How to crop gridded data with shapefile

[jlacko]

I believe you are looking for a combination of raster::mask() and possibly raster::crop().

Have a look at this answer from a while back, it seems the issue is similar.

temperature maps in R

I can not reproduce your code, but allow me to illustrate the approach on a similar use case; I have used temperature data from Copernicus and cropped it to shape of the Czech Republic from GADM. This approach requires only two packages (raster and sf) + tidyverse, just because :)) It uses two steps: remove the extra data points via raster::mask() crop the file down to size via raster::crop() library(tidyverse) # because tidyverse library(raster) # raster spatial data processing library(sf) # vector spatial data processing data <- raster("./src/tg_0.25deg_day_2019_grid_ensmean.nc") # your ncdf file borders <- readRDS("./src/gadm36_CZE_0_sf.rds") # country borders in sf …

Also note that you will be better off with reading the country polygon in with sf::st_read(), as the {sf} package format is newer and IMHO more user friendly than the older {sp}.