For the month of May on #reddit, with over 100 million comments, moderators removed ~2.07% of all user comments. However, users themselves removed ~3.56% of their own comments.
Reddit users for the month of May, 2018 removed more of their own comments than moderators.
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I am using this based off my RC_2018-05.xz Reddit comment dump. When a user removes their comment, the metadata remains but the author and body fields become [deleted]. When a mod removes a comment, the body field is [removed] and the author field is still [deleted].
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Does this 2.07% include comments removed by Automod and other bots?
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Yes. Since moderators put rules in for automod and moderators give bots access to their subreddits, I considered automod removed content under the umbrella of moderator removed content.