mdro and 1st isolate improvements

NEWS.md

@@ -17,17 +17,20 @@
 * Fix for `portion_*(..., as_percent = TRUE)` when minimal amount of isolates would not be met
 * Added parameter `also_single_tested` for `portion_*` and `count_*` functions to also include cases where not all antibiotics were tested but at least one of the tested antibiotics includes the target antimicribial interpretation, see `?portion`
 * Using `portion_*` functions now throws a warning when total available isolate is below parameter `minimum`
-* Functions `as.mo`, `as.rsi`, `as.mic` and `as.atc` will not set package name as attribute anymore
+* Functions `as.mo`, `as.rsi`, `as.mic`, `as.atc` and `freq` will not set package name as attribute anymore
-* Data set `septic_patients` is now a `data.frame`, not a tibble anymore
+* Frequency tables - `freq()`:
   * Check for `hms::is.hms` in frequency tables (`freq()`)
-* New parameter `header` for frequency tables to turn them off (default when `markdown = TRUE`)
+  * Now prints in markdown at default in non-interactive sessions
-* Freq now prints in markdown at default in non-interactive sessions
+  * No longer adds the factor level column and sorts factors on count again
-* Freq no longer add the factor level column and sorts factors on count again
+  * Gained `na` parameter, to choose with character to print for empty values
+  * Support for class `difftime`
+  * New parameter `header` to turn it off (default when `markdown = TRUE`)
+* `first_isolate` now tries to find columns to use as input when parameters are left blank
+* Improvement for MDRO algorithm
+* 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
-* Freq gained `na` parameter, to choose with character to print for empty values
 * Fix for `mo_property` not working properly
 * Fix for `EUCAST_rules` where some Streptococci would become ceftazidime R in EUCAST rule 4.5
-* Support for class `difftime` in frequency tables
 * 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/first_isolate.R

@@ -20,9 +20,9 @@
 #'
 #' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.
 #' @param tbl a \code{data.frame} containing isolates.
-#' @param col_date column name of the result date (or date that is was received on the lab)
+#' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column of class \code{Date}
-#' @param col_patient_id column name of the unique IDs of the patients
+#' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' (case insensitive)
-#' @param col_mo column name of the unique IDs of the microorganisms, see \code{\link{mo}}. If this column has another class than \code{"mo"}, values will be coerced using \code{\link{as.mo}}.
+#' @param col_mo column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. If this column has another class than \code{"mo"}, values will be coerced using \code{\link{as.mo}}.
 #' @param col_testcode column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation.
 #' @param col_specimen column name of the specimen type or group
 #' @param col_icu column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)
@@ -125,42 +125,63 @@
 #'                 col_keyantibiotics = 'keyab')
 #' }
 first_isolate <- function(tbl,
-                          col_date,
+                          col_date = NULL,
-                          col_patient_id,
+                          col_patient_id = NULL,
-                          col_mo = NA,
+                          col_mo = NULL,
-                          col_testcode = NA,
+                          col_testcode = NULL,
-                          col_specimen = NA,
+                          col_specimen = NULL,
-                          col_icu = NA,
+                          col_icu = NULL,
-                          col_keyantibiotics = NA,
+                          col_keyantibiotics = NULL,
                           episode_days = 365,
-                          testcodes_exclude = '',
+                          testcodes_exclude = NULL,
                           icu_exclude = FALSE,
-                          filter_specimen = NA,
+                          filter_specimen = NULL,
                           output_logical = TRUE,
                           type = "keyantibiotics",
                           ignore_I = TRUE,
                           points_threshold = 2,
                           info = TRUE,
-                          col_bactid = NA,
+                          col_bactid = NULL,
-                          col_genus = NA,
+                          col_genus = NULL,
-                          col_species = NA) {
+                          col_species = NULL) {
 
-  if (!is.na(col_bactid)) {
+  if (!is.data.frame(tbl)) {
+    stop("`tbl` must be a data frame.", call. = FALSE)
+  }
+
+  # try to find columns based on type
+  # -- mo
+  if (!is.null(col_bactid)) {
     col_mo <- col_bactid
     warning("Use of `col_bactid` is deprecated. Use `col_mo` instead.")
+  } else if (is.null(col_mo) & "mo" %in% lapply(tbl, class)) {
+    col_mo <- colnames(tbl)[lapply(tbl, class) == "mo"]
+    message("NOTE: Using column `", col_mo, "` as input for `col_mo`.")
   }
+  # -- date
+  if (is.null(col_date) & "Date" %in% lapply(tbl, class)) {
+    col_date <- colnames(tbl)[lapply(tbl, class) == "Date"]
+    message("NOTE: Using column `", col_date, "` as input for `col_date`.")
+  }
+  # -- patient id
+  if (is.null(col_patient_id) & any(colnames(tbl) %like% "^patient")) {
+    col_patient_id <- colnames(tbl)[colnames(tbl) %like% "^patient"][1]
+    message("NOTE: Using column `", col_patient_id, "` as input for `col_patient_id`.")
+  }
+
   # bactid OR genus+species must be available
-  if (is.na(col_mo) & (is.na(col_genus) | is.na(col_species))) {
+  if (is.null(col_mo) & (is.null(col_genus) | is.null(col_species))) {
     stop('`col_mo` or both `col_genus` and `col_species` must be available.')
   }
 
+
   # check if columns exist
   check_columns_existance <- function(column, tblname = tbl) {
     if (NROW(tblname) <= 1 | NCOL(tblname) <= 1) {
       stop('Please check tbl for existance.')
     }
 
-    if (!is.na(column)) {
+    if (!is.null(column)) {
       if (!(column %in% colnames(tblname))) {
         stop('Column `', column, '` not found.')
       }
@@ -176,7 +197,7 @@ first_isolate <- function(tbl,
   check_columns_existance(col_icu)
   check_columns_existance(col_keyantibiotics)
 
-  if (!is.na(col_mo)) {
+  if (!is.null(col_mo)) {
     if (!tbl %>% pull(col_mo) %>% is.mo()) {
       tbl[, col_mo] <- as.mo(tbl[, col_mo])
     }
@@ -186,41 +207,37 @@ first_isolate <- function(tbl,
     col_species <- "species"
   }
 
-  if (is.na(col_testcode)) {
+  if (is.null(col_testcode)) {
-    testcodes_exclude <- NA
+    testcodes_exclude <- NULL
   }
   # remove testcodes
-  if (!is.na(testcodes_exclude[1]) & testcodes_exclude[1] != '' & info == TRUE) {
+  if (!is.null(testcodes_exclude) & info == TRUE) {
     cat('[Criteria] Excluded test codes:\n', toString(testcodes_exclude), '\n')
   }
 
-  if (is.na(col_icu)) {
+  if (is.null(col_icu)) {
     icu_exclude <- FALSE
   } else {
     tbl <- tbl %>%
       mutate(col_icu = tbl %>% pull(col_icu) %>% as.logical())
   }
 
-  if (is.na(col_specimen)) {
+  if (is.null(col_specimen)) {
-    filter_specimen <- ''
+    filter_specimen <- NULL
   }
 
   # filter on specimen group and keyantibiotics when they are filled in
-  if (!is.na(filter_specimen) & filter_specimen != '') {
+  if (!is.null(filter_specimen)) {
     check_columns_existance(col_specimen, tbl)
     if (info == TRUE) {
       cat('[Criteria] Excluded other than specimen group \'', filter_specimen, '\'\n', sep = '')
     }
-  } else {
-    filter_specimen <- ''
   }
-  if (col_keyantibiotics %in% c(NA, '')) {
+  if (!is.null(col_keyantibiotics)) {
-    col_keyantibiotics <- ''
-  } else {
     tbl <- tbl %>% mutate(key_ab = tbl %>% pull(col_keyantibiotics))
   }
 
-  if (is.na(testcodes_exclude[1])) {
+  if (is.null(testcodes_exclude)) {
     testcodes_exclude <- ''
   }
 
@@ -234,10 +251,10 @@ first_isolate <- function(tbl,
     mutate(species = if_else(is.na(species) | species == "(no MO)", "", species),
            genus = if_else(is.na(genus) | genus == "(no MO)", "", genus))
 
-  if (filter_specimen == '') {
+  if (is.null(filter_specimen)) {
-
+    # not filtering on specimen
     if (icu_exclude == FALSE) {
-      if (info == TRUE & !is.na(col_icu)) {
+      if (info == TRUE & !is.null(col_icu)) {
         cat('[Criteria] Included isolates from ICU.\n')
       }
       tbl <- tbl %>%
@@ -267,9 +284,9 @@ first_isolate <- function(tbl,
     }
 
   } else {
-    # sort on specimen and only analyse these row to save time
+    # filtering on specimen and only analyse these row to save time
     if (icu_exclude == FALSE) {
-      if (info == TRUE & !is.na(col_icu)) {
+      if (info == TRUE & !is.null(col_icu)) {
         cat('[Criteria] Included isolates from ICU.\n')
       }
       tbl <- tbl %>%
@@ -344,7 +361,7 @@ first_isolate <- function(tbl,
                                0))
 
   weighted.notice <- ''
-  if (col_keyantibiotics != '') {
+  if (!is.null(col_keyantibiotics)) {
     weighted.notice <- 'weighted '
     if (info == TRUE) {
       if (type == 'keyantibiotics') {
@@ -402,7 +419,7 @@ first_isolate <- function(tbl,
   # first one as TRUE
   all_first[row.start, 'real_first_isolate'] <- TRUE
   # no tests that should be included, or ICU
-  if (!is.na(col_testcode)) {
+  if (!is.null(col_testcode)) {
     all_first[which(all_first[, col_testcode] %in% tolower(testcodes_exclude)), 'real_first_isolate'] <- FALSE
   }
   if (icu_exclude == TRUE) {

R/mdro.R

@@ -29,6 +29,8 @@
 #' @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}.
 #' @rdname MDRO
+#' @importFrom dplyr %>%
+#' @importFrom crayon red blue
 #' @export
 #' @examples
 #' library(dplyr)
@@ -38,7 +40,7 @@
 #'          BRMO = BRMO(.))
 MDRO <- function(tbl,
                  country = NULL,
-                 col_mo = 'mo',
+                 col_mo = NULL,
                  info = TRUE,
                  amcl = 'amcl',
                  amik = 'amik',
@@ -99,13 +101,21 @@ MDRO <- function(tbl,
                  trim = 'trim',
                  trsu = 'trsu',
                  vanc = 'vanc',
-                 col_bactid = 'bactid') {
+                 col_bactid = NULL) {
 
-  if (col_bactid %in% colnames(tbl)) {
+  if (!is.data.frame(tbl)) {
+    stop("`tbl` must be a data frame.", call. = FALSE)
+  }
+
+  # try to find columns based on type
+  # -- mo
+  if (!is.null(col_bactid)) {
     col_mo <- col_bactid
     warning("Use of `col_bactid` is deprecated. Use `col_mo` instead.")
-  }
+  } else if (is.null(col_mo) & "mo" %in% lapply(tbl, class)) {
-  if (!col_mo %in% colnames(tbl)) {
+    col_mo <- colnames(tbl)[lapply(tbl, class) == "mo"]
+    message("NOTE: Using column `", col_mo, "` as input for `col_mo`.")
+  } else if (!col_mo %in% colnames(tbl)) {
     stop('Column ', col_mo, ' not found.', call. = FALSE)
   }
 
@@ -142,23 +152,17 @@ MDRO <- function(tbl,
     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:
-  # } else if (country$code == 'AA') {
+  # } else if (country$code == 'xx') {
   #   country$name <- 'country name'
   } else {
     stop('This country code is currently unsupported: ', guideline$country$code, call. = FALSE)
   }
 
-  # Console colours
-  # source: http://www.tldp.org/HOWTO/Bash-Prompt-HOWTO/x329.html
-  ANSI_red <- "\033[31m"
-  ANSI_blue <- "\033[34m"
-  ANSI_reset <- "\033[0m"
-
   if (info == TRUE) {
     cat("Determining multidrug-resistant organisms (MDRO), according to:\n",
-        "Guideline: ", ANSI_red, guideline$name, ", ", guideline$version, ANSI_reset, "\n",
+        "Guideline: ", red(paste0(guideline$name, ", ", guideline$version, "\n")),
-        "Country  : ", ANSI_red, guideline$country$name, ANSI_reset, "\n",
+        "Country  : ", red(paste0(guideline$country$name, "\n")),
-        "Source   : ", ANSI_blue, guideline$source, ANSI_reset, "\n",
+        "Source   : ", blue(paste0(guideline$source, "\n")),
         "\n", sep = "")
   }
 
@@ -231,18 +235,11 @@ MDRO <- function(tbl,
   vanc <- col.list[vanc]
 
   # antibiotic classes
-  aminoglycosides <- c(tobr, gent, kana, neom, neti, siso)
+  aminoglycosides <- c(tobr, gent) # can also be kana but that one is often intrinsic R
-  tetracyclines <- c(doxy, mino, tetr) # since EUCAST v3.1 tige(cycline) is set apart
-  polymyxins <- c(poly, coli)
-  macrolides <- c(eryt, azit, roxi, clar) # since EUCAST v3.1 clin(damycin) is set apart
-  glycopeptides <- c(vanc, teic)
-  streptogramins <- qida # should officially also be pristinamycin and quinupristin/dalfopristin
   cephalosporins <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol)
   cephalosporins_3rd <- c(cfot, cftr, cfta)
   carbapenems <- c(erta, imip, mero)
-  aminopenicillins <- c(ampi, amox)
+  fluoroquinolones <- c(oflo, cipr, levo, moxi)
-  ureidopenicillins <- pita # should officially also be azlo and mezlo
-  fluoroquinolones <- c(oflo, cipr, norf, levo, moxi)
 
   # helper function for editing the table
   trans_tbl <- function(to, rows, cols) {
@@ -254,10 +251,15 @@ MDRO <- function(tbl,
     }
   }
 
-  # join microorganisms
+  if (!tbl %>% pull(col_mo) %>% is.mo()) {
-  tbl <- tbl %>% left_join_microorganisms(col_mo)
+    tbl[, col_mo] <- as.mo(tbl[, col_mo])
+  }
 
-  tbl$MDRO <- NA_integer_
+  tbl <- tbl %>%
+    # 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_))
 
   if (guideline$country$code == 'eucast') {
     # EUCAST ------------------------------------------------------------------
@@ -327,6 +329,11 @@ MDRO <- function(tbl,
       & rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
       & rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1
     ), 'MDRO'] <- 4
+    a <<- tbl[which(
+      tbl$family == 'Enterobacteriaceae'
+      & rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
+      & rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1
+    ), ]
     tbl[which(
       tbl$family == 'Enterobacteriaceae'
       & rowSums(tbl[, carbapenems] == 'R', na.rm = TRUE) >= 1
@@ -363,13 +370,18 @@ MDRO <- function(tbl,
       & tbl$MDRO == 1
     ), 'MDRO'] <- 2
 
+    tbl <- tbl %>% mutate(
+      psae = 0,
+      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)
+    )
     tbl[which(
       tbl$fullname %like% 'Pseudomonas aeruginosa'
-      & sum(rowSums(tbl[, carbapenems] == 'R', na.rm = TRUE) >= 1,
+      & tbl$psae >= 3
-           rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1,
-           rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1,
-           tbl[, cfta] == 'R',
-           tbl[, pita] == 'R') >= 3
     ), 'MDRO'] <- 4
     # rest of Pseudomonas is negative
     tbl[which(
@@ -405,7 +417,7 @@ MDRO <- function(tbl,
 
   factor(x =  tbl$MDRO,
          levels = c(1:4),
-         labels = c('Unknown', 'Negative', 'Unconfirmed', 'Positive'),
+         labels = c('Not evaluated', 'Negative', 'Unconfirmed', 'Positive'),
          ordered = TRUE)
 }
 

man/first_isolate.Rd

@@ -7,22 +7,23 @@
 Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
 }
 \usage{
-first_isolate(tbl, col_date, col_patient_id, col_mo = NA,
+first_isolate(tbl, col_date = NULL, col_patient_id = NULL,
-  col_testcode = NA, col_specimen = NA, col_icu = NA,
+  col_mo = NULL, col_testcode = NULL, col_specimen = NULL,
-  col_keyantibiotics = NA, episode_days = 365,
+  col_icu = NULL, col_keyantibiotics = NULL, episode_days = 365,
-  testcodes_exclude = "", icu_exclude = FALSE, filter_specimen = NA,
+  testcodes_exclude = NULL, icu_exclude = FALSE,
-  output_logical = TRUE, type = "keyantibiotics", ignore_I = TRUE,
+  filter_specimen = NULL, output_logical = TRUE,
-  points_threshold = 2, info = TRUE, col_bactid = NA,
+  type = "keyantibiotics", ignore_I = TRUE, points_threshold = 2,
-  col_genus = NA, col_species = NA)
+  info = TRUE, col_bactid = NULL, col_genus = NULL,
+  col_species = NULL)
 }
 \arguments{
 \item{tbl}{a \code{data.frame} containing isolates.}
 
-\item{col_date}{column name of the result date (or date that is was received on the lab)}
+\item{col_date}{column name of the result date (or date that is was received on the lab), defaults to the first column of class \code{Date}}
 
-\item{col_patient_id}{column name of the unique IDs of the patients}
+\item{col_patient_id}{column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' (case insensitive)}
 
-\item{col_mo}{column name of the unique IDs of the microorganisms, see \code{\link{mo}}. If this column has another class than \code{"mo"}, values will be coerced using \code{\link{as.mo}}.}
+\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. If this column has another class than \code{"mo"}, values will be coerced using \code{\link{as.mo}}.}
 
 \item{col_testcode}{column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation.}
 

man/freq.Rd

@@ -10,11 +10,12 @@
 frequency_tbl(x, ..., sort.count = TRUE,
   nmax = getOption("max.print.freq"), na.rm = TRUE, row.names = TRUE,
   markdown = !interactive(), digits = 2, quote = FALSE,
-  header = !markdown, sep = " ")
+  header = !markdown, na = "<NA>", sep = " ")
 
 freq(x, ..., sort.count = TRUE, nmax = getOption("max.print.freq"),
   na.rm = TRUE, row.names = TRUE, markdown = !interactive(),
-  digits = 2, quote = FALSE, header = !markdown, sep = " ")
+  digits = 2, quote = FALSE, header = !markdown, na = "<NA>",
+  sep = " ")
 
 top_freq(f, n)
 
@@ -30,7 +31,7 @@ top_freq(f, n)
 
 \item{nmax}{number of row to print. The default, \code{15}, uses \code{\link{getOption}("max.print.freq")}. Use \code{nmax = 0}, \code{nmax = Inf}, \code{nmax = NULL} or \code{nmax = NA} to print all rows.}
 
-\item{na.rm}{a logical value indicating whether \code{NA} values should be removed from the frequency table. The header will always print the amount of \code{NA}s.}
+\item{na.rm}{a logical value indicating whether \code{NA} values should be removed from the frequency table. The header (if set) will always print the amount of \code{NA}s.}
 
 \item{row.names}{a logical value indicating whether row indices should be printed as \code{1:nrow(x)}}
 
@@ -42,6 +43,8 @@ top_freq(f, n)
 
 \item{header}{a logical value indicating whether an informative header should be printed}
 
+\item{na}{a character string to should be used to show empty (\code{NA}) values (only useful when \code{na.rm = FALSE})}
+
 \item{sep}{a character string to separate the terms when selecting multiple columns}
 
 \item{f}{a frequency table}

man/key_antibiotics.Rd

@@ -20,7 +20,7 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
 \arguments{
 \item{tbl}{table with antibiotics coloms, like \code{amox} and \code{amcl}.}
 
-\item{col_mo}{column name of the unique IDs of the microorganisms, see \code{\link{mo}}. If this column has another class than \code{"mo"}, values will be coerced using \code{\link{as.mo}}.}
+\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. If this column has another class than \code{"mo"}, values will be coerced using \code{\link{as.mo}}.}
 
 \item{universal_1, universal_2, universal_3, universal_4, universal_5, universal_6}{column names of \strong{broad-spectrum} antibiotics, case-insensitive}
 

tests/testthat/test-first_isolate.R

@@ -119,11 +119,18 @@ test_that("first isolates work", {
 
   # errors
   expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
-  expect_error(first_isolate(septic_patients))
   expect_error(first_isolate(septic_patients,
                              col_date = "non-existing col",
                              col_mo = "mo"))
 
+  # look for columns itself
+  expect_message(first_isolate(septic_patients))
+  expect_message(first_isolate(septic_patients %>%
+                                 mutate(mo = as.character(mo)) %>%
+                                 left_join_microorganisms(),
+                               col_genus = "genus",
+                               col_species = "species"))
+
   # if mo is not an mo class, result should be the same
   expect_identical(septic_patients %>%
                    mutate(mo = as.character(mo)) %>%

tests/testthat/test-mdro.R

@@ -20,7 +20,7 @@ test_that("MDRO works", {
 
   # septic_patients should have these finding using Dutch guidelines
   expect_equal(outcome %>% freq() %>% pull(count),
-               c(2, 14)) # 2 unconfirmed, 14 positive
+               c(1167, 817, 14, 2)) # 1167 not eval., 817 neg, 14 pos, 2 unconfirmed
 
   expect_equal(BRMO(septic_patients, info = FALSE), MDRO(septic_patients, "nl", info = FALSE))