removeBrokenSpeciesListLinks filter not working properly

[nmprista]

removeBrokenSpeciesListLinks is filtering only on SLspeciesListName. Needs to filter based on SLyear, SLcatchFraction and SLcountry.

[davidcurrie2001]

I will create an example

[davidcurrie2001]

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"]])

[nicholascarey]

Revised and should be working now but needs tested.

[rix133]

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