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I have a project with many click boxes and one drag and drop quiz question. In one section, I created a page with 4 click boxes, each one jumps to a different scenario. I only need the learner to go through one of the scenarios, so I set up a variable for each and conditional actions to navigate appropriately. I have ToC showing and this section doesn't get checked as complete and my course doesn't score properly.
1) how do I get that section to track correctly?
2) Is there a way to see a list of everything that's being included in a quiz?
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To have a proper score when using Branching, you'll have to check the Branch Aware option for the Quiz. It will limit navigation however, but the quizzing system variables will be dynamic: maximum score, obtained score and percentage, number of correct questions will adapt to the slides taken by the learner. More info in:
Branch Aware Quiz - Captivate blog
The Advanced Interaction panel (F9) is indispensable and too little known if you are working with quizzes (your last question): it will give an overview of all scored objects.
However the checkmarks in the TOC will only appear when that slide was visited. InfoSemantics has a widget that can take care of that, but I think it only works for SWF output. Is it a good idea to show the TOC for a project where user will only take one branch? You could always use a 'custom' TOC that is showing only the slides visited by the user.
As for Completion setup: are ou talking about SCORM? Cannot you base the completion criterion on the quiz?