Convert sf to unmarked ppp

Question

I wish to convert an sf object to an unmarked ppp. (Conversion from sf to ppp is now supported, according to this post.)

library(sf)

#Initialise sf object
pp <- structure(list(X = c(959207.877070254, 959660.734838225, 951483.685462513,  951527.767554883, 958310.673042469, 950492.05212104, 959660.734838225,  959207.877070254, 960500.020456073, 959660.734838225), Y = c(1944457.42827898,  1955543.76027363, 1939982.16629396, 1940216.55143212, 1954704.68186897,  1951434.68524296, 1955543.76027363, 1944457.42827898, 1955292.64874361,  1955543.76027363), geometry = structure(list(structure(c(959207.877070254,  1944457.42827898), class = c("XY", "POINT", "sfg")), structure(c(959660.734838225,  1955543.76027363), class = c("XY", "POINT", "sfg")), structure(c(951483.685462513,  1939982.16629396), class = c("XY", "POINT", "sfg")), structure(c(951527.767554883,  1940216.55143212), class = c("XY", "POINT", "sfg")), structure(c(958310.673042469,  1954704.68186897), class = c("XY", "POINT", "sfg")), structure(c(950492.05212104,  1951434.68524296), class = c("XY", "POINT", "sfg")), structure(c(959660.734838225,  1955543.76027363), class = c("XY", "POINT", "sfg")), structure(c(959207.877070254,  1944457.42827898), class = c("XY", "POINT", "sfg")), structure(c(960500.020456073,  1955292.64874361), class = c("XY", "POINT", "sfg")), structure(c(959660.734838225,  1955543.76027363), class = c("XY", "POINT", "sfg"))), class = c("sfc_POINT",  "sfc"), precision = 0, bbox = structure(c(xmin = 950492.05212104,  ymin = 1939982.16629396, xmax = 960500.020456073, ymax = 1955543.76027363 ), class = "bbox"), crs = structure(list(input = "EPSG:5179",      wkt = "PROJCRS[\"Korea 2000 / Unified CS\",\n    BASEGEOGCRS[\"Korea 2000\",\n        DATUM[\"Geocentric datum of Korea\",\n            ELLIPSOID[\"GRS 1980\",6378137,298.257222101,\n                LENGTHUNIT[\"metre\",1]]],\n        PRIMEM[\"Greenwich\",0,\n            ANGLEUNIT[\"degree\",0.0174532925199433]],\n        ID[\"EPSG\",4737]],\n    CONVERSION[\"Korea Unified Belt\",\n        METHOD[\"Transverse Mercator\",\n            ID[\"EPSG\",9807]],\n        PARAMETER[\"Latitude of natural origin\",38,\n            ANGLEUNIT[\"degree\",0.0174532925199433],\n            ID[\"EPSG\",8801]],\n        PARAMETER[\"Longitude of natural origin\",127.5,\n            ANGLEUNIT[\"degree\",0.0174532925199433],\n            ID[\"EPSG\",8802]],\n        PARAMETER[\"Scale factor at natural origin\",0.9996,\n            SCALEUNIT[\"unity\",1],\n            ID[\"EPSG\",8805]],\n        PARAMETER[\"False easting\",1000000,\n            LENGTHUNIT[\"metre\",1],\n            ID[\"EPSG\",8806]],\n        PARAMETER[\"False northing\",2000000,\n            LENGTHUNIT[\"metre\",1],\n            ID[\"EPSG\",8807]]],\n    CS[Cartesian,2],\n        AXIS[\"northing (X)\",north,\n            ORDER[1],\n            LENGTHUNIT[\"metre\",1]],\n        AXIS[\"easting (Y)\",east,\n            ORDER[2],\n            LENGTHUNIT[\"metre\",1]],\n    USAGE[\n        SCOPE[\"unknown\"],\n        AREA[\"Korea, Republic of (South Korea)\"],\n        BBOX[28.6,122.71,40.27,134.28]],\n    ID[\"EPSG\",5179]]"), class = "crs"), n_empty = 0L)), row.names = c(4177L,  15721L, 21365L, 21973L, 24836L, 59359L, 66313L, 70379L, 83277L,  90828L), class = c("sf", "data.frame"), sf_column = "geometry", agr = structure(c(X = NA_integer_,  Y = NA_integer_), .Label = c("constant", "aggregate", "identity" ), class = "factor"))

library(spatstat)

#Convert to ppp format: method 1
pp1 <- as.ppp(pp)
#Warning message:
#In as.ppp.sf(pp) : only first attribute column is used for marks
pp1 <- unmark(pp1)

#Convert to ppp format: method 2
pp2 <- as.ppp(st_coordinates(pp), st_convex_hull(st_union(pp)))
#Warning message:
#data contain duplicated points

identical(pp1, pp2)
[1] FALSE

The first method requires marks and I haven't been able to find out how to turn that off (specifying marks=NULL does not work). I remove marks afterwards but that is a workaround.

The second method is probably wrong, considering the warning, although I based it on this solution. The 2 outputs are not identical.

Is any of these methods correct? Why does method 2 produce duplicated points? Is there a more straightforward method of conversion, with no workarounds?

Answer 1

I'm not sure that the following answer works for every version of spatstat, but I think that if you want to generate an unmarked ppp object, you should run

# packages
suppressPackageStartupMessages({
  library(sf)
  library(spatstat)
})

# Initialise sf object
pp <- structure(list(X = c(959207.877070254, 959660.734838225, 951483.685462513,  951527.767554883, 958310.673042469, 950492.05212104, 959660.734838225,  959207.877070254, 960500.020456073, 959660.734838225), Y = c(1944457.42827898,  1955543.76027363, 1939982.16629396, 1940216.55143212, 1954704.68186897,  1951434.68524296, 1955543.76027363, 1944457.42827898, 1955292.64874361,  1955543.76027363), geometry = structure(list(structure(c(959207.877070254,  1944457.42827898), class = c("XY", "POINT", "sfg")), structure(c(959660.734838225,  1955543.76027363), class = c("XY", "POINT", "sfg")), structure(c(951483.685462513,  1939982.16629396), class = c("XY", "POINT", "sfg")), structure(c(951527.767554883,  1940216.55143212), class = c("XY", "POINT", "sfg")), structure(c(958310.673042469,  1954704.68186897), class = c("XY", "POINT", "sfg")), structure(c(950492.05212104,  1951434.68524296), class = c("XY", "POINT", "sfg")), structure(c(959660.734838225,  1955543.76027363), class = c("XY", "POINT", "sfg")), structure(c(959207.877070254,  1944457.42827898), class = c("XY", "POINT", "sfg")), structure(c(960500.020456073,  1955292.64874361), class = c("XY", "POINT", "sfg")), structure(c(959660.734838225,  1955543.76027363), class = c("XY", "POINT", "sfg"))), class = c("sfc_POINT",  "sfc"), precision = 0, bbox = structure(c(xmin = 950492.05212104,  ymin = 1939982.16629396, xmax = 960500.020456073, ymax = 1955543.76027363 ), class = "bbox"), crs = structure(list(input = "EPSG:5179",      wkt = "PROJCRS[\"Korea 2000 / Unified CS\",\n    BASEGEOGCRS[\"Korea 2000\",\n        DATUM[\"Geocentric datum of Korea\",\n            ELLIPSOID[\"GRS 1980\",6378137,298.257222101,\n                LENGTHUNIT[\"metre\",1]]],\n        PRIMEM[\"Greenwich\",0,\n            ANGLEUNIT[\"degree\",0.0174532925199433]],\n        ID[\"EPSG\",4737]],\n    CONVERSION[\"Korea Unified Belt\",\n        METHOD[\"Transverse Mercator\",\n            ID[\"EPSG\",9807]],\n        PARAMETER[\"Latitude of natural origin\",38,\n            ANGLEUNIT[\"degree\",0.0174532925199433],\n            ID[\"EPSG\",8801]],\n        PARAMETER[\"Longitude of natural origin\",127.5,\n            ANGLEUNIT[\"degree\",0.0174532925199433],\n            ID[\"EPSG\",8802]],\n        PARAMETER[\"Scale factor at natural origin\",0.9996,\n            SCALEUNIT[\"unity\",1],\n            ID[\"EPSG\",8805]],\n        PARAMETER[\"False easting\",1000000,\n            LENGTHUNIT[\"metre\",1],\n            ID[\"EPSG\",8806]],\n        PARAMETER[\"False northing\",2000000,\n            LENGTHUNIT[\"metre\",1],\n            ID[\"EPSG\",8807]]],\n    CS[Cartesian,2],\n        AXIS[\"northing (X)\",north,\n            ORDER[1],\n            LENGTHUNIT[\"metre\",1]],\n        AXIS[\"easting (Y)\",east,\n            ORDER[2],\n            LENGTHUNIT[\"metre\",1]],\n    USAGE[\n        SCOPE[\"unknown\"],\n        AREA[\"Korea, Republic of (South Korea)\"],\n        BBOX[28.6,122.71,40.27,134.28]],\n    ID[\"EPSG\",5179]]"), class = "crs"), n_empty = 0L)), row.names = c(4177L,  15721L, 21365L, 21973L, 24836L, 59359L, 66313L, 70379L, 83277L,  90828L), class = c("sf", "data.frame"), sf_column = "geometry", agr = structure(c(X = NA_integer_,  Y = NA_integer_), .Label = c("constant", "aggregate", "identity" ), class = "factor"))

# Convert to ppp format: method 1
(pp1 <- as.ppp(st_geometry(pp)))
#> Planar point pattern: 10 points
#> window: rectangle = [950492.1, 960500] x [1939982.2, 1955543.8] units

^{Created on 2021-03-01 by the reprex package (v0.3.0)}

The two methods that you present are not equivalent because the as.ppp.sfc function defined in the sf package uses a rectangular owin object:

# packages
suppressPackageStartupMessages({
  library(sf)
  library(spatstat)
})

#Initialise sf object
pp <- structure(list(X = c(959207.877070254, 959660.734838225, 951483.685462513,  951527.767554883, 958310.673042469, 950492.05212104, 959660.734838225,  959207.877070254, 960500.020456073, 959660.734838225), Y = c(1944457.42827898,  1955543.76027363, 1939982.16629396, 1940216.55143212, 1954704.68186897,  1951434.68524296, 1955543.76027363, 1944457.42827898, 1955292.64874361,  1955543.76027363), geometry = structure(list(structure(c(959207.877070254,  1944457.42827898), class = c("XY", "POINT", "sfg")), structure(c(959660.734838225,  1955543.76027363), class = c("XY", "POINT", "sfg")), structure(c(951483.685462513,  1939982.16629396), class = c("XY", "POINT", "sfg")), structure(c(951527.767554883,  1940216.55143212), class = c("XY", "POINT", "sfg")), structure(c(958310.673042469,  1954704.68186897), class = c("XY", "POINT", "sfg")), structure(c(950492.05212104,  1951434.68524296), class = c("XY", "POINT", "sfg")), structure(c(959660.734838225,  1955543.76027363), class = c("XY", "POINT", "sfg")), structure(c(959207.877070254,  1944457.42827898), class = c("XY", "POINT", "sfg")), structure(c(960500.020456073,  1955292.64874361), class = c("XY", "POINT", "sfg")), structure(c(959660.734838225,  1955543.76027363), class = c("XY", "POINT", "sfg"))), class = c("sfc_POINT",  "sfc"), precision = 0, bbox = structure(c(xmin = 950492.05212104,  ymin = 1939982.16629396, xmax = 960500.020456073, ymax = 1955543.76027363 ), class = "bbox"), crs = structure(list(input = "EPSG:5179",      wkt = "PROJCRS[\"Korea 2000 / Unified CS\",\n    BASEGEOGCRS[\"Korea 2000\",\n        DATUM[\"Geocentric datum of Korea\",\n            ELLIPSOID[\"GRS 1980\",6378137,298.257222101,\n                LENGTHUNIT[\"metre\",1]]],\n        PRIMEM[\"Greenwich\",0,\n            ANGLEUNIT[\"degree\",0.0174532925199433]],\n        ID[\"EPSG\",4737]],\n    CONVERSION[\"Korea Unified Belt\",\n        METHOD[\"Transverse Mercator\",\n            ID[\"EPSG\",9807]],\n        PARAMETER[\"Latitude of natural origin\",38,\n            ANGLEUNIT[\"degree\",0.0174532925199433],\n            ID[\"EPSG\",8801]],\n        PARAMETER[\"Longitude of natural origin\",127.5,\n            ANGLEUNIT[\"degree\",0.0174532925199433],\n            ID[\"EPSG\",8802]],\n        PARAMETER[\"Scale factor at natural origin\",0.9996,\n            SCALEUNIT[\"unity\",1],\n            ID[\"EPSG\",8805]],\n        PARAMETER[\"False easting\",1000000,\n            LENGTHUNIT[\"metre\",1],\n            ID[\"EPSG\",8806]],\n        PARAMETER[\"False northing\",2000000,\n            LENGTHUNIT[\"metre\",1],\n            ID[\"EPSG\",8807]]],\n    CS[Cartesian,2],\n        AXIS[\"northing (X)\",north,\n            ORDER[1],\n            LENGTHUNIT[\"metre\",1]],\n        AXIS[\"easting (Y)\",east,\n            ORDER[2],\n            LENGTHUNIT[\"metre\",1]],\n    USAGE[\n        SCOPE[\"unknown\"],\n        AREA[\"Korea, Republic of (South Korea)\"],\n        BBOX[28.6,122.71,40.27,134.28]],\n    ID[\"EPSG\",5179]]"), class = "crs"), n_empty = 0L)), row.names = c(4177L,  15721L, 21365L, 21973L, 24836L, 59359L, 66313L, 70379L, 83277L,  90828L), class = c("sf", "data.frame"), sf_column = "geometry", agr = structure(c(X = NA_integer_,  Y = NA_integer_), .Label = c("constant", "aggregate", "identity" ), class = "factor"))

# Convert to ppp format: method 1
(pp1 <- as.ppp(st_geometry(pp)))
#> Planar point pattern: 10 points
#> window: rectangle = [950492.1, 960500] x [1939982.2, 1955543.8] units

# Method 2
(pp2 <- as.ppp(
  X = st_coordinates(pp), 
  W = as.owin(st_bbox(pp))
))
#> Warning: data contain duplicated points
#> Planar point pattern: 10 points
#> window: rectangle = [950492.1, 960500] x [1939982.2, 1955543.8] units

identical(pp1, pp2)
#> [1] TRUE

Moreover, the first method returns no warning message since the authors set check = FALSE.

anyDuplicated(pp1)
#> [1] TRUE

^{Created on 2021-03-01 by the reprex package (v0.3.0)}

See here for more details.

Answer 2

The two commands should give the same result. Getting different results is a temporary problem caused by recent changes to the spatstat package.

(These changes break some assumptions made by the packages sf, maptools and sp, causing the second command to fail to find the correct method for as.owin, so that it defaults to a rectangular window).

There's nothing wrong with the first approach. The data pp contain mark values, so as.ppp handles the marks, with a warning that it only used the first column. If you don't want the marks, just use unmark afterward.

The warning you get in the second approach tells you that some of the data points are at the same location. You don't get this warning in the first approach because the points at the same location have different mark values.

Warnings are not errors. Both these approaches are OK apart from the temporary problem with the dispatch of as.owin.

I suggest you use the first approach.

If you really need to use the second approach, you'll need to update all these packages, and in the case of spatstat, install the development version available at the github repository. If that still causes trouble, please wait a week or so until the completed package updates for all four packages are published on CRAN.