This is an R package whose primary purpose is to extend the functionality of the R package lavaan. When incomplete data have been multiply imputed, the lavaan.mi package allows users to fit structural equation models as they would using the lavaan package.
The development version can be installed from GitHub using the remotes package:
remotes::install_github("TDJorgensen/lavaan.mi")
The top 4 lines of the table below indicate the lavaan.mi::lavaan.mi() function corresponds to the lavaan::lavaan() function, as do the wrappers cfa.mi(), sem.mi(), and growth.mi(), all of which return an object of class lavaan.mi.
lavaan Function |
lavaan.mi Function |
|---|---|
lavaan() |
lavaan.mi() |
cfa() |
cfa.mi() |
sem() |
sem.mi() |
growth() |
growth.mi() |
parameterEstimates() |
parameterEstimates.mi() |
standardizedSolution() |
standardizedSolution.mi() |
lavTestLRT() |
lavTestLRT.mi() |
lavTestWald() |
lavTestWald.mi() |
lavTestScore() |
lavTestScore.mi() |
modIndices() |
modIndices.mi() |
lavResiduals() |
lavResiduals.mi() |
The data= argument must be a list of data.frames rather than a single data.frame, and the specified lavaan::model.syntax will be applied to each data.frame in the list.
The lavaan.mi class inherits from class lavaanList (from the lavaan package), extending it with a few additional and customized slots (see class?lavaanList and class?lavaan.mi for details).
It is not wise to use "lazy loading" (i.e., calling lavaan.mi::lavaan.mi() without loading library(lavaan.mi) explicitly) because R may have trouble finding the correct methods in the package for applying generic functions (e.g., summary) to lavaan.mi-class objects. This occasionally happened in the semTools package as well. When the correct methods are not found, then the generic function will revert to the methods written for lavaanList-class objects (e.g., summary() will only have an est.ave column for the average estimate across data sets). In most cases (e.g., fitted(), anova(), residuals(), etc.), this will cause an error because few methods have been written for lavaanList-class objects.
Additional lavaan output can be obtained per imputation using the FUN= argument, which is applied to a lavaan-class object formed from the result of each imputation (prior to its being stored more succinctly in a lavaanList-class object). The last ?lavaan.mi help-page example demonstrates how to obtain and extract additional output.
Many remaining methods written for lavaan-class objects are also available for lavaan.mi-class objects (also see class?lavaan.mi for a list and descriptions of arguments):
show()summary()fitMeasures()anova(), which simply callslavTestLRT.mi()nobs()coef()vcov()fitted.values()and aliasfitted()residuals()and aliasresid(), which calllavResiduals.mi()
Many of the functions in the semTools package continue to be available for lavaan.mi-class objects (e.g., semTools::reliability()), and functions such as semTools::parcelAllocation() and semTools::plausibleValues() are enhanced by allowing their output to be analyzed using lavaan.mi().