Interpreting CLSI values (blood) about amr HOT 12 CLOSED

No, just do:

remotes::install_github("msberends/AMR")

It will install the latest beta version to your computer and then you can just run your code again (you might need to refresh your R session). But this issue is not yet fixed, I'm now also fixing your other issue in one go 🙂

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In addition looking at the https://github.com/msberends/AMR/blob/master/data-raw/DRGLST1.xlsx table I think the values here are for animals

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Looking at the code I believe an additional filter here is required

filter(HOST=='HUMAN') %>%

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Nice catch! I removed all animal records from the file, and now:

data.frame(mo = "E. coli",
           AMC = 4) %>%
  as.rsi(guideline = "CLSI 2019")
#> NOTE: Using column `mo` as input for `col_mo`.
#> NOTE: Assuming column `AMC` (amoxicillin/clavulanic acid) contains MIC values.
#> => Interpreting MIC values of `AMC` (amoxicillin/clavulanic acid) using guideline CLSI 2019 ... OK.
#>        mo AMC
#> 1 E. coli   S

I'm running checks now and will then upload it to the master branch. I'll let you know when it's done!

You're just in time, I was about to release a new version to CRAN! So if you can confirm this is fixed, I will 😉

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Great - thank you.
How do I install locally. Check out code and devtools build?

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Survey completed

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No, just do:

remotes::install_github("msberends/AMR")

It will install the latest beta version to your computer and then you can just run your code again (you might need to refresh your R session). But this issue is not yet fixed, I'm now also fixing your other issue in one go 🙂

Let me know when it's ready for testing

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Ready! You can test the 'new' as.rsi() 😄

Thanks for filling in the survey!

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Sorry for the late reply. Was checking out my comparison and it's much improved. The fixes for human only and the conserve_capped_values work a treat.

I was running into some more discrepancies.

It turns out that exports from Vitek have values such as <=.25 (i.e with no leading 0). as.mic can't interpret this and converts the value to NA

I can solve this by transforming my dataframe as follows

 dplyr::mutate(across(-c(id,Species), str_replace, "([<>]=*)\\.", "\\10.")) 

would you consider making a modification to the as.mic function to accommodate this? Should I raise a new issue?

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No problem about the late reply, wasn’t that late!

Using across() already, nice 😜

Sure thing, I’ll fix it in the morning. New issue would be best, I’ll handle it. Many thanks again!

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Fix released to official R repository

Just a small notice: we released a new software version, containing the fix to this issue. Please update your version using either the user interface of your software, or by running:

install.packages("AMR")

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