error in densityplot mice- missing data example - r

Question

I have the following data:
dput(example)
structure(list(q1 = c(5, 22, 16, 24, 9, 20, 21, 16, 28, 28, 24,
25, 34, 22, 29, NA, 24, 13, 10, 17, 24, 21, 22, 35, 20, 25, 25,
23, 22, 20, 27, 22, 20, 23, 5, 21, 19, 17, 27, 20, 35, 35, 10,
16, 22, 34, 34, 23, 25, 23, 25, 30, 18, 21, 15, 23, 5, 35, 5,
30), q2 = c(5, 5, 24, 15, 5, 5, 26, 23, 24, 9, 24, 5, 15, 26,
30, 14, 14, 19, 11, 25, 20, 5, 14, 13, 11, 10, 13, 16, 16, 21,
10, 12, 20, 9, 15, 5, 13, 5, 30, 18, 12, 27, 10, 9, 20, 5, 9,
10, 11, 26, 22, 8, 6, 5, 15, 6, 5, 35, 10, 18), q3 = c(11, 22,
NA, 22, 6, 18, 30, 6, 26, NA, 17, 22, 33, 19, 22, 25, 23, 13,
13, 15, 16, 16, 23, 24, 6, 25, 27, 12, 25, 17, 28, 15, 20, 31,
5, 17, 17, 20, 24, 7, 35, 35, 10, 10, 20, 10, 31, 21, 16, 32,
25, 30, 10, 24, 15, 24, 5, 35, 9, 26), q4 = c(14, 15, 23, 21,
NA, 25, 30, 23, 28, 20, 25, 5, 35, 30, 19, 23, 30, 5, 23, 18,
30, 15, 30, 22, 8, 29, 35, 23, 23, 24, 25, 25, 20, 25, 5, 15,
34, 8, 32, 35, 35, 35, 10, 6, 21, 10, 24, 27, 10, 30, 35, 15,
6, 21, 15, 15, 5, 35, 19, 26), q5 = c(5, 18, 21, 19, 5, 6, 5,
29, 20, 23, 22, 5, 16, 22, 12, 13, 18, 5, 17, 15, 18, 16, 20,
8, 12, 19, 12, 23, 9, 16, 5, 29, 20, 5, 5, 5, 5, 5, 30, 22, 32,
35, 10, 13, 20, 13, 12, 16, 5, 24, 22, 17, 5, 20, 14, 5, 5, 35,
15, 16), q6 = c(15, 9, 25, 26, 6, 17, 28, 32, 26, 28, 24, 25,
11, 24, 31, 18, 19, 6, 20, 26, 29, 17, 21, 24, 7, 29, 17, 17,
14, 25, 24, 35, 24, 6, 16, 6, 9, 6, 38, 19, 30, 42, 12, 20, 27,
26, 25, 13, 9, 36, 27, 27, 7, 24, 22, 6, 16, 42, 14, 11)), class = "data.frame", row.names = c(NA,
-60L))
I then use mice:
*edit: forgot the complete line
library(mice)
imp <- mice(example,m=5,maxit=50,meth='pmm',seed=500)
example_i <- complete(imp,1)
But when trying to get a densityplot I get the following error:
densityplot(imp)
Error in str2lang(x) : <text>:2:0: unexpected end of input
1: ~
^
My questions are:
Is there something fundamentally wrong about my approach to impute missing data? (this is just a small example)
Am I using properly the MICE arguments?
What am I doing wrong with the density plot, as I have gotten it for all of the other scales I am working with?

Answer 1

Answer
You need to supply a formula to densityplot, otherwise it will plot all variables with > 2 missing values. Since you don't have any variables with 2 > missing values, and since densityplot doesn't expect that, it produces this cryptic error.
Example that works
example$q4[1:10] <- NA
imp <- mice(example, m = 5, maxit = 50, meth = "pmm", seed = 500)
densityplot(imp)
# equivalent: densityplot(imp, ~ q4)
Rationale
imp is of class mids, so you are calling densityplot.mids. Normally, densityplot.mids requires you to provide a formula (data argument), so that it knows which variables to plot (see ?densityplot.mids). If you want to plot q4, then the code is densityplot(imp, ~ q4).
Inside densityplot.mids, we see:
if (missing(data)) {
vnames <- vnames[!allfactors & x$nmis > 2 & x$nmis <
nrow(x$data) - 1]
formula <- as.formula(paste("~", paste(vnames,
collapse = "+", sep = ""), sep = ""))
}
If we use traceback() right after getting your error, then you will see that the last line above is the line that throws the error.
In the first line, you can see the condition xnmis > 2, which means that it will grab all the columns with more than 2 missing values. When no columns satisfy the conditions, then vnames will evaluate to character(0), and so the subsequent line yields as output ~, i.e. the code that you see in your error.
So, why does it give an error when there are too few missings? That's because densityplot plots a distribution, and plotting a distribution of 1 or 2 points is just not doable.
Suggestion
The package maintainers could improve the error by simply checking whether vnames has any content, and if not, they can throw an error that is informative. You may want to add this as an issue on Github if you think it is useful.