Do the traffic graphs for a given project include the traffic data for the associated Pages site?
I.e. does https://github.com/blackberry/Alice/graphs/traffic
include traffic to http://github.com/blackberry/Alice
If not, is that information available anywhere?
Yep, it appears that Github counts your own visits to your repositories too. In this image, the "Traffic' page has 8 views from 1 visitor. Given that, the Traffic page is available only to the owner of the repository, you can deduct that Github counts your own visits too.
If you are logged in to GitHub then your own page views won't be counted. Visitors is the total visits to your repo. Unique visitors refers to the number of individual users who have visited your repository and these are only counted once, regardless of how many times they visit the repo.
In the top right corner of GitHub.com, click your profile photo, then click Your organizations. Click the name of your organization. Under your organization name, click Insights. Optionally, in the upper-right corner of the page, choose to view data for the last 1 week, 1 month, or 1 year.
No, if you want stats for your Pages site you need to use something like google analytics. GitHub doesn't touch the content of your Pages.
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