# Structural Equation Modeling With the sem Package in R

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STRUCTURAL EQUATION MODELING, 13(3), 465–486 Copyright © 2006, Lawrence Erlbaum Associates, Inc. TEACHER’S CORNER Structural Equation Modeling With the sem Package in R John Fox McMaster University R is free, open-source, cooperatively developed software that implements the S sta- tistical programming language and computing environment. The current capabilities of R are extensive, and it is in wide use, especially among statisticians. The sem package provides basic structural equation modeling facilities in R, including the ability to fit structural equations in observed variable models by two-stage least squares, and to fit latent variable models by full information maximum likelihood as- suming multinormality. This article briefly describes R, and then proceeds to illus- trate the use of the tsls and sem functions in the sem package. The article also demonstrates the integration of the sem package with other facilities available in R, for example for computing polychoric correlations and for bootstrapping. R (Ihaka & Gentleman, 1996; R Development Core Team, 2005) is a free, open-source, cooperatively developed implementation of the S statistical program- ming language and computing environment (Becker, Chambers, & Wilks, 1988; Chambers, 1998; Chambers & Hastie, 1992).1 Since its introduction in the mid-1990s, R has rapidly become one of the most widely used facilities for statisti- cal computing, especially among statisticians, and arguably now has broader cov- erage of statistical methods than any other statistical software. The basic R system, with capabilities roughly comparable to (say) a basic installation of SAS, can be augmented by contributed packages, which now number more than 700. These Correspondence should be addressed to John Fox, Department of Sociology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M4. E-mail: jfox@mcmaster.ca 1There is also a commercial implementation of the S statistical computing environment called S-PLUS, which antedates R, and which is distributed by Insightful Corporation (http://www.insight- ful.com/products/splus/). The sem package for R described in this article could be adapted for use with S-PLUS without too much trouble, but it does not work with S-PLUS in its current form.

466 FOX packages, along with the basic R software, are available on the Comprehensive R Archive Network (CRAN) Web sites, with the main CRAN archive in Vienna (at http://cran.r-project.org/; see also the R home page, at http://www.r-project.org/). R runs on all of the major computing platforms, including Linux/UNIX systems, Microsoft Windows systems, and Macintoshes under OS/X. This article describes the sem package in R, which provides a basic structural equation modeling (SEM) facility, including the ability to estimate structural equa- tions in observed variable models by two-stage least squares (2SLS), and to fit gen- eral (including latent variable) models by full information maximum likelihood (FIML) assuming multinormality. There is, in addition, the systemfit package, not described here, which implements a variety of observed variable structural equation estimators. The first section of this article provides a brief introduction to computing in R. Subsequent sections describe the use of the tsls function for 2SLS estimation and the sem function for fitting general structural equation models. A concluding section suggests possible future directions for the sem package. BACKGROUND: A BRIEF INTRODUCTION TO R It is not possible within the confines of this article to give more than a cursory in- troduction to R. The purpose of this section is to provide some background and ori- enting information. Beyond that, R comes with a complete set of manuals, includ- ing a good introductory manual; other documentation is available on the R Web site and in a number of books (e.g., Fox, 2002; Venables & Ripley, 2002). R also has an extensive online help system, reachable through the help command, ? op- erator, and some other commands, such as help.search. Although one can build graphical interfaces to R—for example, the Rcmdr (“R Commander”) package provides a basic statistics graphical user interface—R is fundamentally a command-driven system. The user interacts with the R interpreter either directly at a command prompt in the R console or through a programming editor; the Windows version of R incorporates a simple script editor. Figure 1 shows the main R window as it appears at start-up on a Microsoft Win- dows XP system. The greater than (>) symbol to the left of the block cursor in the R console is the command prompt; commands entered at the prompt are statements in the S language, and may include mathematical and other expressions to be eval- uated along with function calls. The following are some examples of simple R commands: > 1 + 2*3^2 # an arithmetic expression [1] 19 > c(1, 2, 3)*2 # vectorized arithmetic [1] 2 4 6

STRUCTURAL EQUATION MODELING IN R 467 FIGURE 1 The Windows version of R at start-up, showing the main R window and the R console. > 2:5 # the sequence operator [1] 2 3 4 5 > (2:5)/c(2, 2, 3, 3) [1] 1.000000 1.500000 1.333333 1.666667 > x x # print x [1] 0.7115833 1.4496708 0.2819413 0.9289971 1.1364372 0.6987258 [7] -2.2418103 -0.2712084 0.1998054 -1.1573525 > mean(x) [1] 0.1736790 > mean(rnorm(100)) [1] -0.2394827 • The first command is an arithmetic expression representing 1 + 2 × 32; the normal precedence of arithmetic operators applies, and so exponentiation precedes multiplication, which precedes addition. The spaces in the command are optional,

468 FOX and are meant to clarify the expression. The pound sign (#) is a comment charac- ter: Everything to its right is ignored by the R interpreter. • The second command illustrates vectorized arithmetic, in which each ele- ment of a three-element vector is multiplied by 2; here c is the combine function, which constructs a vector from its arguments. As is general in S, the arguments to the c function are specified in parentheses and are separated by commas; argu- ments may be specified by position or by (abbreviated) name, in which case they need not appear in order. In many commands, some arguments have default values and therefore need not be specified explicitly. • In the third command, the sequence operator (:) is used to generate a vector of consecutive integers, and in the following command, this vector is divided by a vector of the same length, with the operation performed element-wise on corre- sponding entries of the two vectors. As here, parentheses may be used to clarify ex- pressions, or to alter the normal order of evaluation. • In the next command, the rnorm function is called with the argument 10 to sample 10 pseudo-random numbers from the standard normal distribution; the re- sult is assigned to a variable named x. Enter ?rnorm or help(rnorm) at the command prompt to see the help page for the rnorm function. The symbol

STRUCTURAL EQUATION MODELING IN R 469 and through programs. Moreover, the functions (programs) that the user writes are syntactically indistinguishable from the functions provided with R. Related sets of functions, data, and documentation can be collected into R pack- ages, and either maintained for private use or contributed to CRAN. The sophisti- cated tools provided for writing, maintaining, building, and checking packages are one of the strengths of R. 2SLS ESTIMATION OF OBSERVED VARIABLE MODELS The tsls function in the sem package fits structural equations by two-stage least squares (2SLS) using the general S “formula” interface. S model formulas imple- ment a variant of Wilkinson and Rogers’s (1973) notation for linear models; for- mulas are used in a wide variety of model-fitting functions in R (e.g., the basic lm and glm functions for fitting linear and generalized linear models, respectively). 2SLS estimation is illustrated using a classical application of SEM in econo- metrics: Klein’s “Model I” of the U.S. economy (Klein, 1950; see also, e.g., Greene, 1993, pp. 581–582). Klein’s data, a time-series data set for the years 1920 to 1941, are included in the data frame Klein in the sem package: > library(sem) > data(Klein) > Klein Year C P Wp I K.lag X Wg G T 1 1920 39.8 12.7 28.8 2.7 180.1 44.9 2.2 2.4 3.4 2 1921 41.9 12.4 25.5 -0.2 182.8 45.6 2.7 3.9 7.7 3 1922 45.0 16.9 29.3 1.9 182.6 50.1 2.9 3.2 3.9 . . . 21 1940 65.0 21.1 45.0 3.3 201.2 75.7 8.0 7.4 9.6 22 1941 69.7 23.5 53.3 4.9 204.5 88.4 8.5 13.8 11.6 The library command loads the sem package, and the data command reads the Klein data set into memory. (The ellipses, … , represent lines elided from the output.) Greene (1993, p. 581) wrote Klein’s model as follows: Ct = α 0 + α1Pt + α 2 Pt-1 + α 3 (W pt + W gt ) + ε1t It = β0 + β1Pt + β2 Pt-1 + β3 Kt-1 + ε2t W pt = γ 0 + γ1 Xt + γ 2 Xt-1 + γ 3 At + ε3t Xt = Ct + It + Gt Pt = Xt - Tt - W pt Kt = Kt-1 + It The last three equations are identities, and do not figure directly in the 2SLS esti- mation of the model. The variables in the model, again as given by Greene, are C

470 FOX (consumption), I (investment), Wp (private wages), Wg (government wages), X (equilibrium demand), P (private profits), K (capital stock), A (a trend variable, ex- pressed as year–1931), and G (government nonwage spending). The subscript t in- dexes observations. Because the model includes lagged variables that are not directly supplied in the data set, the observation for the first year, 1920, is effectively lost to estimation. The lagged variables can be added to the data frame as follows, printing the first three observations: > Klein$P.lag Klein$X.lag Klein[1:3,] Year C P Wp I K.lag X Wg G T P.lag X.lag 1 1920 39.8 12.7 28.8 2.7 180.1 44.9 2.2 2.4 3.4 NA NA 2 1921 41.9 12.4 25.5 -0.2 182.8 45.6 2.7 3.9 7.7 12.7 44.9 3 1922 45.0 16.9 29.3 1.9 182.6 50.1 2.9 3.2 3.9 12.4 45.6 In S, NA (not available) represents missing data, and, consistent with standard sta- tistical notation, a negative subscript, such as -22, drops observations. Square brackets are used to index objects such as data frames (e.g., Klein[1:3,]), vec- tors (e.g., Klein$P[-22]), matrices, arrays, and lists. The dollar sign ($) can be used to index elements of data frames or lists. The available instrumental variables are the exogenous variables G, T, Wg, A, and the constant regressor, and the predetermined variables Kt – 1, Pt – 1, and Xt – 1. Using these instrumental variables, the structural equations can be estimated: > Klein.eqn1 Klein.eqn2 Klein.eqn3

STRUCTURAL EQUATION MODELING IN R 471 functions such as summary, residuals, fitted.values, and anova have methods for handling tsls objects appropriately. The same generics are used for other classes of objects, such as linear and generalized linear models. • We can perform arithmetic operations and function calls within a model for- mula. Thus I(Wp + Wg) forms a single regressor by summing the two wage vari- ables; it is necessary to protect this operation with the identify function I (which re- turns its argument unchanged) because otherwise an arithmetic operator such as + would be accorded special meaning in a model formula; specifically, + means add a term to the model, and therefore, without protection, Wp + Wg would enter the two variables into the regression separately. We can read the model formula for Equation 1 as, “Regress C on P, P.lag, and the sum of Wp and Wc.” Were factors (categorical predictors) included in the model, R would automatically have generated contrasts to represent the factors, by default using dummy-coded (0/1) regressors. Interac- tions, nesting, transformations of variables, etc., can also be specified on the right side of a model formula, and ordinary arithmetic operations and function calls on the left side. Unless it is explicitly suppressed (by including -1 on the right side of the model formula), a constant regressor is included in the model. • The instruments argument to tsls specifies the instrumental variables as a one-sided model formula. As in the specification of the structural equation, the constant variable is automatically included among the instruments. • When an R command is syntactically incomplete, it is continued to the next line, as indicated in the listing by the + prompt, which is supplied at the beginning of each continuation line by the interpreter. To produce a printed summary for the first structural equation: > summary(Klein.eqn1) 2SLS Estimates Model Formula: C ~ P + P.lag + I(Wp + Wg) Instruments: ~G + T + Wg + I(Year - 1931) + K.lag + P.lag + X.lag Residuals: Min. 1st Qu. Median Mean 3rd Qu. Max. -1.89e+00 -6.16e-01 -2.46e-01 -6.60e-11 8.85e-01 2.00e+00 Estimate Std. Error t value Pr(>|t|) (Intercept) 16.55476 1.46798 11.2772 2.587e-09 P 0.01730 0.13120 0.1319 8.966e-01 P.lag 0.21623 0.11922 1.8137 8.741e-02 I(Wp + Wg) 0.81018 0.04474 18.1107 1.505e-12 Residual standard error: 1.1357 on 17 degrees of freedom To save space, the summaries for Equations 2 and 3 are omitted. The coefficient estimates are identical to those in Greene (1993), but the coeffi- cient standard errors differ slightly, because the summary method for tsls ob-

472 FOX jects uses residual degrees of freedom (17) rather than the number of observations (21) to estimate the error variance. To recover Greene’s asymptotic standard errors, the covariance matrix of the coefficients can be extracted and adjusted, illustrating a computation on a tsls object: > sqrt(diag(vcov(Klein.eqn1)*17/21)) (Intercept) P P.lag I(Wp + Wg) 1.32079242 0.11804941 0.10726796 0.04024971 vcov is a generic function that returns a variance–covariance matrix, here for the tsls object Klein.eqn1, and diag extracts the main diagonal of this matrix. ESTIMATING GENERAL STRUCTURAL EQUATION MODELS A Structural Equation Model With Latent Exogenous and Endogenous Variables Like Klein’s Model I, Wheaton, Muthén, Alwin, and Summers’s (1977) panel data on the stability of alienation have been a staple of the SEM literature, making an appearance, for example, in both the LISREL manual (Jöreskog & Sörbom, 1989) and in the documentation for the CALIS procedure in SAS (SAS Institute, 2004). The path diagram in Figure 2 is for a model fit to the Wheaton et al. data in the LISREL manual (Jöreskog & Sörbom, 1989, pp. 169–177). This diagram employs the usual conventions, representing observed variables by Roman letters enclosed in rectangles and unobserved variables (including latent variables and errors) by Greek letters enclosed in ellipses and circles. Directed arrows designate regression coefficients, and bidirectional arrows signify covariances. The covariances repre- sented by the two bidirectional arrows with broken lines are not included in an ini- tial model specified for these data. The directed arrows are labeled with Greek let- ters representing the corresponding regression coefficients. Anomia and Powerlessness are two subscales of a standard alienation scale, with data collected on a panel of individuals from rural Illinois in both 1967 and 1971. (In this version of the model, data on these variables from a 1966 wave of the study are ignored.) Education is measured in years, and SEI represents a socioeco- nomic index based on the respondent’s occupation. The latent variable SES stands for socioeconomic status.2 2It is curious that the various forms of the Wheaton model treat SES as a cause of the indicators Ed- ucation and SEI, rather than treating these variables as constitutive of SES (i.e., reversing the arrows in the path diagram, which produces an observationally indistinguishable model), but for consistency with the literature that specification is retained here.

STRUCTURAL EQUATION MODELING IN R 473 FIGURE 2 Conventional path diagram for Jöreskog and Sörbom’s model for the Wheaton alienation data. Adapted with permission from Figure 6.5 in Jöreskog and Sörbom (1989, 171). Using the common LISREL notation, this model consists of a structural submodel with two equations for the two latent endogenous variables (Alienation 67 and Alienation 71), and a measurement submodel with equations for the six in- dicators of the latent variables: Structural submodel η1 = γ1ξ + ζ1 η2 = γ 2 ξ + βη1 + ζ 2 Measurement submodel y1 = 1η1 + ε1 y2 = λ1η1 + ε2 y3 = 1η2 + ε3 y4 = λ 2 η2 + ε 4 x1 = 1ξ + δ1 x2 = λ 3 ξ + δ 2

474 FOX In these equations, the variables—observed and unobserved—are expressed as deviations from their expectations, suppressing the regression constant in each equation.3 The parameters of the model to be estimated include not just re- gression coefficients (i.e., structural parameters and factor loadings relating observed indicators to latent variables), but also the measurement-error vari- ances, V (εi ) = θεii , V (δ j ) = θδ jj ; the variances of the structural disturbances, V (ζ i ) = ψ ii ; the variance of the latent exogenous variable, V (ξ) = φ ; and, in some models considered next, certain measurement-error covariances C(εi , εi ' ) = θεii ' . The 1s in the measurement submodel reflect normalizing re- strictions, establishing the scales of the latent variables. Internally, the sem function, which is used to fit general structural equation models in R, employs the recticular action model (RAM) formulation of the model, due to McArdle (1980) and McArdle and McDonald (1984), and it is there- fore helpful to understand the structure of this model; the notation used here is from McDonald and Hartmann (1992). In the RAM model, the vector v contains indicator variables, directly observed exogenous variables, and latent exogenous and endogenous variables; the vector u (which may overlap with v) contains directly observed and latent exogenous vari- ables, measurement-error variables, and structural-error variables (i.e., the inputs to the system). Not all classes of variables are present in every model; for example, there are no directly observed exogenous variables in the Wheaton model. The v and u vectors are related by the equation v = Av + u, and, therefore, the matrix A contains regression coefficients (both structural parameters and factor loadings). For example, for the Wheaton model, we have é y1 ù é 0 0 0 0 0 0 1 0 0ù é y1 ù é ε1 ù ê ú ê ú ê ú ê ú ê y2 ú ê 0 0 0 0 0 0 λ1 0 0 úú ê y2 ú ê ε2 ú ê ú ê ê ú ê ú ê y3 ú ê 0 0 0 0 0 0 0 1 0 úú ê y3 ú ê ε3 ú ê ú ê ê ú ê ú ê y ú ê0 0 0 0 0 0 0 λ2 0 úú ê y ú êε ú ê 4ú ê ê 4ú ê 4ú ê ú=ê ú ê ú+ê ú ê x1 ú ê 0 0 0 0 0 0 0 0 1ú ê x1 ú ê δ1 ú ê ú ê ú ê ú ê ú ê x2 ú ê 0 0 0 0 0 0 0 0 λ3 ú ê x2 ú ê δ 2 ú ê ú ê ú ê ú ê ú ê η1 ú ê 0 0 0 0 0 0 0 0 γ1 ú ê η1 ú ê ζ1 ú ê ú ê ú ê ú ê ú êη2 ú ê 0 0 0 0 0 0 0 β γ2 ú êη2 ú êζ 2 ú ê ú ê ú ê ú ê ú êê ξ úú êê 0 0 0 0 0 0 0 0 0 úûú êê ξ úú êê ξ úú ë û ë ë û ë û 3A model with intercepts can be estimated by the sem function (described later) using a raw (i.e., uncorrected) moment matrix of mean sums of squares and cross-products in place of the covariance matrix among the observed variables in the model. This matrix includes sums of squares and products with a vector of ones, representing the constant regressor (see, e.g., McArdle & Epstein, 1987). The raw.moments function in the sem package will compute a raw-moments matrix from a model formula, numeric data frame, or numeric data matrix. To get correct degrees of freedom, set the argument raw = TRUE in sem.

STRUCTURAL EQUATION MODELING IN R 475 As is typically the case, most of the entries of A are prespecified to be 0, whereas others are set to 1. In the RAM formulation, the matrix P contains covariances among the elements of u. For the Wheaton model: é ε1 ù éθε11 0 θε13 0 0 0 0 0 0ù ê ú ê ú ê ε2 ú ê 0 θε 0 θε 0 0 0 0 0úú ê ú ê 22 24 ê ε3 ú êθε13 0 θε 0 0 0 0 0 0úú ê ú ê 33 êε ú ê 0 θε 0 θε 0 0 0 0 0úú ê 4ú ê 24 44 P = V êê δ1 úú = êê 0 0 0 0 θδ11 0 0 0 0ú ú ê ú ê ú ê δ2 ú ê 0 0 0 0 0 θδ22 0 0 0ú ê ú ê ú ê ζ1 ú ê 0 0 0 0 0 0 ψ11 0 0ú ê ú ê ú êζ 2 ú ê 0 0 0 0 0 0 0 ψ12 0ú ê ú ê ú êê ξ úú êê 0 0 0 0 0 0 0 0 φúúû ë û ë Once again, as is typically true, the P matrix is very sparse. Let m represent the number of variables in v, and let the first n entries of v be the observed variables of the model. Then the m × n selection matrix é I n 0ù J=ê ú ê 0 0ú ë û picks out the observed variables, where In is an order-n identity matrix and the 0s are zero matrices of appropriate order. Covariances among the observed variables are therefore given by C = E ( Jvv¢ J ¢) = J ( I m - A)-1 P[( I m - A)-1 ]¢ J ¢ Let S denote the covariances among the observed variables computed directly from a sample of data. Estimating the parameters of the model—the unconstrained entries of A and P—entails picking values of the parameters that make C close in some sense to S. In particular, under the assumption that the latent variables and er- rors are multinormally distributed, maximum likelihood (ML) estimates of the pa- rameters minimize the fitting criterion F ( A, P) = trace(SC-1 ) - n + loge det C - loge det S The sem function minimizes the ML fitting criterion numerically using the nlm optimizer in R, which employs a Newton-type algorithm; sem by default uses an analytic gradient, but a numerical gradient may be optionally employed. The covariance matrix of the parameter estimates is based on the numerical Hessian re-

476 FOX FIGURE 3 Modified RAM-format path diagram, with variables and parameters labeled for input to the sem function. turn by nlm. Start values for the parameters may be supplied by the user or are computed by a slightly modified version of the approach given in McDonald and Hartmann (1992). One advantage of the RAM formulation of a structural equation model is that the elements of the A and P matrices can be read off the path diagram for the model, with single-headed arrows corresponding to elements of A and dou- ble-headed arrows to elements of P, taking into account the fact that variances (as opposed to covariances) of exogenous variables and errors do not appear directly in the path diagram. To make the variances explicit, it helps to modify the path dia- gram slightly, as in Figure 3, eliminating the error variables and showing variances as self-directed double-headed arrows. The names of variables and free parameters have been replaced with names suitable for specifying the model in R. Model specification in the sem package is handled most conveniently via the specify.model function: > mod.wh.1 Anomia67, NA, 1 2: Alienation67 -> Powerless67, lam1, NA 3: Alienation71 -> Anomia71, NA, 1 4: Alienation71 -> Powerless71, lam2, NA

STRUCTURAL EQUATION MODELING IN R 477 5: SES -> Education, NA, 1 6: SES -> SEI, lam3, NA 7: Alienation67 -> Alienation71, beta, NA 8: SES -> Alienation67, gam1, NA 9: SES -> Alienation71, gam2, NA 10: SES SES, phi, NA 11: Alienation67 Alienation67, psi1, NA 12: Alienation71 Alienation71, psi2, NA 13: Anomia67 Anomia67, the11, NA 14: Powerless67 Powerless67, the22, NA 15: Anomia71 Anomia71, the33, NA 16: Powerless71 Powerless71, the44, NA 17: Education Education, thd1, NA 18: SEI SEI, thd2, NA 19: Read 18 records This specification is largely self-explanatory, but note the following: • The line-number prompts are supplied by specify.model, which is called here without any arguments. The entries are terminated by a blank line. The specify-model function can also read the model specification from a text file. • There are three entries in each line, separated by commas. • A single-headed arrow in the first entry indicates a regression coefficient and corresponds to a single-headed arrow in the path diagram; likewise a dou- ble-headed arrow represents a variance or covariance and corresponds to a dou- ble-headed arrow in the modified path diagram in Figure 3 (disregarding for now the broken arrows labeled the13 and the24 in the diagram). • The second entry in each line gives the (arbitrary) name of a free parameter to be estimated. Entering the name NA (missing) indicates that a parameter is to be fixed to a particular value. Assigning the same name to two or more arrows estab- lishes an equality constraint between the corresponding parameters. For example, substituting lam for both lam1 and lam2 would imply that these two factor load- ings are represented by the same parameter and hence are equal. • The third entry in each line either assigns a value to a fixed parameter or sets a start value for a free parameter; in the latter case, entering NA causes sem to pick the start value. • Finally, a word of caution: A common error in specifying models is to omit double-headed arrows representing variances of exogenous variables or error vari- ances. To estimate the model, the covariance or raw-moment matrix among the ob- served variables has to be computed. In the case of the Wheaton data, the

478 FOX covariances rather than the original data are available, and consequently the covariance matrix is entered directly: > S.wh > rownames(S.wh) Chisq) = 2.0417e-13 Goodness-of-fit index = 0.97517 Adjusted goodness-of-fit index = 0.91309 RMSEA index = 0.10826 90 % CI: (0.086585, 0.13145) BIC = 19.695 Normalized Residuals Min. 1st Qu. Median Mean 3rd Qu. Max. -1.26e+00 -2.12e-01 -8.35e-05 -1.53e-02 2.44e-01 1.33e+00 Parameter Estimates Estimate Std Error z value Pr(>|z|) lam1 0.88854 0.043196 20.5699 0.0000e+00 Powerless67

STRUCTURAL EQUATION MODELING IN R 479 psi1 5.30697 0.484105 10.9624 0.0000e+00 Alienation67 Alienation67 psi2 3.74127 0.388844 9.6215 0.0000e+00 Alienation71 Alienation71 the11 4.01554 0.358989 11.1857 0.0000e+00 Anomia67 Anomia67 the22 3.19131 0.283900 11.2410 0.0000e+00 Powerless67 Powerless67 the33 3.70111 0.391894 9.4441 0.0000e+00 Anomia71 Anomia71 the44 3.62481 0.304365 11.9094 0.0000e+00 Powerless71 Powerless71 thd1 2.94419 0.501395 5.8720 4.3057e-09 Education Education thd2 260.99237 18.278663 14.2785 0.0000e+00 SEI SEI Iterations = 83 • The first argument to sem is the model-specification object returned by specify.model. • The second argument, S.wh, is the input covariance matrix. • The third argument is the number of observations on which the covariances are based. • There are other optional arguments, which are explained in the sem help page (type ?sem to see it). One other argument is worth mentioning here: fixed.x takes a vector of quoted names of fixed exogenous variables, ob- viating the tedious necessity of enumerating the variances and covariances among these variables in the model specification. In this case, there are no fixed exogenous variables. As is typical of R programs, sem returns an object rather than a printed report. The summary method for sem objects produces the printout shown previously. One can perform additional computations on sem objects, for example, producing various kinds of residual covariances or modification indexes4 (e.g., Sörbom, 1989): > mod.indices(sem.wh.1) 5 largest modification indices, A matrix: Anomia71:Anomia67 Anomia67:Anomia71 Powerless71:Anomia67 10.378667 9.086581 9.024746 Anomia67:Powerless71 Powerless67:Anomia71 7.712109 7.285830 5 largest modification indices, P matrix: Anomia71:Anomia67 Powerless71:Anomia67 Anomia71:Powerless67 40.944815 35.377847 32.051155 Powerless71:Powerless67 Education:Powerless67 26.512979 5.878679 4The modification indexes returned by mod.indices are slightly in error because of an apparent bug that has to this point been elusive.

480 FOX The object returned by mod.indices is simply printed, which produces a brief report; the summary method for these objects produces a more complete report, showing all modification indexes along with approximations to the esti- mates that would result were each omitted parameter included in the model. Recall that the A matrix contains regression coefficients whereas the P matrix contains covariances. The modification indexes suggest that a better fit to the data would be achieved by freeing one or more of the covariances among the measure- ment errors of the latent endogenous variables; the largest modification index is for the two anomia measures, corresponding to the broken arrow labeled the13 in Figure 3. Adding this parameter to the model produces a much better fit (but subse- quently adding a parameter for the measurement error covariance the24, not shown, yields little additional improvement): > mod.wh.2 Anomia67, NA, 1 2: Alienation67 -> Powerless67, lam1, NA 3: Alienation71 -> Anomia71, NA, 1 4: Alienation71 -> Powerless71, lam2, NA 5: SES -> Education, NA, 1 6: SES -> SEI, lam3, NA 7: Alienation67 -> Alienation71, beta, NA 8: SES -> Alienation67, gam1, NA 9: SES -> Alienation71, gam2, NA 10: SES SES, phi, NA 11: Alienation67 Alienation67, psi1, NA 12: Alienation71 Alienation71, psi2, NA 13: Anomia67 Anomia67, the11, NA 14: Powerless67 Powerless67, the22, NA 15: Anomia71 Anomia71, the33, NA 16: Powerless71 Powerless71, the44, NA 17: Anomia67 Anomia71, the13, NA 18: Education Education, thd1, NA 19: SEI SEI, thd2, NA 20: Read 19 records > sem.wh.2 summary(sem.wh.2) Model Chisquare = 6.3307 Df = 5 Pr(>Chisq) = 0.27536 Goodness-of-fit index = 0.99773 Adjusted goodness-of-fit index = 0.99047 RMSEA index = 0.016908 90 % CI: (NA, 0.050905) BIC = -36.815

STRUCTURAL EQUATION MODELING IN R 481 Normalized Residuals Min. 1st Qu. Median Mean 3rd Qu. Max. -9.57e-01 -1.34e-01 -4.26e-02 -9.17e-02 1.82e-05 5.46e-01 Parameter Estimates Estimate Std Error z value Pr(>|z|) lam1 1.02653 0.053421 19.2159 0.0000e+00 Powerless67

482 FOX These variables originated as responses to the following statements on the mail-back component of the election study: MBSA2: “We should be more tolerant of people who choose to live according to their own standards, even if they are very different from our own.” MBSA7: “Newer lifestyles are contributing to the breakdown of our society.” MBSA8: “The world is always changing and we should adapt our view of moral behaviour to these changes.” MBSA9: “This country would have many fewer problems if there were more emphasis on traditional family values.” The hetcor function in the polycor package computes heterogeneous cor- relation matrices among ordinal and numeric variables: the product–moment cor- relation between two numeric variables, the polychoric correlation between two factors (assumed to be properly ordered), and the point-polyserial correlation be- tween a factor and a numeric variable. For the CNES data, for example: > data(CNES) > CNES[1:5,] # first 5 observations MBSA2 MBSA7 MBSA8 MBSA9 1 StronglyAgree Agree Disagree Disagree 2 Agree StronglyAgree StronglyDisagree StronglyAgree 3 Agree Disagree Disagree Agree 4 StronglyAgree Agree StronglyDisagree StronglyAgree 5 Agree StronglyDisagree Agree Disagree > library(polycor) > hetcor(CNES, ML=TRUE) Maximum-Likelihood Estimates Correlations/Type of Correlation: MBSA2 MBSA7 MBSA8 MBSA9 MBSA2 1 Polychoric Polychoric Polychoric MBSA7 -0.3028 1 Polychoric Polychoric MBSA8 0.2826 -0.344 1 Polychoric MBSA9 -0.2229 0.5469 -0.3213 1 Standard Errors: MBSA2 MBSA7 MBSA8 MBSA2 MBSA7 0.02737 MBSA8 0.02773 0.02642 MBSA9 0.02901 0.02193 0.02742 n = 1529

STRUCTURAL EQUATION MODELING IN R 483 P-values for Tests of Bivariate Normality: MBSA2 MBSA7 MBSA8 MBSA2 MBSA7 1.277e-07 MBSA8 1.852e-07 2.631e-23 MBSA9 5.085e-09 2.356e-10 1.500e-19 By default, the hetcor function computes polychoric and polyserial correla- tions by a relatively quick two-step procedure (see Drasgow, 1986; Olsson, 1979); specifying the argument ML=TRUE causes hetcor to compute pairwise ML esti- mates instead; in this instance (and as is typically the case), the two procedures produce very similar results (see later), so the faster procedure was used for boot- strapping. The tests of bivariate normality, applied to the contingency table for each pair of variables, are highly statistically significant, indicating departures from binormality. Even though a nonparametric bootstrap is employed later, non- normality suggests that it might not be appropriate to summarize the relations be- tween the variables with correlations; on the other hand, the sample size (N = 1,529) is fairly large, making these tests quite sensitive. The hetcor function returns an object with correlations and other informa- tion, but for fitting and bootstrapping a structural equation model, only the correla- tion matrix is used. The following simple function (from the boot.sem help page), entered at the command prompt, does the trick: > hcor R.CNES R.CNES MBSA2 MBSA7 MBSA8 MBSA9 MBSA2 1.0000000 -0.3017953 0.2820608 -0.2230010 MBSA7 -0.3017953 1.0000000 -0.3422176 0.5449886 MBSA8 0.2820608 -0.3422176 1.0000000 -0.3206524 MBSA9 -0.2230010 0.5449886 -0.3206524 1.0000000 Using sem to fit a one-factor confirmatory factor analysis model to the poly- choric correlations produces these results: > model.CNES MBSA2, lam1, NA 2: F -> MBSA7, lam2, NA 3: F -> MBSA8, lam3, NA 4: F -> MBSA9, lam4, NA 5: F F, NA, 1 6: MBSA2 MBSA2, the1, NA 7: MBSA7 MBSA7, the2, NA 8: MBSA8 MBSA8, the3, NA 9: MBSA9 MBSA9, the4, NA 10: Read 9 records

484 FOX > sem.CNES summary(sem. CNES) Model Chisquare = 33.211 Df = 2 Pr(>Chisq) = 6.1407e-08 Goodness-of-fit index = 0.98934 Adjusted goodness-of-fit index = 0.94668 RMSEA index = 0.10106 90 % CI: (0.07261, 0.13261) BIC = 15.774 Normalized Residuals Min. 1st Qu. Median Mean 3rd Qu. Max. -1.76e-05 3.00e-02 2.08e-01 8.48e-01 1.04e+00 3.83e+00 Parameter Estimates Estimate Std Error z value Pr(>|z|) lam1 -0.38933 0.028901 -13.471 0 MBSA2

STRUCTURAL EQUATION MODELING IN R 485 Lower and upper limits are for the 95 percent norm confidence interval Estimate Bias Std.Error Lower Upper lam1 -0.3893278 0.003473333 0.03203950 -0.4555973 -0.3300048 lam2 0.7779153 0.008113908 0.03728210 0.6967299 0.8428730 lam3 -0.4686838 0.007162961 0.03258827 -0.5397186 -0.4119749 lam4 0.6867992 -0.001208898 0.03160963 0.6260544 0.7499619 the1 0.8484245 0.001675460 0.02456932 0.7985941 0.8949041 the2 0.3948479 -0.014065971 0.05897530 0.2933244 0.5245034 the3 0.7803349 0.005612135 0.03004934 0.7158271 0.8336184 the4 0.5283057 0.000671089 0.04377695 0.4418334 0.6134359 The system.time function was used to time the computation, which took 114 sec on a 3 GHz Windows XP machine; the argument gcFirst=TRUE speci- fies that “garbage collection” take place just before the command is executed, pro- ducing a more accurate timing. Notice that boot.sem automatically loads the boot package. The arguments to boot.sem include the data set to be resampled (CNES), the sem object for the model (sem.CNES), the number of bootstrap rep- lications (R=100, which should be sufficient for standard errors and nor- mal-theory confidence intervals), and the function to be used in computing a covariance matrix from the resampled data (here, the hcor function). The boot- strap standard errors are mostly somewhat larger than the standard errors assuming multinormal numeric variables computed by sem. FURTHER DEVELOPMENT OF THE sem PACKAGE The latent variable modeling facility provided by the sem function is relatively ba- sic compared to special-purpose structural equation software such as AMOS, EQS, LISREL, or Mplus. One possible future direction for the sem package, therefore, would be to expand capabilities in areas such as multiple-group models and alternative fitting functions. Some enhancements—for example, multi- ple-group models—should be relatively straightforward, whereas others—for ex- ample, Browne’s (1984) asymptotically distribution-free estimator—would likely require implementation in compiled code to achieve acceptable levels of perfor- mance. At present, the sem package is coded entirely in R, but R makes provisions for the incorporation of portable compiled code in C and Fortran. A second area in which the sem package could be improved is the user inter- face: It would be desirable to provide a graphical interface in which the user speci- fies a model via its path diagram. Currently, the path.diagram function in sem provides only the inverse facility, producing a description of the path diagram from a fitted model, which subsequently can be rendered by the graph-drawing program dot (Gansner, Koutsofios, & North, 2002). Although R provides tools for the con-

486 FOX struction of graphical interfaces, making a path-drawing interface feasible, imple- menting such an interface would be a substantial undertaking. The specific future trajectory of the sem package, and the rapidity with which it is developed, will depend on user interest. REFERENCES Becker, R. A., Chambers, J. M., & Wilks, A. R. (1988). The new S language: A programming environ- ment for data analysis and graphics. Pacific Grove, CA: Wadsworth. Bollen, K. A. (1989). Structural equations with latent variables. New York: Wiley. Browne, M. W. (1984). Asymptotically distribution-free methods for the analysis of covariance struc- tures. British Journal of Mathematical and Statistical Psychology, 37, 62–83. Chambers, J. M. (1998). Programming with data: A guide to the S language. New York: Springer. Chambers, J. M., & Hastie, T. J. (Eds.). (1992). Statistical models in S. Pacific Grove, CA: Wadsworth. Davison, A. C., & Hinkley, D. V. (1997). Bootstrap methods and their application. Cambridge, UK: Cambridge University Press. Drasgow, F. (1986). Polychoric and polyserial correlations. In S. Kotz & N. Johnson (Eds.), The ency- clopedia of statistics (Vol. 7, pp. 68–74). New York: Wiley. Fox, J. (2002). An R and S-PLUS companion to applied regression. Thousand Oaks, CA: Sage. Gansner, E., Koutsofios, E., & North, S. (2002). Drawing graphs with dot. Retrieved June 13, 2005, from http://www.graphviz.org/Documentation/dotguide.pdf Greene, W. H. (1993). Econometric analysis (2nd ed.). New York: Macmillan. Ihaka, R., & Gentleman, R. (1996). R: A language for data analysis and graphics. Journal of Computa- tional and Graphical Statistics, 5, 299–314. Jöreskog, K. G., & Sörbom, D. (1989). LISREL 7: A guide to the program and applications (2nd ed.). Chicago: SPSS. Klein, L. (1950). Economic fluctuations in the United States 1921–1941. New York: Wiley. McArdle, J. J. (1980). Causal modeling applied to psychonomic systems simulation. Behavior Re- search Methods and Instrumentation, 12, 193–209. McArdle, J. J., & Epstein, D. (1987). Latent growth curves within developmental structural equation models. Child Development, 58, 110–133. McArdle, J. J., & McDonald, R. P. (1984). Some algebraic properties of the reticular action model. Brit- ish Journal of Mathematical and Statistical Psychology, 37, 234–251. McDonald, R. P., & Hartmann, W. M. (1992). A procedure for obtaining initial values of parameters in the RAM model. Multivariate Behavioral Research, 27, 57–76. Olsson, U. (1979). Maximum likelihood estimation of the polychoric correlation coefficient. Psycho- metrika, 44, 443–460. R Development Core Team. (2005). R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. SAS Institute. (2004). SAS 9.1.3 help and documentation. Cary, NC: Author. Sörbom, D. (1989). Model modification. Psychometrika, 54, 371–384. Venables, W. N., & Ripley, B. D. (2002). Modern applied statistics with S (4th ed.). New York: Springer. Wheaton, B., Muthén, B., Alwin, D. F., & Summers, G. F. (1977). Assessing reliability and stability in panel models. In D. R. Heise (Ed.), Sociological methodology 1977 (pp. 84–136). San Francisco: Jossey-Bass. Wilkinson, G. N., & Rogers, C. E. (1973). Symbolic description of factorial models for analysis of vari- ance. Applied Statistics, 22, 392–399.

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