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(v3.0.1.9041) add breakpoints 2026

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dr. M.S. (Matthijs) Berends
2026-03-30 10:01:49 +02:00
parent 9c95aa455c
commit 3a736bc484
37 changed files with 5975 additions and 345 deletions
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index.md
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@@ -10,7 +10,7 @@
even WISCA
- Provides the **full microbiological taxonomy** of ~79 000 distinct
species and extensive info of ~620 antimicrobial drugs
- Applies **CLSI 2011-2025** and **EUCAST 2011-2025** clinical and
- Applies **CLSI 2011-2026** and **EUCAST 2011-2026** clinical and
veterinary breakpoints, and ECOFFs, for MIC and disk zone
interpretation
- Corrects for duplicate isolates, **calculates** and **predicts** AMR
@@ -68,7 +68,7 @@ species**](./reference/microorganisms.html) (updated June 2024) and all
drugs**](./reference/antimicrobials.html) by name and code (including
ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all
about valid SIR and MIC values. The integral clinical breakpoint
guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are included, even
guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even
with epidemiological cut-off (ECOFF) values. It supports and can read
any data format, including WHONET data. This package works on Windows,
macOS and Linux with all versions of R since R-3.0 (April 2013). **It
@@ -171,14 +171,14 @@ example_isolates %>%
select(bacteria,
aminoglycosides(),
carbapenems())
#> ℹ Using column 'mo' as input for `mo_fullname()`
#> ℹ Using column 'mo' as input for `mo_is_gram_negative()`
#> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`
#> ℹ Using column mo as input for `mo_fullname()`
#> ℹ Using column mo as input for `mo_is_gram_negative()`
#> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant
#> Phenotypes' v1.2 (2023). This note will be shown once per session.
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 35 × 7
#> bacteria GEN TOB AMK KAN IPM MEM
#> <chr> <sir> <sir> <sir> <sir> <sir> <sir>
@@ -215,9 +215,9 @@ output format automatically (such as markdown, LaTeX, HTML, etc.).
``` r
antibiogram(example_isolates,
antimicrobials = c(aminoglycosides(), carbapenems()))
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
```
| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
@@ -344,15 +344,15 @@ out <- example_isolates %>%
# calculate AMR using resistance(), over all aminoglycosides and polymyxins:
summarise(across(c(aminoglycosides(), polymyxins()),
resistance))
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `polymyxins()` using column 'COL' (colistin)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `polymyxins()` using column COL (colistin)
#> Warning: There was 1 warning in `summarise()`.
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
#> ℹ In group 3: `ward = "Outpatient"`.
#> Caused by warning:
#> ! Introducing NA: only 23 results available for KAN in group: ward =
#> "Outpatient" (`minimum` = 30).
#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient"
#> (whilst `minimum = 30`).
out
#> # A tibble: 3 × 6
#> ward GEN TOB AMK KAN COL