To "be in" is, figuratively speaking, to be present inside a building. This usually applies to a place of occupation or employment, but can be stretched without problems.
Conversely, to "not be in" is to be absent.
Example: "Is Doctor Adams in?" "No, he's not in today. Can I take a message?"
This means that Doctor Adams is not present at the health center for that day. Doctors at health centers tend to work on alternating schedules, so this does not mean anything bad has happened to Dr. Adams.