How to subset a SpatRaster by value in R

Question

How do I subset a SpatRaster from the R terra package by value? This is the raster:

> rh10
class       : SpatRaster 
dimensions  : 2732, 4379, 1  (nrow, ncol, nlyr)
resolution  : 1000, 1000  (x, y)
extent      : -1950750, 2428250, -1785500, 946500  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=lcc +lat_0=42.5 +lon_0=-100 +lat_1=25 +lat_2=60 +x_0=0 +y_0=0 +ellps=WGS84 +units=m +no_defs 
source      : memory 
name        :     vp_1 
min value   : 0.096915 
max value   : 1.291845 
time        : 2009-01-01 12:00:00 

> typeof(rh10)
[1] "S4"

The raster has relative humidity values in the cells. I inspected the raster.

> summary(rh10)
      vp_1      
 Min.   :0.106  
 1st Qu.:0.513  
 Median :0.594  
 Mean   :0.581  
 3rd Qu.:0.678  
 Max.   :1.283  
 NA's   :22329  
Warning message:
[summary] used a sample 

Because it's supposed to be relative humidity, I was expecting values less than 1. I guess greater than 1 is possible, but I'm trying to figure out which cells in the raster are over 1. I can't figure out how to subset the raster to begin with.

> length(rh10$vp_1 > 1.0)
[1] 1
> length(rh10 > 1.0)
[1] 1
> rh10[rh10[]> 1.0]
Error in rh10[rh10[] > 1] : object of type 'S4' is not subsettable

How should I go about figuring which are the uncommon cells? I'd like to see how many there are and where specifically they occur in the raster? Even my idea of subsetting is not correct, I'd like to know how I should properly subset the raster by cell values in addition to answering the related questions of how many and where.

Answer 1

With these example data

library(terra)
f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)
r
#class       : SpatRaster 
#dimensions  : 90, 95, 1  (nrow, ncol, nlyr)
#resolution  : 0.008333333, 0.008333333  (x, y)
#extent      : 5.741667, 6.533333, 49.44167, 50.19167  (xmin, xmax, ymin, ymax)
#coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#source      : elev.tif 
#name        : elevation 
#min value   :       141 
#max value   :       547 

Say you want to set values over 300 to 300

x <- clamp(r, upper=300)

Or to NA

x <- clamp(r, upper=300, value=FALSE)

You can also use ifel

y <- ifel(r > 300, 300, r)

Or classify

z <- classify(r, cbind(300, Inf, 300))

It is best to avoid approaches like the one below. They are inefficient and not safe with large datasets.

r[r > 300] <- NA

There is no specific method to subset multiple values (as suggested in a comment), but you could do

y <- subst(r, c(280, 284, 295, 300), c(280, 284, 295, 300), others=NA)
#or
y <- mask(r, r, c(280, 284, 295, 300), inverse=TRUE)

Or (a less favorably viewed) equivalent

y <- mask(r, r %in% c(280, 284, 295, 300), maskvalue=FALSE)

Answer 2

Either use only the > operator to make a boolean raster of the values over 1.

library(terra)

rast <- terra::rast("path/to/my.tif")

gt.1 <- rast > 1

plot(gt.1)

Or if you want to filter the true values, you can set the rest to NA:

rast <- terra::rast("path/to/my.tif")

rast[rast < 1] <- NA

plot(rast)