You go by the medical way of counting. I even have a book that says things like (in big letters) Sixth week and then in little letters (Fourth week since conception). All the milestones for a developing embryo are listed using the medical way of timing a pregnancy.
I just checked my books, and Babycenter, and Parents.com, and they all use the medical way of counting. So at week 1 they just say things like "Something exciting is about to happen!" and stuff like that, since obviously you haven't even conceived yet at week 1 counted the medical way. But again, it may depend on the book. The way you can tell is by looking at week 1 and week 2. If the baby isn't even a cluster of cells yet, they are timing the pregnancy the medical way, by the first day of your last period.
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