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(v1.7.1.9005) ab class selectors for R-3.0 and R-3.1

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dr. M.S. (Matthijs) Berends
2021-06-22 12:16:42 +02:00
parent c44d9392ca
commit d04e83f494
41 changed files with 227 additions and 279 deletions
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22
index.md
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@ -25,16 +25,12 @@ library(AMR)
library(dplyr)
example_isolates %>%
mutate(bacteria = mo_fullname(mo)) %>%
filter(mo_is_gram_negative(), mo_is_intrinsic_resistant(ab = "cefotax")) %>%
select(bacteria, aminoglycosides(), carbapenems())
#> 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 For `aminoglycosides()` using columns: 'AMK' (amikacin), 'GEN' (gentamicin), 'KAN'
#> (kanamycin) and 'TOB' (tobramycin)
#> ℹ For `carbapenems()` using columns: 'IPM' (imipenem) and 'MEM' (meropenem)
mutate(bacteria = mo_fullname()) %>%
filter(mo_is_gram_negative(),
mo_is_intrinsic_resistant(ab = "cefotax")) %>%
select(bacteria,
aminoglycosides(),
carbapenems())
```
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:
@ -114,9 +110,9 @@ It will be downloaded and installed automatically. For RStudio, click on the men
#### Latest development version
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The latest and unpublished development version can be installed from GitHub in two ways: