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Function for fast spatial thinning of geographic coordinates
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| thin_coordinates = function(coords, threshold){ | |
| # Function for faster spatial thinning of coordinates | |
| # coords: geographic coordinates in lon/lat format | |
| # threshold: minimum distance between points in meters | |
| coords_dist = geosphere::distm(coords, fun = distHaversine) # Great circle distance between points | |
| coords_dist[upper.tri(coords_dist, diag = T)] = NA # Triangular distance matrix | |
| coords_flagged = which(coords_dist < threshold, arr.ind=TRUE) # Two-column matrix of coordinate-pairs that are below threshold | |
| pts_remove = c() | |
| while(nrow(coords_flagged) > 0){ | |
| pts_count = sort(table(c(coords_flagged))) # Count number of occurrences of points in flagged coords | |
| pts_count_max = pts_count[pts_count == max(pts_count)] # Points with most neighbors below threshold | |
| pt_target = as.integer(sample(names(pts_count_max), 1)) # Choose one randomly | |
| pt_ind = which(coords_flagged[,1] == pt_target | coords_flagged[,2] == pt_target) # Find all pairs that involve target point | |
| coords_flagged = coords_flagged[-pt_ind,,drop = F] # Remove those pairs from coords_flagged | |
| pts_remove = c(pts_remove, pt_target) | |
| } | |
| return(coords[-pts_remove,]) | |
| } |
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