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reference/as.sir.md
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@@ -2,16 +2,13 @@
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/pkg/data.table/man/fctr.html) containing the
levels `S`, `SDD`, `I`, `R`, `NI`.
EUCAST or CLSI. \[as.sir()\] transforms the input to a new class
\[\`sir\`\], which is an ordered \[factor\] containing the levels \`S\`,
\`SDD\`, \`I\`, \`R\`, \`NI\`.
Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI
2011-2026, see *Details*. All breakpoints used for interpretation are
available in our
[clinical_breakpoints](https://amr-for-r.org/reference/clinical_breakpoints.md)
data set.
Breakpoints are currently implemented from EUCAST \`r
min(as.integer(gsub("\[^0-9\]", "", subset(AMR::clinical_breakpoints,
guideline
## Usage
@@ -367,8 +364,7 @@ disk diffusion diameters:
## Value
Ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with new
class `sir`
Ordered \[factor\] with new class \`sir\`
## Details
@@ -667,10 +663,10 @@ 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 2026-04-30 17:47:55 1 MIC amoxicillin Escherich… human 8
#> 2 2026-04-30 17:47:55 1 MIC cipro Escherich… human 0.256
#> 3 2026-04-30 17:47:55 1 DISK tobra Escherich… human 16
#> 4 2026-04-30 17:47:55 1 DISK genta Escherich… human 18
#> 1 2026-05-02 13:02:42 1 MIC amoxicillin Escherich… human 8
#> 2 2026-05-02 13:02:42 1 MIC cipro Escherich… human 0.256
#> 3 2026-05-02 13:02:42 1 DISK tobra Escherich… human 16
#> 4 2026-05-02 13:02:43 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>