The Importance of the Normality Assumption in Large Public Health Data Sets
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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. -
Simple Linear Regression with Least Square Estimation: an Overview
Aditya N More et al, / (IJCSIT) International Journal of Computer Science and Information Technologies, Vol. 7 (6) , 2016, 2394-2396 Simple Linear Regression with Least Square Estimation: An Overview Aditya N More#1, Puneet S Kohli*2, Kshitija H Kulkarni#3 #1-2Information Technology Department,#3 Electronics and Communication Department College of Engineering Pune Shivajinagar, Pune – 411005, Maharashtra, India Abstract— Linear Regression involves modelling a relationship amongst dependent and independent variables in the form of a (2.1) linear equation. Least Square Estimation is a method to determine the constants in a Linear model in the most accurate way without much complexity of solving. Metrics where such as Coefficient of Determination and Mean Square Error is the ith value of the sample data point determine how good the estimation is. Statistical Packages is the ith value of y on the predicted regression such as R and Microsoft Excel have built in tools to perform Least Square Estimation over a given data set. line The above equation can be geometrically depicted by Keywords— Linear Regression, Machine Learning, Least Squares Estimation, R programming figure 2.1. If we draw a square at each point whose length is equal to the absolute difference between the sample data point and the predicted value as shown, each of the square would then represent the residual error in placing the I. INTRODUCTION regression line. The aim of the least square method would Linear Regression involves establishing linear be to place the regression line so as to minimize the sum of relationships between dependent and independent variables. -
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. -
Generalized Linear Models
Generalized Linear Models Advanced Methods for Data Analysis (36-402/36-608) Spring 2014 1 Generalized linear models 1.1 Introduction: two regressions • So far we've seen two canonical settings for regression. Let X 2 Rp be a vector of predictors. In linear regression, we observe Y 2 R, and assume a linear model: T E(Y jX) = β X; for some coefficients β 2 Rp. In logistic regression, we observe Y 2 f0; 1g, and we assume a logistic model (Y = 1jX) log P = βT X: 1 − P(Y = 1jX) • What's the similarity here? Note that in the logistic regression setting, P(Y = 1jX) = E(Y jX). Therefore, in both settings, we are assuming that a transformation of the conditional expec- tation E(Y jX) is a linear function of X, i.e., T g E(Y jX) = β X; for some function g. In linear regression, this transformation was the identity transformation g(u) = u; in logistic regression, it was the logit transformation g(u) = log(u=(1 − u)) • Different transformations might be appropriate for different types of data. E.g., the identity transformation g(u) = u is not really appropriate for logistic regression (why?), and the logit transformation g(u) = log(u=(1 − u)) not appropriate for linear regression (why?), but each is appropriate in their own intended domain • For a third data type, it is entirely possible that transformation neither is really appropriate. What to do then? We think of another transformation g that is in fact appropriate, and this is the basic idea behind a generalized linear model 1.2 Generalized linear models • Given predictors X 2 Rp and an outcome Y , a generalized linear model is defined by three components: a random component, that specifies a distribution for Y jX; a systematic compo- nent, that relates a parameter η to the predictors X; and a link function, that connects the random and systematic components • The random component specifies a distribution for the outcome variable (conditional on X). -
Lecture 18: Regression in Practice
Regression in Practice Regression in Practice ● Regression Errors ● Regression Diagnostics ● Data Transformations Regression Errors Ice Cream Sales vs. Temperature Image source Linear Regression in R > summary(lm(sales ~ temp)) Call: lm(formula = sales ~ temp) Residuals: Min 1Q Median 3Q Max -74.467 -17.359 3.085 23.180 42.040 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) -122.988 54.761 -2.246 0.0513 . temp 28.427 2.816 10.096 3.31e-06 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 35.07 on 9 degrees of freedom Multiple R-squared: 0.9189, Adjusted R-squared: 0.9098 F-statistic: 101.9 on 1 and 9 DF, p-value: 3.306e-06 Some Goodness-of-fit Statistics ● Residual standard error ● R2 and adjusted R2 ● F statistic Anatomy of Regression Errors Image Source Residual Standard Error ● A residual is a difference between a fitted value and an observed value. ● The total residual error (RSS) is the sum of the squared residuals. ○ Intuitively, RSS is the error that the model does not explain. ● It is a measure of how far the data are from the regression line (i.e., the model), on average, expressed in the units of the dependent variable. ● The standard error of the residuals is roughly the square root of the average residual error (RSS / n). ○ Technically, it’s not √(RSS / n), it’s √(RSS / (n - 2)); it’s adjusted by degrees of freedom. R2: Coefficient of Determination ● R2 = ESS / TSS ● Interpretations: ○ The proportion of the variance in the dependent variable that the model explains. -
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). -
1 Simple Linear Regression I – Least Squares Estimation
1 Simple Linear Regression I – Least Squares Estimation Textbook Sections: 18.1–18.3 Previously, we have worked with a random variable x that comes from a population that is normally distributed with mean µ and variance σ2. We have seen that we can write x in terms of µ and a random error component ε, that is, x = µ + ε. For the time being, we are going to change our notation for our random variable from x to y. So, we now write y = µ + ε. We will now find it useful to call the random variable y a dependent or response variable. Many times, the response variable of interest may be related to the value(s) of one or more known or controllable independent or predictor variables. Consider the following situations: LR1 A college recruiter would like to be able to predict a potential incoming student’s first–year GPA (y) based on known information concerning high school GPA (x1) and college entrance examination score (x2). She feels that the student’s first–year GPA will be related to the values of these two known variables. LR2 A marketer is interested in the effect of changing shelf height (x1) and shelf width (x2)on the weekly sales (y) of her brand of laundry detergent in a grocery store. LR3 A psychologist is interested in testing whether the amount of time to become proficient in a foreign language (y) is related to the child’s age (x). In each case we have at least one variable that is known (in some cases it is controllable), and a response variable that is a random variable. -
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. -
Chapter 19: Logistic Regression
DISCOVERING STATISTICS USING SPSS Chapter 19: Logistic regression Smart Alex’s Solutions Task 1 A ‘display rule’ refers to displaying an appropriate emotion in a given situation. For example, if you receive a Christmas present that you don’t like, the appropriate emotional display is to smile politely and say ‘Thank you Why did you buy me this Auntie Kate, I’ve always wanted a rotting cabbage’. The crappy statistics textbook for Christmas, Auntie Kate? inappropriate emotional display is to start crying and scream ‘Why did you buy me a rotting cabbage, you selfish old bag?’ A psychologist measured children’s understanding of display rules (with a task that they could either pass or fail), their age (months), and their ability to understand others’ mental states (‘theory of mind’, measured with a false-belief task that they could pass or fail). The data are in Display.sav. Can display rule understanding (did the child pass the test: yes/no?) be predicted from the theory of mind (did the child pass the false-belief task: yes/no?), age and their interaction? The main analysis To carry out logistic regression, the data must be entered as for normal regression: they are arranged in the data editor in three columns (one representing each variable). Open the file Display.sav. Looking at the data editor, you should notice that both of the categorical variables have been entered as coding variables; that is, numbers have been specified to represent categories. For ease of interpretation, the outcome variable should be coded 1 (event occurred) and 0 (event did not occur); in this case, 1 represents having display rule understanding, and 0 represents an absence of display rule understanding.