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/

msberends/AMR Issues

two genera/species that I can't seem to be able to classify using as.mo()
Updated 4 months ago1
Implement mathematically sound WISCA algorithm
Updated 4 months ago
AMR for R as a One Health approach
Updated 4 months ago
Support for working with multiple patient species for veterinary antibiograms?
Closed 5 months ago1
MIC decimals on dark RStudio too black
Closed 5 months ago
Improvements for `as.mic()` and MIC plotting
Closed 5 months ago
Errors in CLSI interpretation
Closed 7 months ago3
Add more LOINC codes for antibiotics
Closed 7 months ago1
Add `keep_synonyms = TRUE` to internal 1st isolate determination
Closed 7 months ago
Phenotype-based first isolate determination selects too many isolates
Closed 7 months ago1
Decrease time in printing tibbles
Closed 7 months ago1
EUCAST rules where there shouldn't be interpretations
Closed a year ago3
Report ATU of EUCAST guidelines
Closed a year ago1
Rework EUCAST Expert Rules
Closed 10 months ago1
UTI coding not being recognised in SIR interpretation
Closed 10 months ago12
how are IE cut-offs used in MIC graphs
Closed 10 months ago7
Possibility of adding EUCAST ECOFF values
Closed a year ago9
Update clinical_breakpoints to WHONET 2023
Closed a year ago
In `clinical_breakpoints`, some values in `ref_tbl` are missing
Closed a year ago
Problem with getting S. coagulans instead of old S. schleiferi coagulans
Closed a year ago
`minimum_matching_score` not always considered
Closed a year ago
typo in function name in tutorial for "Predicting future antimicrobial resistance using regression models"
Closed a year ago3
First isolate: ICU filtering based on wrong ordering
Closed a year ago
NA converted to first defined custom micro-organism
Closed a year ago5
Breakpoints prefer PK/PD
Closed a year ago
Clinical breakpoints for *Burkholderia mallei* and *Burkholderia pseudomallei* for all antibiotic might be wrong
Closed a year ago2
help with %like%
Closed a year ago3
as.sir function not found
Closed a year ago2
strange results, when using first isolate()
Closed a year ago3
set body site for SIR intepretation
Closed a year ago6
Checklist for v2.0.0
Closed a year ago
Azithromycin vs Salmonella spp.
Closed a year ago6
g.test doesn't handle zero counts
Closed a year ago4
Add `mo_pathogenicity()`
Closed a year ago1
Add Bartlett et al. (2022) for human pathogenicity?
Closed a year ago1
Antibiotic resistance prediction challenge 1
Closed a year ago2
Incorporate new GBIF backbone
Closed a year ago1
Gram stain does not recognise Actinomycetota
Closed a year ago
mdro function giving error for Table 5 Acinetobacter
Closed a year ago6
Candida auris mapped to only Candida by as.mo()
Closed a year ago6
No support for coercing antivirals
Closed 2 years ago1
Getting Error: RStudio not running after `mo_uncertainties()`
Closed 2 years ago1
Implement EUCAST System for Antimicrobial Abbreviations
Closed 2 years ago2
Add confidence intervals for AMR calculation
Closed 2 years ago2
Only mention determination of mo column once in dplyr groups
Closed 2 years ago1
New MICs to support
Closed 2 years ago1
Prevent unknown ATC codes from getting coerced
Closed 2 years ago
Clean up `mo_is_yeast()`
Closed 2 years ago1
Regard `""` as `NA` in `as.disk()`
Closed 2 years ago1
Add Ukrainian translation
Closed 2 years ago7