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I recommend using OGR because it will leverage a Shapefile Spatial Index, either .sbn/.sbx or .qix. Iterating thru each group, you can first perform a faster Overlap test between BoundingBox geometries (lyr.SetSpatialFilterRect). When true, test for overlap on the real geometries. Another option, Spatialite is easy to setup and offers PostGIS like functions ...


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I have done something similar for possible habitats analysis. For each shapefile in the analysis (criteria types for habitats), I created a field (integer) called weighting and assigned it the value 1. Then I used the union tool to union all the layers. In the newly created union shapefile, I created a tally field and tallied up all the weighting fields to ...


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Try using this suggestion and this tutorial. Vector -> Analysis -> Distance Matrix



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