Whilst you are right, even fatal train accidents generally lead to far fewer casualties than fatal plane crashes, because a 'fatal plane crash' quite often means everybody in the plane dies, whereas a 'fatal train crash' may merely be 1-2 wagons being crashed, multiple deaths occuring, but still having a majority of the passengers surviving the crash.

Besides that, your amount of Amtrak accidents per 1m train miles also includes non-fatal accidents, and even accidents without any injuries.

Besides that, planes are a lot faster, so whilst the fatality rate per 'unit of distance of your choice' are far lower for planes (0.05 (plane) VS 0.6 deaths per 1 billion kilometers, thus making trains seem 12x more deadly), your odds of dying per 'amount of time spent traveling' are almost equal, but slightly higher for planes (30.8 (plane) VS 30 (train) deaths per 1 billiion hours spent traveling by mode of transport)

So yeah, it depends on your perspective, but looking at time spent air travel would be more dangerous than travelling by train - counteracted by the fact that people generally spend way more time in their lives commuting by train, rather than by plane

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