# Get Properties of an Antibiotic
Use these functions to return a specific property of an antibiotic from
the [antimicrobials](https://amr-for-r.org/reference/antimicrobials.md)
data set. All input values will be evaluated internally with
[`as.ab()`](https://amr-for-r.org/reference/as.ab.md).
## Usage
``` r
ab_name(x, language = get_AMR_locale(), tolower = FALSE, ...)
ab_cid(x, ...)
ab_synonyms(x, ...)
ab_tradenames(x, ...)
ab_group(x, language = get_AMR_locale(), ...)
ab_atc(x, only_first = FALSE, ...)
ab_atc_group1(x, language = get_AMR_locale(), ...)
ab_atc_group2(x, language = get_AMR_locale(), ...)
ab_loinc(x, ...)
ab_ddd(x, administration = "oral", ...)
ab_ddd_units(x, administration = "oral", ...)
ab_info(x, language = get_AMR_locale(), ...)
ab_url(x, open = FALSE, ...)
ab_property(x, property = "name", language = get_AMR_locale(), ...)
set_ab_names(data, ..., property = "name", language = get_AMR_locale(),
snake_case = NULL)
```
## Arguments
- x:
Any (vector of) text that can be coerced to a valid antibiotic drug
code with [`as.ab()`](https://amr-for-r.org/reference/as.ab.md).
- language:
Language of the returned text - the default is the current system
language (see
[`get_AMR_locale()`](https://amr-for-r.org/reference/translate.md))
and can also be set with the package option
[`AMR_locale`](https://amr-for-r.org/reference/AMR-options.md). Use
`language = NULL` or `language = ""` to prevent translation.
- tolower:
A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
the first [character](https://rdrr.io/r/base/character.html) of every
output should be transformed to a lower case
[character](https://rdrr.io/r/base/character.html). This will lead to
e.g. "polymyxin B" and not "polymyxin b".
- ...:
In case of `set_ab_names()` and `data` is a
[data.frame](https://rdrr.io/r/base/data.frame.html): columns to
select (supports tidy selection such as `column1:column4`), otherwise
other arguments passed on to
[`as.ab()`](https://amr-for-r.org/reference/as.ab.md).
- only_first:
A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
only the first ATC code must be returned, with giving preference to
J0-codes (i.e., the antimicrobial drug group).
- administration:
Way of administration, either `"oral"` or `"iv"`.
- open:
Browse the URL using
[`utils::browseURL()`](https://rdrr.io/r/utils/browseURL.html).
- property:
One of the column names of one of the
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md)
data set: `vector_or(colnames(antimicrobials), sort = FALSE)`.
- data:
A [data.frame](https://rdrr.io/r/base/data.frame.html) of which the
columns need to be renamed, or a
[character](https://rdrr.io/r/base/character.html) vector of column
names.
- snake_case:
A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
the names should be in so-called [snake
case](https://en.wikipedia.org/wiki/Snake_case): in lower case and all
spaces/slashes replaced with an underscore (`_`).
## Value
- An [integer](https://rdrr.io/r/base/integer.html) in case of
`ab_cid()`
- A named [list](https://rdrr.io/r/base/list.html) in case of
`ab_info()` and multiple `ab_atc()`/`ab_synonyms()`/`ab_tradenames()`
- A [double](https://rdrr.io/r/base/double.html) in case of `ab_ddd()`
- A [data.frame](https://rdrr.io/r/base/data.frame.html) in case of
`set_ab_names()`
- A [character](https://rdrr.io/r/base/character.html) in all other
cases
## Details
All output [will be
translated](https://amr-for-r.org/reference/translate.md) where
possible.
The function `ab_url()` will return the direct URL to the official WHO
website. A warning will be returned if the required ATC code is not
available.
The function `set_ab_names()` is a special column renaming function for
[data.frame](https://rdrr.io/r/base/data.frame.html)s. It renames
columns names that resemble antimicrobial drugs. It always makes sure
that the new column names are unique. If `property = "atc"` is set,
preference is given to ATC codes from the J-group.
## Source
World Health Organization (WHO) Collaborating Centre for Drug Statistics
Methodology:
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER:
## Download Our Reference Data
All reference data sets in the AMR package - including information on
microorganisms, antimicrobials, and clinical breakpoints - are freely
available for download in multiple formats: R, MS Excel, Apache Feather,
Apache Parquet, SPSS, and Stata.
For maximum compatibility, we also provide machine-readable,
tab-separated plain text files suitable for use in any software,
including laboratory information systems.
Visit [our website for direct download
links](https://amr-for-r.org/articles/datasets.html), or explore the
actual files in [our GitHub
repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
## See also
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md)
## Examples
``` r
# all properties:
ab_name("AMX")
#> [1] "Amoxicillin"
ab_atc("AMX")
#> [1] "J01CA04" "QG51AA03" "QJ01CA04"
ab_cid("AMX")
#> [1] 33613
ab_synonyms("AMX")
#> [1] "acuotricina" "alfamox" "alfida" "amitron"
#> [5] "amoclen" "amodex" "amoksicillin" "amolin"
#> [9] "amopen" "amopenixin" "amophar" "amoran"
#> [13] "amoxi" "amoxicaps" "amoxicilina" "amoxicilline"
#> [17] "amoxicillinum" "amoxidal" "amoxiden" "amoxil"
#> [21] "amoxillat" "amoxina" "amoxine" "amoxipen"
#> [25] "amoxivet" "amoxycillin" "amoxycillinsalt" "amoxyke"
#> [29] "anemolin" "aspenil" "atoksilin" "bristamox"
#> [33] "cemoxin" "ciblor" "clamoxyl" "damoxy"
#> [37] "danoxillin" "delacillin" "demoksil" "dispermox"
#> [41] "efpenix" "eupen" "flemoxin" "flemoxine"
#> [45] "galenamox" "gramidil" "hiconcil" "himinomax"
#> [49] "histocillin" "ibiamox" "imacillin" "izoltil"
#> [53] "kentrocyllin" "lamoxy" "largopen" "larotid"
#> [57] "matasedrin" "metifarma" "moksilin" "moxacin"
#> [61] "moxal" "moxaline" "moxatag" "neotetranase"
#> [65] "novabritine" "ospamox" "pacetocin" "pamocil"
#> [69] "paradroxil" "pasetocin" "penamox" "piramox"
#> [73] "promoxil" "quimiopen" "remoxil" "riotapen"
#> [77] "robamox" "sawacillin" "siganopen" "simplamox"
#> [81] "sintopen" "sumox" "topramoxin" "trifamox"
#> [85] "trimox" "unicillin" "utimox" "velamox"
#> [89] "vetramox" "wymox" "zamocillin" "zamocilline"
#> [93] "zimox"
ab_tradenames("AMX")
#> [1] "acuotricina" "alfamox" "alfida" "amitron"
#> [5] "amoclen" "amodex" "amoksicillin" "amolin"
#> [9] "amopen" "amopenixin" "amophar" "amoran"
#> [13] "amoxi" "amoxicaps" "amoxicilina" "amoxicilline"
#> [17] "amoxicillinum" "amoxidal" "amoxiden" "amoxil"
#> [21] "amoxillat" "amoxina" "amoxine" "amoxipen"
#> [25] "amoxivet" "amoxycillin" "amoxycillinsalt" "amoxyke"
#> [29] "anemolin" "aspenil" "atoksilin" "bristamox"
#> [33] "cemoxin" "ciblor" "clamoxyl" "damoxy"
#> [37] "danoxillin" "delacillin" "demoksil" "dispermox"
#> [41] "efpenix" "eupen" "flemoxin" "flemoxine"
#> [45] "galenamox" "gramidil" "hiconcil" "himinomax"
#> [49] "histocillin" "ibiamox" "imacillin" "izoltil"
#> [53] "kentrocyllin" "lamoxy" "largopen" "larotid"
#> [57] "matasedrin" "metifarma" "moksilin" "moxacin"
#> [61] "moxal" "moxaline" "moxatag" "neotetranase"
#> [65] "novabritine" "ospamox" "pacetocin" "pamocil"
#> [69] "paradroxil" "pasetocin" "penamox" "piramox"
#> [73] "promoxil" "quimiopen" "remoxil" "riotapen"
#> [77] "robamox" "sawacillin" "siganopen" "simplamox"
#> [81] "sintopen" "sumox" "topramoxin" "trifamox"
#> [85] "trimox" "unicillin" "utimox" "velamox"
#> [89] "vetramox" "wymox" "zamocillin" "zamocilline"
#> [93] "zimox"
ab_group("AMX")
#> [1] "Beta-lactams/penicillins"
ab_atc_group1("AMX")
#> [1] "Beta-lactam antibacterials, penicillins"
ab_atc_group2("AMX")
#> [1] "Penicillins with extended spectrum"
ab_url("AMX")
#> Amoxicillin
#> "https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04&showdescription=no"
# smart lowercase transformation
ab_name(x = c("AMC", "PLB"))
#> [1] "Amoxicillin/clavulanic acid" "Polymyxin B"
ab_name(x = c("AMC", "PLB"), tolower = TRUE)
#> [1] "amoxicillin/clavulanic acid" "polymyxin B"
# defined daily doses (DDD)
ab_ddd("AMX", "oral")
#> [1] 1.5
ab_ddd_units("AMX", "oral")
#> [1] "g"
ab_ddd("AMX", "iv")
#> [1] 3
ab_ddd_units("AMX", "iv")
#> [1] "g"
ab_info("AMX") # all properties as a list
#> $ab
#> [1] "AMX"
#>
#> $cid
#> [1] 33613
#>
#> $name
#> [1] "Amoxicillin"
#>
#> $group
#> [1] "Beta-lactams/penicillins"
#>
#> $atc
#> [1] "J01CA04" "QG51AA03" "QJ01CA04"
#>
#> $atc_group1
#> [1] "Beta-lactam antibacterials, penicillins"
#>
#> $atc_group2
#> [1] "Penicillins with extended spectrum"
#>
#> $tradenames
#> [1] "acuotricina" "alfamox" "alfida" "amitron"
#> [5] "amoclen" "amodex" "amoksicillin" "amolin"
#> [9] "amopen" "amopenixin" "amophar" "amoran"
#> [13] "amoxi" "amoxicaps" "amoxicilina" "amoxicilline"
#> [17] "amoxicillinum" "amoxidal" "amoxiden" "amoxil"
#> [21] "amoxillat" "amoxina" "amoxine" "amoxipen"
#> [25] "amoxivet" "amoxycillin" "amoxycillinsalt" "amoxyke"
#> [29] "anemolin" "aspenil" "atoksilin" "bristamox"
#> [33] "cemoxin" "ciblor" "clamoxyl" "damoxy"
#> [37] "danoxillin" "delacillin" "demoksil" "dispermox"
#> [41] "efpenix" "eupen" "flemoxin" "flemoxine"
#> [45] "galenamox" "gramidil" "hiconcil" "himinomax"
#> [49] "histocillin" "ibiamox" "imacillin" "izoltil"
#> [53] "kentrocyllin" "lamoxy" "largopen" "larotid"
#> [57] "matasedrin" "metifarma" "moksilin" "moxacin"
#> [61] "moxal" "moxaline" "moxatag" "neotetranase"
#> [65] "novabritine" "ospamox" "pacetocin" "pamocil"
#> [69] "paradroxil" "pasetocin" "penamox" "piramox"
#> [73] "promoxil" "quimiopen" "remoxil" "riotapen"
#> [77] "robamox" "sawacillin" "siganopen" "simplamox"
#> [81] "sintopen" "sumox" "topramoxin" "trifamox"
#> [85] "trimox" "unicillin" "utimox" "velamox"
#> [89] "vetramox" "wymox" "zamocillin" "zamocilline"
#> [93] "zimox"
#>
#> $loinc
#> [1] "101498-4" "15-8" "16-6" "16365-9" "17-4" "18-2"
#> [7] "18861-5" "18862-3" "19-0" "20-8" "21-6" "22-4"
#> [13] "25274-2" "25310-4" "3344-9" "55614-2" "55615-9" "55616-7"
#> [19] "6976-5" "6977-3" "80133-2"
#>
#> $ddd
#> $ddd$oral
#> $ddd$oral$amount
#> [1] 1.5
#>
#> $ddd$oral$units
#> [1] "g"
#>
#>
#> $ddd$iv
#> $ddd$iv$amount
#> [1] 3
#>
#> $ddd$iv$units
#> [1] "g"
#>
#>
#>
# all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':
ab_atc("AMP")
#> [1] "J01CA01" "QJ01CA01" "QJ51CA01" "QS01AA19" "S01AA19"
ab_group("J01CA01")
#> [1] "Beta-lactams/penicillins"
ab_loinc("ampicillin")
#> [1] "101477-8" "101478-6" "18864-9" "18865-6" "20374-5" "21066-6"
#> [7] "23618-2" "27-3" "28-1" "29-9" "30-7" "31-5"
#> [13] "32-3" "33-1" "3355-5" "33562-0" "33919-2" "34-9"
#> [19] "43883-8" "43884-6" "6979-9" "6980-7" "87604-5"
ab_name("21066-6")
#> [1] "Ampicillin"
ab_name(6249)
#> [1] "Ampicillin"
ab_name("J01CA01")
#> [1] "Ampicillin"
# spelling from different languages and dyslexia are no problem
ab_atc("ceftriaxon")
#> [1] "J01DD04" "QJ01DD04"
ab_atc("cephtriaxone")
#> [1] "J01DD04" "QJ01DD04"
ab_atc("cephthriaxone")
#> [1] "J01DD04" "QJ01DD04"
ab_atc("seephthriaaksone")
#> [1] "J01DD04" "QJ01DD04"
# use set_ab_names() for renaming columns
colnames(example_isolates)
#> [1] "date" "patient" "age" "gender" "ward" "mo" "PEN"
#> [8] "OXA" "FLC" "AMX" "AMC" "AMP" "TZP" "CZO"
#> [15] "FEP" "CXM" "FOX" "CTX" "CAZ" "CRO" "GEN"
#> [22] "TOB" "AMK" "KAN" "TMP" "SXT" "NIT" "FOS"
#> [29] "LNZ" "CIP" "MFX" "VAN" "TEC" "TCY" "TGC"
#> [36] "DOX" "ERY" "CLI" "AZM" "IPM" "MEM" "MTR"
#> [43] "CHL" "COL" "MUP" "RIF"
colnames(set_ab_names(example_isolates))
#> [1] "date" "patient"
#> [3] "age" "gender"
#> [5] "ward" "mo"
#> [7] "benzylpenicillin" "oxacillin"
#> [9] "flucloxacillin" "amoxicillin"
#> [11] "amoxicillin_clavulanic_acid" "ampicillin"
#> [13] "piperacillin_tazobactam" "cefazolin"
#> [15] "cefepime" "cefuroxime"
#> [17] "cefoxitin" "cefotaxime"
#> [19] "ceftazidime" "ceftriaxone"
#> [21] "gentamicin" "tobramycin"
#> [23] "amikacin" "kanamycin"
#> [25] "trimethoprim" "trimethoprim_sulfamethoxazole"
#> [27] "nitrofurantoin" "fosfomycin"
#> [29] "linezolid" "ciprofloxacin"
#> [31] "moxifloxacin" "vancomycin"
#> [33] "teicoplanin" "tetracycline"
#> [35] "tigecycline" "doxycycline"
#> [37] "erythromycin" "clindamycin"
#> [39] "azithromycin" "imipenem"
#> [41] "meropenem" "metronidazole"
#> [43] "chloramphenicol" "colistin"
#> [45] "mupirocin" "rifampicin"
colnames(set_ab_names(example_isolates, NIT:VAN))
#> [1] "date" "patient" "age" "gender"
#> [5] "ward" "mo" "PEN" "OXA"
#> [9] "FLC" "AMX" "AMC" "AMP"
#> [13] "TZP" "CZO" "FEP" "CXM"
#> [17] "FOX" "CTX" "CAZ" "CRO"
#> [21] "GEN" "TOB" "AMK" "KAN"
#> [25] "TMP" "SXT" "nitrofurantoin" "fosfomycin"
#> [29] "linezolid" "ciprofloxacin" "moxifloxacin" "vancomycin"
#> [33] "TEC" "TCY" "TGC" "DOX"
#> [37] "ERY" "CLI" "AZM" "IPM"
#> [41] "MEM" "MTR" "CHL" "COL"
#> [45] "MUP" "RIF"
# \donttest{
if (require("dplyr")) {
example_isolates %>%
set_ab_names()
# this does the same:
example_isolates %>%
rename_with(set_ab_names)
# set_ab_names() works with any AB property:
example_isolates %>%
set_ab_names(property = "atc")
example_isolates %>%
set_ab_names(where(is.sir)) %>%
colnames()
example_isolates %>%
set_ab_names(NIT:VAN) %>%
colnames()
}
#> [1] "date" "patient" "age" "gender"
#> [5] "ward" "mo" "PEN" "OXA"
#> [9] "FLC" "AMX" "AMC" "AMP"
#> [13] "TZP" "CZO" "FEP" "CXM"
#> [17] "FOX" "CTX" "CAZ" "CRO"
#> [21] "GEN" "TOB" "AMK" "KAN"
#> [25] "TMP" "SXT" "nitrofurantoin" "fosfomycin"
#> [29] "linezolid" "ciprofloxacin" "moxifloxacin" "vancomycin"
#> [33] "TEC" "TCY" "TGC" "DOX"
#> [37] "ERY" "CLI" "AZM" "IPM"
#> [41] "MEM" "MTR" "CHL" "COL"
#> [45] "MUP" "RIF"
# }
```