NTES is the salt of Railfanning. IRI is the sugar. - Kirti Solanki

As per the new TE.
1. There is a flag that a train has definitely passed a certain station, specifying the exact passing time/departure time.
2. There is a flag for the LAST station that was definitely passed by that train, and at what time. The last station passed could be either a halt or an intermediate station.
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The...
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above 2 pieces of info are not predictions, but seem to be noted down and recorded at the respective stations. This gives us information on the delay at the individual stations as well as the current delay as per the last crossing/halt. Also, if a train is being shown as beyond a station, then it means it has definitely crossed that station.
Let us say that the train is running 20 minutes late, and has definitely crossed Raja Ki Mandi. As per the 20 minute delay status, it should ALSO have crossed Agra Cantt. by now. But AGC has not flagged that train as "passed" yet. So the train will be shown before AGC, even though it should have reached AGC by now based on the 20 minute delay status.
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Also, the new TE makes some predictions. For example, if the train is running 20 minutes late, it will predict that GWL and future stations will be on time.
However, IRI takes a more conservative stance, and will continue to calculate based on the 20 minute delay status for all future stations. Since this info is just a prediction, users may make their own prediction that "the train will make up time".
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On the whole, it seems that since the train passing is definitively recorded and flagged, we won't have situations where we say: "Site says train has crossed, but it has not yet reached such and such station". Also, in cases of diversions or other mishaps, the TT will not wrongly show that the train has crossed all future stations based on the current delay status.
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Congratulations to IR on the implementation of this system, which is as good as it gets sans GPS.
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We shall observe and act on feedback, if any discrepancies are received, as far as this site is concerned.
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Thanks. Please do inform if you see discrepancies. There are a couple of bugs here and there in IRI which will be fixed within the next couple of days.