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(v0.8.0.9009) unit test

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dr. M.S. (Matthijs) Berends
2019-11-03 22:41:29 +01:00
parent 29e448883d
commit 0bb531f3e0
18 changed files with 35 additions and 33 deletions
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2
man/age_groups.Rd
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@ -60,6 +60,7 @@ age_groups(ages, "children")
# same:
age_groups(ages, c(1, 2, 4, 6, 13, 17))
\dontrun{
# resistance of ciprofloxacine per age group
library(dplyr)
example_isolates \%>\%
@ -69,6 +70,7 @@ example_isolates \%>\%
select(age_group, CIP) \%>\%
ggplot_rsi(x = "age_group")
}
}
\seealso{
To determine ages, based on one or more reference dates, use the \code{\link{age}} function.
}

5
man/ggplot_rsi.Rd
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@ -148,6 +148,8 @@ example_isolates \%>\%
example_isolates \%>\%
select(AMX) \%>\%
ggplot_rsi(colours = c(SI = "yellow"))
\dontrun{
# resistance of ciprofloxacine per age group
example_isolates \%>\%
@ -159,8 +161,7 @@ example_isolates \%>\%
select(age_group,
CIP) \%>\%
ggplot_rsi(x = "age_group")
\donttest{
# for colourblind mode, use divergent colours from the viridis package:
example_isolates \%>\%
select(AMX, NIT, FOS, TMP, CIP) \%>\%

4
man/mdro.Rd
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@ -34,13 +34,11 @@ eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
\item{info}{print progress}
\item{verbose}{print additional info: missing antibiotic columns per parameter}
\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
\item{pct_required_classes}{minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for \emph{S. aureus}. Setting this \code{pct_required_classes} argument to \code{0.5} (default) means that for every \emph{S. aureus} isolate at least 8 different classes must be available. Any lower number of available classes will return \code{NA} for that isolate.}
\item{...}{column name of an antibiotic, see section Antibiotics}
\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
}
\value{
\itemize{