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(v1.4.0.9033) documentation update

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dr. M.S. (Matthijs) Berends
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@ -15,13 +15,43 @@ After installing this package, R knows [**~70,000 distinct microbial species**](
This package is [fully independent of any other R package](https://en.wikipedia.org/wiki/Dependency_hell) and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package is [actively maintained](./news) and is free software (see [Copyright](#copyright)).
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<div class="main-content" style="display: inline-block;">
<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 and to also see the names of the countries.</p><br><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>
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##### With `AMR` (for R), you'll always have a knowledgeable microbiologist at your side!
```r
# AMR works great with dplyr, but it's not required or neccesary
library(AMR)
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)
```
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:
| 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 |
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