warning message/logged event of factor levels.

[Michael-Covell]

I'm getting a warning message/logged event that returns in the output field some of a factor variable's factor levels. I get this type of logged event whenever I include factor variables. What does this mean?

xyz$loggedEvents3.txt

[stefvanbuuren]

it	im	dep	meth	out
1	1	broilers_boosted	norm	"menu_aggMeat, menu_aggNA, menu_aggPizza"
1	2	broilers_boosted	norm	"menu_aggMeat, menu_aggNA, menu_aggPizza"
2	1	broilers_boosted	norm	"menu_aggMeat, menu_aggNA, menu_aggPizza"
2	2	broilers_boosted	norm	"menu_aggMeat, menu_aggNA, menu_aggPizza"
3	1	broilers_boosted	norm	"menu_aggMeat, menu_aggNA, menu_aggPizza"
3	2	broilers_boosted	norm	"menu_aggMeat, menu_aggNA, menu_aggPizza"
4	1	broilers_boosted	norm	"menu_aggMeat, menu_aggNA, menu_aggPizza"
4	2	broilers_boosted	norm	"menu_aggMeat, menu_aggNA, menu_aggPizza"
5	1	broilers_boosted	norm	"menu_aggMeat, menu_aggNA, menu_aggPizza"
5	2	broilers_boosted	norm	"menu_aggMeat, menu_aggNA, menu_aggPizza"

Variables menu_aggMeat, menu_aggNA and menu_aggPizza are removed from the imputation model for broilers_boosted because of linear dependencies among the predictors. Remove these variables using the predictorMatrix.

See https://stefvanbuuren.name/fimd/sec-toomany.html#finding-problems-loggedevents

[Michael-Covell]

Thanks, menu_aggMeat, menu_aggNA and menu_aggPizza are not variables though. They are levels of a categorical variable. Do you mean that these 3 levels are removed and the others (not listed) are used in imputations? If so, then removing variable menu_agg from the predictorMatrix could remove information from the model.

[stefvanbuuren]

Yes, mice removes the dummies variables for these categories.

There might be, for example, another categorical predictor with the same cases in its category. In that case, you may end up with two identical dummy variables. One needs to leave.