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update to septic_patients, speed improvements

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dr. M.S. (Matthijs) Berends
2018-07-25 14:17:04 +02:00
parent 03a3cb397b
commit d9e204031d
26 changed files with 273 additions and 233 deletions
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21
man/septic_patients.Rd
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@@ -4,7 +4,7 @@
\name{septic_patients}
\alias{septic_patients}
\title{Dataset with 2000 blood culture isolates of septic patients}
\format{A data.frame with 2000 observations and 47 variables:
\format{A data.frame with 2000 observations and 49 variables:
\describe{
\item{\code{date}}{date of receipt at the laboratory}
\item{\code{hospital_id}}{ID of the hospital}
@@ -15,11 +15,8 @@
\item{\code{sex}}{sex of the patient}
\item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information}
\item{\code{bactid}}{ID of microorganism, see \code{\link{microorganisms}}}
\item{\code{peni:mupi}}{38 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} and can be translated with \code{\link{abname}}}
\item{\code{peni:rifa}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{abname}}}
}}
\source{
MOLIS (LIS of Certe) - \url{https://www.certe.nl}
}
\usage{
septic_patients
}
@@ -45,15 +42,15 @@ my_data <- my_data \%>\%
# ANALYSIS #
# -------- #
# 1. Get the amoxicillin resistance percentages
# of E. coli, divided by hospital:
# 1. Get the amoxicillin resistance percentages (p)
# and numbers (n) of E. coli, divided by hospital:
my_data \%>\%
filter(bactid == "ESCCOL",
filter(bactid == guess_bactid("E. coli"),
first_isolates == TRUE) \%>\%
group_by(hospital_id) \%>\%
summarise(n = n(),
amoxicillin_resistance = rsi(amox))
summarise(n = n_rsi(amox),
p = resistance(amox))
# 2. Get the amoxicillin/clavulanic acid resistance
@@ -63,7 +60,7 @@ my_data \%>\%
filter(bactid == guess_bactid("E. coli"),
first_isolates == TRUE) \%>\%
group_by(year = format(date, "\%Y")) \%>\%
summarise(n = n(),
amoxclav_resistance = rsi(amcl, minimum = 20))
summarise(n = n_rsi(amcl),
p = resistance(amcl, minimum = 20))
}
\keyword{datasets}