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atc_groups

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dr. M.S. (Matthijs) Berends
2018-06-19 10:05:38 +02:00
parent 0a5898b17d
commit bdc860e29c
14 changed files with 234 additions and 92 deletions
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2
man/abname.Rd
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@ -13,7 +13,7 @@ abname(abcode, from = c("guess", "atc", "molis", "umcg"), to = "official",
\arguments{
\item{abcode}{a code or name, like \code{"AMOX"}, \code{"AMCL"} or \code{"J01CA04"}}
\item{from, to}{type to transform from and to. See \code{\link{antibiotics}} for its column names. WIth \code{from = "guess"} the from will be guessed from \code{"atc"}, \code{"molis"} and \code{"umcg"}.}
\item{from, to}{type to transform from and to. See \code{\link{antibiotics}} for its column names. WIth \code{from = "guess"} the from will be guessed from \code{"atc"}, \code{"molis"} and \code{"umcg"}. When using \code{to = "atc"}, the ATC code will be search using \code{\link{guess_atc}}.}
\item{textbetween}{text to put between multiple returned texts}

3
man/as.mic.Rd
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@ -24,6 +24,9 @@ This transforms a vector to a new class\code{mic}, which is an ordered factor wi
mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
is.mic(mic_data)
# this can also coerce combined MIC/RSI values:
as.mic("<=0.002; R") # will return <=0.002
plot(mic_data)
barplot(mic_data)
}

3
man/as.rsi.Rd
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@ -23,6 +23,9 @@ rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370)))
rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370), "A", "B", "C"))
is.rsi(rsi_data)
# this can also coerce combined MIC/RSI values:
as.rsi("<= 0.002; R") # will return R
plot(rsi_data) # for percentages
barplot(rsi_data) # for frequencies
}

34
man/atc_property.Rd
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@ -2,6 +2,8 @@
% Please edit documentation in R/atc.R
\name{atc_property}
\alias{atc_property}
\alias{atc_groups}
\alias{atc_ddd}
\title{Properties of an ATC code}
\source{
\url{https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/}
@ -9,21 +11,27 @@
\usage{
atc_property(atc_code, property, administration = "O",
url = "https://www.whocc.no/atc_ddd_index/?code=\%s&showdescription=no")
atc_groups(atc_code, ...)
atc_ddd(atc_code, ...)
}
\arguments{
\item{atc_code}{a character or character vector with ATC code(s) of antibiotic(s)}
\item{property}{property of an ATC code. Valid values are \code{"ATC code"}, \code{"Name"}, \code{"DDD"}, \code{"U"} (\code{"unit"}), \code{"Adm.R"} en \code{"Note"}.}
\item{property}{property of an ATC code. Valid values are \code{"ATC"}, \code{"Name"}, \code{"DDD"}, \code{"U"} (\code{"unit"}), \code{"Adm.R"}, \code{"Note"} and \code{groups}. For this last option, all hierarchical groups of an ATC code will be returned, see Examples.}
\item{administration}{type of administration, see \emph{Details}}
\item{administration}{type of administration when using \code{property = "Adm.R"}, see Details}
\item{url}{url of website of the WHO. The sign \code{\%s} can be used as a placeholder for ATC codes.}
\item{...}{parameters to pass on to \code{atc_property}}
}
\description{
Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit. \strong{This function requires an internet connection.}
Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit. \cr \strong{This function requires an internet connection.}
}
\details{
Abbreviations for the property \code{"Adm.R"} (parameter \code{administration}):
Options for parameter \code{administration}:
\itemize{
\item{\code{"Implant"}}{ = Implant}
\item{\code{"Inhal"}}{ = Inhalation}
@ -37,7 +45,7 @@ Abbreviations for the property \code{"Adm.R"} (parameter \code{administration}):
\item{\code{"V"}}{ = vaginal}
}
Abbreviations for the property \code{"U"} (unit):
Abbreviations of return values when using \code{property = "U"} (unit):
\itemize{
\item{\code{"g"}}{ = gram}
\item{\code{"mg"}}{ = milligram}
@ -51,7 +59,19 @@ Abbreviations for the property \code{"U"} (unit):
}
\examples{
\donttest{
atc_property("J01CA04", "DDD", "O") # oral DDD (Defined Daily Dose) of amoxicillin
atc_property("J01CA04", "DDD", "P") # parenteral DDD (Defined Daily Dose) of amoxicillin
# What's the ATC of amoxicillin?
guess_atc("Amoxicillin")
# [1] "J01CA04"
# oral DDD (Defined Daily Dose) of amoxicillin
atc_property("J01CA04", "DDD", "O")
# parenteral DDD (Defined Daily Dose) of amoxicillin
atc_property("J01CA04", "DDD", "P")
atc_property("J01CA04", property = "groups") # search hierarchical groups of amoxicillin
# [1] "ANTIINFECTIVES FOR SYSTEMIC USE"
# [2] "ANTIBACTERIALS FOR SYSTEMIC USE"
# [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"
# [4] "Penicillins with extended spectrum"
}
}

2
man/guess_bactid.Rd
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@ -35,7 +35,7 @@ df$bactid <- df \%>\% select(microorganism_name) \%>\% guess_bactid()
# and can even contain 2 columns, which is convenient for genus/species combinations:
df$bactid <- df \%>\% select(genus, species) \%>\% guess_bactid()
# same result:
df <- df \%>\% mutate(bactid = paste(genus, species) \%>\% guess_bactid())
df <- df \%>\% mutate(bactid = paste(genus, species)) \%>\% guess_bactid())
}
}
\seealso{