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2026-03-22 19:55:49 +00:00
parent 3560dfd611
commit c95646d39c
120 changed files with 617 additions and 675 deletions
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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 2026-03-20 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
#> 1 2026-03-22 19:51:52 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-22 19:51:52 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-22 19:51:52 1 DISK tobra Escherich… human 16
#> 4 2026-03-22 19:51:53 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>
@@ -672,15 +672,15 @@ sir_interpretation_history()
# using parallel computing, which is available in base R:
as.sir(df_wide, parallel = TRUE, info = TRUE)
#> 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.
#> `?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
#>
#> ℹ Run `sir_interpretation_history()` (`?AMR::sir_interpretation_history()`) to
#> retrieve a logbook with all details of the breakpoint interpretations.
#> ℹ Run `?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
@@ -792,7 +792,7 @@ if (require("dplyr")) {
df_wide %>%
mutate_at(vars(cipro:genta), as.sir, mo = "E. coli", uti = TRUE)
}
#> ℹ For `aminopenicillins()` using column 'amoxicillin'
#> ℹ For `?aminopenicillins()` using column amoxicillin
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(...)`.
#> Caused by warning:
@@ -847,7 +847,7 @@ as.sir(
ab = "AMP",
guideline = "EUCAST"
)
#> Class 'sir'
#> Class <sir>
#> [1] R
as.sir(
@@ -856,30 +856,28 @@ as.sir(
ab = "ampicillin", # and `ab` with as.ab()
guideline = "EUCAST"
)
#> Class 'sir'
#> Class <sir>
#> [1] R
# For CLEANING existing SIR values -------------------------------------
as.sir(c("S", "SDD", "I", "R", "NI", "A", "B", "C"))
#> Warning: in `as.sir()` (`?AMR::as.sir()`): 3 results truncated (38%) that were invalid
#> antimicrobial interpretations: "A", "B", and "C"
#> Class 'sir'
#> 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"
#> Class 'sir'
#> Class <sir>
#> [1] S
as.sir(c(1, 2, 3))
#> ℹ in `as.sir()` (`?AMR::as.sir()`): Interpreting input value 1 as "S", 2 as
#> "I", and 3 as "R"
#> Class 'sir'
#> ℹ `?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()` (`?AMR::as.sir()`): Interpreting input value 1 as "R", 2 as
#> "I", and 3 as "S"
#> Class 'sir'
#> ℹ `?as.sir()`: Interpreting input value 1 as "R", 2 as "I", and 3 as "S"
#> Class <sir>
#> [1] R I S
sir_data <- as.sir(c(rep("S", 474), rep("I", 36), rep("R", 370)))