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109
reference/interpretive_rules.md
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@@ -15,58 +15,46 @@ at default, see *Details*.
## Usage
``` r
interpretive_rules(x, col_mo = NULL, info = interactive(),
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 = 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, add_if_missing = TRUE, ...)
"expected_phenotypes")),
guideline = getOption("AMR_guideline", "EUCAST"),
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,
add_if_missing = TRUE,
...
)
eucast_rules(x, col_mo = NULL, info = interactive(),
eucast_rules(
x,
col_mo = NULL,
info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), ...)
"expected_phenotypes")),
...
)
clsi_rules(x, col_mo = NULL, info = interactive(),
clsi_rules(
x,
col_mo = NULL,
info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), ...)
"expected_phenotypes")),
...
)
eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
```
## Source
- EUCAST Expert Rules. Version 2.0, 2012.
Leclercq et al. **EUCAST expert rules in antimicrobial susceptibility
testing.** *Clin Microbiol Infect.* 2013;19(2):141-60;
[doi:10.1111/j.1469-0691.2011.03703.x](https://doi.org/10.1111/j.1469-0691.2011.03703.x)
- EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes
Tables. Version 3.1, 2016.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf)
- EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf)
- EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf)
- EUCAST Breakpoint tables for interpretation of MICs and zone
diameters. Version 9.0, 2019.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx)
- EUCAST Breakpoint tables for interpretation of MICs and zone
diameters. Version 10.0, 2020.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx)
- EUCAST Breakpoint tables for interpretation of MICs and zone
diameters. Version 11.0, 2021.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx)
- EUCAST Breakpoint tables for interpretation of MICs and zone
diameters. Version 12.0, 2022.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.xlsx)
## Arguments
- x:
@@ -232,7 +220,7 @@ The file containing all interpretive rules is located here:
where applicable. For example, *Ochrobactrum anthropi* was renamed to
*Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did
not yet contain this new taxonomic name. The `AMR` package contains the
full microbial taxonomy updated until June 24th, 2024, see
full microbial taxonomy updated until 7th of May, 2026, see
[microorganisms](https://amr-for-r.org/reference/microorganisms.md).
### Custom Rules
@@ -285,6 +273,39 @@ links](https://amr-for-r.org/articles/datasets.html), or explore the
actual files in [our GitHub
repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
## References
- EUCAST Expert Rules. Version 2.0, 2012.
Leclercq et al. **EUCAST expert rules in antimicrobial susceptibility
testing.** *Clin Microbiol Infect.* 2013;19(2):141-60;
[doi:10.1111/j.1469-0691.2011.03703.x](https://doi.org/10.1111/j.1469-0691.2011.03703.x)
- EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes
Tables. Version 3.1, 2016.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf)
- EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf)
- EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf)
- EUCAST Breakpoint tables for interpretation of MICs and zone
diameters. Version 9.0, 2019.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx)
- EUCAST Breakpoint tables for interpretation of MICs and zone
diameters. Version 10.0, 2020.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx)
- EUCAST Breakpoint tables for interpretation of MICs and zone
diameters. Version 11.0, 2021.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx)
- EUCAST Breakpoint tables for interpretation of MICs and zone
diameters. Version 12.0, 2022.
[(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.xlsx)
## Examples
``` r