how are IE cut-offs used in MIC graphs
theanita1 opened this issue · comments
Hi Mattjis
For P. aeruginosa and Gentamicin using EUCAST 2022, there are no defined cut-offs, rather it sends you to the MIC distribution database.
However, in my MIC graph for that same drug/bug combo it appears as such:
I have another MIC graph where there are no cut-offs available (S. aureus and Mupirocin) and the bars are grey
Can you explain what's going on with the P. aero/Gentamicin chart? I've got PKPD turned off in my MIC interpretation
Cheers
I will have a look at this. Might be due to species groups that WHONET introduced which we use. I'll get back to you!
That's because PK/PD rules are (or actually: were) always used for getting the interpretations in plots. That should be settable by the user , so that's now fixed, all plotting functions gained the include_PKPD argument that as.sir() also has. So, if you've set this to FALSE, you will now get this:
Moreover, the subtitle will now always contain the reference table from the guideline, like this:
Still working on some internal tests, it's not on GitHub yet, but will be in a moment :)
All is right it seems!
Thanks for the update, I'm not sure it's working for me, but that's because all my Pseudomonas charts are now interpreting as Acinetobacter?
autoplot(pseudo_mic$GEN, mo = "Pseudomonas", ab = "Gentamicin", guideline = "EUCAST 2022", include_PKPD = F)
Yes, that’s because Pseudomonas are Coryneform bacteria. According to WHONET, Pseudomonas species are part of that group and should be interpreted as such. I’ll look up the EUCAST guideline today to see if this is right or wrong.
Appeared to be the same bug introduced in #108