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Using QGIS3.10, I have tried Distance Matrix and NNJoin (distance results 0 - 10.32 for both, likely in degrees). I have 93 points of 2 types in one shapefile. I have the same distance issue if the points are in 2 files. UTM projections are problematic in this region because the study area spans at least 2 and often 3 UTM zones (e.g., x: -63 to -78). The CRS is WGS84 (EPSG: 4326). The points (caribou locations) fall into 3 clusters 150-300 km apart, but one point is in a central position between the 3 clusters and it is about 154 km from its nearest neighbor (i.e., QGIS's Measure Line tool readily provides km for WGS84).

How could I resolve this to get nearest neighbor distances in km?

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One quick way would be to choose North Pole Azimuthal Equidistant (EPSG:102016), but it may not return satisfying result if your study area is not close enough to the north pole.

Second option: Create custom projection by modifying the above mentioned EPSG:102016. For instance, if your central position is located at (latitude: 86, longitude: 135), then the proj4 string is +proj=aeqd +lat_0=86 +lon_0=135 +x_0=0 +y_0=0 +a=6371000 +b=6371000 +units=m +no_defs.

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On a separate note, working on proj4 string on QGIS custom projection has been tricky recently- due to ongoing PROJ improvements. It seems I had luck with QGIS 3.12.3; please carefully test it in your environment.

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  • Thanks for this suggestion. It led me to search for polar projections, then to projectionwizard.org, that provides PROJ WKT code. I entered the area extent as N: 68.1, S: 61.75, E: -61.1, W: -78.4. Equal-area option provided very long codes with unrecognizable names. The Conformal option provided: Lambert conformal conic (most realistic landform shapes, but maybe not for NN distances?), and PROJ WKT code: +proj=lcc +lon_0=-69.75 +lat_1=62.8083333 +lat_2=67.0416667 +lat_0=64.925 +datum=WGS84 +units=m +no_defs (to be continued)
    – Mike
    Commented Jun 22, 2020 at 5:49
  • Continuation ... Equidistant option provided: "Oblique azimuthal equidistant PROJ WKT - distance correct along any line passing through the center of the map (i.e., great circle)", and PROJ WKT code: +proj=aeqd +lon_0=-69.75 +lat_0=64.925 +datum=WGS84 +units=m +no_defs The code looks very similar to your suggestion, with the center corrected. How might it compare to the Conformal option?
    – Mike
    Commented Jun 22, 2020 at 5:54
  • @Mike It's a vast area, and a little bit far from the north pole. So please forget the suggested aeqd option, which is valid only for distances which involves the center point. I like your Lambert conformal conic option which two standard parallels are close to NS extents of your working area.
    – Kazuhito
    Commented Jun 22, 2020 at 9:10
  • @Kazukito. Thanks for your confirmation. It agrees with a technical report DOI: 10.13140/RG.2.1.2809.2240 that I just found, which recommended Azimuthal Polar Equidistant and AP Stereographic for the high Arctic (71-90 N), and Lambert Conic Conformal and LC Equidistant for the sub-Arctic (50-75 N).
    – Mike
    Commented Jun 23, 2020 at 21:15

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