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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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as.sir reports invalid results as coming from wrong columns #150

Closed andrewjmc closed 4 months ago

andrewjmc commented 4 months ago

Hello,

Sorry not to have a reproducible example to share, but I found that as.sir told me about two columns with inappropriate values.

in as.sir(): 77 results in column 'Minocycline' truncated (0%) that were invalid antimicrobial interpretations: "N", "P", and "PP"

However, on inspection the columns with the inappropriate values were actually near adjacent (+1 and +2 in each case). I wonder if the function is making a small error in the logic to pull out the column names.

Best wishes,

Andrew

msberends commented 4 months ago

I’ll look into it! Could you share the column names you have?

andrewjmc commented 4 months ago

Actually in trying to rerun it to make it do the same it hasn't failed. I wondered if it was due to previously duplicated antibiotic columns [e.g. Gentamicin (Low) and Gentamicin (High)] but that doesn't seem to be the case. I'll close and if I see it again investigate in more detail!