time and geographical subset of netcdf raster stack or raster brick using R - r

Question

For the following netcdf file with daily global sea surface temperatures for 2016, I'm trying to (i) subset temporally, (ii) subset geographically, (iii) then take long-term means for each pixel and create a basic plot.
Link to file: here
library(raster)
library(ncdf4)
open the netcdf after setting my working directory
nc_data <- nc_open('sst.day.mean.2016.v2.nc')
change the time variable so it's easy to interpret
time <- ncdf4::ncvar_get(nc_data, varid="time")
head(time)
change to dates that I can interpret
time_d <- as.Date(time, format="%j", origin=as.Date("1800-01-01"))
Now I'd like to subset only September 1 to October 15, but can't figure that out...
Following temporal subset, create raster brick (or stack) and geographical subset
b <- brick('sst.day.mean.2016.v2.nc') # I would change this name to my file with time subest
subset geographically
b <- crop(b, extent(144, 146, 14, 16))
Finally, I'd like to take the average for each pixel across all my days of data, assign this to a single raster, and make a simple plot...
Thanks for any help and guidance.

Answer 1

After b <- brick('sst.day.mean.2016.v2.nc'), we can type b to see information of the raster brick.
b
# class : RasterBrick
# dimensions : 720, 1440, 1036800, 366 (nrow, ncol, ncell, nlayers)
# resolution : 0.25, 0.25 (x, y)
# extent : 0, 360, -90, 90 (xmin, xmax, ymin, ymax)
# coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
# data source : C:\Users\basaw\Downloads\sst.day.mean.2016.v2.nc
# names : X2016.01.01, X2016.01.02, X2016.01.03, X2016.01.04, X2016.01.05, X2016.01.06, X2016.01.07, X2016.01.08, X2016.01.09, X2016.01.10, X2016.01.11, X2016.01.12, X2016.01.13, X2016.01.14, X2016.01.15, ...
# Date : 2016-01-01, 2016-12-31 (min, max)
# varname : sst
Notice that the Date slot has information from 2016-01-01 to 2016-12-31, which means the Z values already has date information and we can use that to subset the raster brick.
We can use the getZ function to access the values stored in the Z values. Type getZ(b) we can see a series of dates.
head(getZ(b))
# [1] "2016-01-01" "2016-01-02" "2016-01-03" "2016-01-04" "2016-01-05" "2016-01-06"
class(getZ(b))
# [1] "Date"
We can thus use the following code to subset the raster brick.
b2 <- b[[which(getZ(b) >= as.Date("2016-09-01") & getZ(b) <= as.Date("2016-10-15"))]]
We can then crop the image based on the code you provided.
b3 <- crop(b2, extent(144, 146, 14, 16))
To calculate the average, just use the mean function.
b4 <- mean(b3, na.rm = TRUE)
Finally, we can plot the average.
plot(b4)

Answer 2

The subsetting and averaging task is easy to do in CDO:
cdo timmean -sellonlatbox,lon1,lon2,lat1,lat2 -seldate,date1,date2 in.nc out.nc
where the lon1,lon2 etc define the lon-lat area to cut out and date1,date2 are the date bounds.
You can call this command directly from R using the climate operators package as per this question.
So for example, without the piping, on 3 lines would be in R:
cdo("seldate,date1,date2",in.fname,out1.fname,debug=TRUE)
cdo("sellonlatbox,lon1,lon2,lat1,lat", out1.fname,out2.fname,debug=TRUE)
cdo("timmean",out2.fname,out.fname,debug=TRUE)