R raster::calc calculating quantile with na.rm = FALSE - r

Question

I use raster::calc to compute quantile for each cell across different layers but I do not understand the behaviour when na.rm = FALSE, like in the example below.
Let's create a sample raster and remove 5 values from random cells.
library(raster)
r <- raster::raster(nrow = 2, ncol = 2)
r[] <- 1:4
s <- raster::stack(r, r*2, r * 3, r * 4, r * 5)
s[]
set.seed(1)
s[][sample(1:4, 1), sample(1:5, 1)] <- NA
s[][sample(1:4, 1), sample(1:5, 1)] <- NA
s[][sample(1:4, 1), sample(1:5, 1)] <- NA
s[][sample(1:4, 1), sample(1:5, 1)] <- NA
s[][sample(1:4, 1), sample(1:5, 1)] <- NA
s[]
If I remove NAs, the code below works!
fun <- function(x) {quantile(x, probs = 0.50, na.rm = TRUE)}
p <- raster::calc(s, fun)
p[]
However, if I want to exclude the cells where there is at least one NA, the code does not work!
fun <- function(x) {quantile(x, probs = 0.50, na.rm = FALSE)}
p <- raster::calc(s, fun)
I was expecting a vector containing 4 NAs, but the code above throws this error instead:
Error in .calcTest(x[1:5], fun, na.rm, forcefun, forceapply) :
cannot use this function
Could anybody help me understand why this happens? And what should I do to get the behaviour I was expecting?

Answer 1

I think the error message is straightforward, and it may not be related to the raster package. The basic idea is if you apply the quantile function to values with any NA, the quantile function returns an error message.
Considering the following example.
# Set na.rm = TRUE
quantile(c(1, NA, 3, 4), probs = 0.50, na.rm = TRUE)
50%
3
# Set na.rm = FALSE
quantile(c(1, NA, 3, 4), probs = 0.50, na.rm = FALSE)
Error in quantile.default(c(1, NA, 3, 4), probs = 0.5, na.rm = FALSE) :
missing values and NaN's not allowed if 'na.rm' is FALSE
When setting na.rm = FALSE the second example just returned an error. This is the same when applying quantile to raster. na.rm needs to be TRUE.
Update
To illustrate how to apply the quantile functions while some cells are NA, I modified the example dataset from the OP a little.
s <- raster::stack(r, r*2, r * 3, r * 4, r * 5)
s[]
set.seed(1)
s[][sample(1:4, 1), sample(1:5, 1)] <- NA
s[][sample(1:4, 1), sample(1:5, 1)] <- NA
s[][sample(1:4, 1), sample(1:5, 1)] <- NA
s[]
layer.1 layer.2 layer.3 layer.4 layer.5
[1,] 1 2 3 4 NA
[2,] 2 NA 6 8 10
[3,] 3 6 9 12 NA
[4,] 4 8 12 16 20
See the last row, which has no any NA.
We can then create a function. This function will return NA if there are any NA from any layers of a location. Otherwise, it will calculate the quantile.
# Design a function
quantile_fun <- function(x, probs = 0.50){
if (anyNA(x)){
return(NA)
} else {
return(quantile(x, probs = probs))
}
}
After that, we can apply this function using calc
p <- raster::calc(s, quantile_fun)
p[]
[1] NA NA NA 12