NA converted to first defined custom micro-organism

[bennsal]

When a data frame has an NA in the list of isolate names and you define a custom microorganism, then run as.mo, the NA is replaced with the name of the custom microorganism

 library(AMR)
Isolates <- c("Salmonella typhi", NA ,"Escherichia coli","Taleromyces marneffei")
Numbers <- c(1,2,3,4)
names <- data.frame(Isolates,Numbers)
as.mo(names$Isolates)
add_custom_microorganisms(
  data.frame(
    genus = "Talaromyces",
    species = "marneffei")) 
as.mo(names$Isolates)

[msberends]

Thanks for using our package!

True, that's a bug! Seems easy to fix, I'll look into it.

Many thanks for catching it.

[msberends]

I want to point out though, in your Isolates <- ... line you have Taleromyces with an 'E', while in the add_custom_microorganisms() call you have Talaromyces with an 'A' 🙂

Should not be much of a problem since the matching score will be high enough to end up with
Talaromyces marneffei (which is the correct name).

[bennsal]

My incoming files have a lot of odd spellings in them, though this was my typo! AMRforR does a great job of regularising them - thank you!

[msberends]

The problem was (strangely enough) an internal issue with SNOMED codes when using NA as input and using custom microorganism codes. Anyway, fixed now!

You're welcome to test the latest beta:

remotes::install_github("msberends/AMR")

[bennsal]

Thanks for the super quick fix!

On Mon, 8 May 2023, at 12:07 PM, Dr. Matthijs Berends wrote: The problem was (strangely enough) an internal issue with SNOMED codes when using `NA` as input and using custom microorganism codes. Anyway, fixed now! You're welcome to test the latest beta: `remotes::install_github("msberends/AMR")

`

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