Error in writeOGR when trying to export spatial polygons as shapefile in R

Question

I am trying to export polygons that i have created for home range data but when i go to export them get this error message:

Error in writeOGR(colkud95[1, ], ".", "colonyhomerange", driver = "ESRI Shapefile") : 
  Spatial Polygons objects should have valid ordering comments
use rgeos::createSPComment()

# main package for this analysis
library(adehabitatHR)  
library(sp)
library(rgdal)

tracks.utm <- dput(new("SpatialPointsDataFrame", data = structure(list(TripID = c(1, 
1, 1, 1, 1, 1, 1, 1, 1, 1), `Breeding stage` = c(1, 1, 1, 1, 
1, 1, 1, 1, 1, 1)), row.names = c(NA, -10L), class = c("tbl_df", 
"tbl", "data.frame")), coords.nrs = 1:2, coords = structure(c(174.78327, 
174.78326, 174.78332, 174.78323, 174.78325, 174.78277, 174.78238, 
174.78238, 174.78244, 174.78278, -41.09482, -41.09491, -41.09484, 
-41.09491, -41.09496, -41.09564, -41.09637, -41.09685, -41.09747, 
-41.09771), .Dim = c(10L, 2L), .Dimnames = list(NULL, c("x", 
"y"))), bbox = structure(c(174.78238, -41.09771, 174.78332, -41.09482
), .Dim = c(2L, 2L), .Dimnames = list(c("x", "y"), c("min", "max"
))), proj4string = new("CRS", 
projargs = "+proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null +wktext +no_defs")))

# Organising variable 1 refers to Trip ID
colkud<-kernelUD(tracks.utm[,1],h="href", 
                 grid=1000,same4all=T)

# Organising variable 2 refers to Breeding stage
colkudb<-kernelUD(tracks.utm[,2],h="href", 
                  grid=1000,same4all=T)

kernel.area(colkud,percent=50)
kernel.area(colkudb,percent=50)
kernel.area(colkud,percent=95)
kernel.area(colkudb,percent=95)

colkud95<- getverticeshr(colkud, percent=95)
colkud50<- getverticeshr(colkud, percent=50)
colkud95b<- getverticeshr(colkudb, percent=95)
colkud50b<- getverticeshr(colkudb, percent=50)

# This is where the error occurs
writeOGR(colkud95,".",layer="colkud95",driver="ESRI Shapefile")

I haven't had any luck searching for an answer to this, my aim is to create polygons for home range and then export them as a shapefile to be used in QGIS.

Answer 1

First, check that you have a valid object to export to a shapefile in the first place. Your example is not reproducible and returns an error:

The grid is too small to allow the estimation of home-range

As I recall, depending on how the functions are parametrized, it is possible for adehabitatHR::getverticeshr to return a SpatialPolygons object, which lacks attributes and do not reflect the output in the functions example. You can check output using class(colkud95). For writing a shapefile, you are after a SpatialPolygonsDataFrame, if the object is a SpatialPolygons type you will need to convert it to an exportable object.

If you have a spatial object with attributes, I highly recommend using sf, as opposed to rgdal, to write the shapefile. It is faster and the syntax is a bit easier. You will have to coerce your sp object to sf but, that is easily done on the fly using as. The function st_write parses the correct format based on the file extension.

sf::st_write(as(colkud95, "sf"), "out_shpfile.shp")

Please note that if I increase the grid size to 2500, I can get your example to run but, the largest volume contour I can produce is 75%, which I find odd because if it can create a KDE it should be able to return all of the volume contours for the density estimate. The output is, in fact, a SpatialPolygonsDataFrame object. So, you really need to look closely at your output(s) as there is likely something invalid.

colkud <- kernelUD(tracks.utm[,1],h="href", grid=2500, 
                   same4all=TRUE)
  kernel.area(colkud, percent=50)
  kernel.area(colkud, percent=75)
  colkud50<- getverticeshr(colkud, percent=50)
  colkud75 <- getverticeshr(colkud, percent=75)

Here is a workaround using the raster class and directly calculating the percent volume(s) using spatialEco::raster.vol. In this example, we use adehabitatHR::estUDm2spixdf to create a KDE raster of an individual animal, calculate the 75% volume contour then, plot the result to compare with the result from adehabitatHR::kernel.area and adehabitatHR::getverticeshr. You can convert each raster volume contour to a polygon and then export to shapefiles.

library(raster)
library(spatialEco)

colkud.kde <- raster(adehabitatHR::estUDm2spixdf(colkud))
  kde75 <- raster.vol(colkud.kde, p = 0.75)
  colkud75 <- getverticeshr(colkud, percent=75)
    plot(kde75)
      plot(colkud75, add=TRUE)