simongrund1/mitml

Error when viewing output from testEstimates function

Closed this issue · 2 comments

L-J-Robinson commented

This may or may not be an error related to your package, but I receive the error: "Error in fmt[isLarge] <- sub(paste0(postfix, "$"), "e", fmt[isLarge]) : NAs are not allowed in subscripted assignments" when running the final line of code in this example to undertake mediation analysis on multiply imputed datasets. Are you able to clarify for me whether it is an issue with the package?

simongrund1 commented

I think the issue is that the extracted parameters (qhat) in this example include non-free parameters that shouldn't really be pooled. This produces NaN values that weren't formatted correctly, hence the error. I've uploaded a fix, so the example should run fine now.

However, notice that mitml supports lavaan natively since version 0.4-3, so you can use the simplified code below to run your model and pool the results. This automatically omits non-free parameters (unless they are user-defined).

library(mice)
library(miceadds)
library(mitml)

data <- airquality

# create missing data
data[80:81, 3] <- rep(NA, 2)
data[4:15, 3] <- rep(NA, 12)
data[1:5, 2] <- rep(NA, 5)

# remove categorical variables
data <- data[-c(5,6)]
summary(data)

# impute
imp <- mice(data, m = 5, maxit = 10, meth = 'pmm', seed = 500)
summary(imp)

# create list of imputed data sets
implist <- mids2mitml.list(imp)

# create mediation model
mediation <- ' 
# DV
Temp ~ cprime*Ozone + b*Solar.R

# mediator 
Solar.R ~ a*Ozone

# indirect effect
indirect := a*b
direct := cprime
total := direct + indirect
'

# fit model
mod2 <- with(implist, lavaan::sem(mediation), include.data = TRUE)

# pool results
res2 <- mitml::testEstimates(model = mod2)
res2

# Call:
# 
# mitml::testEstimates(model = mod2)
# 
# Final parameter estimates and inferences obtained from 5 imputed data sets.
# 
#                                      Estimate Std.Error   t.value        df   P(>|t|)       RIV       FMI 
# Temp~Ozone               (cprime)       0.188     0.024     7.683    24.974     0.000     0.667     0.443 
# Temp~Solar.R             (b)            0.011     0.008     1.309    32.891     0.200     0.535     0.385 
# Solar.R~Ozone            (a)            0.957     0.254     3.767    62.484     0.000     0.339     0.276 
# Temp~~Temp                             48.800     5.709     8.547  2006.556     0.000     0.047     0.046 
# Solar.R~~Solar.R                     7406.932   897.781     8.250   334.923     0.000     0.123     0.115 
# indirect:=a*b            (indirect)     0.010     0.008     1.257    51.989     0.215     0.384     0.304 
# direct:=cprime           (direct)       0.188     0.024     7.683    24.974     0.000     0.667     0.443 
# total:=direct+indirect   (total)        0.198     0.022     8.876    33.198     0.000     0.532     0.383 
# 
# Unadjusted hypothesis test as appropriate in larger samples.
L-J-Robinson commented