The Times chose to investigate claims by transit agencies of high, on-time performance of LIRR, Metro-North, and NJ Transit by doing their own analysis and found major discrepancies. The article also indicates the infrastructure problems responsible.
The best performing trains in the NY metro area are Metro-North, serving Westchester and Connecticut, followed by the Long Island Rail Road. New Jersey? Forgetaboutit!
"Long Island Rail Road officials said the railroad had delays at rush hour in part because of the paucity of platforms at Penn Station, which must handle dozens of trains arriving and departing each hour.
Metro-North's" lines to Connecticut and Westchester, which have the best performance in the region, benefit from having spacious Grand Central Terminal to themselves. Still, trains on the New Haven line perform worse than the others, primarily because the cars are holdovers from the 1970s and some of the track uses overhead electrical wires that are nearly a century old and prone to damage.
New Jersey Transit's (trains to Penn Station, NY), which recorded the worst performance of the three railroads...must pass through a two-track tunnel under the Hudson River that is shared with Amtrak."
FULL STORY: 95% of Trains Are on Time? Riders Beg to Differ

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Urban Design for Planners 1: Software Tools
This six-course series explores essential urban design concepts using open source software and equips planners with the tools they need to participate fully in the urban design process.
Planning for Universal Design
Learn the tools for implementing Universal Design in planning regulations.
City of Albany
UCLA Lewis Center for Regional Policy Studies
Mpact (formerly Rail~Volution)
Chaddick Institute at DePaul University
City of Piedmont, CA
Great Falls Development Authority, Inc.
HUDs Office of Policy Development and Research