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I am trying to download time series data (2017-01-01 to 2018-12-31) of different optical indices (e.g. NDVI) from the COPERNICUS/S2_SR dataset. The chart I plot only ever contains few values per year and if I export the .csv I seem to have the complete data from Oct 2018 onward but most of 2018 and 2017 is missing.

I was working with the same code end of April/beginning of May and at that time 2018 data was more or less complete.

https://code.earthengine.google.com/f871b1f713bb9ed25bb80f33d63f8b52

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    You're right about the missing data. It depends on the area you're working with. Some areas may have data back to March 2017, but some only have data from the beginning of 2019.
    – Kevin
    Jul 3, 2019 at 14:47

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July 2019, most part of the world (specially Americas) are more than 20 days delayed compared to raw dataset.

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See this for reporting missing images: https://developers.google.com/earth-engine/help_missing_images#sentinel

Earlier years didn't have full S2 SR coverage by the provider, though this might improve with ongoing production of Collection 1.

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