Cannot specify column for species designation in mdro() about amr

[msberends]

Great! Many thanks for your reply.

I squashed the bug. For mdro() and eucast_rules(), the col_mo argument can now contain any column name of your data. The problem was that the column name that you picked was also present in the microorganisms data set, leading to conflicting code.

The development version nows contains the fix to this issue. If you like, you can try the latest version yourself using:

install.packages("remotes") # if you haven't already
remotes::install_github("msberends/AMR")

[msberends]

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")

[msberends]

Hi Jane, many thanks for using our package!

No, that’s absolutely not the way it should behave. The intended behaviour is that it just works without requiring you to think about it 🙂

Would you be able to share the structure of your data here, by pasting the output of str(vitek_spp)? Feel free to remove the actual data it prints, I’m just curious for the column names and data types.

I think the problem might be that the microorganisms data set also contains a column ‘species’, but that should not pose a problem. Could you also try:

vitek_spp %>%
  rename(mybugs = species) %>%
  mdro()

Then my last question, which AMR package version are you using?

[jhawkey]

Okay, after running the following command (which converts the species column from character to the mo class, and then displaying the output of str(vitek_spp):

vitek_spp <-vitek_spp %>% select(-acquired_esbl) %>% filter(!is.na(AMP)) %>% mutate(species=as.mo(species))
str(vitek_spp)
tibble [403 × 20] (S3: tbl_df/tbl/data.frame)
 $ sampleID: chr [1:403] ...
 $ species : 'mo' chr [1:403] "B_KLBSL_PNMN" "B_KLBSL_PNMN" "B_KLBSL_PNMN" "B_KLBSL_PNMN" ...
 $ AMP     : chr [1:403] "R" "R" "R" "R" ...
 $ AUG     : chr [1:403] "R" "R" "S" "R" ...
[etc]

If I rename the species column to 'mybugs', then the mdro() function works correctly.