What is multilevel regression modeling?

Consider an educational study with data from students in many schools, predicting in each school the students' grades y on a standardized test given their scores on a pre-test x and other information. A separate regression model can be fit within each school, and the parameters from these schools can themselves be modeled as depending on school characteristics (such as the socioeconomic status of the school's neighborhood, whether the school is public or private, and so on). The student-level regression and the school-level regression here are the two levels of a multilevel model.

In this example, a multilevel model can be expressed in (at least) three equivalent ways as a student-level regression:

• A model in which the coefficients vary by school (thus, instead of a model such as y = α + βx + error, we have y = αj + βjx + error, where the subscripts j index schools),

• A model with more than one variance component (student-level and school-level variation),

• A regression with many predictors, including an indicator variable for each school in the data.

More generally, we consider a multilevel model to be a regression (a linear or generalized linear model) in which the parameters—the regression coefficients—are given a probability model. This second-level model has parameters of its own—the hyperparameters of the model—which are also estimated from data.

The two key parts of a multilevel model are varying coefficients, and a model for those varying coefficients (which can itself include group-level predictors).

Statistical graphics are sometimes summarized as “exploratory data analysis” or “presentation” or “data display.” But these only capture part of the story. Graphs are a way to communicate graphical and spatial information to ourselves and others. Long before worrying about how to convince others, you first have to understand what's happening yourself.

Why to graph

Going back through the dozens of examples in this book, what are our motivations for graphing data and fitted models? Ultimately, the goal is communication (to self or others). More immediately, graphs are comparisons (to zero, to other graphs, to horizontal lines, and so forth). We “read” a graph both by pulling out the expected (for example, the slope of a fitted regression line, the comparisons of a series of confidence intervals to zero and each other) and the unexpected.

In our experience, the unexpected is usually not an “outlier” or aberrant point but rather a systematic pattern in some part of the data. For example, consider the binned residual plots in Section 5.6 for the well-switching models. There was an unexpectedly low rate of switching from wells that were just barely over the dangerous level for arsenic, possibly suggesting that people were moderating their decisions when in this ambiguous zone, or that there was other information not included in the model that could explain these decisions.

Analysis of variance (ANOVA) refers to a specific set of methods for data analysis and to a way of summarizing multilevel models:

• As a tool for data analysis, ANOVA is typically used to learn the relative importance of different sources of variation in a dataset. For example, Figure 13.8 displays success rates of pilots at a flight simulator under five different treatments at eight different airports. How much of the variation in the data is explained by treatments, how much by airports, and how much remains after these factors have been included in a linear model?

• If a multilevel model has already been fit, it can be summarized by the variation in each of its batches of coefficients. For example, in the radon modeling in Chapter 12, how much variation in radon levels is explained by floor of measurement and how much by geographical variation? Or, in the analysis of public opinion by state in Section 14.1, how much of the variation is explained by demographic factors (sex, age, ethnicity, education), and how much by states and regions? These “analysis of variance” questions can be of interest even for models that are primarily intended for prediction, or for estimating particular regression coefficients.

The sections of this chapter address the different roles of ANOVA in multilevel data analysis. We begin in Section 22.1 with a brief review of the goals and methods of classical analysis of variance, outlining how they fit into our general multilevel modeling approach.

Linear regression is a method that summarizes how the average values of a numerical outcome variable vary over subpopulations defined by linear functions of predictors. Introductory statistics and regression texts often focus on how regression can be used to represent relationships between variables, rather than as a comparison of average outcomes. By focusing on regression as a comparison of averages, we are being explicit about its limitations for defining these relationships causally, an issue to which we return in Chapter 9. Regression can be used to predict an outcome given a linear function of these predictors, and regression coefficients can be thought of as comparisons across predicted values or as comparisons among averages in the data.

One predictor

We begin by understanding the coefficients without worrying about issues of estimation and uncertainty. We shall fit a series of regressions predicting cognitive test scores of three- and four-year-old children given characteristics of their mothers, using data from a survey of adult American women and their children (a subsample from the National Longitudinal Survey of Youth).

We start by modeling the children's test scores given an indicator for whether the mother graduated from high school (coded as 1) or not (coded as 0).

Getting started with R, Bugs, and a text editor

Follow the instructions at www.stat.columbia.edu/∼gelman/arm/software/ to download, install, and set up R and Bugs on your Windows computer. The webpage is occasionally updated as the software improves, so we recommend checking back occasionally. R, OpenBugs, and WinBugs have online help with more information available at www.r-project.org, www.math.helsinki.fi/openbugs/, and www.mrc-bsu.cam.ac.uk/bugs/.

Set up a working directory on your computer for your R work. Every time you enter R, your working directory will automatically be set, and the necessary functions will be loaded in.

Configuring your computer display for efficient data analysis

We recommend working with three nonoverlapping open windows, as pictured in Figure C.1: an R console, the R graphics window, and a text editor (ideally a program such as Emacs or WinEdt that allows split windows, or the script window in the Windows version of R). When programming in Bugs, the text editor will have two windows open: a file (for example, project. R) with R commands, and a file (for example, project.bug) with the Bugs model. It is simplest to type commands into the text file with R commands and then cut and paste them into the R console. This is preferable to typing in the R console directly because copying and altering the commands is easier in the text editor. To run Bugs, there is no need to open a Bugs window; R will do this automatically when the function bugs() is called (assuming you have set up your computer as just described, which includes loading the R2WinBUGS package in R).

Multilevel modeling can be thought of in two equivalent ways:

• We can think of a generalization of linear regression, where intercepts, and possibly slopes, are allowed to vary by group. For example, starting with a regression model with one predictor, yi = α + βxi + ∈i, we can generalize to the varyingintercept model, yi = αj[i] + βxi + ∈i, and the varying-intercept, varying-slope model, yi = αj[i] + βj[i]xi + ∈i (see Figure 11.1 on page 238).

• Equivalently, we can think of multilevel modeling as a regression that includes a categorical input variable representing group membership. From this perspective, the group index is a factor with J levels, corresponding to J predictors in the regression model (or 2J if they are interacted with a predictor x in a varying-intercept, varying-slope model; or 3J if they are interacted with two predictors X(1), X(2); and so forth).

In either case, J−1 linear predictors are added to the model (or, to put it another way, the constant term in the regression is replaced by J separate intercept terms). The crucial multilevel modeling step is that these J coefficients are then themselves given a model (most simply, a common distribution for the J parameters αj or, more generally, a regression model for the αj's given group-level predictors). The group-level model is estimated simultaneously with the data-level regression of y.

We next explain how to fit multilevel models in Bugs, as called from R. We illustrate with several examples and discuss some general issues in model fitting and tricks that can help us estimate multilevel models using less computer time. We also present the basics of Bayesian inference (as a generalization of the least squares and maximum likelihood methods used for classical regression), which is the approach used in problems such as multilevel models with potentially large numbers of parameters.

Appendix C discusses some software that is available to quickly and approximately fit multilevel models. We recommend using Bugs for its flexibility in modeling; however, these simpler approaches can be useful to get started, explore models quickly, and check results.

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) for binary data from a linear predictor with an inverselogit transformation. A generalized linear model involves:

1. A data vector y = (y1, …, yn)

2. Predictors X and coefficients β, forming a linear predictor Xβ

3. A link function g, yielding a vector of transformed data ŷ = g−1(Xβ) that are used to model the data

4. A data distribution, p(y|ŷ)

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, the transformation is the identity (that is, g(u) ≡ u) and the data distribution is normal, with standard deviation σ estimated from data.

• In logistic regression, the transformation is the inverse-logit, g−1(u) = logit−1(u) (see Figure 5.2a on page 80) and the data distribution is defined by the probability for binary data: Pr(y = 1) = ŷ.

We now go through the steps of understanding and working with multilevel regressions, including designing studies, summarizing inferences, checking the fit of models to data, and imputing missing data.

Now that we can fit multilevel models, we should consider how to understand and summarize the parameters (and important transformations of these parameters) thus estimated.

Inferences from classical regression are typically summarized by a table of coefficient estimates and standard errors, sometimes with additional information on residuals and statistical significance (see, for example, the R output on page 39). With multilevel models, however, the sheer number of parameters adds a challenge to interpretation. The coefficient list in a multilevel model can be arbitrarily long (for example, the radon analysis has 85 county-level coefficients for the varying-intercept model, or 170 coefficients if the slope is allowed to vary also), and it is unrealistic to expect even the person who fit the model to be able to interpret each number separately. We prefer graphical displays such as the generic plot of a Bugs object or plots of fitted multilevel models such as displayed in the examples in Part 2A of this book.

Our general plan is to follow the same structures when plotting as when modeling. Thus, we plot data with data-level regressions (as in Figure 12.5 on page 266), and estimated group coefficients with group-level regressions (as in Figure 12.6). More complicated plots can be appropriate for non-nested models (for example, Figure 13.10 on page 291 and Figure 13.12 on page 293). More conventional plots of parameter estimates and standard errors (such as Figure 14.1 on page 306) can be helpful in multilevel models too.

Once data and a model have been set up, we face the challenge of debugging or, more generally, building confidence in the model and estimation. The steps of Bugs and R as we have described them are straightforward, but cumulatively they require a bit of effort, both in setting up the model and checking it—adding many lines of code produces many opportunities for typos and confusion. In Section 19.1 we discuss some specific issues in Bugs and general strategies for debugging and confidence building. Another problem that often arises is computational speed, and in Sections 19.2–19.5 we discuss several specific methods to get reliable inferences faster when fitting multilevel models. The chapter concludes with Section 19.6, which is not about computation at all, but rather is a discussion of prior distributions for variance parameters. The section is included here because it discusses models that were inspired by the computational idea described in Section 19.5. It thus illustrates the interplay between computation and modeling which has often been so helpful in multilevel data analysis.

Debugging and confidence building

Our general approach to finding problems in statistical modeling software is to get various crude models (for example, complete pooling and no pooling, or models with no predictors) to work and then to gradually build up to the model we want to fit.

Causal inference using regression has an inherent multilevel structure—the data give comparisons between units, but the desired causal inferences are within units. Experimental designs such as pairing and blocking assign different treatments to different units within a group. Observational analyses such as pairing or panel study attempt to capture groups of similar observations with variation in treatment assignment within groups.

Multilevel aspects of data collection

Hierarchical analysis of a paired design

Section 9.3 describes an experiment applied to school classrooms with a paired design: within each grade, two classes were chosen within each of several schools, and each pair was randomized, with the treatment assigned to one class and the control assigned to the other. The appropriate analysis then controls for grade and pair.

Including pair indicators in the Electric Company experiment. As in Section 9.3, we perform a separate analysis for each grade, which could be thought of as a model including interactions of treatment with grade indicators. Within any grade, let n be the number of classes (recall that the treatment and measurements are at the classroom, not the student, level) and J be the number of pairs, which is n/2 in this case. (We use the general notation n, J rather than simply “hard-coding” J = n/2 so that our analysis can also be used for more general randomized block designs with arbitrary numbers of units within each block.)

Aim of this book

This book originated as lecture notes for a course in regression and multilevel modeling, offered by the statistics department at Columbia University and attended by graduate students and postdoctoral researchers in social sciences (political science, economics, psychology, education, business, social work, and public health) and statistics. The prerequisite is statistics up to and including an introduction to multiple regression.

Advanced mathematics is not assumed—it is important to understand the linear model in regression, but it is not necessary to follow the matrix algebra in the derivation of least squares computations. It is useful to be familiar with exponents and logarithms, especially when working with generalized linear models.

After completing Part 1 of this book, you should be able to fit classical linear and generalized linear regression models—and do more with these models than simply look at their coefficients and their statistical significance. Applied goals include causal inference, prediction, comparison, and data description. After completing Part 2, you should be able to fit regression models for multilevel data. Part 3 takes you from data collection, through model understanding (looking at a table of estimated coefficients is usually not enough), to model checking and missing data. The appendixes include some reference materials on key tips, statistical graphics, and software for model fitting.

We now introduce multilevel linear and generalized linear models, including issues such as varying intercepts and slopes and non-nested models. We view multilevel models either as regressions with potentially large numbers of coefficients that are themselves modeled, or as regressions with coefficients that can vary by group.