Aggregate nc file using specific condition in R

Question

I need your help again. I have.nc file, metadata: File minty.nc (NC_FORMAT_64BIT):

 1 variables (excluding dimension variables):
    short mn2t[longitude,latitude,time]   
        scale_factor: 0.000940940342005054
        add_offset: 259.294916797895
        _FillValue: -32767
        missing_value: -32767
        units: K
        long_name: Minimum temperature at 2 metres since previous post-processing

 3 dimensions:
    longitude  Size:57
        units: degrees_east
        long_name: longitude
    latitude  Size:49
        units: degrees_north
        long_name: latitude
    time  Size:90240
        units: hours since 1900-01-01 00:00:00.0
        long_name: time
        calendar: gregorian

2 global attributes:
    Conventions: CF-1.6
    

I have a code, which works well with smaller.nc files:

 library(raster)
 library(rgdal)
 library(ggplot2)
 nc_data = nc_open('file.nc')
 lon = ncvar_get(nc_data, "longitude")
 lat = ncvar_get(nc_data, "latitude", verbose = F)
 t = ncvar_get(nc_data, "time")
 head(lon)
 head(t)
 head(lat)
 mint.array = ncvar_get(nc_data, "mn2t")
 dim(mint.array)
 fillvalue = ncatt_get(nc_data, "mn2t", "_FillValue")
 fillvalue
 mint.array[mint.array == fillvalue$value] <- NA
 r_brick <- brick(mint.array, xmn=min(lat), xmx=max(lat), ymn=min(lon), ymx=max(lon), crs=CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs+ towgs84=0,0,0"))
 r_brick = flip(t(r_brick), direction = 'y')

Because of the large file size, I got an error: "cannot allocate vector of size 1.4 Mb" I also used gc() to clear unused memory. It didn't help. I do not need all the data in my file.nc. In this case, I need somehow to aggregate this. For my further calculations, I need only daily minima. In this case, for df I used: df(ff) <- aggregate(df, list(rep(1:(nrow(df)%(%n+1), each=24, len=nrow(df))), min)

Unfortunately, I find it difficult to adapt this code for.nc file. Maybe someone could help me. Thank you in advance!

Answer 1

To avoid memory problems, you can do this instead:

library(raster)
r_brick <- brick('file.nc', "mn2t")

It also prevents mistakes. For example, in your code, this is wrong in two ways:

xmn=min(lat), xmx=max(lat), ymn=min(lon), ymx=max(lon)

because x should be lon and y should be lat and because the ncdf coordinates refer to the centers of the cells, whereas xmn , xmx , ymn , and ymx refer to the borders.

You can also use the modern equivalent

library(terra)
r <- rast('file.nc')