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reference/as.sir.md
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@@ -3,7 +3,8 @@
Clean up existing SIR values, or interpret minimum inhibitory
concentration (MIC) values and disk diffusion diameters according to
EUCAST or CLSI. `as.sir()` transforms the input to a new class `sir`,
which is an ordered [factor](https://rdrr.io/r/base/factor.html)
which is an ordered
[factor](https://rdatatable.gitlab.io/data.table/reference/fctr.html)
containing the levels `S`, `SDD`, `I`, `R`, `NI`.
Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI
@@ -349,8 +350,9 @@ disk diffusion diameters:
## Value
Ordered [factor](https://rdrr.io/r/base/factor.html) with new class
`sir`
Ordered
[factor](https://rdatatable.gitlab.io/data.table/reference/fctr.html)
with new class `sir`
## Details
@@ -648,10 +650,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2025-12-23 10:09:01 1 MIC amoxicillin Escherich… human 8
#> 2 2025-12-23 10:09:02 1 MIC cipro Escherich… human 0.256
#> 3 2025-12-23 10:09:02 1 DISK tobra Escherich… human 16
#> 4 2025-12-23 10:09:02 1 DISK genta Escherich… human 18
#> 1 2026-01-06 22:18:05 1 MIC amoxicillin Escherich… human 8
#> 2 2026-01-06 22:18:05 1 MIC cipro Escherich… human 0.256
#> 3 2026-01-06 22:18:05 1 DISK tobra Escherich… human 16
#> 4 2026-01-06 22:18:06 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr>