Various Errors in runMI: error in getMethod and not fitMeasures

[Angelika]

Dear forum,

I am quite new to lavaan and basically, I would like to do an EFA with the WLSMV estimator and multiple imputation via mice ('pmm') (and if I can figure it out apply rotation) by using semTools. 

Unfortunately, I get various errors and I cannot figure out the problem behind it. I installed the development version of semTools various times and first it went ok, but when I ran the code a second and third time, the errors occured and the summary output was different. Additionally, I would like to get the "pooled" standardized loadings and I could not figure out how to get them. I would be very grateful for any help!

I used the following code:

set.seed(20170110)
HSMiss <- HolzingerSwineford1939[,paste("x", 1:9, sep="")]
randomMiss <- rbinom(prod(dim(HSMiss)), 1, 0.1)
randomMiss <- matrix(as.logical(randomMiss), nrow=nrow(HSMiss))
HSMiss[randomMiss] <- NA

HS.model <- ' visual  =~ x1 + x2 + x3
textual =~ x4 + x5 + x6
speed   =~ x7 + x8 + x9 '

out1 <- runMI(HS.model,
              data=HSMiss,
              m = 5,
              miPackage="mice",
              fun="cfa",
              meanstructure = TRUE)

summary(out1)
lavaanList (0.6-11) -- based on 5 datasets (5 converged)

Latent Variables:
  est.ave
visual =~                
  x1                1.000
x2                0.572
x3                0.760
textual =~              
  x4                1.000
x5                1.157
x6                0.990
speed =~                
  x7                1.000
x8                1.116
x9                1.069

Covariances:
  est.ave
visual ~~                
  textual           0.394
speed             0.275
textual ~~              
  speed             0.176

Intercepts:
  est.ave
.x1                4.909
.x2                6.135
.x3                2.250
.x4                3.059
.x5                4.301
.x6                2.197
.x7                4.215
.x8                5.508
.x9                5.368
visual            0.000
textual           0.000
speed             0.000

Variances:
  est.ave
.x1                0.624
.x2                1.164
.x3                0.856
.x4                0.368
.x5                0.450
.x6                0.381
.x7                0.781
.x8                0.475
.x9                0.582
visual            0.754
textual           0.896
speed             0.376

fitMeasures(out1, "chisq")
Error in getMethod("coef", "lavaan.mi") :
   no method found for function 'coef'and Signatur lavaan.mi

fitMeasures(out1, fit.measures = ("all"), test = "D2", pool.robust=TRUE)
Error in getMethod("resid", "lavaan.mi") :
   no method found for function for 'resid' und Signatur lavaan.mi

>sessionInfo()

R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

Random number generation:
  RNG:     Mersenne-Twister
Normal:  Inversion
Sample:  Rounding

locale:
  [1] LC_COLLATE=German_Germany.utf8  LC_CTYPE=German_Germany.utf8  
[3] LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C                  
[5] LC_TIME=German_Germany.utf8    

attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
  [1] mice_3.14.0        semTools_0.5-5.926 lavaan_0.6-11    

loaded via a namespace (and not attached):
  [1] Rcpp_1.0.8.3        pillar_1.7.0        compiler_4.2.0    
[4] prettyunits_1.1.1   remotes_2.4.2       tools_4.2.0        
[7] testthat_3.1.4      pkgbuild_1.3.1      pkgload_1.2.4      
[10] tibble_3.1.6        memoise_2.0.1       lifecycle_1.0.1    
[13] nlme_3.1-157        lattice_0.20-45     pkgconfig_2.0.3    
[16] rlang_1.0.2         psych_2.2.3         cli_3.3.0          
[19] parallel_4.2.0      pbivnorm_0.6.0      fastmap_1.1.0      
[22] dplyr_1.0.9         withr_2.5.0         generics_0.1.2    
[25] vctrs_0.4.1         desc_1.4.1          fs_1.5.2          
[28] devtools_2.4.3      tidyselect_1.1.2    stats4_4.2.0      
[31] rprojroot_2.0.3     grid_4.2.0          glue_1.6.2        
[34] R6_2.5.1            processx_3.5.3      fansi_1.0.3        
[37] sessioninfo_1.2.2   tidyr_1.2.0         callr_3.7.0        
[40] purrr_0.3.4         magrittr_2.0.3      MASS_7.3-56        
[43] backports_1.4.1     ps_1.7.0            ellipsis_0.3.2    
[46] usethis_2.1.5       mnormt_2.0.2        numDeriv_2016.8-1.1
[49] utf8_1.2.2          broom_0.8.0         cachem_1.0.6      
[52] tmvnsim_1.0-2       crayon_1.5.1        brio_1.1.3

 

[Terrence Jorgensen]

summary(out1)

lavaanList (0.6-11) -- based on 5 datasets (5 converged)

This output indicates it only recognizes the object as a lavaanList (the class from which lavaan.mi inherits).  I have no idea what other packages conflict with semTools, preventing R from finding the correct method for the lavaan.mi object returned by runMI(), but this happens quite commonly.  When I run your syntax without any other packages loaded but semTools (which loads lavaan and its dependencies), I have no problem (using R 4.1.3 and the same versions of lavaan and semTools you have).

I am hoping to resolve this issue by creating a separate lavaan.mi package this week.

I would like to get the "pooled" standardized loadings

 

summary(out1, standardized = "std.all")

See class?lavaan.mi for information about other arguments and methods.

Terrence D. Jorgensen

Assistant Professor, Methods and Statistics

Research Institute for Child Development and Education, the University of Amsterdam

http://www.uva.nl/profile/t.d.jorgensen