mirror of
https://github.com/msberends/AMR.git
synced 2025-12-15 23:10:28 +01:00
132 lines
3.3 KiB
Markdown
132 lines
3.3 KiB
Markdown
# Get ATC Properties from WHOCC Website
|
||
|
||
Gets data from the WHOCC website to determine properties of an
|
||
Anatomical Therapeutic Chemical (ATC) (e.g. an antimicrobial), such as
|
||
the name, defined daily dose (DDD) or standard unit.
|
||
|
||
## Usage
|
||
|
||
``` r
|
||
atc_online_property(atc_code, property, administration = "O",
|
||
url = "https://atcddd.fhi.no/atc_ddd_index/?code=%s&showdescription=no",
|
||
url_vet = "https://atcddd.fhi.no/atcvet/atcvet_index/?code=%s&showdescription=no")
|
||
|
||
atc_online_groups(atc_code, ...)
|
||
|
||
atc_online_ddd(atc_code, ...)
|
||
|
||
atc_online_ddd_units(atc_code, ...)
|
||
```
|
||
|
||
## Source
|
||
|
||
<https://atcddd.fhi.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/>
|
||
|
||
## Arguments
|
||
|
||
- atc_code:
|
||
|
||
A [character](https://rdrr.io/r/base/character.html) (vector) with ATC
|
||
code(s) of antimicrobials, will be coerced with
|
||
[`as.ab()`](https://amr-for-r.org/reference/as.ab.md) and
|
||
[`ab_atc()`](https://amr-for-r.org/reference/ab_property.md)
|
||
internally if not a valid ATC code.
|
||
|
||
- property:
|
||
|
||
Property of an ATC code. Valid values are `"ATC"`, `"Name"`, `"DDD"`,
|
||
`"U"` (`"unit"`), `"Adm.R"`, `"Note"` and `groups`. For this last
|
||
option, all hierarchical groups of an ATC code will be returned, see
|
||
*Examples*.
|
||
|
||
- administration:
|
||
|
||
Type of administration when using `property = "Adm.R"`, see *Details*.
|
||
|
||
- url:
|
||
|
||
URL of website of the WHOCC. The sign `%s` can be used as a
|
||
placeholder for ATC codes.
|
||
|
||
- url_vet:
|
||
|
||
URL of website of the WHOCC for veterinary medicine. The sign `%s` can
|
||
be used as a placeholder for ATC_vet codes (that all start with "Q").
|
||
|
||
- ...:
|
||
|
||
Arguments to pass on to `atc_property`.
|
||
|
||
## Details
|
||
|
||
Options for argument `administration`:
|
||
|
||
- `"Implant"` = Implant
|
||
|
||
- `"Inhal"` = Inhalation
|
||
|
||
- `"Instill"` = Instillation
|
||
|
||
- `"N"` = nasal
|
||
|
||
- `"O"` = oral
|
||
|
||
- `"P"` = parenteral
|
||
|
||
- `"R"` = rectal
|
||
|
||
- `"SL"` = sublingual/buccal
|
||
|
||
- `"TD"` = transdermal
|
||
|
||
- `"V"` = vaginal
|
||
|
||
Abbreviations of return values when using `property = "U"` (unit):
|
||
|
||
- `"g"` = gram
|
||
|
||
- `"mg"` = milligram
|
||
|
||
- `"mcg"` = microgram
|
||
|
||
- `"U"` = unit
|
||
|
||
- `"TU"` = thousand units
|
||
|
||
- `"MU"` = million units
|
||
|
||
- `"mmol"` = millimole
|
||
|
||
- `"ml"` = millilitre (e.g. eyedrops)
|
||
|
||
**N.B. This function requires an internet connection and only works if
|
||
the following packages are installed: `curl`, `rvest`, `xml2`.**
|
||
|
||
## Examples
|
||
|
||
``` r
|
||
# \donttest{
|
||
if (requireNamespace("curl") && requireNamespace("rvest") && requireNamespace("xml2")) {
|
||
# oral DDD (Defined Daily Dose) of amoxicillin
|
||
atc_online_property("J01CA04", "DDD", "O")
|
||
atc_online_ddd(ab_atc("amox"))
|
||
|
||
# parenteral DDD (Defined Daily Dose) of amoxicillin
|
||
atc_online_property("J01CA04", "DDD", "P")
|
||
|
||
atc_online_property("J01CA04", property = "groups") # search hierarchical groups of amoxicillin
|
||
}
|
||
#> Loading required namespace: rvest
|
||
#> ℹ in `atc_online_property()`: no properties found for ATC QG51AA03. Please
|
||
#> check
|
||
#> https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA03&showdescription=no.
|
||
#> ℹ in `atc_online_property()`: no properties found for ATC QJ01CA04. Please
|
||
#> check
|
||
#> https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&showdescription=no.
|
||
#> [1] "ANTIINFECTIVES FOR SYSTEMIC USE"
|
||
#> [2] "ANTIBACTERIALS FOR SYSTEMIC USE"
|
||
#> [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"
|
||
#> [4] "Penicillins with extended spectrum"
|
||
# }
|
||
```
|