I want to explore the distance of points in a point pattern to the nearest polygon in a polygon shapefile.

Using the R package spatstat, my approach is to calculate the envelope for the function Jfox that consider the distance of my points to the polygons.

My full dataset include point patterns from multiple sites, and I have been successfully using this approach with several sites.

However, when running the envelope on a particular site I get this error:

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.

I cannot figure out what is causing the issue.

Reproducible example:

Datafiles can be found here:

https://www.dropbox.com/sh/fzucl5f6u4s2igx/AAAzgf2Fn-L9cfwzSCwj1RbPa?dl=0

please adapt the code for importing the data according to where you store the files.


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)}) )

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

# 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))

Is there any underlying reason why I get this error or it is a bug (e.g. see the links in the PS)?

My session info is as follow:

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: My search for an explanation lead to similar problems that resulted from a bug in previous version of the spatstat code. here the links:

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

As you can see, though, my statspat and my R versions should be current.

envelope for Foxall Jfox giving "error in Hest" in R spatstat

Reproducible example: