I'm reading in polygons from ArcMap 10.6.1 into R 3.5.1 using raster::shapefile. I sometimes get the following warning:

Warning message: In rgdal::readOGR(dirname(x), fn, stringsAsFactors = stringsAsFactors, : Z-dimension discarded

I'm confused because I'm not even employing rgdal to read in. Area calculations using the resulting SpatialPolygonsDataFrame are incorrect, and I think this error reading in is why. It's projection is

CRS arguments: +proj=utm +zone=12 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0

I've tried readOGR and get the same warning. I am able to read in some other shape files in the same way with the same projection, and they work just fine. Why do I get this warning and how can I remedy it?

Edit: reading in using sp::st_read does not return an issue re: Z-dimensions until I try to convert. However, I need a SpatialPolygonsDataFrame to do what I need to do but this is how the file reads in:

Simple feature collection with 1 feature and 5 fields 
geometry type: MULTIPOLYGON 
dimension:  XYZ 
bbox:    xmin: 365305.5 ymin:5809943 xmax: 476043.9 ymax: 5891941 
epsg (SRID):    32612
proj4string:    +proj=utm +zone=12 +datum=WGS84 +units=m +no_defs

How do I convert to a spdf? df::as_Spatial return this error:

Error in StopZ(zm) : sp supports Z dimension only for POINT and MULTIPOINT. use drop_zm(...) to coerce to XY dimensions

  • Did you get this same warning when using sf::st_read()? Dec 4, 2018 at 20:56
  • No, I don't get the same warning, but I am now struggling with how to convert to a SpatialPointsDataFrame after reading in that way, to have all the same info as I would have using shapefile or readOGR. An answer addressing that would be awesome, and I could edit my question
    – Emily
    Dec 4, 2018 at 21:04
  • 1
    What do you mean by same information? Reading in with st_write() preserves all of the info of your file including projection, number of objects, and attribute data. Maybe edit the question for clarification. Dec 4, 2018 at 21:05
  • Why do you need a spatial polygon dataframe, specifically? What are you trying to do? Your simple features object is the same thing but wrapped in one dataframe-like object. Dec 4, 2018 at 21:26
  • Intersect with another spdf and calculate area, perimeter etc within features of that spdf. When I try to intersect I get "no method for coercing this S4 class to a vector"
    – Emily
    Dec 4, 2018 at 21:28

2 Answers 2


My understanding is that you are seeking to get the intersection of two layers and write that out to a shapefile. Using simple features in R it would look something like this:

# this is assuming your projections are matched

poly_file1 <- st_read("path_to_first_file.shp")
poly_file2 <- st_read("path_to_second_file.shp")

#get the intersection

poly_intersect <- st_intersection(poly_file1, poly_file2)

#write to file
st_write(poly_intersect, "path_to_new_file.shp")

You could add one sentence

x1<-readOGR("**/apple.shp") #读取shp格式文件


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