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(v0.8.0.9031) as.mo() improvements

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dr. M.S. (Matthijs) Berends
2019-11-15 15:25:03 +01:00
parent 248b45da71
commit 09e2730b53
28 changed files with 751 additions and 598 deletions
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17
man/eucast_rules.Rd
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@ -42,12 +42,27 @@ eucast_rules(x, col_mo = NULL, info = TRUE, rules = c("breakpoints",
The input of \code{x}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with all original and new values of the affected bug-drug combinations.
}
\description{
Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details.
}
\details{
\strong{Note:} This function does not translate MIC values to RSI values. Use \code{\link{as.rsi}} for that. \cr
\strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
Before further processing, some non-EUCAST rules are applied to improve the efficacy of the EUCAST rules. These non-EUCAST rules, that are applied to all isolates, are:
\itemize{
\item{Inherit amoxicillin (AMX) from ampicillin (AMP), where amoxicillin (AMX) is unavailable;}
\item{Inherit ampicillin (AMP) from amoxicillin (AMX), where ampicillin (AMP) is unavailable;}
\item{Set amoxicillin (AMX) = R where amoxicillin/clavulanic acid (AMC) = R;}
\item{Set piperacillin (PIP) = R where piperacillin/tazobactam (TZP) = R;}
\item{Set trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R;}
\item{Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;}
\item{Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;}
\item{Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.}
}
To \emph{not} use these rules, please use \code{eucast_rules(..., rules = c("breakpoints", "expert"))}.
The file containing all EUCAST rules is located here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
}
\section{Antibiotics}{