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2026-06-26 07:36:21 +00:00
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88 changed files with 156 additions and 138 deletions
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reference/as.sir.md
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@@ -16,7 +16,7 @@ data set.
## Usage
``` r
as.sir(x, ...)
as.sir(x, ..., enforce_method = "auto")
NA_sir_
@@ -131,6 +131,13 @@ sir_interpretation_history(clean = FALSE)
selectors](https://amr-for-r.org/reference/antimicrobial_selectors.md),
e.g. `as.sir(df, penicillins())`.
- enforce_method:
A [character](https://rdrr.io/r/base/character.html) string to force
interpretation as a specific method, useful when the S3 class of `x`
is lost (e.g., when called from Python via rpy2). Must be one of
`"auto"` (default), `"mic"`, or `"disk"`.
Otherwise: arguments passed on to methods.
- threshold:
@@ -705,10 +712,10 @@ 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 2026-06-24 18:34:31 1 MIC amoxicillin Escherich… human 8
#> 2 2026-06-24 18:34:31 1 MIC cipro Escherich… human 0.256
#> 3 2026-06-24 18:34:32 1 DISK tobra Escherich… human 16
#> 4 2026-06-24 18:34:32 1 DISK genta Escherich… human 18
#> 1 2026-06-26 07:32:01 1 MIC amoxicillin Escherich… human 8
#> 2 2026-06-26 07:32:01 1 MIC cipro Escherich… human 0.256
#> 3 2026-06-26 07:32:01 1 DISK tobra Escherich… human 16
#> 4 2026-06-26 07:32:02 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>
@@ -829,7 +836,7 @@ if (require("dplyr")) {
#> ! 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, ...) ...`.
#> ℹ In argument: `cipro = (function (x, ..., enforce_method = "auto") ...`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> interpretation guideline.
@@ -839,7 +846,7 @@ if (require("dplyr")) {
#> ! 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, ...) ...`.
#> ℹ In argument: `mics = (function (x, ..., enforce_method = "auto") ...`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> interpretation guideline.
@@ -849,7 +856,7 @@ if (require("dplyr")) {
#> ! 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, ...) ...`.
#> ℹ In argument: `cipro = (function (x, ..., enforce_method = "auto") ...`.
#> Caused by warning:
#> ! Some MICs were converted to the nearest higher log2 level, following the CLSI
#> interpretation guideline.