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(v1.4.0.9038) docu update

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dr. M.S. (Matthijs) Berends
2020-12-13 13:44:04 +01:00
parent c8bcecf232
commit ac22b8d5c1
16 changed files with 62 additions and 66 deletions
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index.md
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@ -19,7 +19,7 @@ This package is [fully independent of any other R package](https://en.wikipedia.
<p>
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a>
<strong>Used in 135 countries</strong><br>
Since its first public release in early 2018, this package has been downloaded from 135 countries. Click the map to enlarge.</p><br><br>
Since its first public release in early 2018, this package has been downloaded from 135 countries. Click the map to enlarge and to see the country names.</p>
</div>
##### With `AMR` (for R), there's always a knowledgeable microbiologist by your side!
@ -36,17 +36,15 @@ example_isolates %>%
#> 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)
#> 'KAN' (kanamycin), 'TOB' (tobramycin)
#> Selecting carbapenems: 'IPM' (imipenem), 'MEM' (meropenem)
```
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:
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* | | 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 |