Cropping raster to minimum extent not working in R

Question

I am writing a script that will take any three rasters, and crop them to the minimum possible extent. All three rasters will have the same resolution and projection. However, cropping to the minimum extent does not change the extents for the three rasters. I've tried setExtent and the same thing happens. If anyone can give suggestions I would really appreciate it. Here is sample code:

 library(raster)

#Projection of all three rasters
newproj<- "+proj=utm +zone=4 +datum=WGS84 +units=m +no_defs +ellps=WGS84
+towgs84=0,0,0" 

#Create three rasters with varying extents
raster1p<- raster(crs = newproj)
extent(raster1p)<- c(531247, 691847, 7856684, 7987884) 
res(raster1p)<- c(100, 100)
values(raster1p)<- NA

raster2p<- raster(crs = newproj)
extent(raster2p)<- c(533550.8, 646550.8, 7881307, 7973807) 
res(raster2p)<- c(100, 100)
values(raster2p)<- NA

raster3p<- raster(crs = newproj)
extent(raster3p)<- c(525739, 689839, 7857305, 7996505) 
res(raster3p)<- c(100, 100)
values(raster3p)<- NA


#Find minimum extent
xmin1<- c(xmin(extent(raster1p)), xmin(extent(raster2p)), xmin(extent(raster3p)))
xmax1<- c(xmax(extent(raster1p)), xmax(extent(raster2p)), xmax(extent(raster3p)))
ymin1<- c(ymin(extent(raster1p)), ymin(extent(raster2p)), ymin(extent(raster3p)))
ymax1<- c(ymax(extent(raster1p)), ymax(extent(raster2p)), ymax(extent(raster3p)))
xmin_new<- min(xmin1)
xmax_new<- min(xmax1)
ymin_new<- min(ymin1)
ymax_new<- min(ymax1)
newextent=c(xmin_new, xmax_new, ymin_new, ymax_new)

#Crop rasters to minimum extent
crop(raster1p, newextent)
crop(raster2p, newextent)
crop(raster3p, newextent)

#Compare extents
extent_check<- c(extent(raster1p), extent(raster2p), extent(raster3p))

However, when I look at the extent_check to see if the extents now match, I see that the extents have not changed at all:

> extent_check
[[1]]
class       : Extent 
xmin        : 531247 
xmax        : 691847 
ymin        : 7856684 
ymax        : 7987884 

[[2]]
class       : Extent 
xmin        : 533550.8 
xmax        : 646550.8 
ymin        : 7881307 
ymax        : 7973807 

[[3]]
class       : Extent 
xmin        : 525739 
xmax        : 689839 
ymin        : 7857305 
ymax        : 7996505 

Any idea what I could be doing wrong? Thank you for your time

Answer 1

I think it is not so much about doing something wrong, but rater a misconception (although there is a mistake in your code).

Example data

library(raster)  
prj <- "+proj=utm +zone=4 +datum=WGS84"
r1 <- raster(res=100, ext=extent(c(531247, 691847, 7856684, 7987884)), crs=prj, vals=NA)
r2 <- raster(res=100, ext=extent(c(533550.8, 646550.8, 7881307, 7973807)), crs=prj, vals=NA)
r3 <- raster(res=100, ext=extent(c(525739, 689839, 7857305, 7996505)), crs=prj, vals=NA)

Find the "minimum extent"

e <- intersect(intersect(extent(r1), extent(r2)), extent(r3))

Note that the result is different from yours because you use

xmin_new <- min(xmin1) and ymin_new <- min(ymin1)

Where it should be

xmin_new <- max(xmin1) and ymin_new <- max(ymin1)

Now crop

r1e <- crop(r1, e)
r2e <- crop(r2, e)
r3e <- crop(r3, e)

Inspect the resulting extents

t(sapply(c(r1e, r2e, r3e), function(i) as.vector(extent(i))))
#         [,1]     [,2]    [,3]    [,4]
#[1,] 533547.0 646547.0 7881284 7973784
#[2,] 533550.8 646550.8 7881307 7973807
#[3,] 533539.0 646539.0 7881305 7973805

They are not exactly the same, because that is not possible because the rasters do not align. Their "origins" are different

t(sapply(c(r1e, r2e, r3e), origin))
#      [,1] [,2]
#[1,]  47.0  -16
#[2,] -49.2    7
#[3,]  39.0    5

To make them align, you would need to do something like this

r1e <- crop(r1, e)
r2e <- resample(r2, r1e)
r3e <- resample(r3, r1e)

t(sapply(c(r1e, r2e, r3e), function(i) as.vector(extent(i))))
#       [,1]   [,2]    [,3]    [,4]
#[1,] 533547 646547 7881284 7973784
#[2,] 533547 646547 7881284 7973784
#[3,] 533547 646547 7881284 7973784