removeBrokenSpeciesListLinks filter not working properly #59

Activity

1. nmprista

   added

   2_preparationGenerating probabilities and Zero's, subsetting speciesGenerating probabilities and Zero's, subsetting species

   on Oct 12, 2022
2. nmprista

   changed the title [-]removeBrokenSpeciesListLinks[/-] [+]removeBrokenSpeciesListLinks filter not working properly[/+] on Oct 12, 2022
3. nicholascarey

   self-assigned this

   on Oct 13, 2022
4. davidcurrie2001 commented on Oct 13, 2022

   

   davidcurrie2001

   on Oct 13, 2022

   Contributor

   More actions

   I will create an example
5. davidcurrie2001

   self-assigned this

   on Oct 13, 2022
6. davidcurrie2001 commented on Oct 13, 2022

   

   davidcurrie2001

   on Oct 13, 2022

   Contributor

   More actions

   library(icesRDBES)
   
   # Get some test data - if you get errors or an emptry object check your wd
   myLohr <- importRDBESDownloadData('data-raw/WGRDBES-EST_TEST_LOHR_eg_3_2_3_6.zip')
   
   # Test 1) removeBrokenSpeciesListLinks() works ok - it doesn't remove any SS rows  valid data
   
   # Check number of SS rows before removing broken species list links (300)
   nrow(myLohr[["SS"]])
   # Try removing any broken links
   test1 <- removeBrokenSpeciesListLinks(myLohr)
   # Check number of SS rows after removing broken species list links - no broken links so shoudl be the same (300)
   nrow(test1[["SS"]])
   
   
   # Test 2) removeBrokenSpeciesListLinks() works ok.  Let's try removing all species lists from SL and check all SS rows are removed.
   test2 <- filterRDBESDataObject(myLohr,c("SLspeclistName"),c("xxx"))
   
   # Check number of SS rows before removing broken species list links (300)
   nrow(test2[["SS"]])
   # Try removing any broken links
   test3 <- removeBrokenSpeciesListLinks(test2)
   # Check number of SS rows after removing broken species list links - we've removed all SL rows so all SS entries shoudl be broken - number of SS rows shoudl now be zero - it is :-)
   nrow(test3[["SS"]])
   
   
   # Test 3) removeBrokenSpeciesListLinks() does not work correctly.  Change all SL entries to relate to "Dis" rather than "Lan" - the current removeBrokenSpeciesListLinks() function thinks everything is ok so doesn't remove any SS rows - however the correct behaviour should be to remove all SS rows
   test4 <- myLohr
   test4[["SL"]]$SLcatchFrac <- "Dis"
   # Note that all SS rows are Lan but all SL rows are Dis - we now have a mis-match between SL and SS
   unique(test4[["SS"]]$SScatchFra)
   unique(test4[["SL"]]$SLcatchFrac)
   
   # Check number of SS rows before removing broken species list links (300)
   nrow(test4[["SS"]])
   # Try removing any broken links
   test5 <- removeBrokenSpeciesListLinks(test4)
   # Check number of SS rows after removing broken species list links - we shoudl have zero rows because we don't have an SL entry that matches on Species List Name, catch fraction, country, and year - however we still have 300 rows :-(
   nrow(test5[["SS"]])
   
   
   
7. davidcurrie2001

   removed their assignment

   on Oct 13, 2022
8. nicholascarey commented on Oct 19, 2023

   

   nicholascarey

   on Oct 19, 2023

   Contributor

   More actions

   Revised and should be working now but needs tested.
9. nmprista

   added

   10_priorityChairs-label - priority issue (work on these when you can)Chairs-label - priority issue (work on these when you can)

   on Oct 22, 2023
10. rix133

    added

    9_needs_human_reviewPlease add more tests or review code some other wayPlease add more tests or review code some other way

    on Nov 3, 2023
11. nmprista

    removed

    10_priorityChairs-label - priority issue (work on these when you can)Chairs-label - priority issue (work on these when you can)

    on Nov 17, 2023
12. rix133 commented on Oct 14, 2024

    

    rix133

    on Oct 14, 2024

    Contributor

    More actions

    test-removeBrokenSpeciesListLinks needs the 4 use cases see above implemented as tests
13. rix133

    unassigned

    nicholascarey

    on Oct 7, 2026
14. rix133

    assigned

    Copilot

    and

    rix133

    on Oct 15, 2026
15. Copilot

    linked a pull request that will close this issueAdd tests for removeBrokenSpeciesListLinks matching on catch fraction, year and country #285on Oct 15, 2026