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(v0.7.1.9007) mdro update

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dr. M.S. (Matthijs) Berends
2019-07-04 15:26:07 +02:00
parent 4ff20af123
commit c57ad26c5b
26 changed files with 146 additions and 117 deletions
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6
man/freq.Rd
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@ -10,14 +10,14 @@
\usage{
freq(x, ..., sort.count = TRUE, nmax = getOption("max.print.freq"),
na.rm = TRUE, row.names = TRUE, markdown = !interactive(),
digits = 2, quote = FALSE, header = TRUE, title = NULL,
digits = 2, quote = NULL, header = TRUE, title = NULL,
na = "<NA>", droplevels = TRUE, sep = " ",
decimal.mark = getOption("OutDec"), big.mark = ifelse(decimal.mark !=
",", ",", "."))
frequency_tbl(x, ..., sort.count = TRUE,
nmax = getOption("max.print.freq"), na.rm = TRUE, row.names = TRUE,
markdown = !interactive(), digits = 2, quote = FALSE,
markdown = !interactive(), digits = 2, quote = NULL,
header = TRUE, title = NULL, na = "<NA>", droplevels = TRUE,
sep = " ", decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark != ",", ",", "."))
@ -48,7 +48,7 @@ header(f, property = NULL)
\item{digits}{how many significant digits are to be used for numeric values in the header (not for the items themselves, that depends on \code{\link{getOption}("digits")})}
\item{quote}{a logical value indicating whether or not strings should be printed with surrounding quotes}
\item{quote}{a logical value indicating whether or not strings should be printed with surrounding quotes. Default is to print them only around characters that are actually numeric values.}
\item{header}{a logical value indicating whether an informative header should be printed}

41
man/mdro.Rd
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@ -7,13 +7,20 @@
\alias{mdr_tb}
\alias{eucast_exceptional_phenotypes}
\title{Determine multidrug-resistant organisms (MDRO)}
\source{
EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})
World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link})
Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})
}
\usage{
mdro(x, country = NULL, guideline = NULL, col_mo = NULL,
info = TRUE, verbose = FALSE, ...)
mdro(x, guideline = NULL, col_mo = NULL, info = TRUE,
verbose = FALSE, ...)
brmo(..., country = "nl")
brmo(..., guideline = "BRMO")
mrgn(x, country = "de", ...)
mrgn(x, guideline = "MRGN", ...)
mdr_tb(x, guideline = "TB", ...)
@ -22,9 +29,7 @@ eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
\arguments{
\item{x}{table with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
\item{country}{country code to determine guidelines. Should be or 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.}
\item{guideline}{a specific guideline to mention. For some countries this will be determined automatically, see Details. EUCAST guidelines will be used when left empty, see Details.}
\item{guideline}{a specific guideline to mention, see Details. EUCAST guidelines will be used when left empty, see Details.}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
@ -35,25 +40,23 @@ eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
\item{...}{column name of an antibiotic, see section Antibiotics}
}
\value{
Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}.
For TB (\code{mdr_tb()}): Ordered factor with levels \code{Negative < Mono-resistance < Poly-resistance < Multidrug resistance < Extensive drug resistance}.
For everything else: Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}. The value \code{"Positive, unconfirmed"} means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests.
}
\description{
Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
Determine which isolates are multidrug-resistant organisms (MDRO) according to (country-specific) guidelines.
}
\details{
When \code{country} is set, the parameter guideline will be ignored as these guidelines will be used:
Currently supported guidelines are:
\itemize{
\item{\code{country = "nl"}: Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})}
\item{\code{guideline = "EUCAST"}: EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})}
\item{\code{guideline = "TB"}: World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link})}
\item{\code{guideline = "MRGN"}: (work in progress)}
\item{\code{guideline = "BRMO"}: Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})}
}
Please suggest your own country's specific guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}.
Other currently supported guidelines are:
\itemize{
\item{\code{guideline = "eucast"}: EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})}
\item{\code{guideline = "tb"}: World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link})}
}
Please suggest your own (country-specific) guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}.
}
\section{Antibiotics}{