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Tidyverse methods that remove nodes drop agr attributes #275

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loreabad6 opened this issue Nov 3, 2024 · 0 comments
Open

Tidyverse methods that remove nodes drop agr attributes #275

loreabad6 opened this issue Nov 3, 2024 · 0 comments

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@loreabad6
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loreabad6 commented Nov 3, 2024 •
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Describe the bug
Those tidyverse methods in tidygraph that recreate the network when removing nodes do not preserve the agr attributes from the sf object. It comes from the igraph::delete_vertices() function that is recreating the network. So far I found this for

  • filter.tbl_graph()
  • slice.tbl_graph() and their slice_*.tbl_graph() functions
  • distinct.tbl_graph()

Reproducible example

library(sfnetworks)
library(tidygraph)
library(tidyverse)
library(sf)
#> Linking to GEOS 3.13.0, GDAL 3.9.3, PROJ 9.5.0; sf_use_s2() is TRUE

net = as_sfnetwork(roxel)

net |> 
  activate(edges) |> 
  st_agr()
#>     from       to     name     type 
#>     <NA>     <NA> constant constant 
#> Levels: constant aggregate identity

# filter.tbl_graph()
net |> 
  mutate(foo = sample(1:5, 987, replace = TRUE)) |> 
  filter(foo == 2) |> 
  activate(edges) |> 
  st_agr()
#> from   to name type 
#> <NA> <NA> <NA> <NA> 
#> Levels: constant aggregate identity

# slice.tbl_graph()
net |> 
  slice(3:7) |> 
  activate(edges) |> 
  st_agr()
#> from   to name type 
#> <NA> <NA> <NA> <NA> 
#> Levels: constant aggregate identity

# slice_sample.tbl_graph()
net |> 
  slice_sample(n = 20) |> 
  activate(edges) |> 
  st_agr()
#> from   to name type 
#> <NA> <NA> <NA> <NA> 
#> Levels: constant aggregate identity

# distinct.tbl_graph()
net |> 
  distinct() |> 
  activate(edges) |> 
  st_agr()
#> from   to name type 
#> <NA> <NA> <NA> <NA> 
#> Levels: constant aggregate identity

Expected behavior
The agr attributes are preserved.

R Session Info

sfnetworks v1.0 branch

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.2 (2024-10-31)
#>  os       Ubuntu 24.04.1 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Etc/UTC
#>  date     2024-11-03
#>  pandoc   3.5 @ /usr/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package          * version date (UTC) lib source
#>  abind              1.4-8   2024-09-12 [1] CRAN (R 4.4.2)
#>  class              7.3-22  2023-05-03 [2] CRAN (R 4.4.2)
#>  classInt           0.4-10  2023-09-05 [1] CRAN (R 4.4.2)
#>  cli                3.6.3   2024-06-21 [1] RSPM (R 4.4.0)
#>  colorspace         2.1-1   2024-07-26 [1] RSPM (R 4.4.0)
#>  DBI                1.2.3   2024-06-02 [1] RSPM (R 4.4.0)
#>  deldir             2.0-4   2024-02-28 [1] RSPM (R 4.4.0)
#>  digest             0.6.37  2024-08-19 [1] RSPM (R 4.4.0)
#>  dplyr            * 1.1.4   2023-11-17 [1] RSPM (R 4.4.0)
#>  e1071              1.7-16  2024-09-16 [1] CRAN (R 4.4.2)
#>  evaluate           1.0.1   2024-10-10 [1] RSPM (R 4.4.0)
#>  fansi              1.0.6   2023-12-08 [1] RSPM (R 4.4.0)
#>  fastmap            1.2.0   2024-05-15 [1] RSPM (R 4.4.0)
#>  forcats          * 1.0.0   2023-01-29 [1] RSPM (R 4.4.0)
#>  fs                 1.6.5   2024-10-30 [1] RSPM (R 4.4.0)
#>  generics           0.1.3   2022-07-05 [1] RSPM (R 4.4.0)
#>  ggplot2          * 3.5.1   2024-04-23 [1] RSPM (R 4.4.0)
#>  glue               1.8.0   2024-09-30 [1] RSPM (R 4.4.0)
#>  goftest            1.2-3   2021-10-07 [1] RSPM (R 4.4.0)
#>  gtable             0.3.6   2024-10-25 [1] RSPM (R 4.4.0)
#>  hms                1.1.3   2023-03-21 [1] RSPM (R 4.4.0)
#>  htmltools          0.5.8.1 2024-04-04 [1] RSPM (R 4.4.0)
#>  igraph             2.1.1   2024-10-19 [1] RSPM (R 4.4.0)
#>  KernSmooth         2.23-24 2024-05-17 [2] CRAN (R 4.4.2)
#>  knitr              1.48    2024-07-07 [1] RSPM (R 4.4.0)
#>  lattice            0.22-6  2024-03-20 [2] CRAN (R 4.4.2)
#>  lifecycle          1.0.4   2023-11-07 [1] RSPM (R 4.4.0)
#>  lubridate        * 1.9.3   2023-09-27 [1] RSPM (R 4.4.0)
#>  lwgeom             0.2-15  2024-11-03 [1] Github (r-spatial/lwgeom@4569f09)
#>  magrittr           2.0.3   2022-03-30 [1] RSPM (R 4.4.0)
#>  Matrix             1.7-1   2024-10-18 [2] CRAN (R 4.4.2)
#>  mgcv               1.9-1   2023-12-21 [2] CRAN (R 4.4.2)
#>  munsell            0.5.1   2024-04-01 [1] RSPM (R 4.4.0)
#>  nlme               3.1-166 2024-08-14 [2] CRAN (R 4.4.2)
#>  pillar             1.9.0   2023-03-22 [1] RSPM (R 4.4.0)
#>  pkgconfig          2.0.3   2019-09-22 [1] RSPM (R 4.4.0)
#>  polyclip           1.10-7  2024-07-23 [1] RSPM (R 4.4.0)
#>  proxy              0.4-27  2022-06-09 [1] CRAN (R 4.4.2)
#>  purrr            * 1.0.2   2023-08-10 [1] RSPM (R 4.4.0)
#>  R6                 2.5.1   2021-08-19 [1] RSPM (R 4.4.0)
#>  Rcpp               1.0.13  2024-07-17 [1] RSPM (R 4.4.0)
#>  readr            * 2.1.5   2024-01-10 [1] RSPM (R 4.4.0)
#>  reprex             2.1.1   2024-07-06 [1] RSPM (R 4.4.0)
#>  rlang              1.1.4   2024-06-04 [1] RSPM (R 4.4.0)
#>  rmarkdown          2.28    2024-08-17 [1] RSPM (R 4.4.0)
#>  rpart              4.1.23  2023-12-05 [2] CRAN (R 4.4.2)
#>  rstudioapi         0.17.1  2024-10-22 [1] RSPM (R 4.4.0)
#>  s2                 1.1.7   2024-07-17 [1] CRAN (R 4.4.2)
#>  scales             1.3.0   2023-11-28 [1] RSPM (R 4.4.0)
#>  sessioninfo        1.2.2   2021-12-06 [1] RSPM (R 4.4.0)
#>  sf               * 1.0-19  2024-11-03 [1] Github (r-spatial/sf@dc02f71)
#>  sfheaders          0.4.4   2024-01-17 [1] RSPM (R 4.4.0)
#>  sfnetworks       * 0.6.4   2024-11-03 [1] local
#>  spatstat.data      3.1-2   2024-06-21 [1] RSPM (R 4.4.0)
#>  spatstat.explore   3.3-3   2024-10-22 [1] RSPM (R 4.4.0)
#>  spatstat.geom      3.3-3   2024-09-18 [1] RSPM (R 4.4.0)
#>  spatstat.linnet    3.2-2   2024-09-20 [1] RSPM (R 4.4.0)
#>  spatstat.model     3.3-2   2024-09-19 [1] RSPM (R 4.4.0)
#>  spatstat.random    3.3-2   2024-09-18 [1] RSPM (R 4.4.0)
#>  spatstat.sparse    3.1-0   2024-06-21 [1] RSPM (R 4.4.0)
#>  spatstat.univar    3.0-1   2024-09-05 [1] RSPM (R 4.4.0)
#>  spatstat.utils     3.1-0   2024-08-17 [1] RSPM (R 4.4.0)
#>  stringi            1.8.4   2024-05-06 [1] RSPM (R 4.4.0)
#>  stringr          * 1.5.1   2023-11-14 [1] RSPM (R 4.4.0)
#>  tensor             1.5     2012-05-05 [1] RSPM (R 4.4.0)
#>  tibble           * 3.2.1   2023-03-20 [1] RSPM (R 4.4.0)
#>  tidygraph        * 1.3.1   2024-01-30 [1] RSPM (R 4.4.0)
#>  tidyr            * 1.3.1   2024-01-24 [1] RSPM (R 4.4.0)
#>  tidyselect         1.2.1   2024-03-11 [1] RSPM (R 4.4.0)
#>  tidyverse        * 2.0.0   2023-02-22 [1] RSPM (R 4.4.0)
#>  timechange         0.3.0   2024-01-18 [1] RSPM (R 4.4.0)
#>  tzdb               0.4.0   2023-05-12 [1] RSPM (R 4.4.0)
#>  units              0.8-5   2023-11-28 [1] RSPM (R 4.4.0)
#>  utf8               1.2.4   2023-10-22 [1] RSPM (R 4.4.0)
#>  vctrs              0.6.5   2023-12-01 [1] RSPM (R 4.4.0)
#>  withr              3.0.2   2024-10-28 [1] RSPM (R 4.4.0)
#>  wk                 0.9.4   2024-10-11 [1] CRAN (R 4.4.2)
#>  xfun               0.48    2024-10-03 [1] RSPM (R 4.4.0)
#>  yaml               2.3.10  2024-07-26 [1] RSPM (R 4.4.0)
#> 
#>  [1] /usr/local/lib/R/site-library
#>  [2] /usr/local/lib/R/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────
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