Error in missing value imputation using MICE package

Sonu Mishra Source

I have a huge data (4M x 17) that has missing values. Two columns are categorical, rest all are numerical. I want to use MICE package for missing value imputation. This is what I tried:

> testMice <- mice(myData[1:100000,]) # runs fine  
> testTot <- predict(testMice, myData)
Error in UseMethod("predict") : 
  no applicable method for 'predict' applied to an object of class "mids"

Running the imputation on whole dataset was computationally expensive, so I ran it on only the first 100K observations. Then I am trying to use the output to impute the whole data.

Is there anything wrong with my approach? If yes, what should I do to make it correct? If no, then why am I getting this error?



answered 2 years ago Hack-R #1

You don't use predict() with mice. It's not a model you're fitting per se. Your imputed results are already there for the 100,000 rows.

If you want data for all rows then you have to put all rows in mice. I wouldn't recommend it though, unless you set it up on a large cluster with dozens of CPU cores.

answered 2 years ago Alex W #2

Neither mice nor hmisc provide the parameter estimates from the imputation process. Both Amelia and imputeMulti do. In both cases, you can extract the parameter estimates and use them for imputing your other observations.

  • Amelia assumes your data are distributed as a multivariate normal (eg. X \sim N(\mu, \Sigma).
  • imputeMulti assumes that your data is distributed as a multivariate multinomial distribution. That is the complete cell counts are distributed (X \sim M(n,\theta)) where n is the number of observations.

Fitting can be done as follows, via example data. Examining parameter estimates is shown further below.

data(tract2221, package= "imputeMulti")
test_dat2 <- tract2221[, c("gender", "marital_status","edu_attain", "emp_status")]
# fitting
IM_EM <- multinomial_impute(test_dat2, "EM",conj_prior = "non.informative", verbose= TRUE)
amelia_EM <- amelia(test_dat2, m= 1, noms= c("gender", "marital_status","edu_attain", "emp_status"))
  • The parameter estimates from the amelia function are found in amelia_EM$mu and amelia_EM$theta.
  • The parameter estimates in imputeMulti are found in [email protected]_x_y and can be accessed via the get_parameters method.

imputeMulti has noticeably higher imputation accuracy for categorical data relative to either of the other 3 packages, though it only accepts multinomial (eg. factor) data.

All of this information is in the currently unpublished vignette for imputeMulti. The paper has been submitted to JSS and I am awaiting a response before adding the vignette to the package.

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