Quantcast
Channel: Active questions tagged r - Stack Overflow
Viewing all articles
Browse latest Browse all 201867

Getting estimated means after multiple imputation using the mitml, nlme & geepack R packages

$
0
0

I'm running multilevel multiple imputation through the package mitml (using the panimpute() function) and am fitting linear mixed models and marginal models through the packages nlme and geepack and the mitml:with() function.

I can get the estimates, p-values etc for those through the testEstimates() function but I'm also looking to get estimated means across my model predictors. I've tried the emmeans package, which I normally use for getting estimated means when running nlme & geepack without multiple imputation but doing so emmeans tell me "Can't handle an object of class “mitml.result”".

I'm wondering is there a way to get pooled estimated means from the multiple imputation analyses I've run?

The data frames I'm analyzing are longitudinal/repeated measures and in long format. In the linear mixed model I want to get the estimated means for a 2x2 interaction effect and in the marginal model I'm trying to get estimated means for the 6 levels of 'time' variable. The outcome in all models is continuous.

Here's my code

# mixed model
fml <- Dep + time ~ 1 + (1|id)
imp <- panImpute(data=Data, formula=fml, n.burn=50000, n.iter=5000, m=100, group = "treatment")
summary(imp)
plot(imp, trace="all")
implist <- mitmlComplete(imp, "all", force.list = TRUE)

fit <- with(implist, lme(Dep ~ time*treatment, random = ~ 1|id, method = "ML", na.action = na.exclude, control = list(opt = "optim")))
testEstimates(fit, var.comp = TRUE)
confint.mitml.testEstimates(testEstimates(fit, var.comp = TRUE))

# marginal model
fml <- Dep + time ~ 1 + (1|id)
imp <- panImpute(data=Data, formula=fml, n.burn=50000, n.iter=5000, m=100)
summary(imp)
plot(imp, trace="all")
implist <- mitmlComplete(imp, "all", force.list = TRUE)

fit <- with(implist, geeglm(Dep ~ time, id = id, corstr ="unstructured"))
testEstimates(fit, var.comp = TRUE)
confint.mitml.testEstimates(testEstimates(fit, var.comp = TRUE))

Viewing all articles
Browse latest Browse all 201867

Trending Articles



<script src="https://jsc.adskeeper.com/r/s/rssing.com.1596347.js" async> </script>