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Are there specific data sets about movement of commuters (in cars, trains, buses, etc.) in major US cities? Ideally the data would include numbers of commuters, have detailed location information, and across time (throughout the day, and over weeks/months).

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There's a related question. This answer may be helpful here too Nick.

You can find out information about Americans' commuting habits in relation to specific geographic areas through the U.S. Census American Community Survey. Access to the data is available. For example, if you are looking for how people in Los Angeles County get to work, you can find the answer through the Easy Stats online.

L.A. County Transportation Choices

The longitude and latitude of all U.S. boundaries (from school districts to counties to roads) can be found via TIGER files (topographically integrated geographic encoding and referencing).

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Residence to Workplace Commute Patterns, RPA Counties has some of what you want. not sure about all, i'm not really familiar with it
http://catalog.opendata.city/dataset/residence-to-workplace-commute-patterns-rpa-counties

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Check this dataset: http://data.mytransit.nyc.s3.amazonaws.com/README.HTML. This dataset includes the GTFS schedule data and the historical data for bus system in NYC.

The historical data can be found in the directory named bus_time. It records all the MTA's operated buses' location around every 1 minute and 30 seconds every day.

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