I would like to calculate the overlap between the distributions of two sets of data (predator & prey). The prey set has got about 250 species, the predator set approximately 5000. For each species I have a shape file in .shp format. Has anyone got any suggestions how to calculate the overlap between the pairs?
In the past I've used the function 'pairwiseRangemaps' of the fuzzySim package, but it calculates the overlap between EACH pair (so > 27 million comparisons for a 5250 x 5250 matrix), making it impossible to run on any normal computer (even splitting the data set in dozens of smaller files and taking out the upper triangle would take weeks or months). I'm not interested in the overlap between prey species or between predator species, just between each prey and each predator.
Has anyone got a suggestion how to calculate this in R? I'm thinking of two vectors (one prey, one predator) and then calculating the overlap between just these.
Hi Chris Broeckhoven ,
Have you considered using the sf package? They have a function called st_intersection() that may be useful for you.
https://r-spatial.github.io/sf/reference/geos_binary_ops.html
If you can read in your .shp files with the package and format your information correctly, using that function should be able to retrieve intersecting areas.
You may want to set up some sort of apply / map function that can run through each combination you need, calculate the area / region, and return the data.
You may want to look at the answer found here for an additional example of its use: https://gis.stackexchange.com/a/230161
Hope this helps!
Please take a look at the "Overlapping" package in R:
https://cran.r-project.org/web/packages/overlapping/overlapping.pdf
Hi!! There are many ways to do that, if you do not have many polygons, you can do it with a simple clip and the calculation of the areas in attribute table. Then with the area of the complete and clipped polygon you can calculate the percentage of overlap. If you have many polygons, there are many functions to explore as those recommended the colleagues above. Depending on the software you use, you should google overlay polygons ArcGis, or QGIS, or R..
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