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 format

plot(data) # the big picture

data_masked <- mask(data,borders) %>% # mask the unwanted areas
  crop(borders) # crop to shape

plot(data_masked) # the small picture

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