I have read a single-variable .nc file into R as a SpatRaster object using the excellent terra package, with the intention of fitting geostatistical models based on the cell centroids. For this I need to construct a dataframe with columns corresponding to "lon, lat, value" using data from the SpatRaster. This feels like a task which might have a standard solution, but I'm unfamiliar with R's spatial statistics ecosystem.
Any advice/suggestions would be much appreciated.
It's even more straightforward to use the function terra::as.data.frame(). See https://rspatial.github.io/terra/reference/as.data.frame.html
library(terra)
#> terra version 1.3.4
# make test raster with terra::rast()
a <- terra::rast(ncols = 10, nrows = 10,
xmin = -84, xmax = -83,
ymin = 42, ymax = 43)
# give it some values
values(a) <- 1:ncell(a)
plot(a)
a_df <- terra::as.data.frame(a, xy = TRUE, na.rm = FALSE)
# take special note of default values
head(a_df)
#> x y lyr.1
#> 1 -83.95 42.95 1
#> 2 -83.85 42.95 2
#> 3 -83.75 42.95 3
#> 4 -83.65 42.95 4
#> 5 -83.55 42.95 5
#> 6 -83.45 42.95 6
packageVersion("terra")
#> [1] '1.3.4'
sessionInfo()
#> R version 4.1.0 (2021-05-18)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur 10.16
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] terra_1.3-4
#>
#> loaded via a namespace (and not attached):
#> [1] Rcpp_1.0.7 codetools_0.2-18 lattice_0.20-44 digest_0.6.27
#> [5] withr_2.4.2 grid_4.1.0 magrittr_2.0.1 reprex_2.0.0
#> [9] evaluate_0.14 highr_0.9 rlang_0.4.11 stringi_1.7.3
#> [13] cli_3.0.1 fs_1.5.0 sp_1.4-5 raster_3.4-13
#> [17] rmarkdown_2.9 tools_4.1.0 stringr_1.4.0 glue_1.4.2
#> [21] xfun_0.24 yaml_2.2.1 compiler_4.1.0 htmltools_0.5.1.1
#> [25] knitr_1.33
Created on 2021-10-21 by the reprex package (v2.0.0)
library(terra)
#> Warning: package 'terra' was built under R version 4.0.5
#> terra version 1.3.22
r <- rast(ncol=10, nrow=10)
values(r) <- runif(ncell(r))
plot(r)
p <- terra::as.points(r)
df <- data.frame(values(p), geom(p))
head(df)
#> lyr.1 geom part x y hole
#> 1 0.9557333 1 1 -162 81 0
#> 2 0.2974196 2 1 -126 81 0
#> 3 0.9703617 3 1 -90 81 0
#> 4 0.3046196 4 1 -54 81 0
#> 5 0.7334711 5 1 -18 81 0
#> 6 0.8880635 6 1 18 81 0