On extracting values of a raster to points I find that I have several NA's, and rather than use a buffer and fun arguments of extract function, instead I'd like to extract the nearest non-NA Pixel to a point that overlaps NA.
I am using the basic extract function:
data.extr<-extract(loc.thr, data[,11:10])
Here's a solution without using the buffer. However, it calculates a distance map separately for each point in your dataset, so it might be ineffective if your dataset is large.
set.seed(2)
# create a 10x10 raster
r <- raster(ncol=10,nrow=10, xmn=0, xmx=10, ymn=0,ymx=10)
r[] <- 1:10
r[sample(1:ncell(r), size = 25)] <- NA
# plot the raster
plot(r, axes=F, box=F)
segments(x0 = 0, y0 = 0:10, x1 = 10, y1 = 0:10, lty=2)
segments(y0 = 0, x0 = 0:10, y1 = 10, x1 = 0:10, lty=2)
# create sample points and add them to the plot
xy = data.frame(x=runif(10,1,10), y=runif(10,1,10))
points(xy, pch=3)
text(x = xy$x, y = xy$y, labels = as.character(1:nrow(xy)), pos=4, cex=0.7, xpd=NA)
# use normal extract function to show that NAs are extracted for some points
extracted = extract(x = r, y = xy)
# then take the raster value with lowest distance to point AND non-NA value in the raster
sampled = apply(X = xy, MARGIN = 1, FUN = function(xy) r@data@values[which.min(replace(distanceFromPoints(r, xy), is.na(r), NA))])
# show output of both procedures
print(data.frame(xy, extracted, sampled))
# x y extracted sampled
#1 5.398959 6.644767 6 6
#2 2.343222 8.599861 NA 3
#3 4.213563 3.563835 5 5
#4 9.663796 7.005031 10 10
#5 2.191348 2.354228 NA 2
#6 1.093731 9.835551 2 2
#7 2.481780 3.673097 3 3
#8 8.291729 2.035757 9 9
#9 8.819749 2.468808 9 9
#10 5.628536 9.496376 6 6