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(v1.1.0.9015) new default eucast_rules
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@ -20,7 +20,7 @@ eucast_rules(
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x,
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col_mo = NULL,
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info = interactive(),
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rules = c("breakpoints", "expert", "other", "all"),
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rules = getOption("AMR.eucast_rules", default = c("breakpoints", "expert")),
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verbose = FALSE,
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...
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)
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@ -32,7 +32,7 @@ eucast_rules(
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\item{info}{print progress}
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\item{rules}{a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}}
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\item{rules}{a character vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}. The default value can be set to another value using e.g. \code{options(AMR.eucast_rules = "all")}.}
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\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.}
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@ -42,7 +42,7 @@ eucast_rules(
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The input of \code{x}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{\link{data.frame}} with all original and new values of the affected bug-drug combinations.
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}
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\description{
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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.
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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 and intrinsic resistance and (2) inferred resistance as defined in their breakpoint tables.
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To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details.
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}
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@ -50,7 +50,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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\strong{Note:} This function does not translate MIC values to RSI values. Use \code{\link[=as.rsi]{as.rsi()}} for that. \cr
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\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.
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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:
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Before further processing, some non-EUCAST rules can be applied to improve the efficacy of the EUCAST rules. These non-EUCAST rules, that are then applied to all isolates, are:
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\itemize{
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\item Inherit amoxicillin (AMX) from ampicillin (AMP), where amoxicillin (AMX) is unavailable;
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\item Inherit ampicillin (AMP) from amoxicillin (AMX), where ampicillin (AMP) is unavailable;
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@ -62,7 +62,7 @@ Before further processing, some non-EUCAST rules are applied to improve the effi
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\item Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.
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}
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To \emph{not} use these rules, please use \code{eucast_rules(..., rules = c("breakpoints", "expert"))}.
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These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use \code{eucast_rules(..., rules = "all")}, or set the default behaviour of the \verb{[eucast_rules()]} function with \code{options(AMR.eucast_rules = "all")} (or any other valid input value(s) to the \code{rules} parameter).
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The file containing all EUCAST rules is located here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
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}
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