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"Are they used to calculate the geodesic distance?"
Yes. They are used for geodesic distance.
"The intra-zonal travel cost matrix should be appended to merge all OD matrices at three levels."
The data itself is too special. It requires other datasets to calculate compares to all other pairs. If you really want we can append it to the bottom of the file. And it will be kinda hard to locate,
What are the "X field in ZCTA file" and "Y field in ZCTA file" used for? Are they used to calculate the geodesic distance?
and what should I input for the "OD pair field name in the table"?
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