I’ve been encountering an issue while working with spatial data in R. Specifically, I’m getting an error when trying to calculate centroids for my geometries using the st_centroid function from the sf package. The error message is as follows:

Error in st_centroid.sfc(st_geometry(x)) :
not implemented for objects of class sfc_GEOMETRY
Caused by error in wk_handle.wk_wkb():
! Loop 7 is not valid: Edge 185 crosses edge 187
Backtrace:

1. shapefile_data %>% …
2. sf:::st_centroid.sfc(geometry)
3. s2::s2_centroid(x)
4. sf:::as_s2_geography.sfc(x)
5. sf:::st_as_s2.sfc(x, …, oriented = oriented)
6. s2:::as_s2_geography.WKB(st_as_binary(x), …, oriented = oriented)
7. s2::s2_geog_from_wkb(x, oriented = oriented, check = check)
8. wk:::wk_handle.wk_wkb(…)

I’ve tried using st_make_valid to ensure all geometries are valid, but it hasn’t resolved the issue. Here’s a simplified version of my code:

library(sf)
library(dplyr)

# Load shapefile data
shapefile_path <- "/path/to/shapefile.shp"
shapefile_data <- st_read(shapefile_path)

shapefile_data <- st_make_valid(shapefile_data)

invalid_geometries <- which(!st_is_valid(shapefile_data))
if (length(invalid_geometries) > 0) {
  shapefile_data <- st_make_valid(shapefile_data)
}

shapefile_data <- st_transform(shapefile_data, crs = "+proj=longlat +ellps=WGS84 +datum=WGS84")

shapefile_data <- shapefile_data %>%
  mutate(centroid = st_centroid(geometry),
         lon = st_coordinates(centroid)[, 1],
         lat = st_coordinates(centroid)[, 2])
And the map is look wired too:

Despite these steps, the error still persists. I’m not sure how to proceed to make sure each of polygon is close. I would greatly appreciate any suggestions or solutions to handle this issue.