MDRO update

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.4.0.9010
+Version: 0.4.0.9011
-Date: 2018-11-09
+Date: 2018-11-16
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(

NAMESPACE

@@ -35,11 +35,7 @@ S3method(skewness,matrix)
 S3method(summary,mic)
 S3method(summary,rsi)
 export("%like%")
-export(BRMO)
-export(EUCAST_exceptional_phenotypes)
 export(EUCAST_rules)
-export(MDRO)
-export(MRGN)
 export(ab_atc)
 export(ab_certe)
 export(ab_name)
@@ -58,6 +54,7 @@ export(as.rsi)
 export(atc_ddd)
 export(atc_groups)
 export(atc_property)
+export(brmo)
 export(count_I)
 export(count_IR)
 export(count_R)
@@ -65,6 +62,8 @@ export(count_S)
 export(count_SI)
 export(count_all)
 export(count_df)
+export(eucast_exceptional_phenotypes)
+export(eucast_rules)
 export(facet_rsi)
 export(first_isolate)
 export(freq)
@@ -91,6 +90,7 @@ export(kurtosis)
 export(labels_rsi_count)
 export(left_join_microorganisms)
 export(like)
+export(mdro)
 export(mo_TSN)
 export(mo_authors)
 export(mo_class)
@@ -110,6 +110,7 @@ export(mo_subspecies)
 export(mo_taxonomy)
 export(mo_type)
 export(mo_year)
+export(mrgn)
 export(n_rsi)
 export(p.symbol)
 export(portion_I)

NEWS.md

@@ -9,14 +9,16 @@
 * Functions `mo_authors` and `mo_year` to get specific values about the scientific reference of a taxonomic entry
 
 #### Changed
-* Big changes to the `EUCAST_rules` function:
+* Functions `MDRO`, `BRMO`, `MRGN` and `EUCAST_exceptional_phenotypes` were renamed to `mdro`, `brmo`, `mrgn` and `eucast_exceptional_phenotypes`
+* `EUCAST_rules` was renamed to `eucast_rules`, the old function still exists as a deprecated function
+* Big changes to the `eucast_rules` function:
   * Now also applies rules from the EUCAST 'Breakpoint tables for bacteria', version 8.1, 2018, http://www.eucast.org/clinical_breakpoints/ (see Source of the function)
   * New parameter `rules` to specify which rules should be applied (expert rules, breakpoints, others or all)
   * New parameter `verbose` which can be set to `TRUE` to get very specific messages about which columns and rows were affected
   * Better error handling when rules cannot be applied (i.e. new values could not be inserted)
   * The number of affected values will now only be measured once per row/column combination
   * Data set `septic_patients` now reflects these changes
-  * Added parameter `pipe` for piperacillin (J01CA12), also to the `MDRO` function
+  * Added parameter `pipe` for piperacillin (J01CA12), also to the `mdro` function
   * Small fixes to EUCAST clinical breakpoint rules
 * Added column `kingdom` to the microorganisms data set, and function `mo_kingdom` to look up values
 * Tremendous speed improvement for `as.mo` (and subsequently all `mo_*` functions), as empty values wil be ignored *a priori*
@@ -41,11 +43,11 @@
   * New parameter `header` to turn it off (default when `markdown = TRUE`)
   * New parameter `title` to replace the automatically set title
 * `first_isolate` now tries to find columns to use as input when parameters are left blank
-* Improvement for MDRO algorithm
+* Improvement for MDRO algorithm (function `mdro`)
 * Data set `septic_patients` is now a `data.frame`, not a tibble anymore
 * Removed diacritics from all authors (columns `microorganisms$ref` and `microorganisms.old$ref`) to comply with CRAN policy to only allow ASCII characters
 * Fix for `mo_property` not working properly
-* Fix for `EUCAST_rules` where some Streptococci would become ceftazidime R in EUCAST rule 4.5
+* Fix for `eucast_rules` where some Streptococci would become ceftazidime R in EUCAST rule 4.5
 * Support for named vectors of class `mo`, useful for `top_freq()`
 * `ggplot_rsi` and `scale_y_percent` have `breaks` parameter
 * AI improvements for `as.mo`:

R/eucast_rules.R

@@ -25,7 +25,7 @@
 #' @param verbose a logical to indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected
 #' @param amcl,amik,amox,ampi,azit,azlo,aztr,cefa,cfep,cfot,cfox,cfra,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mezl,mino,moxi,nali,neom,neti,nitr,norf,novo,oflo,oxac,peni,pipe,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column name of an antibiotic, see Details
 #' @param col_bactid deprecated, use \code{col_mo} instead.
-#' @param ... parameters that are passed on to \code{EUCAST_rules}
+#' @param ... parameters that are passed on to \code{eucast_rules}
 #' @inheritParams first_isolate
 #' @details To define antibiotics column names, input a text or use \code{NA} to skip a column (e.g. \code{tica = NA}). Non-existing columns will anyway be skipped with a warning. See the Antibiotics section for an explanation of the abbreviations.
 #' @section Antibiotics:
@@ -94,7 +94,7 @@
 #'  \strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}),
 #'  \strong{vanc}: vancomycin (\emph{J01XA01}).
 #' @keywords interpretive eucast reading resistance
-#' @rdname EUCAST
+#' @rdname eucast_rules
 #' @export
 #' @importFrom dplyr %>% select pull mutate_at vars
 #' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic strip_style
@@ -116,7 +116,7 @@
 #'     }
 #'   }
 #' @examples
-#' a <- EUCAST_rules(septic_patients)
+#' a <- eucast_rules(septic_patients)
 #'
 #' a <- data.frame(mo = c("Staphylococcus aureus",
 #'                        "Enterococcus faecalis",
@@ -140,7 +140,7 @@
 #' # 4  Klebsiella pneumoniae    -    -    -    -    -    S    S
 #' # 5 Pseudomonas aeruginosa    -    -    -    -    -    S    S
 #'
-#' b <- EUCAST_rules(a, "mo") # 18 results are forced as R or S
+#' b <- eucast_rules(a, "mo") # 18 results are forced as R or S
 #'
 #' b
 #' #                       mo vanc amox coli cfta cfur peni cfox
@@ -149,7 +149,7 @@
 #' # 3       Escherichia coli    R    -    -    -    -    R    S
 #' # 4  Klebsiella pneumoniae    R    R    -    -    -    R    S
 #' # 5 Pseudomonas aeruginosa    R    R    -    -    R    R    R
-EUCAST_rules <- function(tbl,
+eucast_rules <- function(tbl,
                          col_mo = NULL,
                          info = TRUE,
                          rules = c("breakpoints", "expert", "other", "all"),
@@ -1745,8 +1745,16 @@ EUCAST_rules <- function(tbl,
   tbl_original
 }
 
-#' @rdname EUCAST
+#' @rdname eucast_rules
+#' @export
+EUCAST_rules <- function(...) {
+  .Deprecated("eucast_rules")
+  eucast_rules(...)
+}
+
+#' @rdname eucast_rules
 #' @export
 interpretive_reading <- function(...) {
-  EUCAST_rules(...)
+  .Deprecated("eucast_rules")
+  eucast_rules(...)
 }

R/mdro.R

@@ -22,13 +22,13 @@
 #' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
 #' @param country country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).
 #' @param info print progress
-#' @inheritParams EUCAST_rules
+#' @inheritParams eucast_rules
 #' @param metr column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.
 #' @param ... parameters that are passed on to methods
-#' @inheritSection EUCAST_rules Antibiotics
+#' @inheritSection eucast_rules Antibiotics
 #' @details When \code{country} will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}).
-#' @return Ordered factor with levels \code{Unknown < Negative < Unconfirmed < Positive}.
+#' @return Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}.
-#' @rdname MDRO
+#' @rdname mdro
 #' @importFrom dplyr %>%
 #' @importFrom crayon red blue
 #' @export
@@ -36,9 +36,9 @@
 #' library(dplyr)
 #'
 #' septic_patients %>%
-#'   mutate(EUCAST = MDRO(.),
+#'   mutate(EUCAST = mdro(.),
-#'          BRMO = BRMO(.))
+#'          BRMO = brmo(.))
-MDRO <- function(tbl,
+mdro <- function(tbl,
                  country = NULL,
                  col_mo = NULL,
                  info = TRUE,
@@ -129,8 +129,8 @@ MDRO <- function(tbl,
     country <- 'EUCAST'
   }
   country <- trimws(country)
-  if (country != 'EUCAST' & !country %like% '^[a-z]{2}$') {
+  if (tolower(country) != 'eucast' & !country %like% '^[a-z]{2}$') {
-    stop('This is not a valid ISO 3166-1 alpha-2 country code: "', country, '". Please see ?MDRO.', call. = FALSE)
+    stop('This is not a valid ISO 3166-1 alpha-2 country code: "', country, '". Please see ?mdro.', call. = FALSE)
   }
 
   # create list and make country code case-independent
@@ -152,9 +152,9 @@ MDRO <- function(tbl,
     guideline$name <- 'WIP-Richtlijn BRMO'
     guideline$version <- 'Revision of December 2017'
     guideline$source <- 'https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH'
-  # add here more countries like this:
+    # add here more countries like this:
-  # } else if (country$code == 'xx') {
+    # } else if (country$code == 'xx') {
-  #   country$name <- 'country name'
+    #   country$name <- 'country name'
   } else {
     stop('This country code is currently unsupported: ', guideline$country$code, call. = FALSE)
   }
@@ -243,10 +243,17 @@ MDRO <- function(tbl,
   fluoroquinolones <- c(oflo, cipr, levo, moxi)
 
   # helper function for editing the table
-  trans_tbl <- function(to, rows, cols) {
+  trans_tbl <- function(to, rows, cols, any_all) {
     cols <- cols[!is.na(cols)]
     if (length(rows) > 0 & length(cols) > 0) {
-      col_filter <- which(tbl[, cols] == 'R')
+      if (any_all == "any") {
+        col_filter <- which(tbl[, cols] == 'R')
+      } else if (any_all == "all") {
+        col_filter <- tbl %>%
+          mutate(index = 1:nrow(.)) %>%
+          filter_at(vars(cols), all_vars(. == "R")) %>%
+          pull((index))
+      }
       rows <- rows[rows %in% col_filter]
       tbl[rows, 'MDRO'] <<- to
     }
@@ -265,52 +272,66 @@ MDRO <- function(tbl,
   if (guideline$country$code == 'eucast') {
     # EUCAST ------------------------------------------------------------------
     # Table 5
-    trans_tbl(4,
+    trans_tbl(3,
               which(tbl$family == 'Enterobacteriaceae'
                     | tbl$fullname %like% '^Pseudomonas aeruginosa'
                     | tbl$genus == 'Acinetobacter'),
-              coli)
+              coli,
-    trans_tbl(4,
+              "all")
+    trans_tbl(3,
               which(tbl$fullname %like% '^Salmonella Typhi'),
-              c(carbapenems, fluoroquinolones))
+              c(carbapenems, fluoroquinolones),
-    trans_tbl(4,
+              "any")
+    trans_tbl(3,
               which(tbl$fullname %like% '^Haemophilus influenzae'),
-              c(cephalosporins_3rd, carbapenems, fluoroquinolones))
+              c(cephalosporins_3rd, carbapenems, fluoroquinolones),
-    trans_tbl(4,
+              "any")
+    trans_tbl(3,
               which(tbl$fullname %like% '^Moraxella catarrhalis'),
-              c(cephalosporins_3rd, fluoroquinolones))
+              c(cephalosporins_3rd, fluoroquinolones),
-    trans_tbl(4,
+              "any")
+    trans_tbl(3,
               which(tbl$fullname %like% '^Neisseria meningitidis'),
-              c(cephalosporins_3rd, fluoroquinolones))
+              c(cephalosporins_3rd, fluoroquinolones),
-    trans_tbl(4,
+              "any")
+    trans_tbl(3,
               which(tbl$fullname %like% '^Neisseria gonorrhoeae'),
-              azit)
+              azit,
+              "any")
     # Table 6
-    trans_tbl(4,
+    trans_tbl(3,
               which(tbl$fullname %like% '^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)'),
-              c(vanc, teic, dapt, line, qida, tige))
+              c(vanc, teic, dapt, line, qida, tige),
-    trans_tbl(4,
+              "any")
+    trans_tbl(3,
               which(tbl$genus == 'Corynebacterium'),
-              c(vanc, teic, dapt, line, qida, tige))
+              c(vanc, teic, dapt, line, qida, tige),
-    trans_tbl(4,
+              "any")
+    trans_tbl(3,
               which(tbl$fullname %like% '^Streptococcus pneumoniae'),
-              c(carbapenems, vanc, teic, dapt, line, qida, tige, rifa))
+              c(carbapenems, vanc, teic, dapt, line, qida, tige, rifa),
-    trans_tbl(4, # Sr. groups A/B/C/G
+              "any")
+    trans_tbl(3, # Sr. groups A/B/C/G
               which(tbl$fullname %like% '^Streptococcus (pyogenes|agalactiae|equisimilis|equi|zooepidemicus|dysgalactiae|anginosus)'),
-              c(peni, cephalosporins, vanc, teic, dapt, line, qida, tige))
+              c(peni, cephalosporins, vanc, teic, dapt, line, qida, tige),
-    trans_tbl(4,
+              "any")
+    trans_tbl(3,
               which(tbl$genus == 'Enterococcus'),
-              c(dapt, line, tige, teic))
+              c(dapt, line, tige, teic),
-    trans_tbl(4,
+              "any")
+    trans_tbl(3,
               which(tbl$fullname %like% '^Enterococcus faecalis'),
-              c(ampi, amox))
+              c(ampi, amox),
+              "any")
     # Table 7
-    trans_tbl(4,
+    trans_tbl(3,
               which(tbl$genus == 'Bacteroides'),
-              metr)
+              metr,
-    trans_tbl(4,
+              "any")
+    trans_tbl(3,
               which(tbl$fullname %like% '^Clostridium difficile'),
-              c(metr, vanc))
+              c(metr, vanc),
+              "any")
   }
 
   if (guideline$country$code == 'de') {
@@ -325,112 +346,88 @@ MDRO <- function(tbl,
     carbapenems <- carbapenems[!is.na(carbapenems)]
 
     # Table 1
-    tbl[which(
+    trans_tbl(3,
-      tbl$family == 'Enterobacteriaceae'
+              which(tbl$family == 'Enterobacteriaceae'),
-      & rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
+              c(aminoglycosides, fluoroquinolones),
-      & rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1
+              "all")
-    ), 'MDRO'] <- 4
+
-    tbl[which(
+    trans_tbl(2,
-      tbl$family == 'Enterobacteriaceae'
+              which(tbl$family == 'Enterobacteriaceae'),
-      & rowSums(tbl[, carbapenems] == 'R', na.rm = TRUE) >= 1
+              c(carbapenems),
-    ), 'MDRO'] <- 3
+              "any")
-    # rest is negative
-    tbl[which(
-      tbl$family == 'Enterobacteriaceae'
-      & tbl$MDRO == 1
-    ), 'MDRO'] <- 2
 
     # Table 2
-    tbl[which(
+    trans_tbl(2,
-      tbl$genus == 'Acinetobacter'
+              which(tbl$genus == 'Acinetobacter'),
-      & rowSums(tbl[, carbapenems] == 'R', na.rm = TRUE) >= 1
+              c(carbapenems),
-    ), 'MDRO'] <- 3
+              "any")
-    tbl[which(
+    trans_tbl(3,
-      tbl$genus == 'Acinetobacter'
+              which(tbl$genus == 'Acinetobacter'),
-      & rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
+              c(aminoglycosides, fluoroquinolones),
-      & rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1
+              "all")
-    ), 'MDRO'] <- 4
-    # rest of Acinetobacter is negative
-    tbl[which(
-      tbl$genus == 'Acinetobacter'
-      & tbl$MDRO == 1
-    ), 'MDRO'] <- 2
 
-    tbl[which(
+    trans_tbl(3,
-      tbl$fullname %like% 'Stenotrophomonas maltophilia'
+              which(tbl$fullname %like% '^Stenotrophomonas maltophilia'),
-      & tbl[, trsu] == 'R'
+              trsu,
-    ), 'MDRO'] <- 4
+              "all")
-    # rest of Stenotrophomonas is negative
-    tbl[which(
-      tbl$fullname %like% 'Stenotrophomonas maltophilia'
-      & tbl$MDRO == 1
-    ), 'MDRO'] <- 2
 
-    tbl <- tbl %>% mutate(
+    if (!is.na(mero) & !is.na(imip)
-      psae = 0,
+        & !is.na(gent) & !is.na(tobr)
-      psae = ifelse(mero == "R" | imip == "R", psae + 1, psae),
+        & !is.na(cipr)
-      psae = ifelse(gent == "R" & tobr == "R", psae + 1, psae),
+        & !is.na(cfta)
-      psae = ifelse(cipr == "R", psae + 1, psae),
+        & !is.na(pita) ) {
-      psae = ifelse(cfta == "R", psae + 1, psae),
+      tbl <- tbl %>% mutate(
-      psae = ifelse(pita == "R", psae + 1, psae),
+        psae = 0,
-      psae = ifelse(is.na(psae), 0, psae)
+        psae = ifelse(mero == "R" | imip == "R", psae + 1, psae),
-    )
+        psae = ifelse(gent == "R" & tobr == "R", psae + 1, psae),
+        psae = ifelse(cipr == "R", psae + 1, psae),
+        psae = ifelse(cfta == "R", psae + 1, psae),
+        psae = ifelse(pita == "R", psae + 1, psae),
+        psae = ifelse(is.na(psae), 0, psae)
+      )
+    } else {
+      tbl$psae <- 0
+    }
     tbl[which(
       tbl$fullname %like% 'Pseudomonas aeruginosa'
       & tbl$psae >= 3
-    ), 'MDRO'] <- 4
+    ), 'MDRO'] <- 3
-    # rest of Pseudomonas is negative
-    tbl[which(
-      tbl$fullname %like% 'Pseudomonas aeruginosa'
-      & tbl$MDRO == 1
-    ), 'MDRO'] <- 2
 
     # Table 3
-    tbl[which(
+    trans_tbl(3,
-      tbl$fullname %like% 'Streptococcus pneumoniae'
+              which(tbl$fullname %like% 'Streptococcus pneumoniae'),
-      & tbl[, peni] == 'R'
+              peni,
-    ), 'MDRO'] <- 4
+              "all")
-    tbl[which(
+    trans_tbl(3,
-      tbl$fullname %like% 'Streptococcus pneumoniae'
+              which(tbl$fullname %like% 'Streptococcus pneumoniae'),
-      & tbl[, vanc] == 'R'
+              vanc,
-    ), 'MDRO'] <- 4
+              "all")
-    # rest of Streptococcus pneumoniae is negative
+    trans_tbl(3,
-    tbl[which(
+              which(tbl$fullname %like% 'Enterococcus faecium'),
-      tbl$fullname %like% 'Streptococcus pneumoniae'
+              c(peni, vanc),
-      & tbl$MDRO == 1
+              "all")
-    ), 'MDRO'] <- 2
-
-    tbl[which(
-      tbl$fullname %like% 'Enterococcus faecium'
-      &  rowSums(tbl[, c(peni, vanc)] == 'R', na.rm = TRUE) >= 1
-    ), 'MDRO'] <- 4
-    # rest of Enterococcus faecium is negative
-    tbl[which(
-      tbl$fullname %like% 'Enterococcus faecium'
-      & tbl$MDRO == 1
-    ), 'MDRO'] <- 2
   }
 
   factor(x =  tbl$MDRO,
-         levels = c(1:4),
+         levels = 1:3,
-         labels = c('Not evaluated', 'Negative', 'Unconfirmed', 'Positive'),
+         labels = c('Negative', 'Positive, unconfirmed', 'Positive'),
          ordered = TRUE)
 }
 
-#' @rdname MDRO
+#' @rdname mdro
 #' @export
-BRMO <- function(tbl, country = "nl", ...) {
+brmo <- function(..., country = "nl") {
-  MDRO(tbl = tbl, country = "nl", ...)
+  mdro(..., country = "nl")
 }
 
-#' @rdname MDRO
+#' @rdname mdro
 #' @export
-MRGN <- function(tbl, country = "de", ...) {
+mrgn <- function(tbl, country = "de", ...) {
-  MDRO(tbl = tbl, country = "de", ...)
+  mdro(tbl = tbl, country = "de", ...)
 }
 
-#' @rdname MDRO
+#' @rdname mdro
 #' @export
-EUCAST_exceptional_phenotypes <- function(tbl, country = "EUCAST", ...) {
+eucast_exceptional_phenotypes <- function(tbl, country = "EUCAST", ...) {
-  MDRO(tbl = tbl, country = "EUCAST", ...)
+  mdro(tbl = tbl, country = "EUCAST", ...)
 }

R/read.4d.R

@@ -110,7 +110,7 @@ read.4D <- function(file,
 
   # backup original column names
   colnames.bak <- toupper(colnames(data_4D))
-  colnames.bak[colnames.bak == "AGE"] <- NULL
+  colnames.bak[colnames.bak == "AGE"] <- NA_character_
 
   # rename of columns
   colnames(data_4D) <- gsub("patientnr", "patient_id", colnames(data_4D), fixed = TRUE)
@@ -162,9 +162,18 @@ read.4D <- function(file,
     message("OK\nSetting original column names as label... ", appendLF = FALSE)
   }
   for (i in 1:ncol(data_4D)) {
-    attr(data_4D[, i], "label") <- colnames.bak[i]
+    if (!is.na(colnames.bak[i])) {
+      attr(data_4D[, i], "label") <- colnames.bak[i]
+    }
   }
 
+  if (info == TRUE) {
+    message("OK\nSetting query as label to data.frame... ", appendLF = FALSE)
+  }
+  qry <- readLines(con <- file(file, open="r"))[1]
+  close(con)
+  attr(data_4D, "label") <- qry
+
   if (info == TRUE) {
     message("OK")
   }

man/eucast_rules.Rd

@@ -1,6 +1,7 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/eucast.R
+% Please edit documentation in R/eucast_rules.R
-\name{EUCAST_rules}
+\name{eucast_rules}
+\alias{eucast_rules}
 \alias{EUCAST_rules}
 \alias{interpretive_reading}
 \title{EUCAST rules}
@@ -22,7 +23,7 @@
   }
 }
 \usage{
-EUCAST_rules(tbl, col_mo = NULL, info = TRUE,
+eucast_rules(tbl, col_mo = NULL, info = TRUE,
   rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE,
   amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
   azit = "azit", azlo = "azlo", aztr = "aztr", cefa = "cefa",
@@ -41,6 +42,8 @@ EUCAST_rules(tbl, col_mo = NULL, info = TRUE,
   tetr = "tetr", tica = "tica", tige = "tige", tobr = "tobr",
   trim = "trim", trsu = "trsu", vanc = "vanc", col_bactid = NULL)
 
+EUCAST_rules(...)
+
 interpretive_reading(...)
 }
 \arguments{
@@ -58,7 +61,7 @@ interpretive_reading(...)
 
 \item{col_bactid}{deprecated, use \code{col_mo} instead.}
 
-\item{...}{parameters that are passed on to \code{EUCAST_rules}}
+\item{...}{parameters that are passed on to \code{eucast_rules}}
 }
 \value{
 The input of \code{tbl}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with verbose info.
@@ -138,7 +141,7 @@ Abbrevations of the column containing antibiotics in the form: \strong{abbreviat
 }
 
 \examples{
-a <- EUCAST_rules(septic_patients)
+a <- eucast_rules(septic_patients)
 
 a <- data.frame(mo = c("Staphylococcus aureus",
                        "Enterococcus faecalis",
@@ -162,7 +165,7 @@ a
 # 4  Klebsiella pneumoniae    -    -    -    -    -    S    S
 # 5 Pseudomonas aeruginosa    -    -    -    -    -    S    S
 
-b <- EUCAST_rules(a, "mo") # 18 results are forced as R or S
+b <- eucast_rules(a, "mo") # 18 results are forced as R or S
 
 b
 #                       mo vanc amox coli cfta cfur peni cfox

man/mdro.Rd

@@ -1,13 +1,13 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/mdro.R
-\name{MDRO}
+\name{mdro}
-\alias{MDRO}
+\alias{mdro}
-\alias{BRMO}
+\alias{brmo}
-\alias{MRGN}
+\alias{mrgn}
-\alias{EUCAST_exceptional_phenotypes}
+\alias{eucast_exceptional_phenotypes}
 \title{Determine multidrug-resistant organisms (MDRO)}
 \usage{
-MDRO(tbl, country = NULL, col_mo = NULL, info = TRUE,
+mdro(tbl, country = NULL, col_mo = NULL, info = TRUE,
   amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
   azit = "azit", aztr = "aztr", cefa = "cefa", cfra = "cfra",
   cfep = "cfep", cfot = "cfot", cfox = "cfox", cfta = "cfta",
@@ -25,11 +25,11 @@ MDRO(tbl, country = NULL, col_mo = NULL, info = TRUE,
   tobr = "tobr", trim = "trim", trsu = "trsu", vanc = "vanc",
   col_bactid = NULL)
 
-BRMO(tbl, country = "nl", ...)
+brmo(..., country = "nl")
 
-MRGN(tbl, country = "de", ...)
+mrgn(tbl, country = "de", ...)
 
-EUCAST_exceptional_phenotypes(tbl, country = "EUCAST", ...)
+eucast_exceptional_phenotypes(tbl, country = "EUCAST", ...)
 }
 \arguments{
 \item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
@@ -165,7 +165,7 @@ EUCAST_exceptional_phenotypes(tbl, country = "EUCAST", ...)
 \item{...}{parameters that are passed on to methods}
 }
 \value{
-Ordered factor with levels \code{Unknown < Negative < Unconfirmed < Positive}.
+Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}.
 }
 \description{
 Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
@@ -245,6 +245,6 @@ Abbrevations of the column containing antibiotics in the form: \strong{abbreviat
 library(dplyr)
 
 septic_patients \%>\%
-  mutate(EUCAST = MDRO(.),
+  mutate(EUCAST = mdro(.),
-         BRMO = BRMO(.))
+         BRMO = brmo(.))
 }

tests/testthat/test-eucast_rules.R

@@ -1,11 +1,11 @@
-context("eucast.R")
+context("eucast_rules.R")
 
 test_that("EUCAST rules work", {
 
-  expect_error(suppressWarnings(EUCAST_rules(septic_patients, col_mo = "Non-existing")))
+  expect_error(suppressWarnings(eucast_rules(septic_patients, col_mo = "Non-existing")))
 
   expect_identical(colnames(septic_patients),
-                   colnames(suppressWarnings(EUCAST_rules(septic_patients))))
+                   colnames(suppressWarnings(eucast_rules(septic_patients))))
 
   a <- data.frame(mo = c("KLEPNE",  # Klebsiella pneumoniae
                          "PSEAER",  # Pseudomonas aeruginosa
@@ -17,7 +17,8 @@ test_that("EUCAST rules work", {
                          "ENTAER"), # Enterobacter aerogenes
                   amox = "R",       # Amoxicillin
                   stringsAsFactors = FALSE)
-  expect_identical(suppressWarnings(EUCAST_rules(a, "mo", info = FALSE)), b)
+  expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
+  expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
   expect_identical(suppressWarnings(interpretive_reading(a, "mo", info = TRUE)), b)
 
   a <- data.frame(mo = c("STAAUR",  # Staphylococcus aureus
@@ -28,7 +29,7 @@ test_that("EUCAST rules work", {
                          "STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
                   coli = "R",       # Colistin
                   stringsAsFactors = FALSE)
-  expect_equal(suppressWarnings(EUCAST_rules(a, "mo", info = FALSE)), b)
+  expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
 
   # piperacillin must be R in Enterobacteriaceae when tica is R
   library(dplyr)
@@ -36,7 +37,7 @@ test_that("EUCAST rules work", {
     septic_patients %>%
       mutate(tica = as.rsi("R"),
              pipe = as.rsi("S")) %>%
-      EUCAST_rules(col_mo = "mo") %>%
+      eucast_rules(col_mo = "mo") %>%
       left_join_microorganisms() %>%
       filter(family == "Enterobacteriaceae") %>%
       pull(pipe) %>%
@@ -51,12 +52,12 @@ test_that("EUCAST rules work", {
                 eryt,
                 azit = as.rsi("R"),
                 clar = as.rsi("R")) %>%
-      EUCAST_rules(col_mo = "mo") %>%
+      eucast_rules(col_mo = "mo") %>%
       pull(clar))
   b <-   suppressWarnings(
     septic_patients %>%
       select(mo, eryt) %>%
-      EUCAST_rules(col_mo = "mo") %>%
+      eucast_rules(col_mo = "mo") %>%
       pull(eryt))
 
   expect_identical(a[!is.na(b)],
@@ -64,7 +65,7 @@ test_that("EUCAST rules work", {
 
   # amox is inferred by benzylpenicillin in Kingella kingae
   expect_equal(
-    as.list(EUCAST_rules(
+    as.list(eucast_rules(
       data.frame(mo = as.mo("Kingella kingae"),
                  peni = "S",
                  amox = "-",
@@ -72,6 +73,6 @@ test_that("EUCAST rules work", {
       , info = FALSE))$amox,
     "S")
 
-  expect_output(suppressWarnings(EUCAST_rules(septic_patients, verbose = TRUE)))
+  expect_output(suppressWarnings(eucast_rules(septic_patients, verbose = TRUE)))
 
 })

tests/testthat/test-mdro.R

@@ -1,30 +1,30 @@
 context("mdro.R")
 
 
-test_that("MDRO works", {
+test_that("mdro works", {
   library(dplyr)
 
-  expect_error(suppressWarnings(MDRO(septic_patients, "invalid", col_bactid = "mo", info = TRUE)))
+  expect_error(suppressWarnings(mdro(septic_patients, "invalid", col_bactid = "mo", info = TRUE)))
-  expect_error(suppressWarnings(MDRO(septic_patients, "fr", col_bactid = "mo", info = TRUE)))
+  expect_error(suppressWarnings(mdro(septic_patients, "fr", col_bactid = "mo", info = TRUE)))
-  expect_error(suppressWarnings(MDRO(septic_patients, country = c("de", "nl"), info = TRUE)))
+  expect_error(suppressWarnings(mdro(septic_patients, country = c("de", "nl"), info = TRUE)))
-  expect_error(suppressWarnings(MDRO(septic_patients, col_mo = "invalid", info = TRUE)))
+  expect_error(suppressWarnings(mdro(septic_patients, col_mo = "invalid", info = TRUE)))
 
-  outcome <- suppressWarnings(MDRO(septic_patients))
+  outcome <- suppressWarnings(mdro(septic_patients))
-  outcome <- suppressWarnings(EUCAST_exceptional_phenotypes(septic_patients, info = TRUE))
+  outcome <- suppressWarnings(eucast_exceptional_phenotypes(septic_patients, info = TRUE))
   # check class
   expect_equal(outcome %>% class(), c('ordered', 'factor'))
 
-  outcome <- suppressWarnings(MDRO(septic_patients, "nl", info = TRUE))
+  outcome <- suppressWarnings(mdro(septic_patients, "nl", info = TRUE))
   # check class
   expect_equal(outcome %>% class(), c('ordered', 'factor'))
 
   # septic_patients should have these finding using Dutch guidelines
   expect_equal(outcome %>% freq() %>% pull(count),
-               c(1167, 817, 14, 2)) # 1167 not eval., 817 neg, 14 pos, 2 unconfirmed
+               c(19989, 9, 2)) # 1167 not eval., 817 neg, 14 pos, 2 unconfirmed
 
-  expect_equal(BRMO(septic_patients, info = FALSE), MDRO(septic_patients, "nl", info = FALSE))
+  expect_equal(brmo(septic_patients, info = FALSE), mdro(septic_patients, "nl", info = FALSE))
 
   # still working on German guidelines
-  expect_error(suppressWarnings(MRGN(septic_patients, info = TRUE)))
+  expect_error(suppressWarnings(mrgn(septic_patients, info = TRUE)))
 
 })