Foxall Jfox 的信封在 R spatstat 中给出 "error in Hest"
envelope for Foxall Jfox giving "error in Hest" in R spatstat
我想探索点模式中的点到多边形 shapefile 中最近的多边形的距离。
使用 R 包 spatstat，我的方法是计算函数 Jfox 的 envelope，考虑我的点到多边形的距离。
我的完整数据集包括来自多个站点的点模式，并且我已经成功地将这种方法用于多个站点。
但是，当 运行 特定站点上的信封出现此错误时：
Generating 99 simulations of CSR with fixed number of points ...
Error : in Hest(X,r) the successive r values must be finely spaced: given spacing = 0.0043766; required spacing <= 0.00393
In addition: Warning messages:
1: In resolve.foxall.window(X, Y, W) :
Trimming the window of X to be a subset of the Frame of Y
2: In resolve.foxall.window(X, Y, W) :
Trimming the window of X to be a subset of the Frame of Y
[retrying]
Error : in Hest(X,r) the successive r values must be finely spaced: given spacing = 0.0043766; required spacing <= 0.00393
In addition: Warning message:
In resolve.foxall.window(X, Y, W) :
Trimming the window of X to be a subset of the Frame of Y
[retrying]
... and so on.
我无法弄清楚是什么导致了这个问题。
可重现的例子：
数据文件可以在这里找到：
https://www.dropbox.com/sh/fzucl5f6u4s2igx/AAAzgf2Fn-L9cfwzSCwj1RbPa?dl=0
请根据您存储文件的位置修改导入数据的代码。
library(tidyverse)
{ # load these two together because spatstat rely on them but I don't know exactely for what.
library(sp)
library(maptools) # needed for method such as as.ppp
}
library(spatstat)
library(sf)
library(xlsx)
# load transect polygon giving the Window of ppp, and make it a owin object
tr_poly_win<-st_read('transect.shp') %>%
select(geometry) %>% as(., 'Spatial') %>% as(.,'SpatialPolygons') %>%
as.owin(tr_poly_sp)
# load points and make them a ppp with correct window
options(digits=15) # this to allow enough decimals
points<-read.table('points.txt', head=T,sep='\t',dec='.') %>%
mutate(geometry=as.character(geometry)) %>%
mutate(lon=as.numeric(sapply(strsplit(geometry, '[(,)]'), "[[", 2)),
lat=as.numeric(sapply(strsplit(geometry, '[(,)]'), "[[", 3))) %>%
st_as_sf(coords=c('lon','lat'),crs= 32619) %>%
as(.,'Spatial') %>%
as.ppp(.)
Window(points)<-tr_poly_win
# load polygons
win<-st_read('polygons.shp') %>% as(.,'Spatial') %>% as(.,'owin')
# create an hyperframe
hyp<-hyperframe(points=points,win=win)
# visualize data:
# points as open circles; points' window as black contour; polygons in red;
# Frame of the polygons as red rectangle; Frame of points as green rectangle
plot(hyp, quote({plot(points,which.marks='pos',type='n')
plot(win,col=2,add=TRUE)
plot(points,which.marks='pos',type='p', add=T)
plot(Frame(win),border=2, add=T)
plot(Frame(points),border=3, add=T)}) )
点为空心圆； points' window 为黑色轮廓；红色的多边形；
多边形的框架为红色矩形；点框为绿色矩形
# computing the Jfox function works
with(hyp,Jfox(points,win))
# try to compute the envelope for the Jfox and you'll get the error
with(hyp,envelope(Y=points, fun=Jfox, funargs=list(Y=win) , nsim=99, fix.n=T))
是否有任何根本原因导致我收到此错误或这是一个错误（例如，请参阅 PS 中的链接）？
我的会话信息如下：
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C LC_TIME=Italian_Italy.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] xlsx_0.6.1 sf_0.7-4 spatstat_1.63-0 rpart_4.1-15 nlme_3.1-140 spatstat.data_1.4-3 maptools_0.9-5 sp_1.3-1 forcats_0.4.0
[10] stringr_1.4.0 dplyr_0.8.3 purrr_0.3.3 readr_1.3.1 tidyr_1.0.0 tibble_2.1.3 ggplot2_3.2.1 tidyverse_1.2.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 lubridate_1.7.4 lattice_0.20-38 deldir_0.1-16 xlsxjars_0.6.1 class_7.3-15 assertthat_0.2.1 zeallot_0.1.0
[9] R6_2.4.0 cellranger_1.1.0 backports_1.1.4 e1071_1.7-1 httr_1.4.1 tensor_1.5 pillar_1.4.0 rlang_0.4.1
[17] lazyeval_0.2.2 readxl_1.3.1 rstudioapi_0.10 Matrix_1.2-18 goftest_1.2-2 splines_3.6.2 rgdal_1.4-3 foreign_0.8-72
[25] polyclip_1.10-0 munsell_0.5.0 broom_0.5.2 compiler_3.6.2 modelr_0.1.5 pkgconfig_2.0.2 mgcv_1.8-31 tidyselect_0.2.5
[33] crayon_1.3.4 withr_2.1.2 grid_3.6.2 jsonlite_1.6 gtable_0.3.0 lifecycle_0.1.0 DBI_1.0.0 magrittr_1.5
[41] units_0.6-3 scales_1.0.0 KernSmooth_2.23-16 cli_1.1.0 stringi_1.4.3 xml2_1.2.2 spatstat.utils_1.17-0 generics_0.0.2
[49] vctrs_0.2.0 tools_3.6.2 glue_1.3.1 hms_0.5.2 abind_1.4-5 colorspace_1.4-1 classInt_0.3-3 rvest_0.3.5
[57] rJava_0.9-11 haven_2.2.0
Ps：我对解释的搜索导致了类似的问题，这些问题是由以前版本的 spatstat 代码中的错误引起的。这里是链接：
http://r-sig-geo.2731867.n2.nabble.com/Error-in-random-labelling-using-the-J-function-td7593210.html
http://r-sig-geo.2731867.n2.nabble.com/Complete-spatial-randomness-testing-td7590425.html
如您所见，我的 statspat 和 R 版本应该是最新的。
这是一个错误。
它现在已在 spatstat 的开发版本（版本 1.63-0.020 及更高版本）中得到修复，可从 repository on GitHub.
获得
我想探索点模式中的点到多边形 shapefile 中最近的多边形的距离。
使用 R 包 spatstat，我的方法是计算函数 Jfox 的 envelope，考虑我的点到多边形的距离。
我的完整数据集包括来自多个站点的点模式，并且我已经成功地将这种方法用于多个站点。
但是，当 运行 特定站点上的信封出现此错误时：
Generating 99 simulations of CSR with fixed number of points ...
Error : in Hest(X,r) the successive r values must be finely spaced: given spacing = 0.0043766; required spacing <= 0.00393
In addition: Warning messages:
1: In resolve.foxall.window(X, Y, W) :
Trimming the window of X to be a subset of the Frame of Y
2: In resolve.foxall.window(X, Y, W) :
Trimming the window of X to be a subset of the Frame of Y
[retrying]
Error : in Hest(X,r) the successive r values must be finely spaced: given spacing = 0.0043766; required spacing <= 0.00393
In addition: Warning message:
In resolve.foxall.window(X, Y, W) :
Trimming the window of X to be a subset of the Frame of Y
[retrying]
... and so on.
我无法弄清楚是什么导致了这个问题。
可重现的例子：
数据文件可以在这里找到：
https://www.dropbox.com/sh/fzucl5f6u4s2igx/AAAzgf2Fn-L9cfwzSCwj1RbPa?dl=0
请根据您存储文件的位置修改导入数据的代码。
library(tidyverse)
{ # load these two together because spatstat rely on them but I don't know exactely for what.
library(sp)
library(maptools) # needed for method such as as.ppp
}
library(spatstat)
library(sf)
library(xlsx)
# load transect polygon giving the Window of ppp, and make it a owin object
tr_poly_win<-st_read('transect.shp') %>%
select(geometry) %>% as(., 'Spatial') %>% as(.,'SpatialPolygons') %>%
as.owin(tr_poly_sp)
# load points and make them a ppp with correct window
options(digits=15) # this to allow enough decimals
points<-read.table('points.txt', head=T,sep='\t',dec='.') %>%
mutate(geometry=as.character(geometry)) %>%
mutate(lon=as.numeric(sapply(strsplit(geometry, '[(,)]'), "[[", 2)),
lat=as.numeric(sapply(strsplit(geometry, '[(,)]'), "[[", 3))) %>%
st_as_sf(coords=c('lon','lat'),crs= 32619) %>%
as(.,'Spatial') %>%
as.ppp(.)
Window(points)<-tr_poly_win
# load polygons
win<-st_read('polygons.shp') %>% as(.,'Spatial') %>% as(.,'owin')
# create an hyperframe
hyp<-hyperframe(points=points,win=win)
# visualize data:
# points as open circles; points' window as black contour; polygons in red;
# Frame of the polygons as red rectangle; Frame of points as green rectangle
plot(hyp, quote({plot(points,which.marks='pos',type='n')
plot(win,col=2,add=TRUE)
plot(points,which.marks='pos',type='p', add=T)
plot(Frame(win),border=2, add=T)
plot(Frame(points),border=3, add=T)}) )
点为空心圆； points' window 为黑色轮廓；红色的多边形； 多边形的框架为红色矩形；点框为绿色矩形
# computing the Jfox function works
with(hyp,Jfox(points,win))
# try to compute the envelope for the Jfox and you'll get the error
with(hyp,envelope(Y=points, fun=Jfox, funargs=list(Y=win) , nsim=99, fix.n=T))
是否有任何根本原因导致我收到此错误或这是一个错误（例如，请参阅 PS 中的链接）？
我的会话信息如下：
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C LC_TIME=Italian_Italy.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] xlsx_0.6.1 sf_0.7-4 spatstat_1.63-0 rpart_4.1-15 nlme_3.1-140 spatstat.data_1.4-3 maptools_0.9-5 sp_1.3-1 forcats_0.4.0
[10] stringr_1.4.0 dplyr_0.8.3 purrr_0.3.3 readr_1.3.1 tidyr_1.0.0 tibble_2.1.3 ggplot2_3.2.1 tidyverse_1.2.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 lubridate_1.7.4 lattice_0.20-38 deldir_0.1-16 xlsxjars_0.6.1 class_7.3-15 assertthat_0.2.1 zeallot_0.1.0
[9] R6_2.4.0 cellranger_1.1.0 backports_1.1.4 e1071_1.7-1 httr_1.4.1 tensor_1.5 pillar_1.4.0 rlang_0.4.1
[17] lazyeval_0.2.2 readxl_1.3.1 rstudioapi_0.10 Matrix_1.2-18 goftest_1.2-2 splines_3.6.2 rgdal_1.4-3 foreign_0.8-72
[25] polyclip_1.10-0 munsell_0.5.0 broom_0.5.2 compiler_3.6.2 modelr_0.1.5 pkgconfig_2.0.2 mgcv_1.8-31 tidyselect_0.2.5
[33] crayon_1.3.4 withr_2.1.2 grid_3.6.2 jsonlite_1.6 gtable_0.3.0 lifecycle_0.1.0 DBI_1.0.0 magrittr_1.5
[41] units_0.6-3 scales_1.0.0 KernSmooth_2.23-16 cli_1.1.0 stringi_1.4.3 xml2_1.2.2 spatstat.utils_1.17-0 generics_0.0.2
[49] vctrs_0.2.0 tools_3.6.2 glue_1.3.1 hms_0.5.2 abind_1.4-5 colorspace_1.4-1 classInt_0.3-3 rvest_0.3.5
[57] rJava_0.9-11 haven_2.2.0
Ps：我对解释的搜索导致了类似的问题，这些问题是由以前版本的 spatstat 代码中的错误引起的。这里是链接：
http://r-sig-geo.2731867.n2.nabble.com/Error-in-random-labelling-using-the-J-function-td7593210.html
http://r-sig-geo.2731867.n2.nabble.com/Complete-spatial-randomness-testing-td7590425.html
如您所见，我的 statspat 和 R 版本应该是最新的。
这是一个错误。
它现在已在 spatstat 的开发版本（版本 1.63-0.020 及更高版本）中得到修复，可从 repository on GitHub.