When it comes to measuring the Long Island Rail Road’s on-time performance, it’s all about the destination, and not the journey.

The LIRR’s practice of only considering the time a train arrives at its final stop is one reason commuters’ experiences don’t always match the agency’s on-time statistics, critics said.

Peter Haynes, a former LIRR systems project specialist who now leads the LIRR Commuters Campaign, an advocacy group, has long questioned the system, which deems a train on time if it ends its run within five minutes and 59 seconds of its published schedule, even if it arrives six minutes or more late at every prior stop on its route.

That could result in artificially inflated on-time performance, Haynes said.

“For the average commuter taking five trips in and five trips out, 90 percent performance means they’re only late one time a week . . . 95 percent would be one trip every two weeks,” Haynes said. “I just don’t know anybody who experiences what the railroad says they’re doing.”

Haynes has called on the LIRR to implement an on-time performance metric that would report “passenger minutes” — measuring the number of riders on a train and the number of minutes that train is late at each stop. The LIRR Commuter Council has also called for a “passenger-based on-time metric” in the past.

LIRR President Patrick Nowakowski said the problem with that formula is that the LIRR’s numbers would always be among the worst of any railroad because it has the highest ridership. He added that the LIRR does keep data on trains’ arrival times at all stations, using “timing points” in place throughout the system, and can use that information to “evaluate the pattern of a particular train over time.”

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Randy Clarke, assistant vice president of operations for the American Public Transportation Association, a nonprofit group, said the LIRR’s method of measuring punctuality is widely used, and while imperfect, provides valuable data, especially because most commuters travel to the same destination every morning.

“It’s kind of like an airline. . . . If you got delayed taking off at LAX [Los Angeles International Airport] but you made it to LaGuardia on time, do you care that you got delayed at LAX? Probably not,” Clarke said. Haynes and Clarke agreed that the quality of data available to railroads, and their customers, will improve with the installation of federally -mandated Positive Train Control technology, which uses GPS systems on trains and radio transmitters along tracks to automatically prevent train collisions. The technology will also provide real-time data on every train’s location at all times.

The LIRR has said it expects to have the technology in place by the end of 2018.