从坐标列表创建Owin对象
从坐标列表创建Owin对象
提问于 2021-05-07 00:30:18
我正在尝试构建物种分布多边形，用于R程序rase。该程序需要一个owin对象，但示例数据还包含一个SpatialPolygonDataFrame。您可以使用以下命令自己获取数据：data(rase_data, package = 'rase')
我从一个坐标列表(每个物种的经度/经度)开始。多亏了这个答案here，我已经能够为列表的每个元素(每个物种)创建一个多边形。我需要找到一个owin对象。这是一些测试数据的dput，然后是我用来达到目的的代码。
#dput(specieslist)
specieslist <- structure(list(Species = c("A", "A", "A", "A", "A", "M", "A", "M", "A", "A", "A", "A", "A", "A", "M", "M", "A", "M", "A", "A", "A", "M", "M", "M", "A", "A", "A", "A", "A", "A", "A", "M", "A", "A", "M", "M", "A", "M", "M", "A"), lat = c(37.407002, 35.65242, 33.33891, 37.65105, 38.90657, 39.06893, 34.53998, 38.18311, 37.40006, 35.65242, 34.53998, 33.33891, 37.65105, 38.90657, 38.18311, 39.06893, 36.252183, 40.32555, 39.575983, 39.73548, 39.73548, 37.82096, 39.71557, 38.7222, 35.58556, 36.3075, 36.208, 33.967875, 35.375, 39.73589, 38.75774, 36.61058, 37.63605, 36.586111, 40.63344, 39.80565, 39.72601, 39.70529, 40.50957, 37.81238), long = c(-122.232016, -120.77931, -116.91402, -119.88513, -121.05138, -120.86546, -119.85962, -120.37691, -122.23219, -120.77931, -119.85962, -116.91402, -119.88513, -121.05138, -120.37691, -120.86546, -121.775867, -121.91209, -121.554167, -121.70126, -121.70126, -120.14661, -121.61181, -120.98745, -120.9122, -121.4806, -121.816, -120.097752, -120.6456, -121.70175, -120.8443, -119.05645, -119.8728, -121.914722, -121.87499, -121.71465, -121.76862, -121.53125, -122.10229, -120.42828)), class = "data.frame", row.names = c(NA, -40L))通过在点周围创建外壳，按物种/点创建多边形：
#create simple feature
library(sf)
df.sf <- specieslist %>%
st_as_sf( coords = c("long", "lat" ), crs = 4326 )
# perform fast visual check using mapview-package
#mapview::mapview( df.sf )
#group and summarise by species, and draw hulls
hulls <- df.sf %>%
group_by( Species ) %>%
summarise( geometry = st_combine( geometry ) ) %>%
st_convex_hull()
##result
#mapview::mapview( list(df.sf, hulls ) )现在我认为df.sf (sf points对象)变成了SpatialPolygonDataFrame，hulls (sf polygon对象)变成了owin对象：
as(df.sf, "Spatial") -> df.sf_SPDF #this formats incorrectly though.
distribution <- st_transform(hulls, crs = 6345)
Dist_owin <- as.owin(as_Spatial(distribution))
#Error: Only projected coordinates may be converted to spatstat class objects#OR
as.owin(distribution)
#Error: 'owin' is not an exported object from 'namespace:spatstat'
maptools::as.owin(distribution)
#Error: 'as.owin' is not an exported object from 'namespace:maptools'问题是：df.sf_SPDF的格式似乎不正确，并且Dist_owin错误。我发现R中的所有这些空间工作都非常令人困惑。我已经在这上面工作好几天了。
更新:如果我尝试另一种方法-将几何图形转换为多边形，然后创建owin。这会产生一个错误：
hulls_poly <- st_cast(distribution$geometry, "POLYGON") #.
Dist_owin <- as.owin(as_Spatial(hulls_poly))
#ERROR: no method or default for coercing “sfc_POLYGON” to “owin”Stack Overflow用户
回答已采纳
发布于 2021-05-08 12:35:13
我对sf的了解还不足以解决这个问题，所以我通过terra展示了它，但重要的部分是操作的顺序。如果您愿意，您可以在sf中再次实现它。应该不需要恢复到旧的Spatial*对象
您的数据
specieslist <- structure(list(Species = c("A", "A", "A", "A", "A", "M", "A", "M", "A", "A", "A", "A", "A", "A", "M", "M", "A", "M", "A", "A", "A", "M", "M", "M", "A", "A", "A", "A", "A", "A", "A", "M", "A", "A", "M", "M", "A", "M", "M", "A"), lat = c(37.407002, 35.65242, 33.33891, 37.65105, 38.90657, 39.06893, 34.53998, 38.18311, 37.40006, 35.65242, 34.53998, 33.33891, 37.65105, 38.90657, 38.18311, 39.06893, 36.252183, 40.32555, 39.575983, 39.73548, 39.73548, 37.82096, 39.71557, 38.7222, 35.58556, 36.3075, 36.208, 33.967875, 35.375, 39.73589, 38.75774, 36.61058, 37.63605, 36.586111, 40.63344, 39.80565, 39.72601, 39.70529, 40.50957, 37.81238), long = c(-122.232016, -120.77931, -116.91402, -119.88513, -121.05138, -120.86546, -119.85962, -120.37691, -122.23219, -120.77931, -119.85962, -116.91402, -119.88513, -121.05138, -120.37691, -120.86546, -121.775867, -121.91209, -121.554167, -121.70126, -121.70126, -120.14661, -121.61181, -120.98745, -120.9122, -121.4806, -121.816, -120.097752, -120.6456, -121.70175, -120.8443, -119.05645, -119.8728, -121.914722, -121.87499, -121.71465, -121.76862, -121.53125, -122.10229, -120.42828)), class = "data.frame", row.names = c(NA, -40L))首先，我创建一个空间对象，在本例中为SpatVector，并将其转换为平面CRS -以避免这种情况。
您选择的epsg:6345，即+proj=utm +zone=16不适合您的数据。16区代表阿拉巴马州的经度。加州覆盖了两个UTM区域，所以你不能使用它。改为使用例如"Teale Albers“如果你所有的数据都被限制在金州。
library(terra)
#terra version 1.2.5
v <- vect(specieslist, c("long", "lat"), crs="epsg:4326")
tacrs <- "+proj=aea +lat_1=34 +lat_2=40.5 +lat_0=0 +lon_0=-120 +x_0=0 +y_0=-4000000 +datum=NAD83 +units=m"
v <- project(v, tacrs)为了简单起见，我展示了一个针对1个物种的工作流程
usp <- unique(v$Species)
sp <- v[v$Species==usp[1]]做一个凸壳，我想你会想要添加一个缓冲区。
ch <- terra::convexhull(sp)
bch <- buffer(ch, 25000)
plot(bch)
points(sp)现在通过sf创建owin
library(sf)
library(spatstat)
sfobj <- st_as_sf(bch)
owin <- as.owin(sfobj)您可以像这样提取新CRS中的点
pxy <- terra::coords(sp)现在创建一个spatstat ppp对象。
x <- ppp(pxy[,1], pxy[,2], window=owin)
#Warning message:
#data contain duplicated points 要避免出现上述警告，您可以在脚本的开头使用specieslist <- unique(specieslist)
x
#Planar point pattern: 27 points
#window: polygonal boundary
#enclosing rectangle: [-222286.97, 312378.62] x [-539742.6, 217425] units页面原文内容由Stack Overflow提供。腾讯云小微IT领域专用引擎提供翻译支持
原文链接：
https://stackoverflow.com/questions/67422336
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