Imputation with R and MICE

Question

A short mice-related question as follows: when running simple mice imputation the function goes through well. But complete() function does not substitute my NA's at all. I guess it must be something wrong with my dataset but I can't see what. It is just a matrix as any other although with roughly equal number of rows and columns. Maybe this is the source of the problem. What should I look into?

Answer 1

My guess is that this arises from including the original dataset. You can specify that by either choosing the 0 dataset or complete(..., action="long", include=TRUE), see below example:

# Generate data
dat=data.frame(x1=c(21, 20, 31, 50), 
               x2=c(0, NA, 18, 3), 
               x3=c(0, 0, 54, 10))

library(mice)
# Do imputation
imp <- mice(dat, m=2)

Now this gives:

> # Look at the original dataset
> complete(imp, 0)
  x1 x2 x3
1 21  0  0
2 20 NA  0
3 31 18 54
4 50  3 10
> 
> # Get all the datasets
> complete(imp, action = "long", include = TRUE)
   .imp .id x1 x2 x3
1     0   1 21  0  0
2     0   2 20 NA  0
3     0   3 31 18 54
4     0   4 50  3 10
5     1   1 21  0  0
6     1   2 20  0  0
7     1   3 31 18 54
8     1   4 50  3 10
9     2   1 21  0  0
10    2   2 20 18  0
11    2   3 31 18 54
12    2   4 50  3 10