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Before computing transformation matrix
... it might be good to compute a trend surface of the square differences between the two sets of coordinates, at the sites of the good coordinates.
## compute square difference:
c$sqdiff <- with(c, sqrt((nx-x)^2 + (ny-y)^2))
##
library(gstat)
##
coordinates(c) <- c('nx', 'ny')
coordinates(d) <- c('x', 'y')
gridded(d) <- TRUE\
x <- gstat(sqdiff ~ 1, data=c, degree=2)
x.trend <- predict(x, newdata=d)
spplot(x.trend, "var1.pred")