistic regression to determine whether the type of trauma for the data set using linear regression carried out by statis- team leader (TTL) impacts emergency department (ED) tical software. The mathematical formula for this relation length-of-stay or survival.1 The purpose of this educa- would be: ED length-of-stay = k(ISS) + c. In this equation, tional primer is to provide an easily understood overview k (the slope of the line) indicates the factor by which of these methods of statistical analysis. We hope that this length-of-stay changes as ISS changes and c (the “con- primer will not only help readers interpret the Cummings stant”) is the value of length-of-stay when ISS equals zero and Mayes study, but also other research that uses similar and crosses the vertical axis.2 In this hypothetical scenario, methodology. -
Application of General Linear Models (GLM) to Assess Nodule Abundance Based on a Photographic Survey (Case Study from IOM Area, Pacific Ocean)
minerals Article Application of General Linear Models (GLM) to Assess Nodule Abundance Based on a Photographic Survey (Case Study from IOM Area, Pacific Ocean) Monika Wasilewska-Błaszczyk * and Jacek Mucha Department of Geology of Mineral Deposits and Mining Geology, Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, 30-059 Cracow, Poland; [email protected] * Correspondence: [email protected] Abstract: The success of the future exploitation of the Pacific polymetallic nodule deposits depends on an accurate estimation of their resources, especially in small batches, scheduled for extraction in the short term. The estimation based only on the results of direct seafloor sampling using box corers is burdened with a large error due to the long sampling interval and high variability of the nodule abundance. Therefore, estimations should take into account the results of bottom photograph analyses performed systematically and in large numbers along the course of a research vessel. For photographs taken at the direct sampling sites, the relationship linking the nodule abundance with the independent variables (the percentage of seafloor nodule coverage, the genetic types of nodules in the context of their fraction distribution, and the degree of sediment coverage of nodules) was determined using the general linear model (GLM). Compared to the estimates obtained with a simple Citation: Wasilewska-Błaszczyk, M.; linear model linking this parameter only with the seafloor nodule coverage, a significant decrease Mucha, J. Application of General in the standard prediction error, from 4.2 to 2.5 kg/m2, was found. The use of the GLM for the Linear Models (GLM) to Assess assessment of nodule abundance in individual sites covered by bottom photographs, outside of Nodule Abundance Based on a direct sampling sites, should contribute to a significant increase in the accuracy of the estimation of Photographic Survey (Case Study nodule resources. -
The Simple Linear Regression Model
The Simple Linear Regression Model Suppose we have a data set consisting of n bivariate observations {(x1, y1),..., (xn, yn)}. Response variable y and predictor variable x satisfy the simple linear model if they obey the model yi = β0 + β1xi + ǫi, i = 1,...,n, (1) where the intercept and slope coefficients β0 and β1 are unknown constants and the random errors {ǫi} satisfy the following conditions: 1. The errors ǫ1, . , ǫn all have mean 0, i.e., µǫi = 0 for all i. 2 2 2 2. The errors ǫ1, . , ǫn all have the same variance σ , i.e., σǫi = σ for all i. 3. The errors ǫ1, . , ǫn are independent random variables. 4. The errors ǫ1, . , ǫn are normally distributed. Note that the author provides these assumptions on page 564 BUT ORDERS THEM DIFFERENTLY. Fitting the Simple Linear Model: Estimating β0 and β1 Suppose we believe our data obey the simple linear model. The next step is to fit the model by estimating the unknown intercept and slope coefficients β0 and β1. There are various ways of estimating these from the data but we will use the Least Squares Criterion invented by Gauss. The least squares estimates of β0 and β1, which we will denote by βˆ0 and βˆ1 respectively, are the values of β0 and β1 which minimize the sum of errors squared S(β0, β1): n 2 S(β0, β1) = X ei i=1 n 2 = X[yi − yˆi] i=1 n 2 = X[yi − (β0 + β1xi)] i=1 where the ith modeling error ei is simply the difference between the ith value of the response variable yi and the fitted/predicted valuey ˆi. -
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. -
Modelling Binary Outcomes
Modelling Binary Outcomes 01/12/2020 Contents 1 Modelling Binary Outcomes 5 1.1 Cross-tabulation . .5 1.1.1 Measures of Effect . .6 1.1.2 Limitations of Tabulation . .6 1.2 Linear Regression and dichotomous outcomes . .6 1.2.1 Probabilities and Odds . .8 1.3 The Binomial Distribution . .9 1.4 The Logistic Regression Model . 10 1.4.1 Parameter Interpretation . 10 1.5 Logistic Regression in Stata . 11 1.5.1 Using predict after logistic ........................ 13 1.6 Other Possible Models for Proportions . 13 1.6.1 Log-binomial . 14 1.6.2 Other Link Functions . 16 2 Logistic Regression Diagnostics 19 2.1 Goodness of Fit . 19 2.1.1 R2 ........................................ 19 2.1.2 Hosmer-Lemeshow test . 19 2.1.3 ROC Curves . 20 2.2 Assessing Fit of Individual Points . 21 2.3 Problems of separation . 23 3 Logistic Regression Practical 25 3.1 Datasets . 25 3.2 Cross-tabulation and Logistic Regression . 25 3.3 Introducing Continuous Variables . 26 3.4 Goodness of Fit . 27 3.5 Diagnostics . 27 3.6 The CHD Data . 28 3 Contents 4 1 Modelling Binary Outcomes 1.1 Cross-tabulation If we are interested in the association between two binary variables, for example the presence or absence of a given disease and the presence or absence of a given exposure. Then we can simply count the number of subjects with the exposure and the disease; those with the exposure but not the disease, those without the exposure who have the disease and those without the exposure who do not have the disease. -
Chapter 2 Simple Linear Regression Analysis the Simple
Chapter 2 Simple Linear Regression Analysis The simple linear regression model We consider the modelling between the dependent and one independent variable. When there is only one independent variable in the linear regression model, the model is generally termed as a simple linear regression model. When there are more than one independent variables in the model, then the linear model is termed as the multiple linear regression model. The linear model Consider a simple linear regression model yX01 where y is termed as the dependent or study variable and X is termed as the independent or explanatory variable. The terms 0 and 1 are the parameters of the model. The parameter 0 is termed as an intercept term, and the parameter 1 is termed as the slope parameter. These parameters are usually called as regression coefficients. The unobservable error component accounts for the failure of data to lie on the straight line and represents the difference between the true and observed realization of y . There can be several reasons for such difference, e.g., the effect of all deleted variables in the model, variables may be qualitative, inherent randomness in the observations etc. We assume that is observed as independent and identically distributed random variable with mean zero and constant variance 2 . Later, we will additionally assume that is normally distributed. The independent variables are viewed as controlled by the experimenter, so it is considered as non-stochastic whereas y is viewed as a random variable with Ey()01 X and Var() y 2 . Sometimes X can also be a random variable. -
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). -
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.