EUCAST rules for MDRO

man/MDRO.Rd

@@ -4,36 +4,58 @@
 \alias{MDRO}
 \alias{BRMO}
 \alias{MRGN}
+\alias{EUCAST_exceptional_phenotypes}
 \title{Determine multidrug-resistant organisms (MDRO)}
 \usage{
-MDRO(tbl, country, col_bactid = "bactid", info = TRUE,
-  aminoglycosides = c("gent", "tobr", "kana"), quinolones = c("cipr",
-  "norf"), carbapenems = c("imip", "mero", "erta"), ceftazidime = "cfta",
-  piperacillin = "pita", trimethoprim_sulfa = "trsu", penicillin = "peni",
-  vancomycin = "vanc")
+MDRO(tbl, country = NULL, col_bactid = "bactid", info = TRUE,
+  amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
+  azit = "azit", aztr = "aztr", cefa = "cefa", cfra = "cfra",
+  cfep = "cfep", cfot = "cfot", cfox = "cfox", cfta = "cfta",
+  cftr = "cftr", cfur = "cfur", chlo = "chlo", cipr = "cipr",
+  clar = "clar", clin = "clin", clox = "clox", coli = "coli",
+  czol = "czol", dapt = "dapt", doxy = "doxy", erta = "erta",
+  eryt = "eryt", fosf = "fosf", fusi = "fusi", gent = "gent",
+  imip = "imip", kana = "kana", levo = "levo", linc = "linc",
+  line = "line", mero = "mero", metr = "metr", mino = "mino",
+  moxi = "moxi", nali = "nali", neom = "neom", neti = "neti",
+  nitr = "nitr", novo = "novo", norf = "norf", oflo = "oflo",
+  peni = "peni", pita = "pita", poly = "poly", qida = "qida",
+  rifa = "rifa", roxi = "roxi", siso = "siso", teic = "teic",
+  tetr = "tetr", tica = "tica", tige = "tige", tobr = "tobr",
+  trim = "trim", trsu = "trsu", vanc = "vanc")
 
 BRMO(tbl, country = "nl", ...)
 
 MRGN(tbl, country = "de", ...)
+
+EUCAST_exceptional_phenotypes(tbl, country = "EUCAST", ...)
 }
 \arguments{
 \item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
 
-\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).}
+\item{country}{country code to determine guidelines. EUCAST rules will be used when left empty, see Details. 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. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).}
 
 \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}}}
 
 \item{info}{print progress}
 
-\item{aminoglycosides, quinolones, carbapenems}{character vector with column names of antibiotics}
+\item{amcl, amik, amox, ampi, azit, aztr, cefa, cfra, cfep, cfot, cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, metr, mino, moxi, nali, neom, neti, nitr, novo, norf, oflo, peni, pita, poly, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column names of antibiotics. column names of antibiotics}
 
-\item{ceftazidime, piperacillin, trimethoprim_sulfa, penicillin, vancomycin}{column names of antibiotics}
-
-\item{...}{parameters that are passed on to \code{MDR}}
+\item{...}{parameters that are passed on to methods}
 }
 \value{
-Ordered factor with values \code{Positive}, \code{Unconfirmed}, \code{Negative}.
+Ordered factor with levels \code{Unknown < Negative < Unconfirmed < Positive}.
 }
 \description{
 Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
 }
+\details{
+When \code{country} will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}).
+}
+\examples{
+library(dplyr)
+
+septic_patients \%>\%
+  mutate(EUCAST = MDRO(.),
+         BRMO = MDRO(., "nl"))
+}

man/antibiotics.Rd

@@ -9,9 +9,11 @@
   \item{\code{atc}}{ATC code, like \code{J01CR02}}
   \item{\code{molis}}{MOLIS code, like \code{amcl}}
   \item{\code{umcg}}{UMCG code, like \code{AMCL}}
+  \item{\code{abbr}}{Abbreviation as used by many countries, to be used for \code{\link{guess_atc}}}
   \item{\code{official}}{Official name by the WHO, like \code{"Amoxicillin and enzyme inhibitor"}}
   \item{\code{official_nl}}{Official name in the Netherlands, like \code{"Amoxicilline met enzymremmer"}}
   \item{\code{trivial_nl}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
+  \item{\code{trade_name}}{Trade name as used by many countries, to be used for \code{\link{guess_atc}}}
   \item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
   \item{\code{oral_units}}{Units of \code{ddd_units}}
   \item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}

man/as.mic.Rd

@@ -15,7 +15,7 @@ is.mic(x)
 \item{na.rm}{a logical indicating whether missing values should be removed}
 }
 \value{
-New class \code{mic}
+Ordered factor with new class \code{mic} and new attributes \code{package} and \code{package.version}
 }
 \description{
 This transforms a vector to a new class\code{mic}, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as \code{NA} with a warning.

man/as.rsi.Rd

@@ -13,7 +13,7 @@ is.rsi(x)
 \item{x}{vector}
 }
 \value{
-New class \code{rsi}
+Ordered factor with new class \code{rsi} and new attributes \code{package} and \code{package.version}
 }
 \description{
 This transforms a vector to a new class \code{rsi}, which is an ordered factor with levels \code{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning.

man/guess_atc.Rd

@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/atc.R
+\name{guess_atc}
+\alias{guess_atc}
+\title{Find ATC code based on antibiotic property}
+\usage{
+guess_atc(x)
+}
+\arguments{
+\item{x}{character vector to determine \code{ATC} code}
+}
+\value{
+Character (vector).
+}
+\description{
+Use this function to determine the ATC code of one or more antibiotics. The dataset \code{\link{antibiotics}} will be searched for abbreviations, official names and trade names.
+}
+\details{
+In the ATC classification system, the active substances are classified in a hierarchy with five different levels.  The system has fourteen main anatomical/pharmacological groups or 1st levels.  Each ATC main group is divided into 2nd levels which could be either pharmacological or therapeutic groups.  The 3rd and 4th levels are chemical, pharmacological or therapeutic subgroups and the 5th level is the chemical substance.  The 2nd, 3rd and 4th levels are often used to identify pharmacological subgroups when that is considered more appropriate than therapeutic or chemical subgroups.
+  Source: \url{https://www.whocc.no/atc/structure_and_principles/}
+}
+\examples{
+# These examples all return "J01FA01", the ATC code of Erythromycin:
+guess_atc("J01FA01")
+guess_atc("Erythromycin")
+guess_atc("eryt")
+guess_atc("ERYT")
+guess_atc("ERY")
+guess_atc("Erythrocin") # Trade name
+guess_atc("Eryzole")    # Trade name
+guess_atc("Pediamycin") # Trade name
+}
+\seealso{
+\code{\link{antibiotics}} for the dataframe that is being used to determine ATC's.
+}