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(v1.4.0.9034) MIC printing update

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dr. M.S. (Matthijs) Berends
2020-12-09 09:40:50 +01:00
parent 2145f1d1ba
commit c9fc7e8a45
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@ -22,7 +22,7 @@ This package is [fully independent of any other R package](https://en.wikipedia.
Since its first public release in early 2018, this package has been downloaded from 135 countries. Click the map to enlarge.</p><br><br>
</div>
##### With `AMR` (for R), you'll always have a knowledgeable microbiologist at your side!
##### With `AMR` (for R), there's always a knowledgeable microbiologist by your side!
```r
# AMR works great with dplyr, but it's not required or neccesary
@ -31,26 +31,27 @@ library(dplyr)
example_isolates %>%
mutate(mo = mo_fullname(mo)) %>%
filter(mo_is_gram_positive()) %>%
select(mo, carbapenems(), glycopeptides())
#> NOTE: Using column 'mo' as input for mo_is_gram_positive()
#> Selecting cephalosporins: 'CAZ' (ceftazidime), 'CRO' (ceftriaxone),
#> 'CTX' (cefotaxime), 'CXM' (cefuroxime),
#> 'CZO' (cefazolin), 'FEP' (cefepime),
#> 'FOX' (cefoxitin)
#> Selecting glycopeptides: 'TEC' (teicoplanin), 'VAN' (vancomycin)
filter(mo_is_gram_negative(), mo_is_intrinsic_resistant(ab = "cefotax")) %>%
select(mo, aminoglycosides(), carbapenems())
#> NOTE: Using column 'mo' as input for mo_is_gram_negative()
#> NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant()
#> Selecting aminoglycosides: 'AMK' (amikacin), 'GEN' (gentamicin),
'KAN' (kanamycin), 'TOB' (tobramycin)
#> Selecting carbapenems: 'IPM' (imipenem), 'MEM' (meropenem)
```
With only having defined a filter on Gram-positive micro-organisms (`mo_is_gram_positive()`) and a selection of two antibiotic groups (`carbapenems()` and `glycopeptides()`), the reference data about [all bugs](./reference/microorganisms.html) and [drugs](./reference/antibiotics.html) in the `AMR` package make sure you get what you meant:
With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (`mo_is_gram_positive()` 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 | CAZ | CRO | CTX | CXM | CZO | FEP | FOX | TEC | VAN |
|:-----------------------------|:---:|:---:|:---:|:---:|:---:|:---:|:---:|:---:|:---:|
| *Enterococcus faecalis* | R | R | R | R | R | R | R | | S |
| *Enterococcus faecalis* | R | | R | R | R | R | R | | S |
| *Enterococcus faecalis* | R | R | R | R | R | R | R | | S |
| *Streptococcus* group B | R | S | S | S | S | S | S | | S |
| *Staphylococcus epidermidis* | R | | | S | | | | | S |
| *Enterococcus faecium* | R | R | R | R | R | R | R | | S |
| mo | 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 |
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