P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 07:41:57 +02:00
Code Releases Activity

(v1.2.0.9017) ab_from_text() improvement

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-06-26 12:31:27 +02:00
parent b31003c0b6
commit 4f6f056077
19 changed files with 239 additions and 118 deletions
Download Patch File Download Diff File Expand all files Collapse all files

34
man/ab_from_text.Rd
View File

@ -2,27 +2,35 @@
% Please edit documentation in R/ab_from_text.R
\name{ab_from_text}
\alias{ab_from_text}
\title{Retrieve antimicrobial drugs from text}
\title{Retrieve antimicrobial drugs from clinical text}
\usage{
ab_from_text(text, collapse = NULL, translate_ab = "name", ...)
ab_from_text(text, collapse = NULL, translate_ab = FALSE, ...)
}
\arguments{
\item{text}{text to analyse}
\item{collapse}{character to pass on to \code{paste(..., collapse = ...)} to only return one character per element of \code{text}, see Examples}
\item{translate_ab}{a column name of the \link{antibiotics} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}. Defaults to "name", which is equal to using \code{TRUE}. Use a value \code{FALSE}, \code{NULL} or \code{NA} to prevent translation of the \verb{<ab>} code.}
\item{translate_ab}{a column name of the \link{antibiotics} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}. Defaults to \code{FALSE}. Using \code{TRUE} is equal to using "name".}
\item{...}{parameters passed on to \code{\link[=as.ab]{as.ab()}}}
}
\value{
A \link{list}, or a \link{character} if \code{collapse} is not \code{NULL}
}
\description{
Use this function on e.g. clinical texts from health care records. It returns a vector of antimicrobial drugs found in the texts.
Use this function on e.g. clinical texts from health care records. It returns a \link{list} with all antimicrobial drugs found in the texts.
}
\details{
To use this for creating a new variable in a data set (e.g. with \code{mutate()}), it could be convenient to paste the outcome together with the \code{collapse} parameter so every value in your new variable will be a character of length 1:\cr
Without using \code{collapse}, this function will return a \link{list}. This can be convenient to use e.g. inside a \code{mutate()}):\cr
\code{df \%>\% mutate(abx = ab_from_text(clinical_text))}
The returned AB codes can be transformed to official names, groups, etc. with all \code{\link[=ab_property]{ab_property()}} functions like \code{\link[=ab_name]{ab_name()}} and \code{\link[=ab_group]{ab_group()}}, or by using the \code{translate_ab} parameter.
With using \code{collapse}, this function will return a \link{character}:\cr
\code{df \%>\% mutate(abx = ab_from_text(clinical_text, collapse = "|"))}
This function is also internally used by \code{\link[=as.ab]{as.ab()}}, although it then only returns the first hit.
This function is also internally used by \code{\link[=as.ab]{as.ab()}}, although it then only returns the first hit and will throw a note if more results could have been returned.
}
\examples{
# mind the bad spelling of amoxicillin in this line,
@ -34,5 +42,17 @@ ab_from_text("administered amoxi/clav and cipro", collapse = ", ")
# if you want to know which antibiotic groups were administered, check it:
abx <- ab_from_text("administered amoxi/clav and cipro")
ab_group(abx)
ab_group(abx[[1]])
if (require(dplyr)) {
tibble(clinical_text = c("given cipro and mero",
"started on doxy today")) \%>\%
mutate(abx = ab_from_text(clinical_text),
abx2 = ab_from_text(clinical_text,
collapse = "|"),
abx3 = ab_from_text(clinical_text,
collapse = "|",
translate_ab = "name"))
}
}

4
man/as.ab.Rd
View File

@ -6,13 +6,15 @@
\alias{is.ab}
\title{Transform to antibiotic ID}
\usage{
as.ab(x, ...)
as.ab(x, flag_multiple_results = TRUE, ...)
is.ab(x)
}
\arguments{
\item{x}{character vector to determine to antibiotic ID}
\item{flag_multiple_results}{logical to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.}
\item{...}{arguments passed on to internal functions}
}
\value{