mirror of https://github.com/msberends/AMR.git
40 lines
1.6 KiB
R
40 lines
1.6 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/mdro.R
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\name{MDRO}
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\alias{MDRO}
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\alias{BRMO}
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\alias{MRGN}
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\title{Determine multidrug-resistant organisms (MDRO)}
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\usage{
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MDRO(tbl, country, col_bactid = "bactid", info = TRUE,
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aminoglycosides = c("gent", "tobr", "kana"), quinolones = c("cipr",
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"norf"), carbapenems = c("imip", "mero", "erta"), ceftazidime = "cfta",
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piperacillin = "pita", trimethoprim_sulfa = "trsu", penicillin = "peni",
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vancomycin = "vanc")
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BRMO(tbl, country = "nl", ...)
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MRGN(tbl, country = "de", ...)
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}
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\arguments{
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\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
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\item{country}{country to determine guidelines. Should be a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).}
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\item{col_bactid}{column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$bactid}, see \code{\link{microorganisms}}}
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\item{info}{print progress}
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\item{aminoglycosides, quinolones, carbapenems}{character vector with column names of antibiotics}
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\item{ceftazidime, piperacillin, trimethoprim_sulfa, penicillin, vancomycin}{column names of antibiotics}
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\item{...}{parameters that are passed on to \code{MDR}}
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}
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\value{
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Ordered factor with values \code{Positive}, \code{Unconfirmed}, \code{Negative}.
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}
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\description{
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Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
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}
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