Psychology 209 – Longitudinal Data Analysis and Bayesian Extensions


Lecture Notes (updated 12/10/14)


    • Assignment 1 – Due: 9/18/14
      • Datafile
      • R syntax printed in assignment
    • Assignment 2 – Due: 9/25/14
      • Datafile
    • Assignment 3 – Due: 10/16/14
    • Assignment 4 – Due: 11/4/14
      • GCM datafile
      • GMM datafile
    • Assignment 5 – Due: 11/18/14
      • LTA datafile
    • Assignment 6 – Due: 12/2/14
      • OpenBUGS syntax and data
    • Assignment 7 – Due: 12/17/14
      • Monte Carlo syntax example
      • Analysis model syntax example
      • Depaoli (2012) – see in list below
    • Term Paper     – Due: 12/15/14 by 8:00pm (to me and your partner)


  • R Script File: Note that additional R code is scattered throughout the lecture notes
    • 8/27
    • 9/16
  • Mplus Files: Note that additional Mplus code is scattered throughout the lecture notes
    • 10/15 GCM
    • 10/15 GCM with predictors
    • 10/17 GMM
  • WinBUGS Files:
    •  Example from class: Repeated measures ANOVA code and data


  • Additional Resources
    • Collins, L. M., & Lanza, S. T. (2010). Latent Class and Latent Transition Analysis. Hoboken, NJ: John Wiley & Sons. Chapter 7.
    • Depaoli, S. (2013). Mixture class recovery in GMM under varying degrees of class separation: Frequentist versus Bayesian estimation. Psychological Methods.
    • Depaoli, S. (2012). The ability for posterior predictive checking to identify model mis-specification in Bayesian growth mixture modeling. Structural Equation Modeling19, 534-560.
    • Grimm, K. A., & Ram, N. (2009). Nonlinear growth models in Mplus and SAS. Structural Equation Modeling16, 676–701.
    • Jasra, A., Holmes, C. C., & Stephens, D. A. (2005). Markov chain Monte Carlo methods and the label switching problem in Bayesian mixture modeling. Statistical Science20, 50–67.
    • Kaplan, D. (2008). An overview of Markov chain methods for the study of stage-sequential developmental processes. Developmental Psychology, 44, 457-467.
    • Kaplan, D., & Depaoli, S. (2012). Bayesian statistical methods. In T. Little (Ed.), Handbook of quantitative methods (pp. TBD). Oxford: Oxford University Press.
    • Kaplan, D. & Walpole, S. (2005). A Stage–Sequential Model of Reading Transitions: Evidence From the Early Childhood Longitudinal Study. Journal of Educational Psychology97, 551–563.
    • Muthen, B. O. (2001). Second-generation structural equation modeling with a combination of categorical and continuous latent variables: New opportunities for latent class/latent growth modeling. In L. M. Collins & A. G. Sayer (Eds.), New methods for the analysis of change (pp. 291–322). Washington DC: APA.
    • Muthen, B. O. (2004). Latent variable analysis: Growth mixture modeling and related techniques for longitudinal data. In D. Kaplan (Ed.), Handbook of quantitative methodology for the social sciences (pp. 345–368). Newbury Park, CA: Sage Publications.
    • Muthen, B. O., & Asparouhov, T. (2008). Growth mixture modeling: Analysis with non-Gaussian random effects. In G. Fitzmaurice, M. Davidian, G. Verbeke, & G. Molenberghs (Eds.), Longitudinal data analysis (pp. 143–165). Boca Raton: Chapman & Hall/CRC Press.
    • Nylund, K. (2007). Latent transition analysis: Modeling extensions and an application to peer victimization. Doctoral dissertation, University of California, Los Angeles.
    • Nylund, K.,  Asparouhov, T. &  Muthen, B. (2007). Deciding on the number of classes in latent class analysis and growth mixture modeling: A Monte Carlo simulation study. Structural Equation Modeling14, 535–569.
    • Sinharay, S. (2004). Experiences with Markov chain Monte Carlo convergence assessment in two psychometric examples. Journal of Educational and Behavioral Statistics29, 461–488.
    • Tofighi, D., & Enders, C. K. (2008). Identifying the correct number of classes in growth mixture models. In G. R. Hancock & K. M. Samuelson (Eds.), Advances in latent variable mixture models (pp. 317–341). Charlotte, NC: Information age Publishing.