How can I get the number of pixels with NA value in a raster that is cliped from a large raster by many polygons?

Question

I am new to this field. Currently I applied cloud mask to a raster image in R, and want to check how many pixels are masked out. But what I really need are only the images within some polygons (400+ of them), so I only want to get the number of pixels with no value within the polygons.

Here is what I have done:

library(raster)
library(rgdal)

##Read the raster files

tb = raster('D:/HLS/NDVI_Month_2018_TB.tif', band = 6)

##Read the polygon (400 polygons)

crops = readOGR('D:/HLS/shapefile/tb/tb.shp')

##reproject the vector

new_crops = spTransform(crops, crs(tb))

##Clip the raster with polygons

cliped = crop(tb, extent(new_crops))
output = mask(cliped, new_crops)

##Check the NA value

freq(output, value = NA)

However what I got from the freq() function seems to be all the pixels within the area (not only the polygons but the area from crop() function). the result of freq()

Any suggestion on how to get the NA value within the polygons would be very helpful! Thank you!

Answer 1

When asking an R question, please provide a minimal, self-contained. reproducible example. That is, do not refer to your actual data, but describe the problem in a more general way with data that come with R or that you create with code. Like this (taken mostly from ?raster::extract

Example raster and polygons

library(raster)
r <- raster(ncol=90, nrow=45)
values(r) <- 1:ncell(r)
r[seq(1,ncell(r),3)] <- NA

p1 <- rbind(c(-180,-20), c(-140,55), c(0, 0), c(-140,-60), c(-180,-20))
p2 <- rbind(c(10,0), c(140,60), c(160,0), c(140,-55), c(10,0))

pols <- spPolygons(p1, p2)

Solution 1

extract(r, pols, fun=function(i, ...) sum(is.na(i)))
#     [,1]
#[1,]  215
#[2,]  178

Solution 2

z <- rasterize(pols, r)
zonal(is.na(r), z, "sum")
#     zone sum
#[1,]    1 215
#[2,]    2 178