Possible error in algorithm - polygon fails to include all points

[AdamCSmithCWS]

Thanks so much for your awesome package. I've been using it a lot.
I've been perplexed lately by some odd situations where the algorithm seems to ignore one or a few points when it's creating the polygon.

I've uploaded a small dataset of coordinates to the issue and I hope the code below provides a full reproducible example.

coordinates_example.csv

I've seen this issue with a number of point datasets recently. The data represent survey locations from a continental scale bird monitoring program, but for this example the geographic aspects of the points are irrelevant (I think).

library(tidyverse)
library(sf)
library(concaveman)
# import text file of coordinates
coords <- read.csv("coordinates_example.csv") %>% 
  st_as_sf(coords = c("X","Y"))

Running the concave() function on these points creates a polygon that does not intersect all points.

concave_poly <- concaveman(coords) %>% 
  mutate(in_poly = TRUE) #adds a column for following join

missed <- coords %>% 
  st_join(.,concave_poly,
          join = st_intersects) %>% 
  filter(is.na(in_poly))

In this case, there are three points that are outside of the polygon. However, two of them are extremely close, such that a 1-unit buffer on the polygon includes them. So not a problem in this context, likely more an issue with the precision of the st_intersects() function. So I added a 1-unit buffer below, but there is still one point outside the polygon, and it's far outside. It seems to be completely ignored by the algorithm.

concave_poly <- concaveman(coords) %>% 
  st_buffer(.,1) %>% #just adds a 1-unit buffer - simplifies st_join
  mutate(in_poly = TRUE) #adds a column for following join

missed <- coords %>% 
  st_join(.,concave_poly,
          join = st_intersects) %>% 
  filter(is.na(in_poly))

# plot the polygon with the missing point in red
display <- ggplot()+
  geom_sf(data = concave_poly)+ #concave polygon
  geom_sf(data = coords,alpha = 0.3)+ #original points
  geom_sf(data = missed,colour = "red")+ #points that do not intersect polygon
  geom_sf_text(data = missed,
               aes(label = point),
               size = 3)+
  labs(title = "red point is far outside the polygon")

display

This plot shows the red point that's completely missed by the polygon.

sessionInfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
 [1] concaveman_1.1.0 sf_1.0-9         forcats_0.5.1   
 [4] stringr_1.5.0    dplyr_1.1.0      purrr_0.3.4     
 [7] readr_2.1.2      tidyr_1.2.0      tibble_3.1.7    
[10] ggplot2_3.4.0    tidyverse_1.3.1 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3       lubridate_1.8.0    class_7.3-20      
 [4] assertthat_0.2.1   digest_0.6.29      utf8_1.2.2        
 [7] V8_4.2.2           R6_2.5.1           cellranger_1.1.0  
[10] backports_1.4.1    reprex_2.0.1       evaluate_0.15     
[13] e1071_1.7-11       httr_1.4.3         pillar_1.7.0      
[16] rlang_1.0.6        curl_4.3.2         readxl_1.4.0      
[19] rstudioapi_0.13    rmarkdown_2.14     munsell_0.5.0     
[22] proxy_0.4-27       broom_0.8.0        compiler_4.2.0    
[25] modelr_0.1.8       xfun_0.31          pkgconfig_2.0.3   
[28] htmltools_0.5.2    tidyselect_1.2.0   fansi_1.0.3       
[31] crayon_1.5.1       tzdb_0.3.0         dbplyr_2.2.1      
[34] withr_2.5.0        grid_4.2.0         jsonlite_1.8.0    
[37] gtable_0.3.0       lifecycle_1.0.3    DBI_1.1.3         
[40] magrittr_2.0.3     units_0.8-0        scales_1.2.0      
[43] KernSmooth_2.23-20 cli_3.6.0          stringi_1.7.6     
[46] farver_2.1.0       fs_1.5.2           xml2_1.3.3        
[49] ellipsis_0.3.2     generics_0.1.2     vctrs_0.5.2       
[52] tools_4.2.0        glue_1.6.2         hms_1.1.1         
[55] fastmap_1.1.0      yaml_2.3.5         colorspace_2.0-3  
[58] classInt_0.4-7     rvest_1.0.2        knitr_1.39        
[61] haven_2.5.0 

[AdamCSmithCWS]

FYI, I updated everything to R 4.3, and the same error occurs:

sessionInfo()
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] concaveman_1.1.0 sf_1.0-12        lubridate_1.9.2  forcats_1.0.0    stringr_1.5.0   
 [6] dplyr_1.1.2      purrr_1.0.1      readr_2.1.4      tidyr_1.3.0      tibble_3.2.1    
[11] ggplot2_3.4.2    tidyverse_2.0.0 

loaded via a namespace (and not attached):
 [1] utf8_1.2.3         generics_0.1.3     class_7.3-21       KernSmooth_2.23-20
 [5] stringi_1.7.12     hms_1.1.3          digest_0.6.31      magrittr_2.0.3    
 [9] evaluate_0.20      grid_4.3.0         timechange_0.2.0   fastmap_1.1.1     
[13] jsonlite_1.8.4     e1071_1.7-13       DBI_1.1.3          fansi_1.0.4       
[17] scales_1.2.1       cli_3.6.1          rlang_1.1.0        units_0.8-1       
[21] munsell_0.5.0      withr_2.5.0        yaml_2.3.7         tools_4.3.0       
[25] tzdb_0.3.0         colorspace_2.1-0   curl_5.0.0         vctrs_0.6.2       
[29] R6_2.5.1           proxy_0.4-27       lifecycle_1.0.3    classInt_0.4-9    
[33] V8_4.3.0           pkgconfig_2.0.3    pillar_1.9.0       gtable_0.3.3      
[37] glue_1.6.2         Rcpp_1.0.10        xfun_0.39          tidyselect_1.2.0  
[41] rstudioapi_0.14    knitr_1.42         farver_2.1.1       htmltools_0.5.5   
[45] rmarkdown_2.21     compiler_4.3.0   

[hunterdanielsmith]

I'm seeing a similar issue.