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reference/as.sir.md
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@@ -4,8 +4,8 @@ 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://rdatatable.gitlab.io/data.table/reference/fctr.html)
containing the levels `S`, `SDD`, `I`, `R`, `NI`.
[factor](https://rdrr.io/pkg/data.table/man/fctr.html) containing the
levels `S`, `SDD`, `I`, `R`, `NI`.
Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI
2011-2025, see *Details*. All breakpoints used for interpretation are
@@ -27,12 +27,14 @@ is_sir_eligible(x, threshold = 0.05)
# Default S3 method
as.sir(x, S = "^(S|U|1)+$", I = "^(I|2)+$",
R = "^(R|3)+$", NI = "^(N|NI|V|4)+$", SDD = "^(SDD|D|H|5)+$",
WT = "^(WT|6)+$", NWT = "^(NWT|7)+$", NS = "^(NS|8)+$",
info = interactive(), ...)
# S3 method for class 'mic'
as.sir(x, mo = NULL, ab = deparse(substitute(x)),
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
capped_mic_handling = getOption("AMR_capped_mic_handling", "standard"),
as_wt_nwt = identical(breakpoint_type, "ECOFF"),
add_intrinsic_resistance = FALSE,
reference_data = AMR::clinical_breakpoints,
substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
@@ -45,6 +47,7 @@ as.sir(x, mo = NULL, ab = deparse(substitute(x)),
# S3 method for class 'disk'
as.sir(x, mo = NULL, ab = deparse(substitute(x)),
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
as_wt_nwt = identical(breakpoint_type, "ECOFF"),
add_intrinsic_resistance = FALSE,
reference_data = AMR::clinical_breakpoints,
substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
@@ -58,6 +61,7 @@ as.sir(x, mo = NULL, ab = deparse(substitute(x)),
as.sir(x, ..., col_mo = NULL,
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
capped_mic_handling = getOption("AMR_capped_mic_handling", "standard"),
as_wt_nwt = identical(breakpoint_type, "ECOFF"),
add_intrinsic_resistance = FALSE,
reference_data = AMR::clinical_breakpoints,
substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
@@ -127,7 +131,7 @@ disk diffusion diameters:
Maximum fraction of invalid antimicrobial interpretations of `x`, see
*Examples*.
- S, I, R, NI, SDD:
- S, I, R, NI, SDD, WT, NWT, NS:
A case-independent [regular
expression](https://rdrr.io/r/base/regex.html) to translate input to
@@ -218,6 +222,12 @@ disk diffusion diameters:
also be set with the package option
[`AMR_capped_mic_handling`](https://amr-for-r.org/reference/AMR-options.md).
- as_wt_nwt:
A [logical](https://rdrr.io/r/base/logical.html) to return
`"WT"`/`"NWT"` instead of `"S"`/`"R"`. Defaults to `TRUE` when using
ECOFFs, i.e., when `breakpoint_type` is set to `"ECOFF"`.
- add_intrinsic_resistance:
*(only useful when using a EUCAST guideline)* a
@@ -350,9 +360,8 @@ disk diffusion diameters:
## Value
Ordered
[factor](https://rdatatable.gitlab.io/data.table/reference/fctr.html)
with new class `sir`
Ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with new
class `sir`
## Details
@@ -495,7 +504,7 @@ options to set before analysis:
### After Interpretation
After using `as.sir()`, you can use the
[`eucast_rules()`](https://amr-for-r.org/reference/eucast_rules.md)
[`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
defined by EUCAST to (1) apply inferred susceptibility and resistance
based on results of other antimicrobials and (2) apply intrinsic
resistance based on taxonomic properties of a microorganism.
@@ -651,10 +660,10 @@ 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 2026-01-16 10:04:38 1 MIC amoxicillin Escherich… human 8
#> 2 2026-01-16 10:04:39 1 MIC cipro Escherich… human 0.256
#> 3 2026-01-16 10:04:39 1 DISK tobra Escherich… human 16
#> 4 2026-01-16 10:04:39 1 DISK genta Escherich… human 18
#> 1 2026-02-08 22:25:52 1 MIC amoxicillin Escherich… human 8
#> 2 2026-02-08 22:25:53 1 MIC cipro Escherich… human 0.256
#> 3 2026-02-08 22:25:53 1 DISK tobra Escherich… human 16
#> 4 2026-02-08 22:25:54 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>