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My suggestion is based on a method I apply to group smaller subcatchments into larger. There are no streams, thus 1st step to compute Euclidean minimum spanning tree: I guess it is some sort of optimisation already. Pick your sink and create directed graph. Picture below shows "Flow Accumulation" in links, i.e. count of nodes discharging into it: ...


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I found the answer to the original question, and will therefore answer it here, and make a new question. Turns out that the points that are omitted are the ones that match exactly , or that has 0 metres between them. New question will be about how I can make a distance matrix with both the nearest points with distance >1 m and the ones that match ...


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I'm in a similar boat as you and this site has been more than helpful: http://www.ing.unitn.it/~grass/docs/tutorial_64_en/htdocs/esercitazione/network_analysis/index.html It goes through the various v.net tools in GRASS - I'm not a coder or anything, but I've become pretty familiar with GRASS over the past few months with the help of this site.



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