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2026-04-02 09:54:05 +00:00
parent d6c59896e9
commit d0fd6aa2cc
103 changed files with 293 additions and 265 deletions
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35
reference/interpretive_rules.md
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@@ -18,7 +18,7 @@ at default, see *Details*.
interpretive_rules(x, col_mo = NULL, info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), guideline = getOption("AMR_guideline", "EUCAST"),
verbose = FALSE, version_breakpoints = 15,
verbose = FALSE, version_breakpoints = 16,
version_expected_phenotypes = 1.2, version_expertrules = 3.3,
ampc_cephalosporin_resistance = NA, only_sir_columns = any(is.sir(x)),
custom_rules = NULL, overwrite = FALSE, ...)
@@ -119,17 +119,18 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
- version_breakpoints:
The version number to use for the EUCAST Clinical Breakpoints
guideline. Can be "15.0", "14.0", "13.1", "12.0", "11.0", or "10.0".
guideline. Can be .val 16.0, .val 15.0, .val 14.0, .val 13.1, .val
12.0, .val 11.0, or .val 10.0.
- version_expected_phenotypes:
The version number to use for the EUCAST Expected Phenotypes. Can be
"1.2".
.val 1.2.
- version_expertrules:
The version number to use for the EUCAST Expert Rules and Intrinsic
Resistance guideline. Can be "3.3", "3.2", or "3.1".
Resistance guideline. Can be .val 3.3, .val 3.2, or .val 3.1.
- ampc_cephalosporin_resistance:
@@ -196,7 +197,8 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
- administration:
Route of administration, either "", "im", "iv", "oral", or NA.
Route of administration, either .val , .val im, .val iv, .val oral, or
NA.
## Value
@@ -206,8 +208,9 @@ with all original and new values of the affected bug-drug combinations.
## Details
**Note:** This function does not translate MIC values to SIR values. Use
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) for that.
**Note:** This function does not translate MIC or disk values to SIR
values. Use [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) for
that.
**Note:** When ampicillin (AMP, J01CA01) is not available but
amoxicillin (AMX, J01CA04) is, the latter will be used for all rules
where there is a dependency on ampicillin. These drugs are
@@ -330,22 +333,22 @@ c <- eucast_rules(a, overwrite = TRUE, verbose = TRUE)
head(c)
#> row col mo_fullname old new rule rule_group
#> 1 1 AMX Staphylococcus aureus - S Breakpoints
#> 2 1 CXM Staphylococcus aureus - S Breakpoints
#> 3 1 CAZ Staphylococcus aureus - R Expected phenotypes
#> 4 1 COL Staphylococcus aureus - R Expected phenotypes
#> 5 2 CAZ Enterococcus faecalis - R Expected phenotypes
#> 6 2 COL Enterococcus faecalis - R Expected phenotypes
#> 2 1 CXM Staphylococcus aureus - I Breakpoints
#> 3 1 CXM Staphylococcus aureus I S Breakpoints
#> 4 1 CAZ Staphylococcus aureus - R Expected phenotypes
#> 5 1 COL Staphylococcus aureus - R Expected phenotypes
#> 6 2 CAZ Enterococcus faecalis - R Expected phenotypes
#> rule_name
#> 1 Staphylococcus
#> 2 Staphylococcus
#> 3 Table 4: Expected resistant phenotype in gram-positive bacteria
#> 3 Staphylococcus
#> 4 Table 4: Expected resistant phenotype in gram-positive bacteria
#> 5 Table 4: Expected resistant phenotype in gram-positive bacteria
#> 6 Table 4: Expected resistant phenotype in gram-positive bacteria
#> rule_source
#> 1 'EUCAST Clinical Breakpoint Tables' v15.0, 2025
#> 2 'EUCAST Clinical Breakpoint Tables' v15.0, 2025
#> 3 'EUCAST Expected Resistant Phenotypes' v1.2, 2023
#> 1 'EUCAST Clinical Breakpoint Tables' v16.0, 2026
#> 2 'EUCAST Clinical Breakpoint Tables' v16.0, 2026
#> 3 'EUCAST Clinical Breakpoint Tables' v16.0, 2026
#> 4 'EUCAST Expected Resistant Phenotypes' v1.2, 2023
#> 5 'EUCAST Expected Resistant Phenotypes' v1.2, 2023
#> 6 'EUCAST Expected Resistant Phenotypes' v1.2, 2023