I allow students two absences before I begin deducting points from the roll call assignment category. Is it possible to input this setting/exception in Canvas or do I need to continue making this adjustment manually at the end of the semester?
Roll Call Attendance does not allow you to configure a number of free absences before withdrawing points. There are workarounds, but they will require manual intervention.
If you have a system that works, you can keep using it. If you're looking fora system, then some of the things you can do are mentioned in this lesson from the Canvas Instructor's Guide: How do I edit the Roll Call Attendance assignment? In particular, pay attention to the blue information box at the top.
You could create an extra assignment to give back the points missed, but that because Roll Call Attendance is percentage based, the calculations become messy until the end of the semester once the course is over. That leads to students having a lower grade than they actually have.
An alternative is to make Roll Call attendance not count towards the grade directly, but create a separate assignment that does count. The problem there is that their grade doesn't automatically reflect attendance and so their grade in Canvas is higher for those students with more than 2 absences and they see a penalty applied at the end. You could manually update the attendance grade periodically, but this takes more of your time.
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