# Confirmatory factor analysis in MPlus

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1 Jan Štochl, Ph.D. Department of Psychiatry University of Cambridge Confirmatory factor analysis in MPlus The Psychometrics Centre

2 Agenda of day 1 General ideas and introduction to factor analysis Introduction to Mplus, fitting basic CFA models Introduction to Goodness of fit Differences between Principal Component Analysis, Eploratory Factor Analysis and Confirmatory Factor Analysis

3 General ideas and introduction to factor analysis A bit of theory

4 What is factor analysis? It is a statistical method used to find a small set of unobserved variables (also called latent variables, constructs or factors) which can account for the covariance (correlations) among a larger set of observed variables (also called manifest variables)

5 Factor analysis useful for: Assessment of dimensionality (i.e. how many latent variables underly your questionnaire, survey ) Assessment of validity of items in questionnaires and surveys, and therefore helps to eliminate less valid items Providing scores of respondent in latent variables Finding correlations among latent variables Answering specific scientific questions about relationship between observed and latent variables Helping to optimize length of questionnaires or surveys And many others.

6 What is observed variable? Sometimes also called indicators, manifest variables It is something what we can measure directly on certain scale Eamples: Height, circumference of head, number of pushups, time necessary to answer question during intelligence testing,.these are called continuous observed variables Eamples: Responses on disagree agree scales, never always scales, school grades,. these are called categorical observed variables Hereafter we denote observed variable as rectangular with its name inside, for eample height will be denoted as Height

7 What is latent variable? Also called constructs (especially in psychology), factors, unobserved variables We cannot measure them directly We assume they are underlying abilities causing respondents to score high or low on observed variables Eample: Testee performs poorly items of mathematical test (these items are observed variables) because his/her mathematical ability (latent variable) is low Eamples of latent variables: Intelligence, well-being, mathematical ability, Parkinson s disease. We denote latent variable as oval with its name inside, that is, e.g. Intelligence

8 Principle of factor analysis D A B C

9 Covariances Describe bivariate relationships cov( X, Y) N i1 ( i )( y N i y) May range from - to + (in theory) Covariance equals 0 for unrelated variables Difficult to say how strong is the relationship without knowing the variances

10 Covariance matri N i k ki k ki N i i k ki N i i i N i k ki i N i i i N i i i N N N N N N ) )( ( ) )( ( ) )( ( ) )( ( ) )( ( ) )( ( matri covariance Suppose we have k variables: k X X X,, 2, 1

11 Some properties of covariances and eample of covariance matri For any constant a: cov( X, a) 0 cov( X, X ) var( X ) Covariance is symmetrical, i.e. cov( X, Y) cov( Y, X ) X1 X2 X3 X4 X5 X6 X X X X X X

12 Correlation Standardized covariance, i.e. cor( X, Y) cov( X, Y) X Y Covariance divided by product of standard deviations of variables Ranges from -1 to +1 If correlation equals 0 then there is no (linear) relationship Allows easy comparison of how strong is the relationship between 2 variables

13 Eample of correlation matri X1 X2 X3 X4 X5 X6 X7 X1 1 X X X X X X

14 One factor is underlying this correlation matri? Epsilons are residuals (their variances are estimated) Observed variables (?) 1 (?) 2 (?) 3 X 1 X 2 X 3 1? 2?? 3 Lambdas are called factor loadings (?) 4 (?) 5 (?) 6 X 4 X 5 X 6 4? 5? 6? 7? f Latent variable 7 (?) X 7 Questionmarks represent parameters of the model

15 Formally (for the 1-factor model) f ( i 1,2,...,7) i i i i i represent mean of each observed variable. It vanishes if the variables are centered around mean Usuall regression assumptions apply Now we can choose scale and origin of f (it does not affect the form of the regression equation), so we choose mean f =0 and standard deviation f= 1, so now Cov( X, X ) i k i k ( i, k 1,2,...,7; i k) We can use this property to make deductions about s and s. i i

16 Practical 1: Fitting 1-factor model Data: Correlation matri 4 by 4 X1 X2 X3 X4 X1 1 X X X

17 Kessler items (K4) b34k1 : frequency of feeling so depressed that nothing could cheer him/her up 0: none of the time 1: a little of the time 2: some of the time 3: most of the time 4: all of the time b34k3 : frequency of feeling restless or fidgety 0: none of the time 1: a little of the time 2: some of the time 3: most of the time 4: all of the time b34k2 : frequency of feeling hopeless 0: none of the time 1: a little of the time 2: some of the time 3: most of the time 4: all of the time b34k4 : frequency of feeling that everything was an effort 0: none of the time 1: a little of the time 2: some of the time 3: most of the time 4: all of the time

18 Determining scale of latent variable 2 possibilities: - fi one loading for every factor to 1 (Mplus default). The latent variable then have the same scale as the item with this fied loading. - fi the variance of latent variable to 1. The scale of the latent factor is then the same as for z-scores. Eample: MODEL: f1 BY X1* X2 X3 X4; Selection of the method is somehow arbitrary and may depend on the research question. Selection of the method does not influence model fit

19 Which estimator should be used? 2 basic types of estimators: Maimum likelihood based or least squares based Default estimator depends on type of analysis and measurement level of observed variables Default estimator can be changed ANALYSIS command Eample: ANALYSIS: Estimator = ML; Available estimators: ML, MLM, MLMV, MLR, MLF, MUML, WLS, WLSM, WLSMV, ULS, ULSMV, GLS More in estimator selection in Mplus user guide Muthén L. K., & Muthén, B. O. ( ). Mplus User s Guide. Sith Edition. Los Angeles, CA. Muthén & Muthén.

20 Eample 2 of correlation matri X1 X2 X3 X4 X5 X6 X7 X1 1 X X X X X X

21 Two factors underlying (?) 1 (?) 2 (?) 3 (?) 4 X1 X2 X3 X4 1?? 2? 3? 4 f1? New parameter here representing correlation between factors (will be close to zero for correlation matri on previous slide) 5 (?) X5 5? 6 (?) X6? 6 f2 7 (?) X7 7?

22 Practical 2: Fitting 2-factor model grant data

24 Sample correlation matri and corresponding residual matri Sample correlation matri X1 X2 X3 X4 X5 X6 X7 X1 1 X X X X X X Residual correlation matri X1 X2 X3 X4 X5 X6 X7 X X X X X X X

25 Goodness of fit Each software provides different goodness of fit statistics They are based on different ideas (e.g. summarizing elements in residual matri, information theory, etc.) Some of them are known to favour certain types of model Fortunately Mplus provides only few of them and the ones that are known to provide good information about model fit Degrees of Freedom = 14 Minimum Fit Function Chi-Square = (P = 0.0) Normal Theory Weighted Least Squares Chi-Square = (P = 0.0) Satorra-Bentler Scaled Chi-Square = (P = 0.010) Chi-Square Corrected for Non-Normality = (P = ) Estimated Non-centrality Parameter (NCP) = Percent Confidence Interval for NCP = (3.33 ; 34.52) Minimum Fit Function Value = 0.60 Population Discrepancy Function Value (F0) = Percent Confidence Interval for F0 = ( ; 0.073) Root Mean Square Error of Approimation (RMSEA) = Percent Confidence Interval for RMSEA = (0.022 ; 0.072) P-Value for Test of Close Fit (RMSEA < 0.05) = 0.52 Epected Cross-Validation Inde (ECVI) = Percent Confidence Interval for ECVI = (0.096 ; 0.16) ECVI for Saturated Model = 0.12 ECVI for Independence Model = Chi-Square for Independence Model with 21 Degrees of Freedom = Independence AIC = Model AIC = Saturated AIC = Independence CAIC = Model CAIC = Saturated CAIC = Normed Fit Inde (NFI) = 0.99 Non-Normed Fit Inde (NNFI) = 1.00 Parsimony Normed Fit Inde (PNFI) = 0.66 Comparative Fit Inde (CFI) = 1.00 Incremental Fit Inde (IFI) = 1.00 Relative Fit Inde (RFI) = 0.99 Critical N (CN) = Root Mean Square Residual (RMR) = Standardized RMR = Goodness of Fit Inde (GFI) = 0.87 Adjusted Goodness of Fit Inde (AGFI) = 0.74 Parsimony Goodness of Fit Inde (PGFI) = 0.44

26 Goodness of fit Chi-square and log-likelihood Testing hypothesis that the population correlation (covariance) matri is equal to correlation (covariance) matri estimated in Mplus. Chi-square is widely use as model fit, although it has certain undesired properties - Sensitive to sample size (the larger sample size the more likely is the rejection of the model) - Sensitive to model compleity (the more comple model the more likely is the rejection of the model) Log-likelihood value can be used to compare nested models (those models in which where the more constrained model has all parameters of less constraint one + applied to same data) -2 loglikelihood follows chi-square distribution with df equal to difference in number of estimated parameters

27 Goodness of fit TLI, CFI So-called comparative fit indices or incremental fit indices (measure improvement of fit) Compare your model with baseline model (model, where all observed variables are mutually uncorrelated) Tucker-Lewis inde (TLI) the higher the better (can eceed 1), at least 0.95 is recommended as cutoff value. TLI is underestimated for small sample sizes (say less than 100) and has large sampling variability. Therefore CFI is preferred. Comparative Fit Inde (CFI) range 0-1, the higher the better, recommended cutoff also 0.95

28 Goodness of fit Error of Approimation Indices Root-mean-square Error of Approimation (RMSEA) RMSEA has known distribution and therefore confidence intervals can be computed Recommended cutoffs: > 0.1 poor fit fair fit < 0.05 close fit

29 Goodness of fit Residual Based Fit Indices Measure average differences between sample and estimated population covariance (correlation) matri. Standardised root mean square residual (SRMR) range 0-1, the smaller the better, recommended cutoff 0.08

30 Goodness of fit - recommendations Always check residual matri you can find source of poor fit Do not make your decisions on the basis of one fit inde. (As Rod McDonald says There is always at least one fit inde that shows good fit of your model ). Chi-square based goodness of fit statistics tend to reject model when the sample size is big or when the model is comple. In that case use other statistics.

31 Degrees of freedom and identifiability of the model This adresses problem of model identification (will be covered in detail tomorrow) Model is underidentified (model parameters have infinite number of solutions) if the number of model parameters (q) eceeds pp ( 1) / 2, where p is the number of observed parameters, that is p( p 1) / 2 q 0. Model is just identified if p( p 1) / 2 q 0. Such model has just one solution. This model, however, cannot be statistically tested (fit is always perfect). We aim at overidentified models, that is p( p 1) / 2 q 0.

32 Number of observed variables per latent variable For 1-factor model, 3 observed variables result in just identified model (0 degrees of freedom), 4 observed variables result in model with 2 degrees of freedom If your model involves many items the situation is more complicated you can have only 2 items to represent factor but then question of domain coverage arises Have this in mind when you design your research tool (survey, questionnaire, ) rather include more items

33 General recommendations for CFA analysis If the input sample correlation matri consists of low correlations (say below 0.3), do not perform factor analysis. There is not much to model! Estimated only models that have substantial meaning Remember that parsimonous models are more appreciated Check standard errors of parameter estimates Check significance of factor loadings for model modification

34 Factor analysis useful for: Assessment of dimensionality (i.e. how many latent variables underly your questionnaire, survey ) Assessment of validity of items in questionnaires and surveys, and therefore helps to eliminate less valid items Providing scores of respondent in latent variables Finding correlations among latent variables Answering specific scientific questions about relationship between observed and latent variables Helping to optimize length of questionnaires or surveys And many others.

35 Types of factor analysis Principal component analysis (PCA) sometimes considered as one type of factor analysis, but PCA is conceptually different from FA!!! Eploratory factor analysis (EFA) data driven automated searching engine for finding underlying factors Confirmatory factor analysis (CFA) theory driven, more parsimonous and scientifically more sound methodology for finding underlying factors We did CFA until now!!

36 Principal component analysis (PCA) It is data reduction technique Reduces the number of observed variables to a smaller number of principal components which account for most of the variance of the observed variables Not model based, treat observed variables as measured without error, components cannot be interpreted as latent variables, not recommended for understanding latent structure of the data Useful e.g. for treatment of collinearity in multiple regression

37 Principal component analysis (PCA) The direction of the effect is different from EFA and CFA Unique variances are missing (thus it does not account for measurement error) X1 X2 X3 X4 X5 X6 X7 f1 f2

38 Eploratory factor analysis (EFA) Is a statistical technique which identifies the number of latent variables and the underlying factor structure of a set of observed variables It is model based (advantage over PCA), automated searching procedure for underlying structure, post-hoc interpretations of latent variables (disadvantage comparing to CFA) Traditionally has been used to eplore the possible underlying factor structure of a set of measured variables without imposing any preconceived structure on the outcome

39 Eploratory factor analysis (EFA) EFA models are generally underidentified (infinite number of solutions) We therefore rotate the solution (actually we rotate coordinates) according to some criteria (e.g. until the variance of squared loadings is maimal in Varima rotation) Number of factors is determined using eigenvalues (usually number of factors=number of eigenvalues over 1) X1 X2 X3 X4 X5 X6 X7 f1 f2

40 Eploratory factor analysis (EFA) Correlations between factors can be controlled by rotation method (orthogonal versus oblique) Usually rotation is necessary to interpret factor loadings. Traditionally has been used to eplore the possible underlying factor structure of a set of measured variables without imposing any preconceived structure on the outcome

41 Similarities and differences between PCA and EFA PCA and EFA may look similar and in practice may look like giving similar results. But the principal components (from PCA analysis) and factors (from EFA analysis) have very different interpretations Use EFA when you are interested in making statements about the factors that are responsible for a set of observed responses Use PCA when you are simply interested in performing data reduction.

42 Further reading General literature on factor analysis McDonald, R. P. (1999). Test theory: A unified treatment. Mahwah: Lawrence Erlbaum Associates, Inc. Bartholomew, D. J., et al. (2008). Analysis of Multivariate Social Science Data. London: CRC Press. Dunteman, G. H. (1989). Principal component analysis. Newbury Park: Sage. Bollen, K. A. (1989). Structural equations with latent variables. New York: John Wiley&sons. Kaplan, D. (2000). Structural equation modeling: Foundations and etensions. Thousand Oaks: Sage Publications. Maruyama, G. M. (1998). Basics of Structural Equation Modeling. Thousand Oaks: Sage Publications. McDonald, R. P. (1985). Factor analysis and related methods. Hillsdale NJ: Lawrence Erlbaum Associates. MPlus Muthén, L. K., & Muthén, B. O. ( ). Mplus User s Guide. Sith Edition. Los Angeles, CA: Muthén & Muthén. Visit for many papers and discussion on Mplus Goodness of fit Hu, L., & Bentler, M. P. (1999). Cutoff criteria for fit indees in covariance structure analysis: Conventional criteria versus new alternatives. Structural Equation Modeling: A Multidisciplinary Journal, 6(1), 1-55.

43 Eercise 1 Decathlon data 1. Open data file decathlon.ls. Prepare dataset for analysis in Mplus (in Ecel, Notepad or N2Mplus) 2. Fit 1-factor model for items 1-5. Use ML estimator and subsequently change it to WLS 3. Fit 1-factor model for items Change the default scaling of latent variable and compare factor validities of items 4. Compare fit indices of 1-factor model for all items and 2-factor model with uncorrelated factors as specified 5. Compare 2-factor model with uncorrelated factors with the one with correlated factor. Which of the models would you prefer? 6. Perform eploratory factor analysis with 1 to 2 factors. Use some ortogonal and oblique rotation. Which solution would you prefer? 7. Try to estimate other models that are theoretically meaningful.

44 Eercise 2 Prediction of side of onset from premorbid handedness in Parkinson s disease 1. Open data file Handedness.ls. Data consist of 7 items measuring premorbid handedness of patients with PD + 1 item measuring side of PD onset (onsetside). All items are categorical (onsetside has 3 categories, other items 5 categories) 2. Prepare dataset for analysis in Mplus (in Ecel, Notepad or N2Mplus) 3. Look at correlation matri and assess how much is side of onset is correlated with other items. 4. Introduce factor handedness that loads to all items. Can you predict side of PD onset from premorbid handedness? 5. Eclude item onsetside from model. Change the scale of factor (fi the variance of factor handedness to 1) and asees the validities of items. Which is the least valid item?

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