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(v1.6.0.9047) filter_ab_class() fixes

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dr. M.S. (Matthijs) Berends
2021-05-18 11:29:31 +02:00
parent 7028dcfa5b
commit 6920c0be41
29 changed files with 226 additions and 136 deletions
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14
index.md
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@ -30,13 +30,13 @@ example_isolates %>%
mutate(bacteria = mo_fullname(mo)) %>%
filter(mo_is_gram_negative(), mo_is_intrinsic_resistant(ab = "cefotax")) %>%
select(bacteria, aminoglycosides(), carbapenems())
#> NOTE: Using column 'mo' as input for mo_is_gram_negative()
#> NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant()
#> NOTE: Determining intrinsic resistance based on 'EUCAST Expert Rules' and
#> 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 (2020).
#> Selecting aminoglycosides: columns 'AMK' (amikacin), 'GEN' (gentamicin),
#> 'KAN' (kanamycin) and 'TOB' (tobramycin)
#> Selecting carbapenems: columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> 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 Expert Rules' and 'EUCAST Intrinsic
#> Resistance and Unusual Phenotypes' v3.2 (2020)
#> ℹ Applying `aminoglycosides()`: selecting columns 'AMK' (amikacin), 'GEN' (gentamicin), 'KAN'
#> (kanamycin) and 'TOB' (tobramycin)
#> ℹ Applying `carbapenems()`: selecting columns 'IPM' (imipenem) and 'MEM' (meropenem)
```
With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (`mo_is_gram_negative()` and `mo_is_intrinsic_resistant()`) and a column selection on two antibiotic groups (`aminoglycosides()` and `carbapenems()`), the reference data about [all microorganisms](./reference/microorganisms.html) and [all antibiotics](./reference/antibiotics.html) in the `AMR` package make sure you get what you meant: