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What can you see if a user opts out of Google Analytics tracking using the browser plugin, can you see that they came, but not much else ie. they show up as a direct visitor, or do they not show up at all (although you can always see them in the server logs.)

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That data will not be reported to you (they do not show up at all).

In fact you can set this up programmatically as well - Tracking Basics. When you do execute the disable tracking command or if the visitor has a disabled Javascript or disabled tracking, then GA will not report that visit.

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