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replaced bactid by mo

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dr. M.S. (Matthijs) Berends
2018-08-31 13:36:19 +02:00
parent 98ff131680
commit 5965d3c794
41 changed files with 786 additions and 411 deletions
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8
man/septic_patients.Rd
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@@ -14,7 +14,7 @@
\item{\code{age}}{age of the patient}
\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{mo}}{ID of microorganism, see \code{\link{microorganisms}}}
\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}}}
}}
\usage{
@@ -36,7 +36,7 @@ library(dplyr)
# Add first isolates to our dataset:
my_data <- my_data \%>\%
mutate(first_isolates = first_isolate(my_data, "date", "patient_id", "bactid"))
mutate(first_isolates = first_isolate(my_data, "date", "patient_id", "mo"))
# -------- #
# ANALYSIS #
@@ -46,7 +46,7 @@ my_data <- my_data \%>\%
# and numbers (n) of E. coli, divided by hospital:
my_data \%>\%
filter(bactid == guess_bactid("E. coli"),
filter(mo == guess_mo("E. coli"),
first_isolates == TRUE) \%>\%
group_by(hospital_id) \%>\%
summarise(n = n_rsi(amox),
@@ -57,7 +57,7 @@ my_data \%>\%
# percentages of E. coli, trend over the years:
my_data \%>\%
filter(bactid == guess_bactid("E. coli"),
filter(mo == guess_mo("E. coli"),
first_isolates == TRUE) \%>\%
group_by(year = format(date, "\%Y")) \%>\%
summarise(n = n_rsi(amcl),