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msberends / AMR

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.
https://msberends.github.io/AMR/
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Issue with Eucast Expert Rules (Stenotrophomonas maltophilia and CAZ) #1

Closed remi-leguern closed 4 years ago

remi-leguern commented 4 years ago

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 commented 4 years ago

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

msberends commented 4 years ago

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 commented 4 years ago

Thank you for your help.

Best wishes,

Rémi

On Wed, 23 Oct 2019 at 15:58, MS Berends notifications@github.com 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 https://github.com/msberends/AMR/commit/3e5ab53209268b84163c34676706608463767092#diff-19486c69b49c3c8fdcf665e230918dff. Thanks again.

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