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(v1.3.0.9002) intrinsic_resistant data set

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dr. M.S. (Matthijs) Berends
2020-08-14 13:36:10 +02:00
parent 7d16bec21f
commit 08d62bb5d5
111 changed files with 50487 additions and 525 deletions
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2
man/antibiotics.Rd
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@ -93,6 +93,6 @@ On our website \url{https://msberends.github.io/AMR} you can find \href{https://
}
\seealso{
\link{microorganisms}
\link{microorganisms}, \link{intrinsic_resistant}
}
\keyword{datasets}

4
man/as.ab.Rd
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@ -6,7 +6,7 @@
\alias{is.ab}
\title{Transform to antibiotic ID}
\usage{
as.ab(x, flag_multiple_results = TRUE, ...)
as.ab(x, flag_multiple_results = TRUE, info = TRUE, ...)
is.ab(x)
}
@ -15,6 +15,8 @@ is.ab(x)
\item{flag_multiple_results}{logical to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.}
\item{info}{logical to indicate whether a progress bar should be printed}
\item{...}{arguments passed on to internal functions}
}
\value{

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man/count.Rd
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@ -97,7 +97,7 @@ This AMR package honours this new insight. Use \code{\link[=susceptibility]{susc
\section{Combination therapy}{
When using more than one variable for \code{...} (= combination therapy)), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:\preformatted{--------------------------------------------------------------------
When using more than one variable for \code{...} (= combination therapy), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:\preformatted{--------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
----------------------- -----------------------
Drug A Drug B include as include as include as include as

41
man/intrinsic_resistant.Rd Normal file
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@ -0,0 +1,41 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{intrinsic_resistant}
\alias{intrinsic_resistant}
\title{Data set with bacterial intrinsic resistance}
\format{
A \code{\link{data.frame}} with 49,462 observations and 2 variables:
\itemize{
\item \code{microorganism}\cr Name of the microorganism
\item \code{antibiotic}\cr Name of the antibiotic drug
}
}
\usage{
intrinsic_resistant
}
\description{
Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.
}
\details{
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt}. This file \strong{allows for machine reading EUCAST guidelines about intrinsic resistance}, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
This data set is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version 3.1, 2016.
}
\section{Read more on our website!}{
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\examples{
if (require("dplyr")) {
intrinsic_resistant \%>\%
filter(antibiotic == "Vancomycin", microorganism \%like\% "Enterococcus") \%>\%
pull(microorganism)
# [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
}
}
\seealso{
\link{intrinsic_resistant}
}
\keyword{datasets}

2
man/lifecycle.Rd
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@ -6,7 +6,7 @@
\description{
Functions in this \code{AMR} package are categorised using \href{https://www.Tidyverse.org/lifecycle}{the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle}.
\if{html}{\figure{lifecycle_Tidyverse.svg}{options: height=200px style=margin-bottom:5px} \cr}
\if{html}{\figure{lifecycle_tidyverse.svg}{options: height=200px style=margin-bottom:5px} \cr}
This page contains a section for every lifecycle (with text borrowed from the aforementioned Tidyverse website), so they can be used in the manual pages of the functions.
}
\section{Experimental lifecycle}{

2
man/microorganisms.Rd
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@ -78,6 +78,6 @@ On our website \url{https://msberends.github.io/AMR} you can find \href{https://
}
\seealso{
\code{\link[=as.mo]{as.mo()}}, \code{\link[=mo_property]{mo_property()}}, \link{microorganisms.codes}
\code{\link[=as.mo]{as.mo()}}, \code{\link[=mo_property]{mo_property()}}, \link{microorganisms.codes}, \link{intrinsic_resistant}
}
\keyword{datasets}

2
man/proportion.Rd
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@ -89,7 +89,7 @@ The function \code{\link[=proportion_df]{proportion_df()}} takes any variable fr
}
\section{Combination therapy}{
When using more than one variable for \code{...} (= combination therapy)), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:\preformatted{--------------------------------------------------------------------
When using more than one variable for \code{...} (= combination therapy), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:\preformatted{--------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
----------------------- -----------------------
Drug A Drug B include as include as include as include as

3
man/rsi_translation.Rd
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@ -33,4 +33,7 @@ The repository of this \code{AMR} package contains a file comprising this exact
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\seealso{
\link{intrinsic_resistant}
}
\keyword{datasets}