mirror of
https://github.com/msberends/AMR.git
synced 2025-07-10 08:22:04 +02:00
(v1.5.0.9011) small dosage update
This commit is contained in:
31
index.md
31
index.md
@ -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())]
|
||||
```
|
||||
|
||||
#### Partners
|
||||
|
Reference in New Issue
Block a user