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reference/as.sir.md
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@@ -93,7 +93,7 @@ disk diffusion diameters:
- **EUCAST Breakpoint tables for interpretation of MICs and zone
diameters**, 2011-2025, *European Committee on Antimicrobial
Susceptibility Testing* (EUCAST).
<https://www.eucast.org/clinical_breakpoints>.
<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/>.
- **WHONET** as a source for machine-reading the clinical breakpoints
([read more
@@ -228,7 +228,7 @@ disk diffusion diameters:
[intrinsic_resistant](https://amr-for-r.org/reference/intrinsic_resistant.md)
data set, that itself is based on ['EUCAST Expert Rules' and 'EUCAST
Intrinsic Resistance and Unusual Phenotypes'
v3.3](https://www.eucast.org/expert_rules_and_expected_phenotypes)
v3.3](https://www.eucast.org/bacteria/important-additional-information/expert-rules/)
(2021).
- reference_data:
@@ -537,7 +537,8 @@ base R's [`NA_character_`](https://rdrr.io/r/base/NA.html).
In 2019, the European Committee on Antimicrobial Susceptibility Testing
(EUCAST) has decided to change the definitions of susceptibility testing
categories S, I, and R (<https://www.eucast.org/newsiandr>).
categories S, I, and R
(<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/>).
This AMR package follows insight; use
[`susceptibility()`](https://amr-for-r.org/reference/proportion.md)
@@ -650,10 +651,10 @@ 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 2026-01-08 13:08:47 1 MIC amoxicillin Escherich… human 8
#> 2 2026-01-08 13:08:47 1 MIC cipro Escherich… human 0.256
#> 3 2026-01-08 13:08:48 1 DISK tobra Escherich… human 16
#> 4 2026-01-08 13:08:48 1 DISK genta Escherich… human 18
#> 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
#> # 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>
@@ -854,13 +855,13 @@ as.sir(
# For CLEANING existing SIR values -------------------------------------
as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C"))
#> Warning: in `as.sir()`: 3 results in index '21' truncated (38%) that were invalid
#> antimicrobial interpretations: "A", "B", and "C"
#> Warning: in `as.sir()`: 3 results truncated (38%) that were invalid antimicrobial
#> interpretations: "A", "B", and "C"
#> Class 'sir'
#> [1] S SDD I R NI <NA> <NA> <NA>
as.sir("<= 0.002; S") # will return "S"
#> Warning: in `as.sir()`: 1 result in index '21' truncated (100%) that were invalid
#> antimicrobial interpretations: "<= 0.002; S"
#> Warning: in `as.sir()`: 1 result truncated (100%) that were invalid antimicrobial
#> interpretations: "<= 0.002; S"
#> Class 'sir'
#> [1] <NA>