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R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> suppressPackageStartupMessages(library(spatstat))
> suppressPackageStartupMessages(library(sf))
>
> data(chicago)
> st_as_sf(chicago)
Simple feature collection with 620 features and 4 fields
geometry type: GEOMETRY
dimension: XY
bbox: xmin: 0.3893523 ymin: 153.1034 xmax: 1281.986 ymax: 1276.56
CRS: NA
First 10 features:
label seg tp marks geom
1 window NA NA <NA> POLYGON ((0.3893523 153.103...
2 segment NA NA <NA> LINESTRING (0.3894739 1253....
3 segment NA NA <NA> LINESTRING (109.683 1251.77...
4 segment NA NA <NA> LINESTRING (109.683 1251.77...
5 segment NA NA <NA> LINESTRING (198.1486 1276.5...
6 segment NA NA <NA> LINESTRING (197.9988 1251.1...
7 segment NA NA <NA> LINESTRING (290.4787 1276.5...
8 segment NA NA <NA> LINESTRING (288.9907 1250.5...
9 segment NA NA <NA> LINESTRING (380.1326 1276.5...
10 segment NA NA <NA> LINESTRING (379.9827 1249.8...
> # ppp:
> g = gorillas
> st_as_sf(g)
Simple feature collection with 648 features and 4 fields
geometry type: GEOMETRY
dimension: XY
bbox: xmin: 580457.9 ymin: 674172.8 xmax: 585934 ymax: 678739.2
CRS: NA
First 10 features:
label group season date geom
NA window <NA> <NA> <NA> POLYGON ((584712 674237.1, ...
1 point major dry 2006-01-06 POINT (582518.4 676886.2)
2 point major dry 2006-01-10 POINT (581823 677422.7)
3 point major dry 2006-01-15 POINT (582131 676937.9)
4 point major dry 2006-01-24 POINT (582111.9 677420)
5 point minor dry 2006-01-27 POINT (582585.1 677509.7)
6 point major dry 2006-01-28 POINT (582302.3 677521.6)
7 point major dry 2006-02-01 POINT (583167.2 676730.5)
8 point major dry 2006-02-03 POINT (583584.5 677207.1)
9 point major dry 2006-02-13 POINT (583117.8 676850.3)
> marks(g) = NULL
> st_as_sf(g)
Simple feature collection with 648 features and 1 field
geometry type: GEOMETRY
dimension: XY
bbox: xmin: 580457.9 ymin: 674172.8 xmax: 585934 ymax: 678739.2
CRS: NA
First 10 features:
label geom
1 window POLYGON ((584712 674237.1, ...
2 point POINT (582518.4 676886.2)
3 point POINT (581823 677422.7)
4 point POINT (582131 676937.9)
5 point POINT (582111.9 677420)
6 point POINT (582585.1 677509.7)
7 point POINT (582302.3 677521.6)
8 point POINT (583167.2 676730.5)
9 point POINT (583584.5 677207.1)
10 point POINT (583117.8 676850.3)
>
> # multipolygon: https://github.com/r-spatial/sf/issues/1161
> window = read_sf(system.file("shape/nc.shp", package = "sf")) %>%
+ st_transform(32119)
>
> win = spatstat::as.owin(window)
>
> set.seed(1331)
> pp2a = runifpoint(n = 50, win = win)
> print(st_as_sf(pp2a))
Simple feature collection with 51 features and 1 field
geometry type: GEOMETRY
dimension: XY
bbox: xmin: 123829 ymin: 14744.69 xmax: 930521.8 ymax: 318259.9
CRS: NA
First 10 features:
label geom
1 window MULTIPOLYGON (((886136 3141...
2 point POINT (339121.3 257815.9)
3 point POINT (827443.1 246572.7)
4 point POINT (451340 207948)
5 point POINT (268749.6 203327.8)
6 point POINT (516677.7 198560.6)
7 point POINT (692368 238647.5)
8 point POINT (843281.2 287246)
9 point POINT (648479.4 235471)
10 point POINT (852595.8 267252.6)
>
> # st_sample going the spatstat way
> x <- sf::st_sfc(sf::st_polygon(list(rbind(c(0, 0), c(10, 0), c(10, 10), c(0, 0)))))
> try(pts <- st_sample(x, type = "thomas"))
Error in st_poly_sample(x, size = size, ..., type = type) :
rthomas is not an exported function from spatstat.
> try(pts <- st_sample(x, kappa = 1, mu = 10, type = "Thomas"))
Error in st_poly_sample(x, size = size, ..., type = type) :
The spatstat function rThomas did not return a valid result. Consult the help file.
Error message from spatstat:
Error : 'scale' should be a single number
> # points expected
> set.seed(1331)
> pts <- st_sample(x, kappa = 1, mu = 10, scale = 0.1, type = "Thomas")
> #plot(x)
> #plot(pts, add = TRUE)
> pts
Simple feature collection with 597 features and 1 field
geometry type: POINT
dimension: XY
bbox: xmin: 1.213108 ymin: 0.02200954 xmax: 9.994943 ymax: 8.82534
CRS: NA
First 10 features:
label geom
2 point POINT (9.076646 8.661168)
3 point POINT (9.347089 8.800523)
4 point POINT (9.207624 8.82534)
5 point POINT (9.403886 8.666932)
6 point POINT (9.437082 8.63911)
7 point POINT (9.254756 8.573871)
8 point POINT (9.29172 8.678031)
9 point POINT (9.735812 1.621866)
10 point POINT (9.853825 1.616409)
11 point POINT (9.665138 1.593111)
>
> # see https://github.com/r-spatial/sf/issues/1233
> # png("/tmp/spa%03d.png")
>
> p1 = st_point(0:1)
> p2 = st_point(1:2)
> p3 = st_point(c(-1,2))
> p = st_sfc(p1, p2, p3)
> as.ppp(p)
Planar point pattern: 3 points
window: rectangle = [-1, 1] x [1, 2] units
> try(as.ppp(st_set_crs(p, 4326)))
Error in as.ppp.sfc(st_set_crs(p, 4326)) :
Only projected coordinates may be converted to spatstat class objects
>
> sf = st_sf(geom = p)
> try(as.ppp(sf))
Planar point pattern: 3 points
window: rectangle = [-1, 1] x [1, 2] units
> sf = st_sf(a = 1:3, geom = p)
> as.ppp(sf)
Marked planar point pattern: 3 points
marks are numeric, of storage type 'integer'
window: rectangle = [-1, 1] x [1, 2] units
> sf = st_sf(a = 1:3, b=3:1, geom = p)
> as.ppp(sf) # warns
Marked planar point pattern: 3 points
marks are numeric, of storage type 'integer'
window: rectangle = [-1, 1] x [1, 2] units
Warning message:
In as.ppp.sf(sf) : only first attribute column is used for marks
>
> w = st_as_sfc(st_bbox(st_sfc(p1, p2)))
> sf = st_sf(a = 1:3, geom = p)
> (p0 = rbind(st_sf(a = 0, geom = w), sf))
Simple feature collection with 4 features and 1 field
geometry type: GEOMETRY
dimension: XY
bbox: xmin: -1 ymin: 1 xmax: 1 ymax: 2
CRS: NA
a geom
1 0 POLYGON ((0 1, 1 1, 1 2, 0 ...
2 1 POINT (0 1)
3 2 POINT (1 2)
4 3 POINT (-1 2)
> try(as.ppp(p0)) # errors: one point outside window
Error in `marks<-.ppp`(`*tmp*`, value = value) :
number of rows of data frame != number of points
In addition: Warning message:
1 point was rejected as lying outside the specified window
>
> w = st_as_sfc(st_bbox(p))
> sf = st_sf(a = 1:3, geom = p)
> (p0 = rbind(st_sf(a = 0, geom = w), sf))
Simple feature collection with 4 features and 1 field
geometry type: GEOMETRY
dimension: XY
bbox: xmin: -1 ymin: 1 xmax: 1 ymax: 2
CRS: NA
a geom
1 0 POLYGON ((-1 1, 1 1, 1 2, -...
2 1 POINT (0 1)
3 2 POINT (1 2)
4 3 POINT (-1 2)
> as.ppp(p0)
Marked planar point pattern: 3 points
marks are numeric, of storage type 'double'
window: polygonal boundary
enclosing rectangle: [-1, 1] x [1, 2] units
>
> # as.owin.sf, as.owin.sfc_*
> nc = st_read(system.file("gpkg/nc.gpkg", package="sf"), check_ring_dir = TRUE)
Reading layer `nc.gpkg' from data source `/home/edzer/git/sf.Rcheck/sf/gpkg/nc.gpkg' using driver `GPKG'
Simple feature collection with 100 features and 14 fields
geometry type: MULTIPOLYGON
dimension: XY
bbox: xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
geographic CRS: NAD27
> try(as.owin(nc)) # should be projected
Error in as.owin.sfc_MULTIPOLYGON(st_cast(W, "MULTIPOLYGON"), ...) :
Only projected coordinates may be converted to spatstat class objects
> nc = st_transform(nc, 32119)
> plot(as.owin(nc), col = 'grey')
> plot(as.owin(st_geometry(nc)), col = 'grey')
>
> sq = rbind(c(-1,-1), c(1, -1), c(1,1), c(-1,1), c(-1,-1))
> pol = st_polygon(list(0.5 * sq, sq[5:1,] * 0.45)) # w hole
> plot(as.owin(pol), col = 'grey')
> plot(as.owin(st_sfc(pol)), col = 'grey')
> mpol = st_multipolygon(list(
+ list(sq, sq[5:1,] * 0.9),
+ list(sq * 2, sq[5:1,] * 1.8)))
> plot(as.owin(mpol), col = 'grey')
> plot(as.owin(st_sfc(mpol)), col = 'grey')
> plot(as.owin(st_sfc(pol, mpol)), col = 'grey')
> plot(as.owin(st_sf(a=1:2, st_sfc(pol, mpol))), col = 'grey')
> (o = as.owin(st_sf(a=1:2, st_sfc(pol, mpol))))
window: polygonal boundary
enclosing rectangle: [-2, 2] x [-2, 2] units
> st_as_sfc(o)
Geometry set for 1 feature
geometry type: MULTIPOLYGON
dimension: XY
bbox: xmin: -2 ymin: -2 xmax: 2 ymax: 2
CRS: NA
MULTIPOLYGON (((2 2, -2 2, -2 -2, 2 -2, 2 2), (...
>
> plot(st_as_sfc(o), col = 'blue', main = 'st_as_sfc(o)')
> plot(st_as_sf(o), col = 'blue', main = 'st_as_sf(o)')
>
> data(nztrees)
> qNZ <- quadratcount(nztrees, nx=4, ny=3)
> ts = as.tess(qNZ)
> plot(st_as_sfc(ts))
>
> ls = st_linestring(rbind(c(0,0), c(1,1), c(2,0)))
> plot(as.psp(ls))
> mls = st_multilinestring(list(rbind(c(0,0), c(1,1), c(2,0)), rbind(c(3,3), c(4,2))))
> plot(as.psp(mls))
>
> plot(as.psp(st_sfc(ls)))
> plot(as.psp(st_sfc(mls)))
> plot(as.psp(st_sfc(ls, mls)))
>
> sf = st_sf(st_cast(st_sfc(ls, mls), "MULTILINESTRING"), marks = 1:2, foo = 2:1)
> as.psp(sf) # picks marks itself
marked planar line segment pattern: 5 line segments
Mark variables: marks, foo
window: rectangle = [0, 4] x [0, 3] units
> as.psp(sf, marks = 5:1)
marked planar line segment pattern: 5 line segments
marks are numeric, of type 'integer'
window: rectangle = [0, 4] x [0, 3] units
>
> (x = st_as_sf(as.psp(sf)))
Simple feature collection with 6 features and 3 fields
geometry type: GEOMETRY
dimension: XY
bbox: xmin: 0 ymin: 0 xmax: 4 ymax: 3
CRS: NA
label marks foo geom
1 window NA NA POLYGON ((0 0, 4 0, 4 3, 0 ...
2 segment 1 2 LINESTRING (0 0, 1 1)
3 segment 1 2 LINESTRING (1 1, 2 0)
4 segment 2 1 LINESTRING (0 0, 1 1)
5 segment 2 1 LINESTRING (1 1, 2 0)
6 segment 2 1 LINESTRING (3 3, 4 2)
> (y = st_as_sfc(as.psp(sf)))
Geometry set for 6 features
geometry type: GEOMETRY
dimension: XY
bbox: xmin: 0 ymin: 0 xmax: 4 ymax: 3
CRS: NA
First 5 geometries:
POLYGON ((0 0, 4 0, 4 3, 0 3, 0 0))
LINESTRING (0 0, 1 1)
LINESTRING (1 1, 2 0)
LINESTRING (0 0, 1 1)
LINESTRING (1 1, 2 0)
> all.equal(st_geometry(x), y)
[1] TRUE
>
> proc.time()
user system elapsed
2.022 0.126 2.145
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