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(v1.5.0.9010) MDRO vignette update, get_episode for < day

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dr. M.S. (Matthijs) Berends
2021-01-24 14:48:56 +01:00
parent 1a88caa119
commit 286eaa9699
52 changed files with 319 additions and 210 deletions
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2
man/antibiotic_class_selectors.Rd
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@ -76,7 +76,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
}
\examples{
# `example_isolates` is a dataset available in the AMR package.
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):

4
man/as.rsi.Rd
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@ -47,7 +47,7 @@ is.rsi.eligible(x, threshold = 0.05)
uti = NULL,
conserve_capped_values = FALSE,
add_intrinsic_resistance = FALSE,
reference_data = rsi_translation
reference_data = AMR::rsi_translation
)
}
\arguments{
@ -57,7 +57,7 @@ is.rsi.eligible(x, threshold = 0.05)
\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, see \emph{Examples}}
\item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}, will be determined automatically if the \code{dplyr} package is installed}
\item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}, can be left empty to determine it automatically}
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}}

4
man/first_isolate.Rd
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@ -93,7 +93,7 @@ A \code{\link{logical}} vector
Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. To determine patient episodes not necessarily based on microorganisms, use \code{\link[=is_new_episode]{is_new_episode()}} that also supports grouping with the \code{dplyr} package.
}
\details{
These functions are context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} argument can be left blank, see \emph{Examples}.
These functions are context-aware. This means that then the \code{x} argument can be left blank, see \emph{Examples}.
The \code{\link[=first_isolate]{first_isolate()}} function is a wrapper around the \code{\link[=is_new_episode]{is_new_episode()}} function, but more efficient for data sets containing microorganism codes or names.
@ -148,7 +148,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
}
\examples{
# `example_isolates` is a dataset available in the AMR package.
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
# basic filtering on first isolates

15
man/get_episode.Rd
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@ -12,9 +12,9 @@ is_new_episode(x, episode_days, ...)
\arguments{
\item{x}{vector of dates (class \code{Date} or \code{POSIXt})}
\item{episode_days}{length of the required episode in days, see \emph{Details}}
\item{episode_days}{length of the required episode length in days, can also be less than a day, see \emph{Details}}
\item{...}{arguments passed on to \code{\link[=as.Date]{as.Date()}}}
\item{...}{arguments passed on to \code{\link[=as.POSIXct]{as.POSIXct()}}}
}
\value{
\itemize{
@ -46,15 +46,20 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
}
\examples{
# `example_isolates` is a dataset available in the AMR package.
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
get_episode(example_isolates$date, episode_days = 60)
is_new_episode(example_isolates$date, episode_days = 60)
get_episode(example_isolates$date, episode_days = 60) # indices
is_new_episode(example_isolates$date, episode_days = 60) # TRUE/FALSE
# filter on results from the third 60-day episode only, using base R
example_isolates[which(get_episode(example_isolates$date, 60) == 3), ]
# the functions also work for less than a day, e.g. to include one per hour:
get_episode(c(Sys.time(),
Sys.time() + 60 * 60),
episode_days = 1/24)
\donttest{
if (require("dplyr")) {
# is_new_episode() can also be used in dplyr verbs to determine patient

2
man/ggplot_pca.Rd
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@ -115,7 +115,7 @@ The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unly
}
\examples{
# `example_isolates` is a dataset available in the AMR package.
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
# See ?pca for more info about Principal Component Analysis (PCA).

6
man/key_antibiotics.Rd
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@ -40,7 +40,7 @@ key_antibiotics_equal(
)
}
\arguments{
\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}.}
\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank to determine automatically}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
@ -68,7 +68,7 @@ key_antibiotics_equal(
These function can be used to determine first isolates (see \code{\link[=first_isolate]{first_isolate()}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first 'weighted' isolates.
}
\details{
The \code{\link[=key_antibiotics]{key_antibiotics()}} function is context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} argument can be left blank, see \emph{Examples}.
The \code{\link[=key_antibiotics]{key_antibiotics()}} function is context-aware. This means that then the \code{x} argument can be left blank, see \emph{Examples}.
The function \code{\link[=key_antibiotics]{key_antibiotics()}} returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using \code{\link[=key_antibiotics_equal]{key_antibiotics_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antibiotics]{key_antibiotics()}} and ignored by \code{\link[=key_antibiotics_equal]{key_antibiotics_equal()}}.
@ -135,7 +135,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
}
\examples{
# `example_isolates` is a dataset available in the AMR package.
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
# output of the `key_antibiotics()` function could be like this:

4
man/mdro.Rd
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@ -77,7 +77,7 @@ Ordered \link{factor} with levels \code{Negative} < \verb{Positive, unconfirmed}
Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines.
}
\details{
These functions are context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} argument can be left blank, see \emph{Examples}.
These functions are context-aware. This means that then the \code{x} argument can be left blank, see \emph{Examples}.
For the \code{pct_required_classes} argument, values above 1 will be divided by 100. This is to support both fractions (\code{0.75} or \code{3/4}) and percentages (\code{75}).
@ -137,7 +137,7 @@ table(x)
#> 43 891 1066
}
The rules set (the \code{custom} object in this case) could be exported to a shared file location using \code{\link[=saveRDS]{saveRDS()}} if you collaborate with multiple users. The custom rules set could then be imported using \code{\link[=readRDS]{readRDS()}},
The rules set (the \code{custom} object in this case) could be exported to a shared file location using \code{\link[=saveRDS]{saveRDS()}} if you collaborate with multiple users. The custom rules set could then be imported using \code{\link[=readRDS]{readRDS()}}.
}
\section{Stable Lifecycle}{

2
man/pca.Rd
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@ -71,7 +71,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
}
\examples{
# `example_isolates` is a dataset available in the AMR package.
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
\donttest{