Comments (12)
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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📋 Please take part in our survey!
Now you're at it, please fill in our short questionnaire! You can fill it in completely anonymously. If you know others using this AMR
package, please ask them to fill it in too.
Your valuable input will help to improve the package and its functionalities 🙂
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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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Related Issues (20)
- two genera/species that I can't seem to be able to classify using as.mo() HOT 2
- AMR for R as a One Health approach
- Implement mathematically sound WISCA algorithm
- Update `microorganisms` data set to latest taxonomy HOT 9
- Add new logo for this AMR package to catch One Health approach
- Incorporate EUCAST 13 and 14 HOT 7
- To-do list for AMR v3.0.0
- CLSI 2024 Veterinary Breakpoints HOT 8
- uti argument in as.sir not working as expected HOT 10
- Veterinary breakpoint substitutions incorrect HOT 5
- MIssing/extra veterinary breakpoints HOT 2
- Need Update Some Microorganisms HOT 1
- AMR HOT 3
- Group isolates HOT 7
- Not all mo_transforms work with antibiogram HOT 1
- Check groups for antibiotics: aminoglycosides all right? HOT 1
- as.sir reports invalid results as coming from wrong columns HOT 2
- extra factor level in class SIR (as.sir/is.sir) HOT 5
- `as.mo()`: give preference to species if subspecies is non-existent
- Add denominators to each antibiotic in antibiogram HOT 2
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