I'm using QGIS 2.18 Las Palmas, and I'm trying to build up a Distance Matrix of a series of points for a Mantel test. Specifically, I have a series of points and I want to calculate the distance of each of them to all the other ones. Now, when I use the 'Distance Matrix' tool in QGIS it gives me a three column table with all the distances, in this way:

InputID,C,254 TargetID,C,254 Distance,C,254 1 1 0 1 2 16.2788206 1 3 19.92485885 1 4 36.138622 1 5 69.23149572

This kind of output file contains all the information I need, but in the wrong format. What I'm looking for is a triangular distance matrix, as I need it as an input file for a Mantel test, like this one:

    1           2           3           4           5

1 0
2 16.2788206 0
3 19.92485885 23.84674 0
4 36.138622 29.4846735 55.68871 0
5 69.23149572 45.22356 66.254128 78.6542212 0

If it is possible to do this with QGIS, how do I do it?

2 Answers 2


If you don't mind a programmatic solution, you can do this easily in R with the dist function and the raster library. Example:

# make sure you have the raster library - you might also need rgdal
install.packages(c('raster', 'rgdal'))

# load the raster library

# define file path
shpFile <- "C:/path/to/shape/file.shp"

# load shapefile
shp <- shapefile(shpFile)

# convert SpatialPointsDataFrame to data.frame
shpDF <- as.data.frame(shp)

# get the distance matrix for coordinate sets
distMat <- dist(shpDF[,2:3])

# print results

          1         2         3
2 192801.33                    
3 261837.21 133653.67          
4 240095.52  60905.06  86724.96

By default it will return the euclidean distance between each point in the shapefile. This should be used for data in a projected coordinate system. If you are using a geographic coordinate system, then look into the distHaversine function in the geosphere library.

  • Thanks, I solved using a plugin on excel, but R would surely be fine! May 9, 2018 at 10:31

QGIS Distance matrix tool has an option to choose Output matrix type. You have probably chosen default Linear (N*k x 3) type.

There is another type, Standard (N x T), which returns a common style Distance matrix.

It is not a triangle (lower half) one, so you may need to edit it using Excel or text editor.

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