The way you've organized your data, you can create a calculated field called "Absent" with definition COUNT([User ID])-Count([UserID (Secondary)]), and then drag Calendar Date to Columns and Absent to Rows.
Null values in UserID (secondary) are automatically excluded, so you get what you want: people who have not logged on are counted as absent.
I assume you joined your data on UserID = UserID (Secondary) AND Calendar Date = Logon Date.
I'm attaching the workbook I produced. Hope this helps.
Book1 (2).twbx 15.8 KB