Issue with Eucast Expert Rules (Stenotrophomonas maltophilia and CAZ)

[remi-leguern]

Using the function eucast_rules(), Stenotrophomonas maltophilia isolates should not be interpreted "R" to ceftazidime.

Indeed, it was updated in v3.1 of EUCAST Expert Rules ( http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf ) :
"Table 2: Ceftazidime R deleted for Stenotrophomonas maltophilia"

Anyways, thank you a lot for your work. This package is very useful to analyze antimicrobial resistance data.

[msberends]

That's completely true, thanks for the catch! Fixing this right away.

[msberends]

Now it keeps quiet 😄

eucast_rules(data.frame(mo = "S. maltophila",
                        cefta = "S"))
#> NOTE: Using column `mo` as input for `col_mo`.
#> NOTE: Auto-guessing columns suitable for analysis...
#> NOTE: Using column `cefta` as input for `CAZ` (ceftazidime).
#
# (...)
#
#> -----------------------------------------------------------------
#> EUCAST rules affected 0 out of 1 rows, making a total of 0 edits
#> => added 0 test results
#> => changed 0 test results
#> -----------------------------------------------------------------

This was fixed here to be precise. Thanks again.

[remi-leguern]

Thank you for your help. Best wishes, Rémi

…

On Wed, 23 Oct 2019 at 15:58, MS Berends ***@***.***> wrote: Now it keeps quiet 😄 eucast_rules(data.frame(mo = "S. maltophila", cefta = "S")) #> NOTE: Using column `mo` as input for `col_mo`. #> NOTE: Auto-guessing columns suitable for analysis... #> NOTE: Using column `cefta` as input for `CAZ` (ceftazidime). # # (...) # #> ----------------------------------------------------------------- #> EUCAST rules affected 0 out of 1 rows, making a total of 0 edits #> => added 0 test results #> => changed 0 test results #> ----------------------------------------------------------------- This was fixed here to be precise <3e5ab53#diff-19486c69b49c3c8fdcf665e230918dff>. Thanks again. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1?email_source=notifications&email_token=ANRZ5Y7DQX6XEJS6XI2N5BLQQBKBNA5CNFSM4JDK3LE2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECBQKUQ#issuecomment-545457490>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANRZ5YY6YOE3OIEYLQV4V53QQBKBNANCNFSM4JDK3LEQ> .