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is.rsi.eligible update

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dr. M.S. (Matthijs) Berends
2019-02-04 12:24:07 +01:00
parent cd07d65734
commit 587e00b7be
25 changed files with 1115 additions and 491 deletions
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4
man/WHONET.Rd
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@ -8,7 +8,7 @@
\describe{
\item{\code{Identification number}}{ID of the sample}
\item{\code{Specimen number}}{ID of the specimen}
\item{\code{Organism}}{Microorganisms, can be coerced with \code{\link{as.mo}}}
\item{\code{Organism}}{Name of the microorganism. Before analysis, you should transform this to a valid microbial class, using \code{\link{as.mo}}.}
\item{\code{Country}}{Country of origin}
\item{\code{Laboratory}}{Name of laboratory}
\item{\code{Last name}}{Last name of patient}
@ -31,7 +31,7 @@
\item{\code{Inducible clindamycin resistance}}{Clindamycin can be induced?}
\item{\code{Comment}}{Other comments}
\item{\code{Date of data entry}}{Date this data was entered in WHONET}
\item{\code{AMP_ND10:CIP_EE}}{27 different antibiotics. You can lookup the abbreviatons in the \code{\link{antibiotics}} data set, or use e.g. \code{\link{atc_name}("AMP")} to get the official name immediately.}
\item{\code{AMP_ND10:CIP_EE}}{27 different antibiotics. You can lookup the abbreviatons in the \code{\link{antibiotics}} data set, or use e.g. \code{\link{atc_name}("AMP")} to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using \code{\link{as.rsi}}.}
}}
\usage{
WHONET

9
man/as.rsi.Rd
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@ -10,10 +10,12 @@ as.rsi(x)
is.rsi(x)
is.rsi.eligible(x)
is.rsi.eligible(x, threshold = 0.05)
}
\arguments{
\item{x}{vector}
\item{threshold}{maximum fraction of \code{x} that is allowed to fail transformation, see Examples}
}
\value{
Ordered factor with new class \code{rsi}
@ -47,10 +49,15 @@ library(dplyr)
septic_patients \%>\%
mutate_at(vars(peni:rifa), as.rsi)
# fastest way to transform all columns with already valid AB results to class `rsi`:
septic_patients \%>\%
mutate_if(is.rsi.eligible,
as.rsi)
# default threshold of `is.rsi.eligible` is 5\%.
is.rsi.eligible(WHONET$`First name`) # fails, >80\% is invalid
is.rsi.eligible(WHONET$`First name`, threhold = 0.9) # succeeds
}
\seealso{
\code{\link{as.mic}}

32
man/availability.Rd Normal file
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@ -0,0 +1,32 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/availability.R
\name{availability}
\alias{availability}
\title{Check availability of columns}
\usage{
availability(tbl)
}
\arguments{
\item{tbl}{a \code{data.frame} or \code{list}}
}
\value{
\code{data.frame} with column names of \code{tbl} as row names and columns: \code{percent_IR}, \code{count}, \code{percent}, \code{visual_availability}.
}
\description{
Easy check for availability of columns in a data set. This makes it easy to get an idea of which antibiotic combination can be used for calculation with e.g. \code{\link{portion_IR}}.
}
\examples{
availability(septic_patients)
library(dplyr)
septic_patients \%>\% availability()
septic_patients \%>\%
select_if(is.rsi) \%>\%
availability()
septic_patients \%>\%
filter(mo == as.mo("E. coli")) \%>\%
select_if(is.rsi) \%>\%
availability()
}