What Exactly Is Random About Random Effects?
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Linear Mixed-Effects Modeling in SPSS: an Introduction to the MIXED Procedure
Technical report Linear Mixed-Effects Modeling in SPSS: An Introduction to the MIXED Procedure Table of contents Introduction. 1 Data preparation for MIXED . 1 Fitting fixed-effects models . 4 Fitting simple mixed-effects models . 7 Fitting mixed-effects models . 13 Multilevel analysis . 16 Custom hypothesis tests . 18 Covariance structure selection. 19 Random coefficient models . 20 Estimated marginal means. 25 References . 28 About SPSS Inc. 28 SPSS is a registered trademark and the other SPSS products named are trademarks of SPSS Inc. All other names are trademarks of their respective owners. © 2005 SPSS Inc. All rights reserved. LMEMWP-0305 Introduction The linear mixed-effects models (MIXED) procedure in SPSS enables you to fit linear mixed-effects models to data sampled from normal distributions. Recent texts, such as those by McCulloch and Searle (2000) and Verbeke and Molenberghs (2000), comprehensively review mixed-effects models. The MIXED procedure fits models more general than those of the general linear model (GLM) procedure and it encompasses all models in the variance components (VARCOMP) procedure. This report illustrates the types of models that MIXED handles. We begin with an explanation of simple models that can be fitted using GLM and VARCOMP, to show how they are translated into MIXED. We then proceed to fit models that are unique to MIXED. The major capabilities that differentiate MIXED from GLM are that MIXED handles correlated data and unequal variances. Correlated data are very common in such situations as repeated measurements of survey respondents or experimental subjects. MIXED extends repeated measures models in GLM to allow an unequal number of repetitions. -
Application of Random-Effects Probit Regression Models
Journal of Consulting and Clinical Psychology Copyright 1994 by the American Psychological Association, Inc. 1994, Vol. 62, No. 2, 285-296 0022-006X/94/S3.00 Application of Random-Effects Probit Regression Models Robert D. Gibbons and Donald Hedeker A random-effects probit model is developed for the case in which the outcome of interest is a series of correlated binary responses. These responses can be obtained as the product of a longitudinal response process where an individual is repeatedly classified on a binary outcome variable (e.g., sick or well on occasion t), or in "multilevel" or "clustered" problems in which individuals within groups (e.g., firms, classes, families, or clinics) are considered to share characteristics that produce similar responses. Both examples produce potentially correlated binary responses and modeling these per- son- or cluster-specific effects is required. The general model permits analysis at both the level of the individual and cluster and at the level at which experimental manipulations are applied (e.g., treat- ment group). The model provides maximum likelihood estimates for time-varying and time-invari- ant covariates in the longitudinal case and covariates which vary at the level of the individual and at the cluster level for multilevel problems. A similar number of individuals within clusters or number of measurement occasions within individuals is not required. Empirical Bayesian estimates of per- son-specific trends or cluster-specific effects are provided. Models are illustrated with data from -
10.1 Topic 10. ANOVA Models for Random and Mixed Effects References
10.1 Topic 10. ANOVA models for random and mixed effects References: ST&DT: Topic 7.5 p.152-153, Topic 9.9 p. 225-227, Topic 15.5 379-384. There is a good discussion in SAS System for Linear Models, 3rd ed. pages 191-198. Note: do not use the rules for expected MS on ST&D page 381. We provide in the notes below updated rules from Chapter 8 from Montgomery D.C. (1991) “Design and analysis of experiments”. 10. 1. Introduction The experiments discussed in previous chapters have dealt primarily with situations in which the experimenter is concerned with making comparisons among specific factor levels. There are other types of experiments, however, in which one wish to determine the sources of variation in a system rather than make particular comparisons. One may also wish to extend the conclusions beyond the set of specific factor levels included in the experiment. The purpose of this chapter is to introduce analysis of variance models that are appropriate to these different kinds of experimental objectives. 10. 2. Fixed and Random Models in One-way Classification Experiments 10. 2. 1. Fixed-effects model A typical fixed-effect analysis of an experiment involves comparing treatment means to one another in an attempt to detect differences. For example, four different forms of nitrogen fertilizer are compared in a CRD with five replications. The analysis of variance takes the following familiar form: Source df Total 19 Treatment (i.e. among groups) 3 Error (i.e. within groups) 16 And the linear model for this experiment is: Yij = µ + i + ij. -
Removing Hidden Confounding by Experimental Grounding
Removing Hidden Confounding by Experimental Grounding Nathan Kallus Aahlad Manas Puli Uri Shalit Cornell University and Cornell Tech New York University Technion New York, NY New York, NY Haifa, Israel [email protected] [email protected] [email protected] Abstract Observational data is increasingly used as a means for making individual-level causal predictions and intervention recommendations. The foremost challenge of causal inference from observational data is hidden confounding, whose presence cannot be tested in data and can invalidate any causal conclusion. Experimental data does not suffer from confounding but is usually limited in both scope and scale. We introduce a novel method of using limited experimental data to correct the hidden confounding in causal effect models trained on larger observational data, even if the observational data does not fully overlap with the experimental data. Our method makes strictly weaker assumptions than existing approaches, and we prove conditions under which it yields a consistent estimator. We demonstrate our method’s efficacy using real-world data from a large educational experiment. 1 Introduction In domains such as healthcare, education, and marketing there is growing interest in using observa- tional data to draw causal conclusions about individual-level effects; for example, using electronic healthcare records to determine which patients should get what treatments, using school records to optimize educational policy interventions, or using past advertising campaign data to refine targeting and maximize lift. Observational datasets, due to their often very large number of samples and exhaustive scope (many measured covariates) in comparison to experimental datasets, offer a unique opportunity to uncover fine-grained effects that may apply to many target populations. -
Confounding Bias, Part I
ERIC NOTEBOOK SERIES Second Edition Confounding Bias, Part I Confounding is one type of Second Edition Authors: Confounding is also a form a systematic error that can occur in bias. Confounding is a bias because it Lorraine K. Alexander, DrPH epidemiologic studies. Other types of can result in a distortion in the systematic error such as information measure of association between an Brettania Lopes, MPH bias or selection bias are discussed exposure and health outcome. in other ERIC notebook issues. Kristen Ricchetti-Masterson, MSPH Confounding may be present in any Confounding is an important concept Karin B. Yeatts, PhD, MS study design (i.e., cohort, case-control, in epidemiology, because, if present, observational, ecological), primarily it can cause an over- or under- because it's not a result of the study estimate of the observed association design. However, of all study designs, between exposure and health ecological studies are the most outcome. The distortion introduced susceptible to confounding, because it by a confounding factor can be large, is more difficult to control for and it can even change the apparent confounders at the aggregate level of direction of an effect. However, data. In all other cases, as long as unlike selection and information there are available data on potential bias, it can be adjusted for in the confounders, they can be adjusted for analysis. during analysis. What is confounding? Confounding should be of concern Confounding is the distortion of the under the following conditions: association between an exposure 1. Evaluating an exposure-health and health outcome by an outcome association. -
Chapter 17 Random Effects and Mixed Effects Models
Chapter 17 Random Effects and Mixed Effects Models Example. Solutions of alcohol are used for calibrating Breathalyzers. The following data show the alcohol concentrations of samples of alcohol solutions taken from six bottles of alcohol solution randomly selected from a large batch. The objective is to determine if all bottles in the batch have the same alcohol concentrations. Bottle Concentration 1 1.4357 1.4348 1.4336 1.4309 2 1.4244 1.4232 1.4213 1.4256 3 1.4153 1.4137 1.4176 1.4164 4 1.4331 1.4325 1.4312 1.4297 5 1.4252 1.4261 1.4293 1.4272 6 1.4179 1.4217 1.4191 1.4204 We are not interested in any difference between the six bottles used in the experiment. We therefore treat the six bottles as a random sample from the population and use a random effects model. If we were interested in the six bottles, we would use a fixed effects model. 17.3. One Random Factor 17.3.1. The Random‐Effects One‐way Model For a completely randomized design, with v treatments of a factor T, the one‐way random effects model is , :0, , :0, , all random variables are independent, i=1, ..., v, t=1, ..., . Note now , and are called variance components. Our interest is to investigate the variation of treatment effects. In a fixed effect model, we can test whether treatment effects are equal. In a random effects model, instead of testing : ..., against : treatment effects not all equal, we use : 0,: 0. If =0, then all random effects are 0. -
Beyond Controlling for Confounding: Design Strategies to Avoid Selection Bias and Improve Efficiency in Observational Studies
September 27, 2018 Beyond Controlling for Confounding: Design Strategies to Avoid Selection Bias and Improve Efficiency in Observational Studies A Case Study of Screening Colonoscopy Our Team Xabier Garcia de Albeniz Martinez +34 93.3624732 [email protected] Bradley Layton 919.541.8885 [email protected] 2 Poll Questions Poll question 1 Ice breaker: Which of the following study designs is best to evaluate the causal effect of a medical intervention? Cross-sectional study Case series Case-control study Prospective cohort study Randomized, controlled clinical trial 3 We All Trust RCTs… Why? • Obvious reasons – No confusion (i.e., exchangeability) • Not so obvious reasons – Exposure represented at all levels of potential confounders (i.e., positivity) – Therapeutic intervention is well defined (i.e., consistency) – … And, because of the alignment of eligibility, exposure assignment and the start of follow-up (we’ll soon see why is this important) ? RCT = randomized clinical trial. 4 Poll Questions We just used the C-word: “causal” effect Poll question 2 Which of the following is true? In pharmacoepidemiology, we work to ensure that drugs are effective and safe for the population In pharmacoepidemiology, we want to know if a drug causes an undesired toxicity Causal inference from observational data can be questionable, but being explicit about the causal goal and the validity conditions help inform a scientific discussion All of the above 5 In Pharmacoepidemiology, We Try to Infer Causes • These are good times to be an epidemiologist -
Study Designs in Biomedical Research
STUDY DESIGNS IN BIOMEDICAL RESEARCH INTRODUCTION TO CLINICAL TRIALS SOME TERMINOLOGIES Research Designs: Methods for data collection Clinical Studies: Class of all scientific approaches to evaluate Disease Prevention, Diagnostics, and Treatments. Clinical Trials: Subset of clinical studies that evaluates Investigational Drugs; they are in prospective/longitudinal form (the basic nature of trials is prospective). TYPICAL CLINICAL TRIAL Study Initiation Study Termination No subjects enrolled after π1 0 π1 π2 Enrollment Period, e.g. Follow-up Period, e.g. three (3) years two (2) years OPERATION: Patients come sequentially; each is enrolled & randomized to receive one of two or several treatments, and followed for varying amount of time- between π1 & π2 In clinical trials, investigators apply an “intervention” and observe the effect on outcomes. The major advantage is the ability to demonstrate causality; in particular: (1) random assigning subjects to intervention helps to reduce or eliminate the influence of confounders, and (2) blinding its administration helps to reduce or eliminate the effect of biases from ascertainment of the outcome. Clinical Trials form a subset of cohort studies but not all cohort studies are clinical trials because not every research question is amenable to the clinical trial design. For example: (1) By ethical reasons, we cannot assign subjects to smoking in a trial in order to learn about its harmful effects, or (2) It is not feasible to study whether drug treatment of high LDL-cholesterol in children will prevent heart attacks many decades later. In addition, clinical trials are generally expensive, time consuming, address narrow clinical questions, and sometimes expose participants to potential harm. -
Design of Engineering Experiments Blocking & Confounding in the 2K
Design of Engineering Experiments Blocking & Confounding in the 2 k • Text reference, Chapter 7 • Blocking is a technique for dealing with controllable nuisance variables • Two cases are considered – Replicated designs – Unreplicated designs Chapter 7 Design & Analysis of Experiments 1 8E 2012 Montgomery Chapter 7 Design & Analysis of Experiments 2 8E 2012 Montgomery Blocking a Replicated Design • This is the same scenario discussed previously in Chapter 5 • If there are n replicates of the design, then each replicate is a block • Each replicate is run in one of the blocks (time periods, batches of raw material, etc.) • Runs within the block are randomized Chapter 7 Design & Analysis of Experiments 3 8E 2012 Montgomery Blocking a Replicated Design Consider the example from Section 6-2 (next slide); k = 2 factors, n = 3 replicates This is the “usual” method for calculating a block 3 B2 y 2 sum of squares =i − ... SS Blocks ∑ i=1 4 12 = 6.50 Chapter 7 Design & Analysis of Experiments 4 8E 2012 Montgomery 6-2: The Simplest Case: The 22 Chemical Process Example (1) (a) (b) (ab) A = reactant concentration, B = catalyst amount, y = recovery ANOVA for the Blocked Design Page 305 Chapter 7 Design & Analysis of Experiments 6 8E 2012 Montgomery Confounding in Blocks • Confounding is a design technique for arranging a complete factorial experiment in blocks, where the block size is smaller than the number of treatment combinations in one replicate. • Now consider the unreplicated case • Clearly the previous discussion does not apply, since there -
Chapter 5 Experiments, Good And
Chapter 5 Experiments, Good and Bad Point of both observational studies and designed experiments is to identify variable or set of variables, called explanatory variables, which are thought to predict outcome or response variable. Confounding between explanatory variables occurs when two or more explanatory variables are not separated and so it is not clear how much each explanatory variable contributes in prediction of response variable. Lurking variable is explanatory variable not considered in study but confounded with one or more explanatory variables in study. Confounding with lurking variables effectively reduced in randomized comparative experiments where subjects are assigned to treatments at random. Confounding with a (only one at a time) lurking variable reduced in observational studies by controlling for it by comparing matched groups. Consequently, experiments much more effec- tive than observed studies at detecting which explanatory variables cause differences in response. In both cases, statistically significant observed differences in average responses implies differences are \real", did not occur by chance alone. Exercise 5.1 (Experiments, Good and Bad) 1. Randomized comparative experiment: effect of temperature on mice rate of oxy- gen consumption. For example, mice rate of oxygen consumption 10.3 mL/sec when subjected to 10o F. temperature (Fo) 0 10 20 30 ROC (mL/sec) 9.7 10.3 11.2 14.0 (a) Explanatory variable considered in study is (choose one) i. temperature ii. rate of oxygen consumption iii. mice iv. mouse weight 25 26 Chapter 5. Experiments, Good and Bad (ATTENDANCE 3) (b) Response is (choose one) i. temperature ii. rate of oxygen consumption iii. -
The Impact of Other Factors: Confounding, Mediation, and Effect Modification Amy Yang
The Impact of Other Factors: Confounding, Mediation, and Effect Modification Amy Yang Senior Statistical Analyst Biostatistics Collaboration Center Oct. 14 2016 BCC: Biostatistics Collaboration Center Who We Are Leah J. Welty, PhD Joan S. Chmiel, PhD Jody D. Ciolino, PhD Kwang-Youn A. Kim, PhD Assoc. Professor Professor Asst. Professor Asst. Professor BCC Director Alfred W. Rademaker, PhD Masha Kocherginsky, PhD Mary J. Kwasny, ScD Julia Lee, PhD, MPH Professor Assoc. Professor Assoc. Professor Assoc. Professor Not Pictured: 1. David A. Aaby, MS Senior Stat. Analyst 2. Tameka L. Brannon Financial | Research Hannah L. Palac, MS Gerald W. Rouleau, MS Amy Yang, MS Administrator Senior Stat. Analyst Stat. Analyst Senior Stat. Analyst Biostatistics Collaboration Center |680 N. Lake Shore Drive, Suite 1400 |Chicago, IL 60611 BCC: Biostatistics Collaboration Center What We Do Our mission is to support FSM investigators in the conduct of high-quality, innovative health-related research by providing expertise in biostatistics, statistical programming, and data management. BCC: Biostatistics Collaboration Center How We Do It Statistical support for Cancer-related projects or The BCC recommends Lurie Children’s should be requesting grant triaged through their support at least 6 -8 available resources. weeks before submission deadline We provide: Study Design BCC faculty serve as Co- YES Investigators; analysts Analysis Plan serve as Biostatisticians. Power Sample Size Are you writing a Recharge Model grant? (hourly rate) Short Short or long term NO collaboration? Long Subscription Model Every investigator is (salary support) provided a FREE initial consultation of up to 2 hours with BCC faculty of staff BCC: Biostatistics Collaboration Center How can you contact us? • Request an Appointment - http://www.feinberg.northwestern.edu/sites/bcc/contact-us/request- form.html • General Inquiries - [email protected] - 312.503.2288 • Visit Our Website - http://www.feinberg.northwestern.edu/sites/bcc/index.html Biostatistics Collaboration Center |680 N. -
Menbreg — Multilevel Mixed-Effects Negative Binomial Regression
Title stata.com menbreg — Multilevel mixed-effects negative binomial regression Syntax Menu Description Options Remarks and examples Stored results Methods and formulas References Also see Syntax menbreg depvar fe equation || re equation || re equation ::: , options where the syntax of fe equation is indepvars if in , fe options and the syntax of re equation is one of the following: for random coefficients and intercepts levelvar: varlist , re options for random effects among the values of a factor variable levelvar: R.varname levelvar is a variable identifying the group structure for the random effects at that level or is all representing one group comprising all observations. fe options Description Model noconstant suppress the constant term from the fixed-effects equation exposure(varnamee) include ln(varnamee) in model with coefficient constrained to 1 offset(varnameo) include varnameo in model with coefficient constrained to 1 re options Description Model covariance(vartype) variance–covariance structure of the random effects noconstant suppress constant term from the random-effects equation 1 2 menbreg — Multilevel mixed-effects negative binomial regression options Description Model dispersion(dispersion) parameterization of the conditional overdispersion; dispersion may be mean (default) or constant constraints(constraints) apply specified linear constraints collinear keep collinear variables SE/Robust vce(vcetype) vcetype may be oim, robust, or cluster clustvar Reporting level(#) set confidence level; default is level(95)