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(v0.9.0.9012) Support for LOINC codes

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dr. M.S. (Matthijs) Berends
2020-01-26 20:20:00 +01:00
parent 19172b1d48
commit 449d9bde35
35 changed files with 92866 additions and 295 deletions
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20
man/ab_property.Rd
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@ -11,6 +11,7 @@
\alias{ab_group}
\alias{ab_atc_group1}
\alias{ab_atc_group2}
\alias{ab_loinc}
\alias{ab_ddd}
\alias{ab_info}
\title{Property of an antibiotic}
@ -31,6 +32,8 @@ ab_atc_group1(x, language = get_locale(), ...)
ab_atc_group2(x, language = get_locale(), ...)
ab_loinc(x, ...)
ab_ddd(x, administration = "oral", units = FALSE, ...)
ab_info(x, language = get_locale(), ...)
@ -91,18 +94,18 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
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_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
ab_atc_group2("AMX") # "Penicillins with extended spectrum"
# 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"
# defined daily doses (DDD)
ab_ddd("AMX", "oral") # 1
ab_ddd("AMX", "oral", units = TRUE) # "g"
ab_ddd("AMX", "iv") # 1
@ -110,12 +113,13 @@ ab_ddd("AMX", "iv", units = TRUE) # "g"
ab_info("AMX") # all properties as a list
# all ab_* functions use as.ab() internally:
ab_name("Fluclox") # "Flucloxacillin"
ab_name("fluklox") # "Flucloxacillin"
ab_name("floxapen") # "Flucloxacillin"
ab_name(21319) # "Flucloxacillin" (using CID)
ab_name("J01CF05") # "Flucloxacillin" (using ATC)
# 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)
# spelling from different languages and dyslexia are no problem
ab_atc("ceftriaxon")

3
man/antibiotics.Rd
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@ -5,7 +5,7 @@
\alias{antibiotics}
\alias{antivirals}
\title{Data sets with ~550 antimicrobials}
\format{\subsection{For the \link{antibiotics} data set: a \code{\link{data.frame}} with 452 observations and 13 variables:}{
\format{\subsection{For the \link{antibiotics} data set: a \code{\link{data.frame}} with 452 observations and 14 variables:}{
\itemize{
\item \code{ab}\cr Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
\item \code{atc}\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}
@ -20,6 +20,7 @@
\item \code{oral_units}\cr Units of \code{oral_ddd}
\item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral treatment
\item \code{iv_units}\cr Units of \code{iv_ddd}
\item \code{loinc}\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the antimicrobial name of the drug. Use \code{\link[=ab_loic]{ab_loic()}} to retrieve them quickly, see \code{\link[=ab_property]{ab_property()}}.
}
}

5
man/eucast_rules.Rd
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@ -3,7 +3,7 @@
\name{eucast_rules}
\alias{eucast_rules}
\alias{EUCAST}
\title{EUCAST rules}
\title{Apply EUCAST rules}
\source{
\itemize{
\item EUCAST Expert Rules. Version 2.0, 2012. \cr
@ -60,9 +60,10 @@ Before further processing, some non-EUCAST rules are applied to improve the effi
\item Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;
\item Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;
\item Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.
To \emph{not} use these rules, please use \code{eucast_rules(..., rules = c("breakpoints", "expert"))}.
}
To \emph{not} use these rules, please use \code{eucast_rules(..., rules = c("breakpoints", "expert"))}.
The file containing all EUCAST rules is located here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
}
\section{Antibiotics}{