I think you can use the sf package to read those data
url <- "https://zenodo.org/record/3386198/files/pc_to_resilience.gpkg?download=1"
temp_file <- tempfile(fileext = ".gpkg")
download.file(url, destfile = temp_file, mode = "wb")
library(sf)
data <- st_read(temp_file)
Several resources to help
There also a book on sf https://keen-swartz-3146c4.netlify.com/intro.html#reading
and another one on geocomputation