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I have a large point dataset of about 5.3 million points. I would like to delete the "lonely" points using QGIS, for example all points with no neighbor within a 5 km radius. The extent of my point dataset limits some of the tools I guess...

I tried the Distance matrix en v.neighbours tools, but QGIS can't handle it and goes irresponsive... Is there another way to work around this problem for large datasets?

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    Make a dissolved Buffer and then delete those with area of a single buffer or less than something, in particular can be <= 5 km – Taras Nov 2 '19 at 21:33
  • Do you think this would work with such a large dataset? – user152287 Nov 2 '19 at 21:36
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    Irresponsive? Maybe you're just impatient :) Under Windows, open the Task Manager to see the QGIS CPU usage; that will inform you if QGIS is still chugging away at the task. – Stu Smith Nov 2 '19 at 22:30
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    As a rule, it's often better to keep features you don't want to delete during a copy than to delete features (and their indexes) directly.. – Vince Nov 3 '19 at 3:44
  • Quick possibility (haven't listed the commands so I wouldn't regard it as an answer) - buffer the points to 5km, then do a "count nodes in polygon" on the buffer. Ensure that there is some sort of primary key to link it back to the original layer. Link it back using a join, then delete any where the counted nodes =1 (as it will still contain the original node). – user25730 Nov 3 '19 at 22:20
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As I understand it, v.neighbors outputs a raster that can hold the number of points within a set distance from each cell, but does not identify whether or not the points themselves have any neighbours (see the manual page).

Anyway, instead you could try a clustering tool, for example DBSCAN clustering. Set the minimum cluster size to 2 and maximum distance to 5 km. Using the default settings, points without neighbours will then get CLUSTER_ID set to null in the attribute table. If you then perform a selection using the expression "CLUSTER_ID" != 'NULL' and save the selected features, you should be left with a layer holding all points with at least one neighbour within 5 km (and still have the original data, as per the comment by Vince)

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