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2026-03-20 16:11:30 +00:00
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reference/as.sir.md
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@@ -660,10 +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 2026-03-18 09:41:20 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-18 09:41:20 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-18 09:41:21 1 DISK tobra Escherich… human 16
#> 4 2026-03-18 09:41:21 1 DISK genta Escherich… human 18
#> 1 2026-03-20 16:07:38 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-20 16:07:38 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-20 16:07:39 1 DISK tobra Escherich… human 16
#> 4 2026-03-20 16:07:39 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>
@@ -671,17 +671,16 @@ sir_interpretation_history()
# \donttest{
# using parallel computing, which is available in base R:
as.sir(df_wide, parallel = TRUE, info = TRUE)
#> ℹ Returning previously coerced values for various antimicrobials. Run
#> `ab_reset_session()` to reset this. This note will be shown once per
#> session.
#> ℹ Returning a previously coerced value for an antimicrobial. Run
#> `ab_reset_session()` (`?AMR::ab_reset_session()`) to reset this. This note
#> will be shown once per session.
#>
#> Running in parallel mode using 3 out of 4 cores, on columns 'amoxicillin',
#> 'cipro', 'tobra', 'genta', and 'ERY'...
#> DONE
#> DONE
#>
#>
#> ℹ Run `sir_interpretation_history()` to retrieve a logbook with all details
#> of the breakpoint interpretations.
#> ℹ Run `sir_interpretation_history()` (`?AMR::sir_interpretation_history()`) to
#> retrieve a logbook with all details of the breakpoint interpretations.
#> microorganism amoxicillin cipro tobra genta ERY
#> 1 Escherichia coli S I S S R
@@ -797,44 +796,43 @@ if (require("dplyr")) {
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(...)`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the
#> CLSI interpretation guideline.
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> interpretation guideline.
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `cipro = (function (x, ...) ...`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the
#> CLSI interpretation guideline.
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> interpretation guideline.
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(...)`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the
#> CLSI interpretation guideline.
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> interpretation guideline.
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `mics = (function (x, ...) ...`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the
#> CLSI interpretation guideline.
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> interpretation guideline.
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(...)`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the
#> CLSI interpretation guideline.
#> Interpreting MIC values: 'antibiotic' (TESTAB, test Antibiotic), CLSI
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> interpretation guideline.
#> Interpreting MIC values: 'antibiotic' (TESTAB, test Antibiotic), CLSI 2025...
#> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic), CLSI
#> 2025...
#> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic), CLSI
#> 2025...
#> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic),
#> CLSI 2025...
#> Interpreting disk diffusion zones: 'antibiotic' (TESTAB, test Antibiotic),
#> CLSI 2025...
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `cipro = (function (x, ...) ...`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the
#> CLSI interpretation guideline.
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> interpretation guideline.
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(...)`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the
#> CLSI interpretation guideline.
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> interpretation guideline.
#> microorganism amoxicillin cipro tobra genta ERY
#> 1 Escherichia coli 8 <NA> S S R
@@ -865,8 +863,8 @@ as.sir(
# For CLEANING existing SIR values -------------------------------------
as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C"))
#> Warning: in `as.sir()`: 3 results truncated (38%) that were invalid antimicrobial
#> interpretations: "A", "B", and "C"
#> Warning: in `as.sir()` (`?AMR::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"
@@ -874,11 +872,13 @@ as.sir("<= 0.002; S") # will return "S"
#> [1] S
as.sir(c(1, 2, 3))
#> ℹ in `as.sir()`: Interpreting input value 1 as "S", 2 as "I", and 3 as "R"
#> ℹ in `as.sir()` (`?AMR::as.sir()`): Interpreting input value 1 as "S", 2 as
#> "I", and 3 as "R"
#> Class 'sir'
#> [1] S I R
as.sir(c(1, 2, 3), S = 3, I = 2, R = 1)
#> ℹ in `as.sir()`: Interpreting input value 1 as "R", 2 as "I", and 3 as "S"
#> ℹ in `as.sir()` (`?AMR::as.sir()`): Interpreting input value 1 as "R", 2 as
#> "I", and 3 as "S"
#> Class 'sir'
#> [1] R I S