Comments (1)
So, the problem here was that the phenotype-based algorithm checked the antimicrobial results in the previous row only.
In the new version of AMR
, antimicrobial results of all isolates found in a patient will be checked. This leads to this result (notice how the phenotype
column are now not all TRUE
anymore):
tibble(mo = as.mo("S. aureus"),
fluclox = as.sir(rep(c("S", "R"), 5)),
cefoxitin = fluclox,
date = Sys.Date() - c(-10:-1),
id = "A") %>%
mutate(phenotype = first_isolate(method = "phenotype", col_patient_id = "id"),
episode = first_isolate(method = "episode", col_patient_id = "id"),
patient = first_isolate(method = "patient", col_patient_id = "id"),
isolate = first_isolate(method = "isolate", col_patient_id = "id"))
When adding another antibiotic, it can clearly be seen that the algorithm now works as expected:
tibble(mo = as.mo("S. aureus"),
fluclox = as.sir(rep(c("S", "R"), 5)),
cefoxitin = fluclox,
genta = as.sir(c(rep("S", 5), rep("R", 5))),
date = Sys.Date() - c(-10:-1),
id = "A") %>%
mutate(phenotype = first_isolate(method = "phenotype", col_patient_id = "id"),
episode = first_isolate(method = "episode", col_patient_id = "id"),
patient = first_isolate(method = "patient", col_patient_id = "id"),
isolate = first_isolate(method = "isolate", col_patient_id = "id"))
As intended, it now only returns TRUE
for each phenotype.
from amr.
Related Issues (20)
- Update clinical_breakpoints to WHONET 2023
- Rework EUCAST Expert Rules HOT 1
- how are IE cut-offs used in MIC graphs HOT 7
- Errors in CLSI interpretation HOT 3
- Decrease time in printing tibbles HOT 1
- Add `keep_synonyms = TRUE` to internal 1st isolate determination
- Add more LOINC codes for antibiotics HOT 1
- Support for working with multiple patient species for veterinary antibiograms? HOT 1
- MIC decimals on dark RStudio too black
- Improvements for `as.mic()` and MIC plotting
- 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
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from amr.