You can go your entire time in San Francisco without visiting Oakland, and all the cities on the Peninsula or North Bay you're likely to visit instead have much, much lower crime rates. I'm not sure why including Oakland is necessary to make an apples-to-apples comparison to Portland, which OP claims was safer than San Francisco.

Sure and you can live in Chicago without venturing to the south-side, most people who live on the west-side in LA only go to south LA for events and stay out of east LA.

My point is that SF is a bit odd in that it's a county and city that ends very abruptly, and Oakland is a 12 minute car or BART or 25 minute ferry ride from Embarcadero, thus the crime stats in the bay don't make much sense until you start averaging them across the metro area. It's not that Oakland is crazy violent, it's just that the a lot of the most violent areas of the metro fall in its borders, it's not that SF has the most vagrant or larcenous population, it's that it has a good climate for it: lots of the soft targets and toothless police force.