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(v1.5.0.9011) small dosage update

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dr. M.S. (Matthijs) Berends
2021-01-24 23:27:11 +01:00
parent 286eaa9699
commit 24eb4453db
29 changed files with 207 additions and 110 deletions
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@ -32,13 +32,13 @@ library(AMR)
library(dplyr)
example_isolates %>%
mutate(mo = mo_fullname(mo)) %>%
mutate(bacteria = mo_fullname(mo)) %>%
filter(mo_is_gram_negative(), mo_is_intrinsic_resistant(ab = "cefotax")) %>%
select(mo, aminoglycosides(), carbapenems())
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 from 2020.
#> 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 (2020).
#> Selecting aminoglycosides: 'AMK' (amikacin), 'GEN' (gentamicin),
#> 'KAN' (kanamycin), 'TOB' (tobramycin)
#> Selecting carbapenems: 'IPM' (imipenem), 'MEM' (meropenem)
@ -46,23 +46,26 @@ example_isolates %>%
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:
| mo | AMK | GEN | KAN | TOB | IPM | MEM |
|:------------------------------|:---------:|:---------:|:---------:|:---------:|:---------:|:---------:|
|*Pseudomonas aeruginosa* | | I | R | S | S | |
|*Pseudomonas aeruginosa* | S | S | R | S | | S |
|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
|*Stenotrophomonas maltophilia* | R | R | R | R | R | R |
|*Pseudomonas aeruginosa* | S | S | R | S | | S |
|bacteria | AMK | GEN | KAN | TOB | IPM | MEM |
|:------------------------------|:---:|:---:|:---:|:---:|:---:|:---:|
|*Pseudomonas aeruginosa* | | I | R | S | S | |
|*Pseudomonas aeruginosa* | | I | R | S | S | |
|*Pseudomonas aeruginosa* | | I | R | S | S | |
|*Pseudomonas aeruginosa* | S | S | R | S | | S |
|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
|*Stenotrophomonas maltophilia* | R | R | R | R | R | R |
|*Pseudomonas aeruginosa* | S | S | R | S | | S |
|*Pseudomonas aeruginosa* | S | S | R | S | | S |
|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
A base R equivalent would be:
```r
example_isolates$mo <- mo_fullname(example_isolates$mo)
example_isolates$bacteria <- mo_fullname(example_isolates$mo)
example_isolates[which(mo_is_gram_negative() &
mo_is_intrinsic_resistant(ab = "cefotax")),
c("mo", aminoglycosides(), carbapenems())]
c("bacteria", aminoglycosides(), carbapenems())]
```
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