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fix for antibiogram(), transform WHONET data set to sir

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dr. M.S. (Matthijs) Berends
2023-02-22 15:40:05 +01:00
parent dad25302f2
commit c2cfc5ef84
10 changed files with 20 additions and 30 deletions
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2
man/WHONET.Rd
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@ -39,7 +39,7 @@ A \link[tibble:tibble]{tibble} with 500 observations and 53 variables:
WHONET
}
\description{
This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our \link{example_isolates} data set. All patient names are created using online surname generators and are only in place for practice purposes.
This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our \link{example_isolates} data set. All patient names were created using online surname generators and are only in place for practice purposes.
}
\details{
Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.

5
man/antibiogram.Rd
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@ -46,7 +46,7 @@ antibiogram(
\arguments{
\item{x}{a \link{data.frame} containing at least a column with microorganisms and columns with antibiotic results (class 'sir', see \code{\link[=as.sir]{as.sir()}})}
\item{antibiotics}{vector of column names, or (any combinations of) \link[=antibiotic_class_selectors]{antibiotic selectors} such as \code{\link[=aminoglycosides]{aminoglycosides()}} or \code{\link[=carbapenems]{carbapenems()}}. For combination antibiograms, this can also be column names separated with \code{"+"}, such as "TZP+TOB" given that the data set contains columns "TZP" and "TOB". See \emph{Examples}.}
\item{antibiotics}{vector of any antibiotic name or code (will be evaluated with \code{\link[=as.ab]{as.ab()}}, column name of \code{x}, or (any combinations of) \link[=antibiotic_class_selectors]{antibiotic selectors} such as \code{\link[=aminoglycosides]{aminoglycosides()}} or \code{\link[=carbapenems]{carbapenems()}}. For combination antibiograms, this can also be set to values separated with \code{"+"}, such as "TZP+TOB" or "cipro + genta", given that columns resembling such antibiotics exist in \code{x}. See \emph{Examples}.}
\item{mo_transform}{a character to transform microorganism input - must be "name", "shortname", "gramstain", or one of the column names of the \link{microorganisms} data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be \code{NULL} to not transform the input.}
@ -194,8 +194,9 @@ antibiogram(example_isolates,
mo_transform = "gramstain"
)
# names of antibiotics do not need to resemble columns exactly:
antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB"),
antibiotics = c("Cipro", "cipro + genta"),
mo_transform = "gramstain",
ab_transform = "name",
sep = " & "