Linear latent variable models: The lava-package

Computational Statistics

Volumn 28, Issue 4, 2013, Pages 1385-1452

  Holst, Klaus Kähler ^a   Budtz Jørgensen, Esben ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Latent variable model; Maximum likelihood; R; Seasonality; Serotonin; SERT; Structural equation model

Indexed keywords

EID: 84881073973     PISSN: 09434062     EISSN: 16139658     Source Type: Journal    
DOI: 10.1007/s00180-012-0344-y     Document Type: Article

References (51)

1. Andersen EB (1971) The asymptotic distribution of conditional likelihood ratio tests. J Am Stat Assoc 66(335): 630-633.
2. Angrist J (2001) Estimation of limited dependent variable models with dummy endogenous regressors: simple strategies for empirical practice. J Bus Econ Stat 19: 2-16.
3. Bates D, Maechler M (2009) lme4: linear mixed-effects models using S4 classes. http://CRAN. R-project. org/package=lme4, R package version 0. 999375-31.
4. Boker S, Neale M, Maes H, Wilde M, Spiegel M, Brick T, Spies J, Estabrook R, Kenny S, Bates T, Mehta P, Fox J (2011) Openmx: an open source extended structural equation modeling framework. Psychometrika 76: 306-317.
5. Bollen K (1996) An alternative two stage least squares (2sls) estimator for latent variable equations. Psychometrika 61(1): 109-121.
6. Bollen KA (1989) Structural equations with latent variables. Applied probability and statistics, Wiley series in probability and mathematical statistics. Wiley, New York.
7. Bollen KA (2001) Two-stage least squares and latent variable models: simultaneous estimation and robustness to misspecification. In: Cudeck R, Sörbom D, Du Toit SHC (eds) Structural equation modeling, present and future: a festschrift in honor of Karl Jöreskog, Scientific Software International, Lincolnwood.
8. Bollen KA, Kirby JB, Curran PJ, Paxton PM, Chen F (2007) Latent variable models under misspecification two-stage least squares (2SLS) and maximum likelihood (ML) estimators. Soc Methods Res 36(1): 48-86. doi: 10. 1177/0049124107301947.
9. Budtz-Jørgensen E, Keiding N, Grandjean P, Weihe P, White RF (2003) Statistical methods for the evaluation of health effects of prenatal mercury exposure. Environmetrics 14: 105-120.
10. Caffo B, Griswold M (2006) A user-friendly introduction to link-probit-normal models. Am Stat 60(2): 139-145.
11. Csardi G, Nepusz T (2006) The igraph software package for complex network research, InterJ, Complex Syst 1695. http://igraph. sf. net.
12. Ditlevsen S, Christensen U, Lynch J, Damsgaard MT, Keiding N (2005) The mediation proportion: a structural equation approach for estimating the proportion of exposure effect on outcome explained by an intermediate variable. Epidemiology 16(1): 114-120. doi: 10. 1097/01. ede. 0000147107. 76079. 07.
13. Erritzoe D, Holst KK, Frokjaer VG, Licht CL, Kalbitzer J, Nielsen FA, Svarer C, Madsen J, Knudsen GM (2010) A nonlinear relationship between cerebral serotonin transporter and 5-HT2A receptor binding: an in vivo molecular imaging study in humans. J Neurosci 30(9): 3391-3397. doi: 10. 1523/JNEUROSCI. 2852-09. 2010. http://www. jneurosci. org/cgi/reprint/30/9/3391. pdf.
14. Fox J (2006) Teacher's corner: structural equation modeling with the sem package in r. Struct Equ Model Multidiscip J 13(13): 465-585. doi: 10. 1207/s15328007sem1303_7.
15. Fox J (2009) Sem: structural equation models. http://CRAN. R-project. org/package=sem, R package version 0. 9-16.
16. Gansner ER, North SC (1999) An open graph visualization system and its applications to software engineering. Softw Pract Exper 30: 1203-1233.
17. Gentleman RC, Carey VJ, Bates DM et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80. http://genomebiology. com/2004/5/10/R80.
18. Gentry J, Long L, Gentleman R, Falcon S, Hahne F, Sarkar D (2009) Rgraphviz: provides plotting capabilities for R graph objects. R package version 1. 20. 3.
19. Genz A, Bretz F, Miwa T, Mi X, Leisch F, Scheipl F, Hothorn T (2009) Mvtnorm: multivariate normal and t distributions. http://CRAN. R-project. org/package=mvtnorm, R package version 0. 9-4.
20. Gilbert P (2009) NumDeriv: accurate numerical derivatives. http://www. bank-banque-canada. ca/pgilbert, R package version 2006. 4-1.
21. Greene WH (2002) Econometric analysis, 5th edn. Prentice Hall, Englewood Cliffs.
22. Holm S (1979) A simple sequentially rejective multiple test procedure. Scand J Stat 6(2): 65-70. doi: 10. 2307/4615733.
23. Holst KK (2011) Lava. tobit: latent variable models with censored and binary outcomes. http://lava. r-forge. r-project. org, R package version 0. 4-3.
24. Holst KK (2012) Gof: model-diagnostics based on cumulative residuals. http://CRAN. R-project. org/package=gof, R package version 0. 8-1.
25. Horvitz DG, Thompson DJ (1952) A generalization of sampling without replacement from a finite universe. J Am Stat Assoc 47(260): 663-685.
26. Hotelling H (1953) New light on the correlation coefficient and its transforms. J R Stat Soc Ser B 15: 193-225 (discussion, 225-232).
27. Jöreskog K (1970) A general method for analysis of covariance structures. Biometrika 57: 239-251.
28. Kalbitzer J, Erritzoe D, Holst KK, Nielsen F, Marner L, Lehel S, Arentzen T, Jernigan TL, Knudsen GM (2010) Seasonal changes in brain serotonin transporter binding in short serotonin transporter linked polymorphic region-allele carriers but not in long-allele homozygotes. Biol Psychiatry 67: 1033-1039. doi: 10. 1016/j. biopsych. 2009. 11. 027.
29. Kenward MG, Molenberghs G (1998) Likelihood based frequentist inference when data are missing at random. Stat Sci 13(3): 236-247. doi: 10. 1214/ss/1028905886.
30. Laird NM, Ware JH (1982) Random-effects models for longitudinal data. Biometrics 38: 963-974.
31. Lehmann EL, Romano JP (2005) Testing statistical hypotheses. Springer texts in statistics. Springer, New York.
32. Liang KY, Zeger S (1986) Longitudinal data analysis using generalized linear models. Biometrika 73(1): 13-22.
33. Little RJA, Rubin DB (2002) Statistical analysis with missing data, 2nd edn. Wiley series in probability and statistics, Wiley, Hoboken.
34. Magnus JR, Neudecker H (1988) Matrix differential calculus with applications in statistics and econometrics. Wiley series in probability and mathematical statistics: Applied probability and statistics. Wiley, Chichester.
35. McArdle JJ, McDonald RP (1984) Some algebraic properties of the reticular action model for moment structures. Br J Math Stat Psychol 37(2): 234-251.
36. Muthén LK, Muthén BO (2007) Mplus user's guide (version 5), 5th edn. Muthén& Muthén, Los Angeles.
37. Paik M (1988) Repeated measurement analysis for nonnormal data in small samples. Commun Stat Simul Comput 17: 1155-1171.
38. Pinheiro JC, Bates DM (2000) Mixed-effects models in S and S-PLUS. Springer, Berlin.
39. Pinheiro JC, Chao EC (2006) Efficient laplacian and adaptive gaussian quadrature algorithms for multilevel generalized linear mixed models. J Comput Graph Stat 15(1): 58-81.
40. R Development Core Team (2010) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. http://www. R-project. org, ISBN 3-900051-07-0.
41. REvolution Computing (2009) Foreach: foreach looping construct for R. http://CRAN. R-project. org/package=foreach, R package version 1. 3. 0.
42. Rabe-Hesketh S, Skrondal A, Pickles A (2004) Generalized multilevel structural equation modeling. Psychometrika 69: 167-190. doi: 10. 1007/BF02295939.
43. Raftery A (1993) Bayesian model selection in structural equation models. In: Bollen K, Long J (eds) Testing structural equation models. Sage, Newbury Park, pp 163-180.
44. Rotnitzky A, Robins JM (1995) Semiparametric regression estimation in the presence of dependent censoring. Biometrika 82(4): 805-820.
45. Sanchez BN, Budtz-Jørgensen E, Ryan LM, Hu H (2005) Structural equation models: a review with applications to environmental epidemiology. J Am Stat Assoc 100: 1443-1455.
46. Sharpsteen C, Bracken C (2010) TikzDevice: a device for R graphics output in PGF/TikZ format. http://R-Forge. R-project. org/projects/tikzdevice, R package version 0. 5. 2/r34.
47. Steiger JH (2001) Driving fast in reverse. J Am Stat Assoc 96(453): 331-338. doi: 10. 1198/016214501750332893.
48. Therneau T, original R port by Thomas Lumley (2009) Survival: survival analysis, including penalised likelihood. http://CRAN. R-project. org/package=survival, R package version 2. 35-8.
49. White H (1982) Maximum likelihood estimation of misspecified models. Econometrica 50(1): 1-26.
50. Williams RL (2000) A note on robust variance estimation for cluster-correlated data. Biometrics 56(2): 645-646. doi: 10. 1111/j. 0006-341X. 2000. 00645. x.
51. Yan J, Fine J (2004) Estimating equations for association structures. Stat Med 23: 859-874. doi: 10. 1002/sim. 1650.