The entire transit system will close for the weekend in preparation for the hurricane - no easy task. More difficult will be restarting the system as damage, included possible washed away Long Island Rail Road tracks on some branches, will have to be surveyed.
"The Metropolitan Transportation Authority said this process would take at least eight hours." The shut-down includes both Metro North and LIRR commuter trains.
"Restarting the system might take even longer.
About 200 subway trains are usually stored in outdoor yards, some of which, like those in the Rockaways, may flood. These trains will be stored underground in tunnels across the city, making it impossible for the agency to provide regular service on those routes
A major concern in the subway is flooding, particularly in open-trench tracks in Brooklyn and the low-lying stations in Lower Manhattan. Train signal systems can also short-circuit in a flood."
Meanwhile, the City itself is shutting down because on the hurricane.
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Irene: Metro-North and NJ Transit commuter rail fare the worst
Correction: clarification of update posted under appropriate Irene-transit article, Planetizen: Back In Service! Most NY Rail Lines Resume Operation
Irvin Dawid, Palo Alto, CA