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reference/clinical_breakpoints.md
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@@ -7,12 +7,12 @@ ECOFFs.
These breakpoints are currently implemented:
- For **clinical microbiology**: EUCAST 2011-2025 and CLSI 2011-2025;
- For **clinical microbiology**: EUCAST 2011-2026 and CLSI 2011-2026;
- For **veterinary microbiology**: EUCAST 2021-2025 and CLSI 2019-2025;
- For **veterinary microbiology**: EUCAST 2021-2026 and CLSI 2019-2026;
- For **ECOFFs** (Epidemiological Cut-off Values): EUCAST 2020-2025 and
CLSI 2022-2025.
- For **ECOFFs** (Epidemiological Cut-off Values): EUCAST 2020-2026 and
CLSI 2022-2026.
Use [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) to transform
MICs or disks measurements to SIR values.
@@ -25,8 +25,8 @@ clinical_breakpoints
## Format
A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 40
217 observations and 14 variables:
A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 45
797 observations and 14 variables:
- `guideline`
Name of the guideline
@@ -80,7 +80,7 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 40
A [logical](https://rdrr.io/r/base/logical.html) value
(`TRUE`/`FALSE`) to indicate whether the intermediate range between
"S" and "R" should be interpreted as "SDD", instead of "I". This
currently applies to 48 breakpoints.
currently applies to 72 breakpoints.
## Details
@@ -154,20 +154,20 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
``` r
clinical_breakpoints
#> # A tibble: 40,217 × 14
#> # A tibble: 45,797 × 14
#> guideline type host method site mo rank_index ab ref_tbl
#> <chr> <chr> <chr> <chr> <chr> <mo> <dbl> <ab> <chr>
#> 1 EUCAST 2025 human human DISK NA B_ACHRMB_XYLS 2 MEM A. xylo…
#> 2 EUCAST 2025 human human MIC NA B_ACHRMB_XYLS 2 MEM A. xylo…
#> 3 EUCAST 2025 human human DISK NA B_ACHRMB_XYLS 2 SXT A. xylo…
#> 4 EUCAST 2025 human human MIC NA B_ACHRMB_XYLS 2 SXT A. xylo…
#> 5 EUCAST 2025 human human DISK NA B_ACHRMB_XYLS 2 TZP A. xylo…
#> 6 EUCAST 2025 human human MIC NA B_ACHRMB_XYLS 2 TZP A. xylo…
#> 7 EUCAST 2025 human human DISK NA B_ACNTB 3 AMK Acineto…
#> 8 EUCAST 2025 human human DISK Uncomp… B_ACNTB 3 AMK Acineto…
#> 9 EUCAST 2025 human human MIC NA B_ACNTB 3 AMK Acineto…
#> 10 EUCAST 2025 human human MIC Uncomp… B_ACNTB 3 AMK Acineto…
#> # ℹ 40,207 more rows
#> 1 EUCAST 2026 human human DISK NA B_ACHRMB_XYLS 2 MEM A. xylo…
#> 2 EUCAST 2026 human human MIC NA B_ACHRMB_XYLS 2 MEM A. xylo…
#> 3 EUCAST 2026 human human DISK NA B_ACHRMB_XYLS 2 SXT A. xylo…
#> 4 EUCAST 2026 human human MIC NA B_ACHRMB_XYLS 2 SXT A. xylo…
#> 5 EUCAST 2026 human human DISK NA B_ACHRMB_XYLS 2 TZP A. xylo…
#> 6 EUCAST 2026 human human MIC NA B_ACHRMB_XYLS 2 TZP A. xylo…
#> 7 EUCAST 2026 human human DISK NA B_ACNTB 3 AMK Acineto…
#> 8 EUCAST 2026 human human DISK Uncomp… B_ACNTB 3 AMK Acineto…
#> 9 EUCAST 2026 human human MIC NA B_ACNTB 3 AMK Acineto…
#> 10 EUCAST 2026 human human MIC Uncomp… B_ACNTB 3 AMK Acineto…
#> # ℹ 45,787 more rows
#> # ℹ 5 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>,
#> # uti <lgl>, is_SDD <lgl>
```