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Abraham, Alan,
On a close approach to earth, or any large solar body, it is no longer a point source. There are gravity influence maps that show irregularities in the force of gravity due to material density changes. Do any of the studies of a flyby anomaly examine the flyby path in relationship to these known variations in the force of gravity?
Many papers that are attempting to describe some spacecraft anomaly do not identify all the parameters about the spacecraft or the spacecraft/object relative dynamics.
One of the parameters that should be identified is whether the spacecraft is or is not spin stabilized, and if spin stabilized, the angular direction of the spin and its angular rate. What is this spin direction relative to the objects rotation? Secondly, on a close encounter, is the spacecraft going in the same direction of the objects rotation or opposite to it? And as Alan pointed out, what angle did the spacecraft pass by the object relative to the objects equator? This also has implications on the force of gravity, as it will be influenced if the object has an equatorial bulge.
Can I assume a flyby anomaly study accounts for the position of any nearby object(s), such as a moon?