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(v1.0.1.9006) added generic CLSI rules

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dr. M.S. (Matthijs) Berends
2020-04-14 14:12:31 +02:00
parent d1cb7d3b6f
commit 7a6f819232
23 changed files with 4318 additions and 496 deletions
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6
man/like.Rd
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@ -26,9 +26,11 @@ x \%like_case\% pattern
A \code{\link{logical}} vector
}
\description{
Convenient wrapper around \code{\link[base:grep]{base::grep()}} to match a pattern: \code{a \%like\% b}. It always returns a \code{\link{logical}} vector and is always case-insensitive (use \code{a \%like_case\% b} for case-sensitive matching). Also, \code{pattern} (\emph{b}) can be as long as \code{x} (\emph{a}) to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.
Convenient wrapper around \code{\link[=grep]{grep()}} to match a pattern: \code{x \%like\% pattern}. It always returns a \code{\link{logical}} vector and is always case-insensitive (use \code{x \%like_case\% pattern} for case-sensitive matching). Also, \code{pattern} can be as long as \code{x} to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.
}
\details{
When running a regular expression fails, these functions try again with \code{base::grepl(..., perl = TRUE)}.
Using RStudio? This function can also be inserted from the Addins menu and can have its own Keyboard Shortcut like \code{Ctrl+Shift+L} or \code{Cmd+Shift+L} (see \code{Tools} > \verb{Modify Keyboard Shortcuts...}).
}
\section{Stable lifecycle}{
@ -62,7 +64,7 @@ a \%like\% b
# get frequencies of bacteria whose name start with 'Ent' or 'ent'
library(dplyr)
example_isolates \%>\%
filter(mo_name(mo) \%like\% '^ent') \%>\%
filter(mo_name(mo) \%like\% "^ent") \%>\%
freq(mo_genus(mo))
}
\seealso{

2
man/rsi_translation.Rd
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@ -5,7 +5,7 @@
\alias{rsi_translation}
\title{Data set for R/SI interpretation}
\format{
A \code{\link{data.frame}} with 15,745 observations and 10 variables:
A \code{\link{data.frame}} with 18,964 observations and 10 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{method}\cr Either "MIC" or "DISK"