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(v0.9.0.9026) update documentation

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dr. M.S. (Matthijs) Berends
2020-02-17 14:38:01 +01:00
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8
man/proportion.Rd
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@ -74,7 +74,7 @@ rsi_df(
A \code{\link{double}} or, when \code{as_percent = TRUE}, a \code{\link{character}}.
}
\description{
These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in \code{\link[dplyr:summarise]{dplyr::summarise()}} and support grouped variables, please see \emph{Examples}.
These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in \code{summarise()}][dplyr::summarise()] and also support grouped variables, please see \emph{Examples}.
\code{\link[=resistance]{resistance()}} should be used to calculate resistance, \code{\link[=susceptibility]{susceptibility()}} should be used to calculate susceptibility.\cr
}
@ -83,13 +83,13 @@ The function \code{\link[=resistance]{resistance()}} is equal to the function \c
\strong{Remember that you should filter your table to let it contain only first isolates!} This is needed to exclude duplicates and to reduce selection bias. Use \code{\link[=first_isolate]{first_isolate()}} to determine them in your data set.
These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the \code{\link[AMR:count]{AMR::count()}} functions to count isolates. The function \code{\link[=susceptibility]{susceptibility()}} is essentially equal to \code{count_susceptible() / count_all()}. \emph{Low counts can infuence the outcome - the \code{proportion} functions may camouflage this, since they only return the proportion (albeit being dependent on the \code{minimum} parameter).}
These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the \code{count()}][AMR::count()] functions to count isolates. The function \code{\link[=susceptibility]{susceptibility()}} is essentially equal to \code{count_susceptible() / count_all()}. \emph{Low counts can influence the outcome - the \code{proportion} functions may camouflage this, since they only return the proportion (albeit being dependent on the \code{minimum} parameter).}
The function \code{\link[=proportion_df]{proportion_df()}} takes any variable from \code{data} that has an \code{\link{rsi}} class (created with \code{\link[=as.rsi]{as.rsi()}}) and calculates the proportions R, I and S. The function \code{\link[=rsi_df]{rsi_df()}} works exactly like \code{\link[=proportion_df]{proportion_df()}}, but adds the number of isolates.
}
\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, Antibiotic A and Antibiotic 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
@ -143,7 +143,7 @@ This AMR package honours this new insight. Use \code{\link[=susceptibility]{susc
\section{Read more on our website!}{
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}
\examples{