(v0.8.0.9004) added MDR guideline by Magiorakos et al.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.8.0.9003
+Version: 0.8.0.9004
-Date: 2019-10-23
+Date: 2019-10-26
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NAMESPACE

@@ -135,6 +135,7 @@ export(kurtosis)
 export(labels_rsi_count)
 export(left_join_microorganisms)
 export(like)
+export(mdr_cmi2012)
 export(mdr_tb)
 export(mdro)
 export(mo_authors)

NEWS.md

@@ -1,11 +1,17 @@
-# AMR 0.8.0.9003
+# AMR 0.8.0.9004
-<small>Last updated: 23-Oct-2019</small>
+<small>Last updated: 26-Oct-2019</small>
+
+### New
+* Support for a new MDRO guideline: Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012). **This is now the new default guideline for the `mdro()` function.**
 
 ### Changes
 * When running `as.rsi()` over a data set, it will now print the guideline that will be used if it is not specified by the user
 * Fix for `eucast_rules()`: *Stenotrophomonas maltophilia* not interpreted "R" to ceftazidime anymore (following EUCAST v3.1)
 * Fix in taxonomic info for genera that are in multiple kingdoms, like *Proteus*
 * Fix for interpreting MIC values with `as.rsi()` where the input is `NA`
+* Added "imi" as allowed abbreviation for Imipenem
+* Fix for automatically determining columns with antibiotic results in `mdro()` and `eucast_rules()`
+* Added ATC codes for ceftaroline, ceftobiprole and faropenem
 
 # AMR 0.8.0
 

R/eucast_rules.R

@@ -47,6 +47,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
 #'  \strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
 #'  \strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
 #'  \strong{AMP}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
+#'  \strong{SAM}: ampicillin/sulbactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR01}{J01CR01}),
 #'  \strong{AZM}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
 #'  \strong{AZL}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
 #'  \strong{ATM}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
@@ -55,17 +56,20 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
 #'  \strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
 #'  \strong{FEP}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
 #'  \strong{CTX}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
+#'  \strong{CTT}: cefotetan (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC05}{J01DC05}),
 #'  \strong{FOX}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
-#'  \strong{CED}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
+#'  \strong{CPT}: ceftaroline (\href{https://www.whocc.no/atc_ddd_index/?code=J01DI02}{J01DI02}),
 #'  \strong{CAZ}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
 #'  \strong{CRO}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
 #'  \strong{CXM}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
+#'  \strong{CED}: cephradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
 #'  \strong{CHL}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
 #'  \strong{CIP}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
 #'  \strong{CLR}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
 #'  \strong{CLI}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
 #'  \strong{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
 #'  \strong{DAP}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
+#'  \strong{DOR}: doripenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH04}{J01DH04}),
 #'  \strong{DOX}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
 #'  \strong{ETP}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
 #'  \strong{ERY}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
@@ -75,6 +79,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
 #'  \strong{FUS}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
 #'  \strong{GAT}: gatifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA16}{J01MA16}),
 #'  \strong{GEN}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
+#'  \strong{GEH}: gentamicin-high (no ATC code),
 #'  \strong{IPM}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
 #'  \strong{INH}: isoniazid (\href{https://www.whocc.no/atc_ddd_index/?code=J04AC01}{J04AC01}),
 #'  \strong{KAN}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
@@ -91,10 +96,10 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
 #'  \strong{NET}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
 #'  \strong{NIT}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
 #'  \strong{NOR}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
-#'  \strong{NOV}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
+#'  \strong{NOV}: novobiocin (\href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
 #'  \strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
 #'  \strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF04}{J01CF04}),
-#'  \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
+#'  \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01RA01}{J01RA01}),
 #'  \strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
 #'  \strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
 #'  \strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
@@ -103,13 +108,15 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
 #'  \strong{QDA}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
 #'  \strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}),
 #'  \strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
-#'  \strong{RIF}: rifampin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
 #'  \strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}),
-#'  \strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
+#'  \strong{RXT}: roxithromicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
 #'  \strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
+#'  \strong{STH}: streptomycin-high (no ATC code),
 #'  \strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
+#'  \strong{TLV}: telavancin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA03}{J01XA03}),
 #'  \strong{TCY}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
 #'  \strong{TIC}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
+#'  \strong{TCC}: ticarcillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR03}{J01CR03}),
 #'  \strong{TGC}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
 #'  \strong{TOB}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
 #'  \strong{TMP}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),

R/guess_ab_col.R

@@ -166,26 +166,31 @@ get_column_abx <- function(x,
 
   # sort on name
   x <- x[order(names(x), x)]
-  duplicates <- x[base::duplicated(x)]
+  duplicates <- c(x[base::duplicated(x)], x[base::duplicated(names(x))]) 
-  x <- x[!names(x) %in% names(duplicates)]
+  duplicates <- duplicates[unique(names(duplicates))]
+  x <- c(x[!names(x) %in% names(duplicates)], duplicates)
+  x <- x[order(names(x), x)]
   
   # succeeded with aut-guessing
   message(blue("OK."))
 
-  if (verbose == TRUE) {
   for (i in seq_len(length(x))) {
+    if (verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
       message(blue(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i],
                           "` (", ab_name(names(x)[i], tolower = TRUE), ").")))
     }
-  } else if (length(duplicates) > 0) {
+    if (names(x[i]) %in% names(duplicates)) {
-    for (i in seq_len(length(duplicates))) {
+      warning(red(paste0("Using column `", bold(x[i]), "` as input for `", names(x)[i],
-      warning(red(paste0("Using column `", bold(duplicates[i]), "` as input for `", names(x[which(x == duplicates[i])]), 
+                         "` (", ab_name(names(x)[i], tolower = TRUE),
-                         "` (", ab_name(names(x[names(which(x == duplicates))[i]]), tolower = TRUE), 
+                         "), although it was matched for multiple antibiotics or columns.")), 
-                         "), although it was matched for multiple antibiotics or columns.")), call. = FALSE)
+              call. = FALSE, 
+              immediate. = verbose)
     }
   }
   
+  
   if (!is.null(hard_dependencies)) {
+    hard_dependencies <- unique(hard_dependencies)
     if (!all(hard_dependencies %in% names(x))) {
       # missing a hard dependency will return NA and consequently the data will not be analysed
       missing <- hard_dependencies[!hard_dependencies %in% names(x)]
@@ -194,6 +199,7 @@ get_column_abx <- function(x,
     }
   }
   if (!is.null(soft_dependencies)) {
+    soft_dependencies <- unique(soft_dependencies)
     if (!all(soft_dependencies %in% names(x))) {
       # missing a soft dependency may lower the reliability
       missing <- soft_dependencies[!soft_dependencies %in% names(x)]
@@ -203,7 +209,7 @@ get_column_abx <- function(x,
         mutate(txt = paste0(bold(missing), " (", missing_names, ")")) %>%
         arrange(missing_names) %>%
         pull(txt)
-      message(blue("NOTE: Reliability might be improved if these antimicrobial results would be available too:",
+      message(blue("NOTE: Reliability will be improved if these antimicrobial results would be available too:",
                    paste(missing_txt, collapse = ", ")))
     }
   }

R/mdro.R

@@ -23,13 +23,14 @@
 #'
 #' Determine which isolates are multidrug-resistant organisms (MDRO) according to (country-specific) guidelines.
 #' @param x table with antibiotic columns, like e.g. \code{AMX} and \code{AMC}
-#' @param guideline a specific guideline to mention, see Details. EUCAST guidelines will be used when left empty, see Details.
+#' @param guideline a specific guideline to follow. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, see Details.
 #' @param info print progress
 #' @inheritParams eucast_rules
 #' @param verbose print additional info: missing antibiotic columns per parameter
 #' @inheritSection eucast_rules Antibiotics
 #' @details Currently supported guidelines are (case-insensitive):
 #' \itemize{
+#'   \item{\code{guideline = "CMI2012"}: Magiorakos AP, Srinivasan A \emph{et al.} "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (\href{https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext}{link})}
 #'   \item{\code{guideline = "EUCAST"}: The European international guideline - 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"}: The international guideline for multi-drug resistant tuberculosis - 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"}: The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6}
@@ -38,25 +39,27 @@
 #'
 #' Please suggest your own (country-specific) guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}.
 #' @return \itemize{
-#'   \item{TB guideline - function \code{mdr_tb()} or \code{mdro(..., guideline = "TB")}:\cr Ordered factor with levels \code{Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensive drug-resistant}}
+#'   \item{CMI 2012 paper - function \code{mdr_cmi2012()} or \code{mdro()}:\cr Ordered factor with levels \code{Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant (XDR) < Pandrug-resistant (PDR)}}
+#'   \item{TB guideline - function \code{mdr_tb()} or \code{mdro(..., guideline = "TB")}:\cr Ordered factor with levels \code{Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensively drug-resistant}}
 #'   \item{German guideline - function \code{mrgn()} or \code{mdro(..., guideline = "MRGN")}:\cr Ordered factor with levels \code{Negative < 3MRGN < 4MRGN}}
 #'   \item{Everything else:\cr 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}
 #' }
 #' @rdname mdro
-#' @importFrom dplyr %>%
+#' @importFrom dplyr %>% filter_all
-#' @importFrom crayon red blue bold
+#' @importFrom crayon blue bold italic
 #' @export
 #' @inheritSection AMR Read more on our website!
 #' @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})
+#' Please see Details for the list of publications used for this function.
-#'
-#' 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})
 #' @examples
 #' library(dplyr)
 #' 
 #' example_isolates %>% 
+#'   mdro() %>% 
+#'   freq()
+#'   
+#' \donttest{
+#' example_isolates %>%
 #'   mutate(EUCAST = mdro(.),
 #'          BRMO = brmo(.),
 #'          MRGN = mrgn(.))
@@ -65,6 +68,7 @@
 #'   rename(PIP = TZP) %>% # no piperacillin, so take piperacillin/tazobactam
 #'   mrgn() %>%            # check German guideline
 #'   freq()                # check frequencies
+#' }
 mdro <- function(x,
                  guideline = NULL,
                  col_mo = NULL,
@@ -86,7 +90,8 @@ mdro <- function(x,
   }
 
   if (is.null(guideline)) {
-    guideline <- "eucast"
+    # default to the paper by Magiorakos et al. (2012)
+    guideline <- "cmi2012"
   }
   if (tolower(guideline) == "nl") {
     guideline <- "BRMO"
@@ -94,7 +99,7 @@ mdro <- function(x,
   if (tolower(guideline) == "de") {
     guideline <- "MRGN"
   }
-  if (!tolower(guideline) %in% c("brmo", "mrgn", "eucast", "tb")) {
+  if (!tolower(guideline) %in% c("brmo", "mrgn", "eucast", "tb", "cmi2012")) {
     stop("invalid guideline: ", guideline, call. = FALSE)
   }
   guideline <- list(code = tolower(guideline))
@@ -114,7 +119,13 @@ mdro <- function(x,
     stop("`col_mo` must be set.", call. = FALSE)
   }
 
-  if (guideline$code == "eucast") {
+  if (guideline$code == "cmi2012") {
+    guideline$name <- "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
+    guideline$author <- "Magiorakos AP, Srinivasan A, Carey RB, ..., Vatopoulos A, Weber JT, Monnet DL"
+    guideline$version <- "N/A"
+    guideline$source <- "Magiorakos et al. (2012) Clinical Microbiology and Infection 18:3. DOI: 10.1111/j.1469-0691.2011.03570.x"
+    
+  } else if (guideline$code == "eucast") {
     guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Exceptional Phenotypes Tables\""
     guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)"
     guideline$version <- "3.1"
@@ -129,9 +140,10 @@ mdro <- function(x,
     # support per country:
   } else if (guideline$code == "mrgn") {
     guideline$name <- "Cross-border comparison of the Dutch and German guidelines on multidrug-resistant Gram-negative microorganisms"
-    guideline$author <- "J. M\u00fcller, A. Voss, R. K\u00f6ck, ..., W.V. Kern, C. Wendt, A.W. Friedrich"
+    guideline$author <- "M\u00fcller J, Voss A, K\u00f6ck R, ..., Kern WV, Wendt C, Friedrich AW"
     guideline$version <- "N/A"
     guideline$source <- "M\u00fcller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6"
+    
   } else if (guideline$code == "brmo") {
     guideline$name <- "WIP-Richtlijn Bijzonder Resistente Micro-organismen (BRMO)"
     guideline$author <- "RIVM (Rijksinstituut voor de Volksgezondheid)"
@@ -141,16 +153,126 @@ mdro <- function(x,
     stop("This guideline is currently unsupported: ", guideline$code, call. = FALSE)
   }
 
-  if (info == TRUE) {
+  if (guideline$code == "cmi2012") {
-    cat("Determining multidrug-resistant organisms (MDRO), according to:\n",
+    cols_ab <- get_column_abx(x = x,
-        "Guideline: ", red(guideline$name), "\n",
+                              soft_dependencies = c(
-        "Version:   ", red(guideline$version), "\n",
+                                # table 1 (S aureus):
-        "Author:    ",    red(guideline$author), "\n",
+                                "GEN",
-        "Source:    ", blue(guideline$source), "\n",
+                                "RIF",
-        "\n", sep = "")
+                                "CPT",
-  }
+                                "OXA",
-
+                                "CIP",
-  if (guideline$code == "tb") {
+                                "MFX",
+                                "SXT",
+                                "FUS",
+                                "VAN",
+                                "TEC",
+                                "TLV",
+                                "TGC",
+                                "CLI",
+                                "DAP",
+                                "ERY",
+                                "LNZ",
+                                "CHL",
+                                "FOS",
+                                "QDA",
+                                "TCY",
+                                "DOX",
+                                "MNO",
+                                # table 2 (Enterococcus)
+                                "GEH",
+                                "STH",
+                                "IPM",
+                                "MEM",
+                                "DOR",
+                                "CIP",
+                                "LVX",
+                                "MFX",
+                                "VAN",
+                                "TEC",
+                                "TGC",
+                                "DAP",
+                                "LNZ",
+                                "AMP",
+                                "QDA",
+                                "DOX",
+                                "MNO",
+                                # table 3 (Enterobacteriaceae)
+                                "GEN",
+                                "TOB",
+                                "AMK",
+                                "NET",
+                                "CPT",
+                                "TCC",
+                                "TZP",
+                                "ETP",
+                                "IPM",
+                                "MEM",
+                                "DOR",
+                                "CZO",
+                                "CXM",
+                                "CTX",
+                                "CAZ",
+                                "FEP",
+                                "FOX",
+                                "CTT",
+                                "CIP",
+                                "SXT",
+                                "TGC",
+                                "ATM",
+                                "AMP",
+                                "AMC",
+                                "SAM",
+                                "CHL",
+                                "FOS",
+                                "COL",
+                                "TCY",
+                                "DOX",
+                                "MNO",
+                                # table 4 (Pseudomonas)
+                                "GEN",
+                                "TOB",
+                                "AMK",
+                                "NET",
+                                "IPM",
+                                "MEM",
+                                "DOR",
+                                "CAZ",
+                                "FEP",
+                                "CIP",
+                                "LVX",
+                                "TCC",
+                                "TZP",
+                                "ATM",
+                                "FOS",
+                                "COL",
+                                "PLB",
+                                # table 5 (Acinetobacter)
+                                "GEN",
+                                "TOB",
+                                "AMK",
+                                "NET",
+                                "IPM",
+                                "MEM",
+                                "DOR",
+                                "CIP",
+                                "LVX",
+                                "TZP",
+                                "TCC",
+                                "CTX",
+                                "CRO",
+                                "CAZ",
+                                "FEP",
+                                "SXT",
+                                "SAM",
+                                "COL",
+                                "PLB",
+                                "TCY",
+                                "DOX",
+                                "MNO"
+                                ),
+                              verbose = verbose, ...)
+  } else if (guideline$code == "tb") {
     cols_ab <- get_column_abx(x = x,
                               soft_dependencies = c("CAP",
                                                     "ETH",
@@ -188,11 +310,14 @@ mdro <- function(x,
   CLI <- cols_ab["CLI"]
   CLR <- cols_ab["CLR"]
   COL <- cols_ab["COL"]
+  CPT <- cols_ab["CPT"]
   CRO <- cols_ab["CRO"]
+  CTT <- cols_ab["CTT"]
   CTX <- cols_ab["CTX"]
   CXM <- cols_ab["CXM"]
   CZO <- cols_ab["CZO"]
   DAP <- cols_ab["DAP"]
+  DOR <- cols_ab["DOR"]
   DOX <- cols_ab["DOX"]
   ERY <- cols_ab["ERY"]
   ETP <- cols_ab["ETP"]
@@ -201,6 +326,7 @@ mdro <- function(x,
   FOS <- cols_ab["FOS"]
   FOX <- cols_ab["FOX"]
   FUS <- cols_ab["FUS"]
+  GEH <- cols_ab["GEH"]
   GEN <- cols_ab["GEN"]
   IPM <- cols_ab["IPM"]
   KAN <- cols_ab["KAN"]
@@ -219,6 +345,7 @@ mdro <- function(x,
   NOR <- cols_ab["NOR"]
   NOV <- cols_ab["NOV"]
   OFX <- cols_ab["OFX"]
+  OXA <- cols_ab["OXA"]
   PEN <- cols_ab["PEN"]
   PIP <- cols_ab["PIP"]
   PLB <- cols_ab["PLB"]
@@ -227,12 +354,16 @@ mdro <- function(x,
   RID <- cols_ab["RID"]
   RIF <- cols_ab["RIF"]
   RXT <- cols_ab["RXT"]
+  SAM <- cols_ab["SAM"]
   SIS <- cols_ab["SIS"]
+  STH <- cols_ab["STH"]
   SXT <- cols_ab["SXT"]
+  TCC <- cols_ab["TCC"]
   TCY <- cols_ab["TCY"]
   TEC <- cols_ab["TEC"]
   TGC <- cols_ab["TGC"]
   TIC <- cols_ab["TIC"]
+  TLV <- cols_ab["TLV"]
   TMP <- cols_ab["TMP"]
   TOB <- cols_ab["TOB"]
   TZP <- cols_ab["TZP"]
@@ -252,9 +383,21 @@ mdro <- function(x,
     stop("No antimycobacterials found in data set.", call. = FALSE)
   }
   
+  if (info == TRUE) {
+    cat("\nDetermining multidrug-resistant organisms (MDRO), according to:\n",
+        bold("Guideline: "), italic(guideline$name), "\n",
+        bold("Version:   "), guideline$version, "\n",
+        bold("Author:    "),    guideline$author, "\n",
+        bold("Source:    "), guideline$source, "\n",
+        "\n", sep = "")
+  }
+
   ab_missing <- function(ab) {
     isTRUE(ab %in% c(NULL, NA)) | length(ab) == 0
   }
+  ab_NA <- function(x) {
+    x[!is.na(x)]
+  }
 
   # antibiotic classes
   aminoglycosides <- c(TOB, GEN)
@@ -280,16 +423,211 @@ mdro <- function(x,
       x[rows, "MDRO"] <<- to
     }
   }
+  trans_tbl2 <- function(txt, rows, lst) {
+    # function specific for the CMI paper of 2012 (Magiorakos et al.)
+    lst_vector <- unlist(lst)[!is.na(unlist(lst))]
+    x$total_groups <- NA_integer_
+    x$affected_groups <- NA_integer_
+    x[rows, "total_groups"] <- length(lst)
+    # now the hard part - using two sapply()s for super fast results:
+    # [1] run through all `rows` with sapply()
+    # [2] within each row, run through all antibiotic groups with another sapply()
+    # [3] determine for each antibiotic group in that row if at least 1 drug is R of I 
+    # [4] sum the number of TRUEs of this determination
+    x[rows, "affected_groups"] <- sapply(rows, 
+                                         function(row, group_tbl = lst) {
+                                           sum(sapply(group_tbl, 
+                                                      function(group) {
+                                                        any(x[row, group[!is.na(group)]] == "R") | 
+                                                          any(x[row, group[!is.na(group)]] == "I") 
+                                                      }),
+                                               na.rm = TRUE) 
+                                         })
+    # now set MDROs: 
+    # MDR (=2): >=3 groups affected
+    x[which(x$row_number %in% rows & x$affected_groups >= 3), "MDRO"] <<- 2
+    # XDR (=3): all but <=2 groups affected
+    x[which(x$row_number %in% rows & x$total_groups - x$affected_groups <= 2), "MDRO"] <<- 3
+    # PDR (=4): all agents are R 
+    x[filter_at(x[rows, ], 
+                vars(lst_vector),
+                all_vars(. %in% c("R", "I")))$row_number,
+      "MDRO"] <<- 4
+  }
   
   x <- x %>%
     mutate_at(vars(col_mo), as.mo) %>%
     # join to microorganisms data set
     left_join_microorganisms(by = col_mo) %>%
     # add unconfirmed to where genus is available
-    mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_)) %>% 
+    mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_),
+           row_number = 1:nrow(x)) %>% 
     # transform to data.frame so subsetting is possible with x[y, z] (might not be the case with tibble/data.table/...)
     as.data.frame(stringsAsFactors = FALSE)
   
+  if (guideline$code == "cmi2012") {
+    # CMI, 2012 ---------------------------------------------------------------
+    # Non-susceptible = R and I
+    # (see header 'Approaches to Creating Definitions for MDR, XDR and PDR' in paper)
+
+    # take amoxicillin if ampicillin is unavailable
+    if (is.na(AMP) & !is.na(AMX)) AMP <- AMX
+    # take ceftriaxone if cefotaxime is unavailable and vice versa
+    if (is.na(CRO) & !is.na(CTX)) CRO <- CTX
+    if (is.na(CTX) & !is.na(CRO)) CTX <- CRO
+    
+    # intrinsic resistant must not be considered for the determination of MDR,
+    # so let's just remove them, meticulously following the paper
+    x[which(x$genus == "Enterococcus" & x$species == "faecium"), ab_NA(IPM)] <- NA
+    x[which(x$genus == "Enterococcus" & x$species == "faecalis"), ab_NA(QDA)] <- NA
+    x[which((x$genus == "Providencia" & x$species == "rettgeri")
+             | (x$genus == "Providencia" & x$species == "stuartii")), ab_NA(c(GEN, TOB, NET))] <- NA
+    x[which(x$genus == "Escherichia" & x$species == "hermannii"), ab_NA(c(TCC, TZP))] <- NA
+    x[which((x$genus == "Citrobacter" & x$species == "freundii")
+            | (x$genus == "Enterobacter" & x$species == "aerogenes")
+            | (x$genus == "Enterobacter" & x$species == "cloacae")
+            | (x$genus == "Hafnia" & x$species == "alvei")
+            | (x$genus == "Morganella" & x$species == "morganii")
+            | (x$genus == "Proteus" & x$species == "penneri")
+            | (x$genus == "Proteus" & x$species == "vulgaris")
+            | (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(CZO)] <- NA
+    x[which((x$genus == "Morganella" & x$species == "morganii")
+            | (x$genus == "Proteus" & x$species == "penneri")
+            | (x$genus == "Proteus" & x$species == "vulgaris")
+            | (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(CXM)] <- NA
+    x[which((x$genus == "Morganella" & x$species == "morganii")
+            | (x$genus == "Proteus" & x$species == "mirabilis")
+            | (x$genus == "Proteus" & x$species == "penneri")
+            | (x$genus == "Proteus" & x$species == "vulgaris")
+            | (x$genus == "Providencia" & x$species == "rettgeri")
+            | (x$genus == "Providencia" & x$species == "stuartii")), ab_NA(TGC)] <- NA
+    x[which((x$genus == "Citrobacter" & x$species == "koseri")
+            | (x$genus == "Citrobacter" & x$species == "freundii")
+            | (x$genus == "Enterobacter" & x$species == "aerogenes")
+            | (x$genus == "Enterobacter" & x$species == "cloacae")
+            | (x$genus == "Escherichia" & x$species == "hermannii")
+            | (x$genus == "Hafnia" & x$species == "alvei")
+            | (x$genus == "Klebsiella")
+            | (x$genus == "Morganella" & x$species == "morganii")
+            | (x$genus == "Proteus" & x$species == "penneri")
+            | (x$genus == "Proteus" & x$species == "vulgaris")
+            | (x$genus == "Providencia" & x$species == "rettgeri")
+            | (x$genus == "Providencia" & x$species == "stuartii")
+            | (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(AMP)] <- NA
+    x[which((x$genus == "Citrobacter" & x$species == "freundii")
+            | (x$genus == "Enterobacter" & x$species == "aerogenes")
+            | (x$genus == "Enterobacter" & x$species == "cloacae")
+            | (x$genus == "Hafnia" & x$species == "alvei")
+            | (x$genus == "Morganella" & x$species == "morganii")
+            | (x$genus == "Providencia" & x$species == "rettgeri")
+            | (x$genus == "Providencia" & x$species == "stuartii")
+            | (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(AMC)] <- NA
+    x[which((x$genus == "Citrobacter" & x$species == "freundii")
+            | (x$genus == "Citrobacter" & x$species == "koseri")
+            | (x$genus == "Enterobacter" & x$species == "aerogenes")
+            | (x$genus == "Enterobacter" & x$species == "cloacae")
+            | (x$genus == "Hafnia" & x$species == "alvei")
+            | (x$genus == "Providencia" & x$species == "rettgeri")
+            | (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(SAM)] <- NA
+    x[which((x$genus == "Morganella" & x$species == "morganii")
+            | (x$genus == "Proteus" & x$species == "mirabilis")
+            | (x$genus == "Proteus" & x$species == "penneri")
+            | (x$genus == "Proteus" & x$species == "vulgaris")
+            | (x$genus == "Providencia" & x$species == "rettgeri")
+            | (x$genus == "Providencia" & x$species == "stuartii")
+            | (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(COL)] <- NA
+    x[which((x$genus == "Morganella" & x$species == "morganii")
+            | (x$genus == "Proteus" & x$species == "mirabilis")
+            | (x$genus == "Proteus" & x$species == "penneri")
+            | (x$genus == "Proteus" & x$species == "vulgaris")
+            | (x$genus == "Providencia" & x$species == "rettgeri")
+            | (x$genus == "Providencia" & x$species == "stuartii")), ab_NA(TCY)] <- NA
+    x[which((x$genus == "Morganella" & x$species == "morganii")
+            | (x$genus == "Proteus" & x$species == "penneri")
+            | (x$genus == "Proteus" & x$species == "vulgaris")
+            | (x$genus == "Providencia" & x$species == "rettgeri")
+            | (x$genus == "Providencia" & x$species == "stuartii")), ab_NA(c(DOX, MNO))] <- NA
+    
+    # now add the MDR levels to the data
+    trans_tbl(2,
+              which(x$genus == "Staphylococcus" & x$species == "aureus"),
+              c(OXA, FOX),
+              "any")
+    trans_tbl2(paste("Table 1 -", italic("S. aureus")),
+               which(x$genus == "Staphylococcus" & x$species == "aureus"),
+               list(GEN,
+                    RIF,
+                    CPT,
+                    c(OXA, FOX),
+                    c(CIP, MFX),
+                    SXT,
+                    FUS,
+                    c(VAN, TEC, TLV),
+                    TGC,
+                    CLI,
+                    DAP,
+                    ERY,
+                    LNZ,
+                    CHL,
+                    FOS,
+                    QDA,
+                    c(TCY, DOX, MNO)))
+    trans_tbl2(paste("Table 2 -", italic("Enterococcus"), "spp"),
+               which(x$genus == "Enterococcus"),
+               list(GEH,
+                    STH,
+                    c(IPM, MEM, DOR),
+                    c(CIP, LVX, MFX),
+                    c(VAN, TEC),
+                    TGC,
+                    DAP,
+                    LNZ,
+                    AMP,
+                    QDA,
+                    c(DOX, MNO)))
+    trans_tbl2(paste("Table 3 -", italic("Enterobacteriaceae")),
+               which(x$family == "Enterobacteriaceae"),
+               list(c(GEN, TOB, AMK, NET),
+                    CPT,
+                    c(TCC, TZP),
+                    c(ETP, IPM, MEM, DOR),
+                    CZO,
+                    CXM,
+                    c(CTX, CAZ, FEP),
+                    c(FOX, CTT),
+                    CIP,
+                    SXT,
+                    TGC,
+                    ATM,
+                    AMP,
+                    c(AMC, SAM),
+                    CHL,
+                    FOS,
+                    COL,
+                    c(TCY, DOX, MNO)))
+    trans_tbl2(paste("Table 4 -", italic("Pseudomonas aeruginosa")),
+               which(x$genus == "Pseudomonas" & x$species == "aeruginosa"),
+               list(c(GEN, TOB, AMK, NET),
+                    c(IPM, MEM, DOR),
+                    c(CAZ, FEP),
+                    c(CIP, LVX),
+                    c(TCC, TZP),
+                    ATM,
+                    FOS,
+                    c(COL, PLB)))
+    trans_tbl2(paste("Table 5 -", italic("Acinetobacter"), "spp"),
+               which(x$genus == "Acinetobacter"),
+               list(c(GEN, TOB, AMK, NET),
+                    c(IPM, MEM, DOR),
+                    c(CIP, LVX),
+                    c(TZP, TCC),
+                    c(CTX, CRO, CAZ, FEP),
+                    SXT,
+                    SAM,
+                    c(COL, PLB),
+                    c(TCY, DOX, MNO)))
+  }
+  
   if (guideline$code == "eucast") {
     # EUCAST ------------------------------------------------------------------
     # Table 5
@@ -534,20 +872,32 @@ mdro <- function(x,
              second = ifelse(drug_is_R(CAP) | drug_is_R(KAN) | drug_is_R(AMK),
                              TRUE, FALSE),
              xdr = ifelse(mdr & xdr & second, TRUE, FALSE)) %>%
-      mutate(mdr_tb = case_when(xdr ~ 5,
+      mutate(MDRO = case_when(xdr ~ 5,
                                 mdr ~ 4,
                                 poly ~ 3,
                                 mono ~ 2,
                                 TRUE ~ 1),
              # keep all real TB, make other species NA
-             mdr_tb = ifelse(x$fullname == "Mycobacterium tuberculosis", mdr_tb, NA_real_))
+             MDRO = ifelse(x$fullname == "Mycobacterium tuberculosis", MDRO, NA_real_))
+  }
+  
+  if (info == TRUE) {
+    cat(bold(paste0("=> Found ", sum(x$MDRO %in% c(2:5), na.rm = TRUE), " MDROs out of ", sum(!is.na(x$MDRO)), 
+                    " possible cases (", percentage(sum(x$MDRO %in% c(2:5), na.rm = TRUE) / sum(!is.na(x$MDRO))), ")")))
   }
 
   # return results
-  if (guideline$code == "tb") {
+  if (guideline$code == "cmi2012") {
-    factor(x =  x$mdr_tb,
+    factor(x =  x$MDRO,
+           levels = 1:4,
+           labels = c("Negative", "Multi-drug-resistant (MDR)", 
+                      "Extensively drug-resistant (XDR)", "Pandrug-resistant (PDR)"),
+           ordered = TRUE)
+  } else if (guideline$code == "tb") {
+    factor(x =  x$MDRO,
            levels = 1:5,
-           labels = c("Negative", "Mono-resistant", "Poly-resistant", "Multi-drug-resistant", "Extensive drug-resistant"),
+           labels = c("Negative", "Mono-resistant", "Poly-resistant", 
+                      "Multi-drug-resistant", "Extensively drug-resistant"),
            ordered = TRUE)
   } else if (guideline$code == "mrgn") {
     factor(x =  x$MDRO,
@@ -580,6 +930,13 @@ mdr_tb <- function(x, guideline = "TB", ...) {
   mdro(x = x, guideline = "TB", ...)
 }
 
+#' @rdname mdro
+#' @export
+mdr_cmi2012 <- function(x, guideline = "CMI2012", ...) {
+  mdro(x = x, guideline = "CMI2012", ...)
+}
+
+
 #' @rdname mdro
 #' @export
 eucast_exceptional_phenotypes <- function(x, guideline = "EUCAST", ...) {

data-raw/reproduction_of_antibiotics.R

@@ -305,9 +305,18 @@ antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]] <- list(c(anti
 antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]] <- list(c("xctl"))
 antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "xct"))
 # High level Gentamcin and Streptomycin
-antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl"))
+antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl", "gentamicin high", "genta high"))
-antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c("sthl"))
+antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c("sthl", "streptomycin high", "strepto high"))
+# add imi to imipenem
+antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]] <- list(c("imip", "imi"))
 
+## new ATC codes
+# ceftaroline
+antibiotics[which(antibiotics$ab == "CPT"), "atc"] <- "J01DI02"
+# faropenem
+antibiotics[which(antibiotics$ab == "FAR"), "atc"] <- "J01DI03"
+# ceftobiprole
+antibiotics[which(antibiotics$ab == "BPR"), "atc"] <- "J01DI01"
 
 antibiotics <- antibiotics %>% arrange(name)
 

docs/404.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9004</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9004</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9004</span>
       </span>
     </div>
 

docs/authors.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9004</span>
       </span>
     </div>
 

docs/index.html

@@ -45,7 +45,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9004</span>
       </span>
     </div>
 

docs/news/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9004</span>
       </span>
     </div>
 
@@ -231,11 +231,19 @@
       
     </div>
 
-    <div id="amr-0-8-0-9003" class="section level1">
+    <div id="amr-0-8-0-9004" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-8-0-9003" class="anchor"></a>AMR 0.8.0.9003<small> Unreleased </small>
+<a href="#amr-0-8-0-9004" class="anchor"></a>AMR 0.8.0.9004<small> Unreleased </small>
 </h1>
-<p><small>Last updated: 23-Oct-2019</small></p>
+<p><small>Last updated: 26-Oct-2019</small></p>
+<div id="new" class="section level3">
+<h3 class="hasAnchor">
+<a href="#new" class="anchor"></a>New</h3>
+<ul>
+<li>Support for a new MDRO guideline: Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012). <strong>This is now the new default guideline for the <code><a href="../reference/mdro.html">mdro()</a></code> function.</strong>
+</li>
+</ul>
+</div>
 <div id="changes" class="section level3">
 <h3 class="hasAnchor">
 <a href="#changes" class="anchor"></a>Changes</h3>
@@ -246,6 +254,10 @@
 </li>
 <li>Fix for interpreting MIC values with <code><a href="../reference/as.rsi.html">as.rsi()</a></code> where the input is <code>NA</code>
 </li>
+<li>Added “imi” as allowed abbreviation for Imipenem</li>
+<li>Fix for automatically determining columns with antibiotic results in <code><a href="../reference/mdro.html">mdro()</a></code> and <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
+</li>
+<li>Added ATC codes for ceftaroline, ceftobiprole and faropenem</li>
 </ul>
 </div>
 </div>
@@ -279,9 +291,9 @@ This is important, because a value like <code>"testvalue"</code> could never be
 <li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
 </ul>
 </div>
-<div id="new" class="section level3">
+<div id="new-1" class="section level3">
 <h3 class="hasAnchor">
-<a href="#new" class="anchor"></a>New</h3>
+<a href="#new-1" class="anchor"></a>New</h3>
 <ul>
 <li>
 <p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
@@ -404,9 +416,9 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
 <h1 class="page-header">
 <a href="#amr-0-7-1" class="anchor"></a>AMR 0.7.1<small> 2019-06-23 </small>
 </h1>
-<div id="new-1" class="section level4">
+<div id="new-2" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-1" class="anchor"></a>New</h4>
+<a href="#new-2" class="anchor"></a>New</h4>
 <ul>
 <li>
 <p>Function <code><a href="../reference/portion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
@@ -485,9 +497,9 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
 <h1 class="page-header">
 <a href="#amr-0-7-0" class="anchor"></a>AMR 0.7.0<small> 2019-06-03 </small>
 </h1>
-<div id="new-2" class="section level4">
+<div id="new-3" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-2" class="anchor"></a>New</h4>
+<a href="#new-3" class="anchor"></a>New</h4>
 <ul>
 <li>Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><a href="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><a href="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
 <li>Function <code><a href="../reference/mo_property.html">mo_name()</a></code> as alias of <code><a href="../reference/mo_property.html">mo_fullname()</a></code>
@@ -602,9 +614,9 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUC
 <li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
 <li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis, import data from WHONET or SPSS and many more.</li>
 </ul>
-<div id="new-3" class="section level4">
+<div id="new-4" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-3" class="anchor"></a>New</h4>
+<a href="#new-4" class="anchor"></a>New</h4>
 <ul>
 <li>
 <strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</li>
@@ -829,9 +841,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <h1 class="page-header">
 <a href="#amr-0-5-0" class="anchor"></a>AMR 0.5.0<small> 2018-11-30 </small>
 </h1>
-<div id="new-4" class="section level4">
+<div id="new-5" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-4" class="anchor"></a>New</h4>
+<a href="#new-5" class="anchor"></a>New</h4>
 <ul>
 <li>Repository moved to GitLab: <a href="https://gitlab.com/msberends/AMR" class="uri">https://gitlab.com/msberends/AMR</a>
 </li>
@@ -956,9 +968,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <h1 class="page-header">
 <a href="#amr-0-4-0" class="anchor"></a>AMR 0.4.0<small> 2018-10-01 </small>
 </h1>
-<div id="new-5" class="section level4">
+<div id="new-6" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-5" class="anchor"></a>New</h4>
+<a href="#new-6" class="anchor"></a>New</h4>
 <ul>
 <li>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <a href="https://itis.gov" class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</li>
 <li>New functions based on the existing function <code>mo_property</code>:
@@ -1091,9 +1103,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <h1 class="page-header">
 <a href="#amr-0-3-0" class="anchor"></a>AMR 0.3.0<small> 2018-08-14 </small>
 </h1>
-<div id="new-6" class="section level4">
+<div id="new-7" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-6" class="anchor"></a>New</h4>
+<a href="#new-7" class="anchor"></a>New</h4>
 <ul>
 <li>
 <strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
@@ -1228,9 +1240,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <h1 class="page-header">
 <a href="#amr-0-2-0" class="anchor"></a>AMR 0.2.0<small> 2018-05-03 </small>
 </h1>
-<div id="new-7" class="section level4">
+<div id="new-8" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-7" class="anchor"></a>New</h4>
+<a href="#new-8" class="anchor"></a>New</h4>
 <ul>
 <li>Full support for Windows, Linux and macOS</li>
 <li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
@@ -1309,7 +1321,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
-        <li><a href="#amr-0-8-0-9003">0.8.0.9003</a></li>
+        <li><a href="#amr-0-8-0-9004">0.8.0.9004</a></li>
         <li><a href="#amr-0-8-0">0.8.0</a></li>
         <li><a href="#amr-0-7-1">0.7.1</a></li>
         <li><a href="#amr-0-7-0">0.7.0</a></li>

docs/reference/eucast_rules.html

@@ -85,7 +85,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9004</span>
       </span>
     </div>
 
@@ -300,6 +300,7 @@
  <strong>AMX</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
  <strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
  <strong>AMP</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
+ <strong>SAM</strong>: ampicillin/sulbactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01'>J01CR01</a>),
  <strong>AZM</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
  <strong>AZL</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
  <strong>ATM</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
@@ -308,17 +309,20 @@
  <strong>CZO</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
  <strong>FEP</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
  <strong>CTX</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
+ <strong>CTT</strong>: cefotetan (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05'>J01DC05</a>),
  <strong>FOX</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
- <strong>CED</strong>: cefradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
+ <strong>CPT</strong>: ceftaroline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DI02'>J01DI02</a>),
  <strong>CAZ</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
  <strong>CRO</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
  <strong>CXM</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
+ <strong>CED</strong>: cephradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
  <strong>CHL</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
  <strong>CIP</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
  <strong>CLR</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
  <strong>CLI</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
  <strong>COL</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
  <strong>DAP</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
+ <strong>DOR</strong>: doripenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH04'>J01DH04</a>),
  <strong>DOX</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
  <strong>ETP</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
  <strong>ERY</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
@@ -328,6 +332,7 @@
  <strong>FUS</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
  <strong>GAT</strong>: gatifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA16'>J01MA16</a>),
  <strong>GEN</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
+ <strong>GEH</strong>: gentamicin-high (no ATC code),
  <strong>IPM</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
  <strong>INH</strong>: isoniazid (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AC01'>J04AC01</a>),
  <strong>KAN</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
@@ -344,10 +349,10 @@
  <strong>NET</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
  <strong>NIT</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
  <strong>NOR</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
- <strong>NOV</strong>: novobiocin (an ATCvet code: <a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
+ <strong>NOV</strong>: novobiocin (<a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
  <strong>OFX</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
  <strong>OXA</strong>: oxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF04'>J01CF04</a>),
- <strong>PEN</strong>: penicillin G (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
+ <strong>PEN</strong>: penicillin G (<a href='https://www.whocc.no/atc_ddd_index/?code=J01RA01'>J01RA01</a>),
  <strong>PIP</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
  <strong>TZP</strong>: piperacillin/tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
  <strong>PLB</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
@@ -356,13 +361,15 @@
  <strong>QDA</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
  <strong>RIB</strong>: rifabutin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB04'>J04AB04</a>),
  <strong>RIF</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
- <strong>RIF</strong>: rifampin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
  <strong>RFP</strong>: rifapentine (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB05'>J04AB05</a>),
- <strong>RXT</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
+ <strong>RXT</strong>: roxithromicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
  <strong>SIS</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
+ <strong>STH</strong>: streptomycin-high (no ATC code),
  <strong>TEC</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
+ <strong>TLV</strong>: telavancin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA03'>J01XA03</a>),
  <strong>TCY</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
  <strong>TIC</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
+ <strong>TCC</strong>: ticarcillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR03'>J01CR03</a>),
  <strong>TGC</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
  <strong>TOB</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
  <strong>TMP</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),

docs/reference/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9004</span>
       </span>
     </div>
 
@@ -354,7 +354,7 @@
       </tr><tr>
         
         <td>
-          <p><code><a href="mdro.html">mdro()</a></code> <code><a href="mdro.html">brmo()</a></code> <code><a href="mdro.html">mrgn()</a></code> <code><a href="mdro.html">mdr_tb()</a></code> <code><a href="mdro.html">eucast_exceptional_phenotypes()</a></code> </p>
+          <p><code><a href="mdro.html">mdro()</a></code> <code><a href="mdro.html">brmo()</a></code> <code><a href="mdro.html">mrgn()</a></code> <code><a href="mdro.html">mdr_tb()</a></code> <code><a href="mdro.html">mdr_cmi2012()</a></code> <code><a href="mdro.html">eucast_exceptional_phenotypes()</a></code> </p>
         </td>
         <td><p>Determine multidrug-resistant organisms (MDRO)</p></td>
       </tr><tr>

docs/reference/mdro.html

@@ -85,7 +85,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9004</span>
       </span>
     </div>
 
@@ -246,6 +246,8 @@
 
 <span class='fu'>mdr_tb</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"TB"</span>, <span class='no'>...</span>)
 
+<span class='fu'>mdr_cmi2012</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"CMI2012"</span>, <span class='no'>...</span>)
+
 <span class='fu'>eucast_exceptional_phenotypes</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='no'>...</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -257,7 +259,7 @@
     </tr>
     <tr>
       <th>guideline</th>
-      <td><p>a specific guideline to mention, see Details. EUCAST guidelines will be used when left empty, see Details.</p></td>
+      <td><p>a specific guideline to follow. When left empty, the publication by Magiorakos <em>et al.</em> (2012, Clinical Microbiology and Infection) will be followed, see Details.</p></td>
     </tr>
     <tr>
       <th>col_mo</th>
@@ -279,14 +281,13 @@
 
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 
-    <p>EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>link</a>)</p>
+    <p>Please see Details for the list of publications used for this function.</p>
-<p>World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<a href='https://www.who.int/tb/publications/pmdt_companionhandbook/en/'>link</a>)</p>
-<p>Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (<a 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</a>)</p>
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     
 <ul>
-<li><p>TB guideline - function <code>mdr_tb()</code> or <code>mdro(..., guideline = "TB")</code>:<br /> Ordered factor with levels <code>Negative &lt; Mono-resistant &lt; Poly-resistant &lt; Multi-drug-resistant &lt; Extensive drug-resistant</code></p></li>
+<li><p>CMI 2012 paper - function <code>mdr_cmi2012()</code> or <code>mdro()</code>:<br /> Ordered factor with levels <code>Negative &lt; Multi-drug-resistant (MDR) &lt; Extensively drug-resistant (XDR) &lt; Pandrug-resistant (PDR)</code></p></li>
+<li><p>TB guideline - function <code>mdr_tb()</code> or <code>mdro(..., guideline = "TB")</code>:<br /> Ordered factor with levels <code>Negative &lt; Mono-resistant &lt; Poly-resistant &lt; Multi-drug-resistant &lt; Extensively drug-resistant</code></p></li>
 <li><p>German guideline - function <code>mrgn()</code> or <code>mdro(..., guideline = "MRGN")</code>:<br /> Ordered factor with levels <code>Negative &lt; 3MRGN &lt; 4MRGN</code></p></li>
 <li><p>Everything else:<br /> Ordered factor with levels <code>Negative &lt; Positive, unconfirmed &lt; Positive</code>. The value <code>"Positive, unconfirmed"</code> 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</p></li>
 </ul>
@@ -294,6 +295,7 @@
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p>Currently supported guidelines are (case-insensitive):</p><ul>
+<li><p><code>guideline = "CMI2012"</code>: Magiorakos AP, Srinivasan A <em>et al.</em> "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (<a href='https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext'>link</a>)</p></li>
 <li><p><code>guideline = "EUCAST"</code>: The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>link</a>)</p></li>
 <li><p><code>guideline = "TB"</code>: The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<a href='https://www.who.int/tb/publications/pmdt_companionhandbook/en/'>link</a>)</p></li>
 <li><p><code>guideline = "MRGN"</code>: The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p></li>
@@ -311,6 +313,7 @@
  <strong>AMX</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
  <strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
  <strong>AMP</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
+ <strong>SAM</strong>: ampicillin/sulbactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01'>J01CR01</a>),
  <strong>AZM</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
  <strong>AZL</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
  <strong>ATM</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
@@ -319,17 +322,20 @@
  <strong>CZO</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
  <strong>FEP</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
  <strong>CTX</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
+ <strong>CTT</strong>: cefotetan (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05'>J01DC05</a>),
  <strong>FOX</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
- <strong>CED</strong>: cefradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
+ <strong>CPT</strong>: ceftaroline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DI02'>J01DI02</a>),
  <strong>CAZ</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
  <strong>CRO</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
  <strong>CXM</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
+ <strong>CED</strong>: cephradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
  <strong>CHL</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
  <strong>CIP</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
  <strong>CLR</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
  <strong>CLI</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
  <strong>COL</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
  <strong>DAP</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
+ <strong>DOR</strong>: doripenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH04'>J01DH04</a>),
  <strong>DOX</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
  <strong>ETP</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
  <strong>ERY</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
@@ -339,6 +345,7 @@
  <strong>FUS</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
  <strong>GAT</strong>: gatifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA16'>J01MA16</a>),
  <strong>GEN</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
+ <strong>GEH</strong>: gentamicin-high (no ATC code),
  <strong>IPM</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
  <strong>INH</strong>: isoniazid (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AC01'>J04AC01</a>),
  <strong>KAN</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
@@ -355,10 +362,10 @@
  <strong>NET</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
  <strong>NIT</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
  <strong>NOR</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
- <strong>NOV</strong>: novobiocin (an ATCvet code: <a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
+ <strong>NOV</strong>: novobiocin (<a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
  <strong>OFX</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
  <strong>OXA</strong>: oxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF04'>J01CF04</a>),
- <strong>PEN</strong>: penicillin G (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
+ <strong>PEN</strong>: penicillin G (<a href='https://www.whocc.no/atc_ddd_index/?code=J01RA01'>J01RA01</a>),
  <strong>PIP</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
  <strong>TZP</strong>: piperacillin/tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
  <strong>PLB</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
@@ -367,13 +374,15 @@
  <strong>QDA</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
  <strong>RIB</strong>: rifabutin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB04'>J04AB04</a>),
  <strong>RIF</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
- <strong>RIF</strong>: rifampin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
  <strong>RFP</strong>: rifapentine (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB05'>J04AB05</a>),
- <strong>RXT</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
+ <strong>RXT</strong>: roxithromicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
  <strong>SIS</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
+ <strong>STH</strong>: streptomycin-high (no ATC code),
  <strong>TEC</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
+ <strong>TLV</strong>: telavancin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA03'>J01XA03</a>),
  <strong>TCY</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
  <strong>TIC</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
+ <strong>TCC</strong>: ticarcillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR03'>J01CR03</a>),
  <strong>TGC</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
  <strong>TOB</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
  <strong>TMP</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
@@ -388,6 +397,11 @@
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
 
+<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
+  <span class='fu'>mdro</span>() <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://rdrr.io/pkg/clean/man/freq.html'>freq</a></span>()
+
+<span class='co'># \donttest{</span>
 <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>mdro</span>(<span class='no'>.</span>),
          <span class='kw'>BRMO</span> <span class='kw'>=</span> <span class='fu'>brmo</span>(<span class='no'>.</span>),
@@ -396,7 +410,8 @@
 <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>rename</a></span>(<span class='kw'>PIP</span> <span class='kw'>=</span> <span class='no'>TZP</span>) <span class='kw'>%&gt;%</span> <span class='co'># no piperacillin, so take piperacillin/tazobactam</span>
   <span class='fu'>mrgn</span>() <span class='kw'>%&gt;%</span>            <span class='co'># check German guideline</span>
-  <span class='fu'><a href='https://rdrr.io/pkg/clean/man/freq.html'>freq</a></span>()                <span class='co'># check frequencies</span></pre>
+  <span class='fu'><a href='https://rdrr.io/pkg/clean/man/freq.html'>freq</a></span>()                <span class='co'># check frequencies</span>
+<span class='co'># }</span></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>

man/eucast_rules.Rd

@@ -59,6 +59,7 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}}
  \strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
  \strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
  \strong{AMP}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
+ \strong{SAM}: ampicillin/sulbactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR01}{J01CR01}),
  \strong{AZM}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
  \strong{AZL}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
  \strong{ATM}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
@@ -67,17 +68,20 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}}
  \strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
  \strong{FEP}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
  \strong{CTX}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
+ \strong{CTT}: cefotetan (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC05}{J01DC05}),
  \strong{FOX}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
- \strong{CED}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
+ \strong{CPT}: ceftaroline (\href{https://www.whocc.no/atc_ddd_index/?code=J01DI02}{J01DI02}),
  \strong{CAZ}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
  \strong{CRO}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
  \strong{CXM}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
+ \strong{CED}: cephradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
  \strong{CHL}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
  \strong{CIP}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
  \strong{CLR}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
  \strong{CLI}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
  \strong{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
  \strong{DAP}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
+ \strong{DOR}: doripenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH04}{J01DH04}),
  \strong{DOX}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
  \strong{ETP}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
  \strong{ERY}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
@@ -87,6 +91,7 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}}
  \strong{FUS}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
  \strong{GAT}: gatifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA16}{J01MA16}),
  \strong{GEN}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
+ \strong{GEH}: gentamicin-high (no ATC code),
  \strong{IPM}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
  \strong{INH}: isoniazid (\href{https://www.whocc.no/atc_ddd_index/?code=J04AC01}{J04AC01}),
  \strong{KAN}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
@@ -103,10 +108,10 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}}
  \strong{NET}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
  \strong{NIT}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
  \strong{NOR}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
- \strong{NOV}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
+ \strong{NOV}: novobiocin (\href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
  \strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
  \strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF04}{J01CF04}),
- \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
+ \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01RA01}{J01RA01}),
  \strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
  \strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
  \strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
@@ -115,13 +120,15 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}}
  \strong{QDA}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
  \strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}),
  \strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
- \strong{RIF}: rifampin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
  \strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}),
- \strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
+ \strong{RXT}: roxithromicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
  \strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
+ \strong{STH}: streptomycin-high (no ATC code),
  \strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
+ \strong{TLV}: telavancin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA03}{J01XA03}),
  \strong{TCY}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
  \strong{TIC}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
+ \strong{TCC}: ticarcillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR03}{J01CR03}),
  \strong{TGC}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
  \strong{TOB}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
  \strong{TMP}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),

man/mdro.Rd

@@ -5,14 +5,11 @@
 \alias{brmo}
 \alias{mrgn}
 \alias{mdr_tb}
+\alias{mdr_cmi2012}
 \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})
+Please see Details for the list of publications used for this function.
-
-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, guideline = NULL, col_mo = NULL, info = TRUE,
@@ -24,12 +21,14 @@ mrgn(x, guideline = "MRGN", ...)
 
 mdr_tb(x, guideline = "TB", ...)
 
+mdr_cmi2012(x, guideline = "CMI2012", ...)
+
 eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
 }
 \arguments{
 \item{x}{table with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
 
-\item{guideline}{a specific guideline to mention, see Details. EUCAST guidelines will be used when left empty, see Details.}
+\item{guideline}{a specific guideline to follow. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, see Details.}
 
 \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
 
@@ -41,7 +40,8 @@ eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
 }
 \value{
 \itemize{
-  \item{TB guideline - function \code{mdr_tb()} or \code{mdro(..., guideline = "TB")}:\cr Ordered factor with levels \code{Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensive drug-resistant}}
+  \item{CMI 2012 paper - function \code{mdr_cmi2012()} or \code{mdro()}:\cr Ordered factor with levels \code{Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant (XDR) < Pandrug-resistant (PDR)}}
+  \item{TB guideline - function \code{mdr_tb()} or \code{mdro(..., guideline = "TB")}:\cr Ordered factor with levels \code{Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensively drug-resistant}}
   \item{German guideline - function \code{mrgn()} or \code{mdro(..., guideline = "MRGN")}:\cr Ordered factor with levels \code{Negative < 3MRGN < 4MRGN}}
   \item{Everything else:\cr 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}
 }
@@ -52,6 +52,7 @@ Determine which isolates are multidrug-resistant organisms (MDRO) according to (
 \details{
 Currently supported guidelines are (case-insensitive):
 \itemize{
+  \item{\code{guideline = "CMI2012"}: Magiorakos AP, Srinivasan A \emph{et al.} "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (\href{https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext}{link})}
   \item{\code{guideline = "EUCAST"}: The European international guideline - 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"}: The international guideline for multi-drug resistant tuberculosis - 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"}: The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6}
@@ -70,6 +71,7 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}}
  \strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
  \strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
  \strong{AMP}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
+ \strong{SAM}: ampicillin/sulbactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR01}{J01CR01}),
  \strong{AZM}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
  \strong{AZL}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
  \strong{ATM}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
@@ -78,17 +80,20 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}}
  \strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
  \strong{FEP}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
  \strong{CTX}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
+ \strong{CTT}: cefotetan (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC05}{J01DC05}),
  \strong{FOX}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
- \strong{CED}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
+ \strong{CPT}: ceftaroline (\href{https://www.whocc.no/atc_ddd_index/?code=J01DI02}{J01DI02}),
  \strong{CAZ}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
  \strong{CRO}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
  \strong{CXM}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
+ \strong{CED}: cephradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
  \strong{CHL}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
  \strong{CIP}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
  \strong{CLR}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
  \strong{CLI}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
  \strong{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
  \strong{DAP}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
+ \strong{DOR}: doripenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH04}{J01DH04}),
  \strong{DOX}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
  \strong{ETP}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
  \strong{ERY}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
@@ -98,6 +103,7 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}}
  \strong{FUS}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
  \strong{GAT}: gatifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA16}{J01MA16}),
  \strong{GEN}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
+ \strong{GEH}: gentamicin-high (no ATC code),
  \strong{IPM}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
  \strong{INH}: isoniazid (\href{https://www.whocc.no/atc_ddd_index/?code=J04AC01}{J04AC01}),
  \strong{KAN}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
@@ -114,10 +120,10 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}}
  \strong{NET}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
  \strong{NIT}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
  \strong{NOR}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
- \strong{NOV}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
+ \strong{NOV}: novobiocin (\href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
  \strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
  \strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF04}{J01CF04}),
- \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
+ \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01RA01}{J01RA01}),
  \strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
  \strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
  \strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
@@ -126,13 +132,15 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}}
  \strong{QDA}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
  \strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}),
  \strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
- \strong{RIF}: rifampin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
  \strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}),
- \strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
+ \strong{RXT}: roxithromicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
  \strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
+ \strong{STH}: streptomycin-high (no ATC code),
  \strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
+ \strong{TLV}: telavancin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA03}{J01XA03}),
  \strong{TCY}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
  \strong{TIC}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
+ \strong{TCC}: ticarcillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR03}{J01CR03}),
  \strong{TGC}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
  \strong{TOB}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
  \strong{TMP}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),
@@ -148,6 +156,11 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 \examples{
 library(dplyr)
 
+example_isolates \%>\% 
+  mdro() \%>\% 
+  freq()
+  
+\donttest{
 example_isolates \%>\%
   mutate(EUCAST = mdro(.),
          BRMO = brmo(.),
@@ -158,3 +171,4 @@ example_isolates \%>\%
   mrgn() \%>\%            # check German guideline
   freq()                # check frequencies
 }
+}

tests/testthat/test-mdro.R

@@ -124,4 +124,50 @@ test_that("mdro works", {
       ,
     2)
   
+  # check the guideline by Magiorakos  et al. (2012), the default guideline
+  stau <- tibble::tribble(
+    ~mo,         ~GEN, ~RIF, ~CPT, ~OXA, ~CIP, ~MFX, ~SXT, ~FUS, ~VAN, ~TEC, ~TLV, ~TGC, ~CLI, ~DAP, ~ERY, ~LNZ, ~CHL, ~FOS, ~QDA, ~TCY, ~DOX, ~MNO,
+    "S. aureus",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
+    "S. aureus",  "R",  "R",  "R",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
+    "S. aureus",  "S",  "S",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",
+    "S. aureus",  "R",  "R",  "I",  "I",  "I",  "I",  "I",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R"
+  )
+  expect_equal(as.integer(mdro(stau)), c(1:4))
+  
+  ente <- tibble::tribble(
+    ~mo,            ~GEH, ~STH, ~IPM, ~MEM, ~DOR, ~CIP, ~LVX, ~MFX, ~VAN, ~TEC, ~TGC, ~DAP, ~LNZ, ~AMP, ~QDA, ~DOX, ~MNO,
+    "Enterococcus",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
+    "Enterococcus",  "R",  "R",  "R",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
+    "Enterococcus",  "S",  "S",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",
+    "Enterococcus",  "R",  "R",  "I",  "I",  "I",  "I",  "I",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R"
+  )
+  expect_equal(as.integer(mdro(ente)), c(1:4))
+  
+  entero <- tibble::tribble(
+    ~mo,       ~GEN, ~TOB, ~AMK, ~NET, ~CPT, ~TCC, ~TZP, ~ETP, ~IPM, ~MEM, ~DOR, ~CZO, ~CXM, ~CTX, ~CAZ, ~FEP, ~FOX, ~CTT, ~CIP, ~SXT, ~TGC, ~ATM, ~AMP, ~AMC, ~SAM, ~CHL, ~FOS, ~COL, ~TCY, ~DOX, ~MNO,
+    "E. coli",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
+    "E. coli",  "R",  "R",  "R",  "R",  "R",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
+    "E. coli",  "S",  "S",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",
+    "E. coli",  "R",  "R",  "I",  "I",  "I",  "I",  "I",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R"
+  )
+  expect_equal(as.integer(mdro(entero)), c(1:4))
+  
+  pseud <- tibble::tribble(
+    ~mo,             ~GEN, ~TOB, ~AMK, ~NET, ~IPM, ~MEM, ~DOR, ~CAZ, ~FEP, ~CIP, ~LVX, ~TCC, ~TZP, ~ATM, ~FOS, ~COL, ~PLB,
+    "P. aeruginosa",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
+    "P. aeruginosa",  "R",  "S",  "S",  "S",  "R",  "S",  "S",  "S",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
+    "P. aeruginosa",  "S",  "S",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",
+    "P. aeruginosa",  "R",  "R",  "I",  "I",  "I",  "I",  "I",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R"
+  )
+  expect_equal(as.integer(mdro(pseud)), c(1:4))
+  
+  acin <- tibble::tribble(
+    ~mo,            ~GEN, ~TOB, ~AMK, ~NET, ~IPM, ~MEM, ~DOR, ~CIP, ~LVX, ~TZP, ~TCC, ~CTX, ~CRO, ~CAZ, ~FEP, ~SXT, ~SAM, ~COL, ~PLB, ~TCY, ~DOX, ~MNO,
+    "A. baumannii",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
+    "A. baumannii",  "R",  "R",  "R",  "R",  "S",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "S",  "R",  "S",  "S",  "S",  "S",  "S",  "S",  "S",
+    "A. baumannii",  "S",  "S",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",
+    "A. baumannii",  "R",  "R",  "I",  "I",  "I",  "I",  "I",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R",  "R"
+  )
+  expect_equal(as.integer(mdro(acin)), c(1:4))
+  
 })