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styled, unit test fix

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dr. M.S. (Matthijs) Berends
2022-08-28 10:31:50 +02:00
parent 4cb1db4554
commit 4d050aef7c
147 changed files with 10897 additions and 8169 deletions
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64
man/ab_property.Rd
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@ -109,36 +109,38 @@ All data sets in this \code{AMR} package (about microorganisms, antibiotics, R/S
\examples{
# all properties:
ab_name("AMX") # "Amoxicillin"
ab_atc("AMX") # "J01CA04" (ATC code from the WHO)
ab_cid("AMX") # 33613 (Compound ID from PubChem)
ab_synonyms("AMX") # a list with brand names of amoxicillin
ab_name("AMX") # "Amoxicillin"
ab_atc("AMX") # "J01CA04" (ATC code from the WHO)
ab_cid("AMX") # 33613 (Compound ID from PubChem)
ab_synonyms("AMX") # a list with brand names of amoxicillin
ab_tradenames("AMX") # same
ab_group("AMX") # "Beta-lactams/penicillins"
ab_group("AMX") # "Beta-lactams/penicillins"
ab_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
ab_atc_group2("AMX") # "Penicillins with extended spectrum"
ab_url("AMX") # link to the official WHO page
ab_url("AMX") # link to the official WHO page
# smart lowercase tranformation
ab_name(x = c("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
ab_name(x = c("AMC", "PLB"),
tolower = TRUE) # "amoxicillin/clavulanic acid" "polymyxin B"
ab_name(x = c("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
ab_name(
x = c("AMC", "PLB"),
tolower = TRUE
) # "amoxicillin/clavulanic acid" "polymyxin B"
# defined daily doses (DDD)
ab_ddd("AMX", "oral") # 1.5
ab_ddd("AMX", "oral") # 1.5
ab_ddd_units("AMX", "oral") # "g"
ab_ddd("AMX", "iv") # 3
ab_ddd_units("AMX", "iv") # "g"
ab_ddd("AMX", "iv") # 3
ab_ddd_units("AMX", "iv") # "g"
ab_info("AMX") # all properties as a list
ab_info("AMX") # all properties as a list
# all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':
ab_atc("AMP") # ATC code of AMP (ampicillin)
ab_group("J01CA01") # Drug group of ampicillins ATC code
ab_loinc("ampicillin") # LOINC codes of ampicillin
ab_name("21066-6") # "Ampicillin" (using LOINC)
ab_name(6249) # "Ampicillin" (using CID)
ab_name("J01CA01") # "Ampicillin" (using ATC)
ab_atc("AMP") # ATC code of AMP (ampicillin)
ab_group("J01CA01") # Drug group of ampicillins ATC code
ab_loinc("ampicillin") # LOINC codes of ampicillin
ab_name("21066-6") # "Ampicillin" (using LOINC)
ab_name(6249) # "Ampicillin" (using CID)
ab_name("J01CA01") # "Ampicillin" (using ATC)
# spelling from different languages and dyslexia are no problem
ab_atc("ceftriaxon")
@ -155,24 +157,24 @@ if (require("dplyr")) {
example_isolates \%>\%
set_ab_names() \%>\%
head()
# this does the same:
example_isolates \%>\%
rename_with(set_ab_names)\%>\%
rename_with(set_ab_names) \%>\%
head()
# set_ab_names() works with any AB property:
example_isolates \%>\%
set_ab_names(property = "atc")\%>\%
set_ab_names(property = "atc") \%>\%
head()
example_isolates \%>\%
set_ab_names(where(is.rsi)) \%>\%
colnames()
example_isolates \%>\%
set_ab_names(NIT:VAN) \%>\%
colnames()
example_isolates \%>\%
set_ab_names(where(is.rsi)) \%>\%
colnames()
example_isolates \%>\%
set_ab_names(NIT:VAN) \%>\%
colnames()
}
}
}