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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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uti is false bug? #163

Open theanita1 opened 3 weeks ago

theanita1 commented 3 weeks ago

ran a transformation of MIC to SIR with the following code agar<- agar %>% mutate_if(is.mic, as.sir, guideline = "EUCAST 2023", add_intrinsic_resistance = F, include_PKPD = F, uti = F) However, in the console, I received the following note: image

When I look at the sir_interpretation_history, overall 10% of the interpretation has been defined as UTI - have a csv of the sir interpretation history but it's too big - if it would be helpful can try and split just let me know

I know we've previously had this conversation (#108) but I can't see anything in there that would help. Am using package version 2.1.1.9068

msberends commented 3 weeks ago

I'll try to check it this week, that's weird.

So you're saying, it should never take UTI-breakpoints if you're setting uti = FALSE explicitly? I would think so myself 🙂

theanita1 commented 3 weeks ago

Yes, all my isolates are blood, so there should be no UTI interpretations

I ran the same code again but with only one year of data and saved as csv if that can be of help to see which drug/bug combos are going awry.

AGAR sir_interpretation_history.zip

Hopefully it's a quick fix because I need to clean my data haha