(v0.8.0.9008) new verbose mode for MDROs

2025-10-31 06:08:14 +01:00 · 2019-11-03 22:24:42 +01:00
parent 09c4b04cd0
commit 29e448883d
42 changed files with 338 additions and 343 deletions
--- a/.gitlab-ci.R
+++ b/.gitlab-ci.R
@@ -23,7 +23,11 @@ install_if_needed <- function(pkg, repos, quiet) {
  package_path <- find.package(pkg, quiet = quiet)
  if (length(package_path) == 0) {
    message("NOTE: pkg ", pkg, " missing, installing...")
-    install.packages(pkg, repos = repos, quiet = quiet)
+    if (pkg == "cleaner") {
+      devtools::install_github("msberends/cleaner")
+    } else {
+      install.packages(pkg, repos = repos, quiet = quiet)
+    }
  }
 }

@@ -41,6 +45,7 @@ gl_update_pkg_all <- function(repos = "https://cran.rstudio.com",
  if (install_lintr == TRUE) {
    install_if_needed(pkg = "lintr", repos = repos, quiet = quiet)
  }
+  install_if_needed(pkg = "cleaner", repos = repos, quiet = quiet)
  
  devtools::install_dev_deps(repos = repos, quiet = quiet, upgrade = TRUE)

--- a/6
+++ b/6
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.8.0.9007
-Date: 2019-10-30
+Version: 0.8.0.9008
+Date: 2019-11-03
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
    person(role = c("aut", "cre"), 
@@ -36,7 +36,7 @@ Depends:
    R (>= 3.1.0)
 Imports:
    backports,
-    clean (>= 1.1.0),
+    cleaner,
    crayon (>= 1.3.0),
    data.table (>= 1.9.0),
    dplyr (>= 0.7.0),
--- a/7
+++ b/7
@@ -232,9 +232,10 @@ exportMethods(skewness.matrix)
 exportMethods(summary.mic)
 exportMethods(summary.mo)
 exportMethods(summary.rsi)
-importFrom(clean,freq)
-importFrom(clean,freq.default)
-importFrom(clean,top_freq)
+importFrom(cleaner,freq)
+importFrom(cleaner,freq.default)
+importFrom(cleaner,percentage)
+importFrom(cleaner,top_freq)
 importFrom(crayon,bgGreen)
 importFrom(crayon,bgRed)
 importFrom(crayon,bgYellow)
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,8 +1,10 @@
-# AMR 0.8.0.9007
-<small>Last updated: 30-Oct-2019</small>
+# AMR 0.8.0.9008
+<small>Last updated: 03-Nov-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.**
+* 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
+  * The new Verbose mode (`mdro(...., verbose = TRUE)`) returns an informative data set where the reason for MDRO determination is given for every isolate

 ### 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
@@ -12,6 +14,10 @@
 * 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 and fixed two typos in the `antibiotics` data set
+* More robust way of determining valid MIC values
+
+### Other
+* Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request

 # AMR 0.8.0

--- a/R/availability.R
+++ b/R/availability.R
@@ -27,7 +27,7 @@
 #' @details The function returns a \code{data.frame} with columns \code{"resistant"} and \code{"visual_resistance"}. The values in that columns are calculated with \code{\link{portion_R}}.
 #' @return \code{data.frame} with column names of \code{tbl} as row names
 #' @inheritSection AMR Read more on our website!
-# @importFrom clean percentage
+#' @importFrom cleaner percentage
 #' @export
 #' @examples
 #' availability(example_isolates)
--- a/R/bug_drug_combinations.R
+++ b/R/bug_drug_combinations.R
@@ -33,7 +33,6 @@
 #' @inheritParams base::formatC
 #' @importFrom dplyr %>% rename group_by select mutate filter summarise ungroup
 #' @importFrom tidyr spread
-# @importFrom clean freq percentage
 #' @details The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S. 
 #' 
 #' The language of the output can be overwritten with \code{options(AMR_locale)}, please see \link{translate}.
@@ -95,6 +94,7 @@ bug_drug_combinations <- function(x,

 #' @importFrom dplyr everything rename %>% ungroup group_by summarise mutate_all arrange everything lag
 #' @importFrom tidyr spread
+#' @importFrom cleaner percentage
 #' @exportMethod format.bug_drug_combinations
 #' @export
 #' @rdname bug_drug_combinations
--- a/R/catalogue_of_life.R
+++ b/R/catalogue_of_life.R
@@ -90,7 +90,6 @@ NULL
 #' @export
 #' @examples
 #' library(dplyr)
-#' library(clean)
 #' microorganisms %>% freq(kingdom)
 #' microorganisms %>% group_by(kingdom) %>% freq(phylum, nmax = NULL)
 catalogue_of_life_version <- function() {
--- a/R/freq.R
+++ b/R/freq.R
@@ -19,14 +19,13 @@
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

-#' @importFrom clean freq
+#' @importFrom cleaner freq
 #' @export
-clean::freq
+cleaner::freq

 #' @exportMethod freq.mo
 #' @importFrom dplyr n_distinct
-#' @importFrom clean freq.default
-# @importFrom clean percentage
+#' @importFrom cleaner freq.default percentage
 #' @export
 #' @noRd
 freq.mo <- function(x, ...) {
@@ -53,7 +52,7 @@ freq.mo <- function(x, ...) {
 }

 #' @exportMethod freq.rsi
-#' @importFrom clean freq.default
+#' @importFrom cleaner freq.default
 #' @export
 #' @noRd
 freq.rsi <- function(x, ...) {
--- a/R/ggplot_rsi.R
+++ b/R/ggplot_rsi.R
@@ -337,7 +337,7 @@ facet_rsi <- function(facet = c("interpretation", "antibiotic"), nrow = NULL) {
 }

 #' @rdname ggplot_rsi
-# @importFrom clean percentage
+#' @importFrom cleaner percentage
 #' @export
 scale_y_percent <- function(breaks = seq(0, 1, 0.1), limits = NULL) {
  stopifnot_installed_package("ggplot2")
@@ -387,7 +387,7 @@ theme_rsi <- function() {

 #' @rdname ggplot_rsi
 #' @importFrom dplyr mutate %>% group_by_at
-# @importFrom clean percentage
+#' @importFrom cleaner percentage
 #' @export
 labels_rsi_count <- function(position = NULL,
                             x = "antibiotic",
--- a/R/like.R
+++ b/R/like.R
@@ -48,7 +48,6 @@
 #'
 #' # get frequencies of bacteria whose name start with 'Ent' or 'ent'
 #' library(dplyr)
-#' library(clean)
 #' example_isolates %>%
 #'   left_join_microorganisms() %>%
 #'   filter(genus %like% '^ent') %>%
--- a/R/mdro.R
+++ b/R/mdro.R
@@ -22,13 +22,16 @@
 #' Determine multidrug-resistant organisms (MDRO)
 #'
 #' 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 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
+#' @param pct_required_classes minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for \emph{S. aureus}. Setting this \code{pct_required_classes} argument to \code{0.5} (default) means that for every \emph{S. aureus} isolate at least 8 different classes must be available. Any lower number of available classes will return \code{NA} for that isolate.
+#' @param verbose a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
 #' @inheritSection eucast_rules Antibiotics
-#' @details Currently supported guidelines are (case-insensitive):
+#' @details 
+#' For the \code{pct_required_classes} argument, values above 1 will be divided by 100. This is to support both fractions (\code{0.75} or \code{3/4}) and percentages (\code{75}).
+#' 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})}
@@ -38,6 +41,7 @@
 #' }
 #'
 #' Please suggest your own (country-specific) guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}.
+#' 
 #' @return \itemize{
 #'   \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}}
@@ -47,6 +51,7 @@
 #' @rdname mdro
 #' @importFrom dplyr %>% filter_all
 #' @importFrom crayon blue bold italic
+#' @importFrom cleaner percentage
 #' @export
 #' @inheritSection AMR Read more on our website!
 #' @source
@@ -54,13 +59,13 @@
 #' @examples
 #' library(dplyr)
 #' 
-#' example_isolates %>% 
-#'   mdro() %>% 
+#' example_isolates %>%
+#'   mdro() %>%
 #'   freq()
 #'   
 #' \donttest{
 #' example_isolates %>%
-#'   mutate(EUCAST = mdro(.),
+#'   mutate(EUCAST = eucast_exceptional_phenotypes(.),
 #'          BRMO = brmo(.),
 #'          MRGN = mrgn(.))
 #'          
@@ -74,13 +79,35 @@ mdro <- function(x,
                 col_mo = NULL,
                 info = TRUE,
                 verbose = FALSE,
+                 pct_required_classes = 0.5,
                 ...) {
-
+  
+  if (verbose == TRUE & interactive()) {
+    txt <- paste0("WARNING: In Verbose mode, the mdro() function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.",
+                  "\n\nThis may overwrite your existing data if you use e.g.:",
+                  "\ndata <- mdro(data, verbose = TRUE)\n\nDo you want to continue?")
+    if ("rstudioapi" %in% rownames(utils::installed.packages())) {
+      q_continue <- rstudioapi::showQuestion("Using verbose = TRUE with mdro()", txt)
+    } else {
+      q_continue <- menu(choices = c("OK", "Cancel"), graphics = TRUE, title = txt)
+    }
+    if (q_continue %in% c(FALSE, 2)) {
+      message("Cancelled, returning original data")
+      return(x)
+    }
+  }
+  
  if (!is.data.frame(x)) {
    stop("`x` must be a data frame.", call. = FALSE)
  }
-
-
+  if (!is.numeric(pct_required_classes)) {
+    stop("`pct_required_classes` must be numeric.", call. = FALSE)
+  }
+  if (pct_required_classes > 1) {
+    # allow pct_required_classes = 75 -> pct_required_classes = 0.75
+    pct_required_classes <- pct_required_classes / 100
+  }
+  
  if (!is.null(list(...)$country)) {
    warning("Using `country` is deprecated, use `guideline` instead. Please see ?mdro.", call. = FALSE)
    guideline <- list(...)$country
@@ -88,7 +115,7 @@ mdro <- function(x,
  if (length(guideline) > 1) {
    stop("`guideline` must be a length one character string.", call. = FALSE)
  }
-
+  
  if (is.null(guideline)) {
    # default to the paper by Magiorakos et al. (2012)
    guideline <- "cmi2012"
@@ -103,7 +130,7 @@ mdro <- function(x,
    stop("invalid guideline: ", guideline, call. = FALSE)
  }
  guideline <- list(code = tolower(guideline))
-
+  
  # try to find columns based on type
  # -- mo
  if (is.null(col_mo)) {
@@ -118,7 +145,7 @@ mdro <- function(x,
  if (is.null(col_mo)) {
    stop("`col_mo` must be set.", call. = FALSE)
  }
-
+  
  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$author <- "Magiorakos AP, Srinivasan A, Carey RB, ..., Vatopoulos A, Weber JT, Monnet DL"
@@ -130,13 +157,13 @@ mdro <- function(x,
    guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)"
    guideline$version <- "3.1"
    guideline$source <- "http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf"
-
+    
  } else if (guideline$code == "tb") {
    guideline$name <- "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis"
    guideline$author <- "WHO (World Health Organization)"
    guideline$version <- "WHO/HTM/TB/2014.11"
    guideline$source <- "https://www.who.int/tb/publications/pmdt_companionhandbook/en/"
-
+    
    # support per country:
  } else if (guideline$code == "mrgn") {
    guideline$name <- "Cross-border comparison of the Dutch and German guidelines on multidrug-resistant Gram-negative microorganisms"
@@ -152,7 +179,7 @@ mdro <- function(x,
  } else {
    stop("This guideline is currently unsupported: ", guideline$code, call. = FALSE)
  }
-
+  
  if (guideline$code == "cmi2012") {
    cols_ab <- get_column_abx(x = x,
                              soft_dependencies = c(
@@ -270,7 +297,7 @@ mdro <- function(x,
                                "TCY",
                                "DOX",
                                "MNO"
-                                ),
+                              ),
                              verbose = verbose, ...)
  } else if (guideline$code == "tb") {
    cols_ab <- get_column_abx(x = x,
@@ -295,7 +322,7 @@ mdro <- function(x,
  } else {
    cols_ab <- get_column_abx(x = x, verbose = verbose, ...)
  }
-
+  
  AMC <- cols_ab["AMC"]
  AMK <- cols_ab["AMK"]
  AMP <- cols_ab["AMP"]
@@ -391,21 +418,23 @@ mdro <- function(x,
        bold("Source:    "), guideline$source, "\n",
        "\n", sep = "")
  }
-
+  
  ab_missing <- function(ab) {
    isTRUE(ab %in% c(NULL, NA)) | length(ab) == 0
  }
  ab_NA <- function(x) {
    x[!is.na(x)]
  }
-
+  
+  verbose_df <- NULL
+  
  # antibiotic classes
  aminoglycosides <- c(TOB, GEN)
  cephalosporins <- c(FEP, CTX, FOX, CED, CAZ, CRO, CXM, CZO)
  cephalosporins_3rd <- c(CTX, CRO, CAZ)
  carbapenems <- c(ETP, IPM, MEM)
  fluoroquinolones <- c(OFX, CIP, LVX, MFX)
-
+  
  # helper function for editing the table
  trans_tbl <- function(to, rows, cols, any_all) {
    cols <- cols[!ab_missing(cols)]
@@ -421,41 +450,41 @@ mdro <- function(x,
      }
      rows <- rows[rows %in% row_filter]
      x[rows, "MDRO"] <<- to
+      x[rows, "reason"] <<- paste0(any_all, " of these ", ifelse(any_all == "any", "is", "are"), " R: ",
+                                   paste(cols, collapse = ", "))
    }
  }
  trans_tbl2 <- function(txt, rows, lst) {
    if (info == TRUE) {
      message(blue(txt, "..."), appendLF = FALSE)
    }
-    # function specific for the CMI paper of 2012 (Magiorakos et al.)
-    lst_vector <- unlist(lst)[!is.na(unlist(lst))]
-    x$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")))$row_number,
-      "MDRO"] <<- 4
+    if (length(rows) > 0) {
+      # function specific for the CMI paper of 2012 (Magiorakos et al.)
+      lst_vector <- unlist(lst)[!is.na(unlist(lst))]
+      x[rows, "classes_in_guideline"] <<- length(lst)
+      x[rows, "classes_available"] <<- sapply(rows, 
+                                             function(row, group_tbl = lst) {
+                                               sum(sapply(group_tbl, function(group) !all(is.na(group))))
+                                             })
+      # now the hard part - using two sapply()s for super fast results:
+      # [1] run through all `rows` with sapply()
+      # [2] within each row, run through all antibiotic classes with another sapply()
+      # [3] determine for each antibiotic group in that row if at least 1 drug is R of I 
+      # [4] sum the number of TRUEs of this determination
+      x[rows, "classes_affected"] <<- sapply(rows, 
+                                            function(row, group_tbl = lst) {
+                                              sum(sapply(group_tbl, 
+                                                         function(group) {
+                                                           any(x[row, group[!is.na(group)]] == "R") | 
+                                                             any(x[row, group[!is.na(group)]] == "I") 
+                                                         }),
+                                                  na.rm = TRUE) 
+                                            })
+      x[filter_at(x[rows,],
+                  vars(lst_vector),
+                  all_vars(. %in% c("R", "I")))$row_number, "classes_affected"] <<- 999
+    }
+    
    if (info == TRUE) {
      message(blue(" OK"))
    }
@@ -465,9 +494,10 @@ mdro <- function(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
+    # add unavailable to where genus is available
    mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_),
-           row_number = seq_len(nrow(.))) %>% 
+           row_number = seq_len(nrow(.)),
+           reason = paste0("not covered by ", toupper(guideline$code), " guideline")) %>% 
    # 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)
  
@@ -475,19 +505,34 @@ mdro <- function(x,
    # 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
+    if (is.na(AMP) & !is.na(AMX)) {
+      if (verbose == TRUE) {
+        message(blue("NOTE: Filling ampicillin (AMP) results with amoxicillin (AMX) results"))
+      }
+      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
+    if (is.na(CRO) & !is.na(CTX)) {
+      if (verbose == TRUE) {
+        message(blue("NOTE: Filling ceftriaxone (CRO) results with cefotaxime (CTX) results"))
+      }
+      CRO <- CTX
+    }
+    if (is.na(CTX) & !is.na(CRO)) {
+      if (verbose == TRUE) {
+        message(blue("NOTE: Filling cefotaxime (CTX) results with ceftriaxone (CRO) results"))
+      }
+      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$genus == "Providencia" & x$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")
@@ -554,6 +599,10 @@ mdro <- function(x,
            | (x$genus == "Providencia" & x$species == "rettgeri")
            | (x$genus == "Providencia" & x$species == "stuartii")), ab_NA(c(DOX, MNO))] <- NA
    
+    x$classes_in_guideline <- NA_integer_
+    x$classes_available <- NA_integer_
+    x$classes_affected <- NA_integer_
+    
    # now add the MDR levels to the data
    trans_tbl(2,
              which(x$genus == "Staphylococcus" & x$species == "aureus"),
@@ -592,7 +641,7 @@ mdro <- function(x,
                    QDA,
                    c(DOX, MNO)))
    trans_tbl2(paste0("Table 3 - ", italic("Enterobacteriaceae"), 
-                     " (before the taxonomic reclassification by Adeolu ", italic("et al."), ", 2016)"),
+                      " (before the taxonomic reclassification by Adeolu ", italic("et al."), ", 2016)"),
               # this new order was previously 'Enterobacteriales' and contained only the family 'Enterobacteriaceae':
               which(x$order == "Enterobacterales"),
               list(c(GEN, TOB, AMK, NET),
@@ -634,6 +683,37 @@ mdro <- function(x,
                    SAM,
                    c(COL, PLB),
                    c(TCY, DOX, MNO)))
+    
+    # now set MDROs: 
+    # MDR (=2): >=3 classes affected
+    x[which(x$classes_affected >= 3), "MDRO"] <- 2
+    if (verbose == TRUE) {
+      x[which(x$classes_affected >= 3), "reason"] <- paste0("at least 3 classes contain R or I: ", x$classes_affected[which(x$classes_affected >= 3)],
+                                                            " out of ", x$classes_available[which(x$classes_affected >= 3)], " available classes")
+    }
+    # XDR (=3): all but <=2 classes affected
+    x[which((x$classes_in_guideline - x$classes_affected) <= 2), "MDRO"] <- 3
+    if (verbose == TRUE) {
+      x[which((x$classes_in_guideline - x$classes_affected) <= 2), "reason"] <- paste0("less than 3 classes remain susceptible (", x$classes_in_guideline[which((x$classes_in_guideline - x$classes_affected) <= 2)] - x$classes_affected[which((x$classes_in_guideline - x$classes_affected) <= 2)],
+                                                                                       " out of ", x$classes_in_guideline[which((x$classes_in_guideline - x$classes_affected) <= 2)], " classes)")
+    }
+    # PDR (=4): all agents are R 
+    x[which(x$classes_affected == 999 & x$classes_in_guideline == x$classes_available), "MDRO"] <- 4
+    if (verbose == TRUE) {
+      x[which(x$classes_affected == 999 & x$classes_in_guideline == x$classes_available), "reason"] <- paste("all antibiotics in all", x$classes_in_guideline[which(x$classes_affected == 999 & x$classes_in_guideline == x$classes_available)], "classes were tested R or I")
+    }
+    
+    # not enough classes available
+    x[which(x$classes_available < base::floor(x$classes_in_guideline * pct_required_classes)), "MDRO"] <- -1
+    if (verbose == TRUE) {
+      x[which(x$classes_available < base::floor(x$classes_in_guideline * pct_required_classes)), "reason"] <- paste0("not enough classes available: ", x$classes_available[which(x$classes_available < base::floor(x$classes_in_guideline * pct_required_classes))], 
+                                                                                                                     " instead of ", (base::floor(x$classes_in_guideline * pct_required_classes))[which(x$classes_available < base::floor(x$classes_in_guideline * pct_required_classes))], 
+                                                                                                                     " (~", percentage(pct_required_classes), " of ", x$classes_in_guideline[which(x$classes_available < base::floor(x$classes_in_guideline * pct_required_classes))], ")")
+    }
+    # some more info on negative results
+    if (verbose == TRUE) {
+      x[which(x$MDRO == 1 & !is.na(x$classes_affected)), "reason"] <- paste0(x$classes_affected[which(x$MDRO == 1 & !is.na(x$classes_affected))], " of ", x$classes_available[which(x$MDRO == 1 & !is.na(x$classes_affected))], " available classes contain R or I (3 required for MDR)")
+    }
  }
  
  if (guideline$code == "eucast") {
@@ -693,14 +773,14 @@ mdro <- function(x,
    # Table 7
    trans_tbl(3,
              which(x$genus == "Bacteroides"),
-               MTR,
+              MTR,
              "any")
    trans_tbl(3,
              which(x$fullname %like% "^Clostridium difficile"),
              c(MTR, VAN),
              "any")
  }
-
+  
  if (guideline$code == "mrgn") {
    # Germany -----------------------------------------------------------------
    CTX_or_CAZ <- CTX %or% CAZ
@@ -715,7 +795,7 @@ mdro <- function(x,
    
    # Table 1
    x[which((x$order == "Enterobacterales" |  # following in fact the old Enterobacteriaceae classification
-              x$fullname %like% "^Acinetobacter baumannii") &
+               x$fullname %like% "^Acinetobacter baumannii") &
              x[, PIP] == "R" &
              x[, CTX_or_CAZ] == "R" &
              x[, IPM_or_MEM] == "S" &
@@ -749,7 +829,7 @@ mdro <- function(x,
              x[, CIP] == "R"),
      "MDRO"] <- 3 # 3 = 4MRGN
  }
-
+  
  if (guideline$code == "brmo") {
    # Netherlands -------------------------------------------------------------
    aminoglycosides <- aminoglycosides[!is.na(aminoglycosides)]
@@ -762,23 +842,23 @@ mdro <- function(x,
    if (length(ESBLs) != 2) {
      ESBLs <- character(0)
    }
-
+    
    # Table 1
    trans_tbl(3,
              which(x$order == "Enterobacterales"), # following in fact the old Enterobacteriaceae classification
              c(aminoglycosides, fluoroquinolones),
              "all")
-
+    
    trans_tbl(2,
              which(x$order == "Enterobacterales"), # following in fact the old Enterobacteriaceae classification
              carbapenems,
              "any")
-
+    
    trans_tbl(2,
              which(x$order == "Enterobacterales"), # following in fact the old Enterobacteriaceae classification
              ESBLs,
              "all")
-
+    
    # Table 2
    trans_tbl(2,
              which(x$genus == "Acinetobacter"),
@@ -788,12 +868,12 @@ mdro <- function(x,
              which(x$genus == "Acinetobacter"),
              c(aminoglycosides, fluoroquinolones),
              "all")
-
+    
    trans_tbl(3,
              which(x$fullname %like% "^Stenotrophomonas maltophilia"),
              SXT,
              "all")
-
+    
    if (!ab_missing(MEM) & !ab_missing(IPM)
        & !ab_missing(GEN) & !ab_missing(TOB)
        & !ab_missing(CIP)
@@ -812,7 +892,7 @@ mdro <- function(x,
      x$fullname %like% "Pseudomonas aeruginosa"
      & x$psae >= 3
    ), "MDRO"] <- 3
-
+    
    # Table 3
    trans_tbl(3,
              which(x$fullname %like% "Streptococcus pneumoniae"),
@@ -827,7 +907,7 @@ mdro <- function(x,
              c(PEN, VAN),
              "all")
  }
-
+  
  prepare_drug <- function(ab) {
    # returns vector values of drug
    # if `ab` is a column name, looks up the values in `x`
@@ -858,7 +938,7 @@ mdro <- function(x,
      ab != "R"
    }
  }
-
+  
  if (guideline$code == "tb") {
    # Tuberculosis ------------------------------------------------------------
    x <- x %>%
@@ -881,43 +961,59 @@ mdro <- function(x,
                             TRUE, FALSE),
             xdr = ifelse(mdr & xdr & second, TRUE, FALSE)) %>%
      mutate(MDRO = case_when(xdr ~ 5,
-                                mdr ~ 4,
-                                poly ~ 3,
-                                mono ~ 2,
-                                TRUE ~ 1),
+                              mdr ~ 4,
+                              poly ~ 3,
+                              mono ~ 2,
+                              TRUE ~ 1),
             # keep all real TB, make other species NA
             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))), ")")))
+                    " tested isolates (", percentage(sum(x$MDRO %in% c(2:5), na.rm = TRUE) / sum(!is.na(x$MDRO))), ")\n")))
  }
-
-  # return results
+  
+  # Results ----
  if (guideline$code == "cmi2012") {
-    factor(x =  x$MDRO,
-           levels = 1:4,
-           labels = c("Negative", "Multi-drug-resistant (MDR)", 
-                      "Extensively drug-resistant (XDR)", "Pandrug-resistant (PDR)"),
-           ordered = TRUE)
+    if (any(x$MDRO == -1)) {
+      warning("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
+              percentage(pct_required_classes), " (set with `pct_required_classes`)")
+      # set these -1s to NA
+      x[which(x$MDRO == -1), "MDRO"] <- NA_integer_
+    }
+    x$MDRO <- factor(x = x$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", "Extensively drug-resistant"),
-           ordered = TRUE)
+    x$MDRO <- factor(x = x$MDRO,
+                     levels = 1:5,
+                     labels = c("Negative", "Mono-resistant", "Poly-resistant", 
+                                "Multi-drug-resistant", "Extensively drug-resistant"),
+                     ordered = TRUE)
  } else if (guideline$code == "mrgn") {
-    factor(x =  x$MDRO,
-           levels = 1:3,
-           labels = c("Negative", "3MRGN", "4MRGN"),
-           ordered = TRUE)
+    x$MDRO <- factor(x = x$MDRO,
+                     levels = 1:3,
+                     labels = c("Negative", "3MRGN", "4MRGN"),
+                     ordered = TRUE)
  } else {
-    factor(x =  x$MDRO,
-           levels = 1:3,
-           labels = c("Negative", "Positive, unconfirmed", "Positive"),
-           ordered = TRUE)
+    x$MDRO <- factor(x = x$MDRO,
+                     levels = 1:3,
+                     labels = c("Negative", "Positive, unconfirmed", "Positive"),
+                     ordered = TRUE)
  }
+  
+  if (verbose == TRUE) {
+    x[, c("row_number",
+          col_mo,
+          "MDRO",
+          "reason")]
+  } else {
+    x$MDRO
+  }
+  
 }

 #' @rdname mdro
--- a/R/mic.R
+++ b/R/mic.R
@@ -51,8 +51,6 @@
 #'
 #' plot(mic_data)
 #' barplot(mic_data)
-#' 
-#' library(clean)
 #' freq(mic_data)
 as.mic <- function(x, na.rm = FALSE) {
  if (is.mic(x)) {
@@ -97,98 +95,15 @@ as.mic <- function(x, na.rm = FALSE) {
    x[x.bak != "" & x == ""] <- "invalid"

    # these are allowed MIC values and will become factor levels
-    lvls <- c("<0.001", "<=0.001", "0.001", ">=0.001", ">0.001",
-              "<0.002", "<=0.002", "0.002", ">=0.002", ">0.002",
-              "<0.003", "<=0.003", "0.003", ">=0.003", ">0.003",
-              "<0.004", "<=0.004", "0.004", ">=0.004", ">0.004",
-              "<0.005", "<=0.005", "0.005", ">=0.005", ">0.005",
-              "<0.006", "<=0.006", "0.006", ">=0.006", ">0.006",
-              "<0.007", "<=0.007", "0.007", ">=0.007", ">0.007",
-              "<0.008", "<=0.008", "0.008", ">=0.008", ">0.008",
-              "<0.009", "<=0.009", "0.009", ">=0.009", ">0.009",
-              "<0.01", "<=0.01", "0.01", ">=0.01", ">0.01",
-              "<0.012", "<=0.012", "0.012", ">=0.012", ">0.012",
-              "<0.0125", "<=0.0125", "0.0125", ">=0.0125", ">0.0125",
-              "<0.016", "<=0.016", "0.016", ">=0.016", ">0.016",
-              "<0.019", "<=0.019", "0.019", ">=0.019", ">0.019",
-              "<0.02", "<=0.02", "0.02", ">=0.02", ">0.02",
-              "<0.023", "<=0.023", "0.023", ">=0.023", ">0.023",
-              "<0.025", "<=0.025", "0.025", ">=0.025", ">0.025",
-              "<0.028", "<=0.028", "0.028", ">=0.028", ">0.028",
-              "<0.03", "<=0.03", "0.03", ">=0.03", ">0.03",
-              "<0.031", "<=0.031", "0.031", ">=0.031", ">0.031",
-              "<0.032", "<=0.032", "0.032", ">=0.032", ">0.032",
-              "<0.038", "<=0.038", "0.038", ">=0.038", ">0.038",
-              "<0.04", "<=0.04", "0.04", ">=0.04", ">0.04",
-              "<0.047", "<=0.047", "0.047", ">=0.047", ">0.047",
-              "<0.05", "<=0.05", "0.05", ">=0.05", ">0.05",
-              "<0.054", "<=0.054", "0.054", ">=0.054", ">0.054",
-              "<0.06", "<=0.06", "0.06", ">=0.06", ">0.06",
-              "<0.0625", "<=0.0625", "0.0625", ">=0.0625", ">0.0625",
-              "<0.063", "<=0.063", "0.063", ">=0.063", ">0.063",
-              "<0.064", "<=0.064", "0.064", ">=0.064", ">0.064",
-              "<0.075", "<=0.075", "0.075", ">=0.075", ">0.075",
-              "<0.08", "<=0.08", "0.08", ">=0.08", ">0.08",
-              "<0.09", "<=0.09", "0.09", ">=0.09", ">0.09",
-              "<0.094", "<=0.094", "0.094", ">=0.094", ">0.094",
-              "<0.095", "<=0.095", "0.095", ">=0.095", ">0.095",
-              "<0.1", "<=0.1", "0.1", ">=0.1", ">0.1",
-              "<0.12", "<=0.12", "0.12", ">=0.12", ">0.12",
-              "<0.125", "<=0.125", "0.125", ">=0.125", ">0.125",
-              "<0.128", "<=0.128", "0.128", ">=0.128", ">0.128",
-              "<0.15", "<=0.15", "0.15", ">=0.15", ">0.15",
-              "<0.16", "<=0.16", "0.16", ">=0.16", ">0.16",
-              "<0.17", "<=0.17", "0.17", ">=0.17", ">0.17",
-              "<0.18", "<=0.18", "0.18", ">=0.18", ">0.18",
-              "<0.19", "<=0.19", "0.19", ">=0.19", ">0.19",
-              "<0.2", "<=0.2", "0.2", ">=0.2", ">0.2",
-              "<0.23", "<=0.23", "0.23", ">=0.23", ">0.23",
-              "<0.25", "<=0.25", "0.25", ">=0.25", ">0.25",
-              "<0.256", "<=0.256", "0.256", ">=0.256", ">0.256",
-              "<0.28", "<=0.28", "0.28", ">=0.28", ">0.28",
-              "<0.3", "<=0.3", "0.3", ">=0.3", ">0.3",
-              "<0.32", "<=0.32", "0.32", ">=0.32", ">0.32",
-              "<0.35", "<=0.35", "0.35", ">=0.35", ">0.35",
-              "<0.36", "<=0.36", "0.36", ">=0.36", ">0.36",
-              "<0.38", "<=0.38", "0.38", ">=0.38", ">0.38",
-              "<0.47", "<=0.47", "0.47", ">=0.47", ">0.47",
-              "<0.5", "<=0.5", "0.5", ">=0.5", ">0.5",
-              "<0.512", "<=0.512", "0.512", ">=0.512", ">0.512",
-              "<0.64", "<=0.64", "0.64", ">=0.64", ">0.64",
-              "<0.73", "<=0.73", "0.73", ">=0.73", ">0.73",
-              "<0.75", "<=0.75", "0.75", ">=0.75", ">0.75",
-              "<0.8", "<=0.8", "0.8", ">=0.8", ">0.8",
-              "<0.94", "<=0.94", "0.94", ">=0.94", ">0.94",
-              "<1", "<=1", "1", ">=1", ">1",
-              "<1.5", "<=1.5", "1.5", ">=1.5", ">1.5",
-              "<2", "<=2", "2", ">=2", ">2",
-              "<3", "<=3", "3", ">=3", ">3",
-              "<4", "<=4", "4", ">=4", ">4",
-              "<5", "<=5", "5", ">=5", ">5",
-              "<6", "<=6", "6", ">=6", ">6",
-              "<7", "<=7", "7", ">=7", ">7",
-              "<8", "<=8", "8", ">=8", ">8",
-              "<10", "<=10", "10", ">=10", ">10",
-              "<12", "<=12", "12", ">=12", ">12",
-              "<16", "<=16", "16", ">=16", ">16",
-              "<20", "<=20", "20", ">=20", ">20",
-              "<24", "<=24", "24", ">=24", ">24",
-              "<32", "<=32", "32", ">=32", ">32",
-              "<40", "<=40", "40", ">=40", ">40",
-              "<48", "<=48", "48", ">=48", ">48",
-              "<64", "<=64", "64", ">=64", ">64",
-              "<80", "<=80", "80", ">=80", ">80",
-              "<96", "<=96", "96", ">=96", ">96",
-              "<128", "<=128", "128", ">=128", ">128",
-              "129",
-              "<160", "<=160", "160", ">=160", ">160",
-              "<256", "<=256", "256", ">=256", ">256",
-              "257",
-              "<320", "<=320", "320", ">=320", ">320",
-              "<512", "<=512", "512", ">=512", ">512",
-              "513",
-              "<1024", "<=1024", "1024", ">=1024", ">1024",
-              "1025")
+    ops <- c("<", "<=", "", ">=", ">")
+    lvls <- c(c(t(sapply(ops, function(x) paste0(x, "0.00", 1:9)))),
+              unique(c(t(sapply(ops, function(x) paste0(x, sort(as.double(paste0("0.0", 
+                                                                                 sort(c(1:99, 125, 128, 256, 512, 625)))))))))),
+              unique(c(t(sapply(ops, function(x) paste0(x, sort(as.double(paste0("0.", 
+                                                                                 c(1:99, 125, 128, 256, 512))))))))),
+              c(t(sapply(ops, function(x) paste0(x, sort(c(1:9, 1.5)))))),
+              c(t(sapply(ops, function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))),
+              c(t(sapply(ops, function(x) paste0(x, sort(c(2 ^ c(7:10), 80 * c(2:12))))))))

    na_before <- x[is.na(x) | x == ""] %>% length()
    x[!x %in% lvls] <- NA
--- a/R/misc.R
+++ b/R/misc.R
@@ -127,45 +127,3 @@ class_integrity_check <- function(value, type, check_vector) {
  }
  value
 }
-
-
-
-
-# Percentages -------------------------------------------------------------
-# Can all be removed when clean 1.2.0 is on CRAN
-
-getdecimalplaces <- function(x, minimum = 0, maximum = 3) {
-  if (maximum < minimum) {
-    maximum <- minimum
-  }
-  if (minimum > maximum) {
-    minimum <- maximum
-  }
-  max_places <- max(unlist(lapply(strsplit(sub("0+$", "", 
-                                               as.character(x * 100)), ".", fixed = TRUE),
-                                  function(y) ifelse(length(y) == 2, nchar(y[2]), 0))), na.rm = TRUE)
-  max(min(max_places,
-          maximum, na.rm = TRUE),
-      minimum, na.rm = TRUE)
-}
-
-round2 <- function(x, digits = 0, force_zero = TRUE) {
-  # https://stackoverflow.com/a/12688836/4575331
-  val <- (trunc((abs(x) * 10 ^ digits) + 0.5) / 10 ^ digits) * sign(x)
-  if (digits > 0 & force_zero == TRUE) {
-    val[val != as.integer(val) & !is.na(val)] <- paste0(val[val != as.integer(val) & !is.na(val)],
-                                          strrep("0", max(0, digits - nchar(gsub(".*[.](.*)$", "\\1", val[val != as.integer(val) & !is.na(val)])))))
-  }
-  val
-}
-
-percentage <- function(x, digits = NULL, ...) {
-  if (is.null(digits)) {
-    digits <- getdecimalplaces(x, minimum = 0, maximum = 1)
-  }
-  # round right: percentage(0.4455) should return "44.6%", not "44.5%"
-  x <- as.numeric(round2(x, digits = digits + 2))
-  x_formatted <- format(as.double(x) * 100, scientific = FALSE, digits = digits, nsmall = digits, ...)
-  x_formatted[!is.na(x)] <- paste0(x_formatted[!is.na(x)], "%")
-  x_formatted
-}
--- a/R/mo.R
+++ b/R/mo.R
@@ -267,7 +267,7 @@ is.mo <- function(x) {
 #' @importFrom dplyr %>% pull left_join n_distinct progress_estimated filter distinct
 #' @importFrom data.table data.table as.data.table setkey
 #' @importFrom crayon magenta red blue silver italic
-# @importFrom clean percentage
+#' @importFrom cleaner percentage
 # param property a column name of AMR::microorganisms
 # param initial_search logical - is FALSE when coming from uncertain tries, which uses exec_as.mo internally too
 # param dyslexia_mode logical - also check for characters that resemble others
@@ -1774,7 +1774,7 @@ pillar_shaft.mo <- function(x, ...) {

 #' @exportMethod summary.mo
 #' @importFrom dplyr n_distinct
-#' @importFrom clean freq top_freq
+#' @importFrom cleaner freq top_freq
 #' @export
 #' @noRd
 summary.mo <- function(object, ...) {
--- a/R/rsi.R
+++ b/R/rsi.R
@@ -73,8 +73,6 @@
 #'
 #' plot(rsi_data)    # for percentages
 #' barplot(rsi_data) # for frequencies
-#' 
-#' library(clean)
 #' freq(rsi_data)    # frequency table with informative header
 #'
 #' # using dplyr's mutate
--- a/R/rsi_calc.R
+++ b/R/rsi_calc.R
@@ -39,7 +39,7 @@ dots2vars <- function(...) {
 }

 #' @importFrom dplyr %>% pull all_vars any_vars filter_all funs mutate_all
-# @importFrom clean percentage
+#' @importFrom cleaner percentage
 rsi_calc <- function(...,
                     ab_result,
                     minimum = 0,
--- a/data-raw/reproduction_of_antibiotics.R
+++ b/data-raw/reproduction_of_antibiotics.R
@@ -308,7 +308,7 @@ antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(anti
 antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl", "gentamicin high", "genta high"))
 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"))
+antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]] <- list(c("imip", "imi", "imp"))

 ## new ATC codes
 # ceftaroline
--- a/data/antibiotics.rda
+++ b/data/antibiotics.rda
--- a/docs/404.html
+++ b/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">0.8.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9008</span>
      </span>
    </div>

--- a/docs/LICENSE-text.html
+++ b/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">0.8.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9008</span>
      </span>
    </div>

--- a/docs/articles/index.html
+++ b/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">0.8.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9008</span>
      </span>
    </div>

--- a/docs/authors.html
+++ b/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">0.8.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9008</span>
      </span>
    </div>

--- a/docs/index.html
+++ b/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">0.8.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9008</span>
      </span>
    </div>

--- a/docs/news/index.html
+++ b/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">0.8.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9008</span>
      </span>
    </div>

@@ -231,16 +231,20 @@
      
    </div>

-    <div id="amr-0-8-0-9007" class="section level1">
+    <div id="amr-0-8-0-9008" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-8-0-9007" class="anchor"></a>AMR 0.8.0.9007<small> Unreleased </small>
+<a href="#amr-0-8-0-9008" class="anchor"></a>AMR 0.8.0.9008<small> Unreleased </small>
 </h1>
-<p><small>Last updated: 30-Oct-2019</small></p>
+<p><small>Last updated: 03-Nov-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>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).
+<ul>
+<li>This is now the new default guideline for the <code><a href="../reference/mdro.html">mdro()</a></code> function</li>
+<li>The new Verbose mode (<code><a href="../reference/mdro.html">mdro(...., verbose = TRUE)</a></code>) returns an informative data set where the reason for MDRO determination is given for every isolate</li>
+</ul>
 </li>
 </ul>
 </div>
@@ -257,6 +261,14 @@
 <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 and fixed two typos in the <code>antibiotics</code> data set</li>
+<li>More robust way of determining valid MIC values</li>
+</ul>
+</div>
+<div id="other" class="section level3">
+<h3 class="hasAnchor">
+<a href="#other" class="anchor"></a>Other</h3>
+<ul>
+<li>Change dependency on <code>clean</code> to <code>cleaner</code>, as this package was renamed accordingly upon CRAN request</li>
 </ul>
 </div>
 </div>
@@ -286,7 +298,7 @@ For WHONET users, this means that all records/isolates with organism code <code>
 <a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co">#&gt; Warning message:</span></a>
 <a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co">#&gt; invalid microorganism code, NA generated</span></a></code></pre></div>
 This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</li>
-<li>Function <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</li>
+<li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</li>
 <li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
 </ul>
 </div>
@@ -401,9 +413,9 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
 </li>
 <li>Added more MIC factor levels (<code><a href="../reference/as.mic.html">as.mic()</a></code>)</li>
 </ul>
-<div id="other" class="section level4">
+<div id="other-1" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other" class="anchor"></a>Other</h4>
+<a href="#other-1" class="anchor"></a>Other</h4>
 <ul>
 <li>Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors</li>
 <li>Cleaned the coding style of every single syntax line in this package with the help of the <code>lintr</code> package</li>
@@ -484,9 +496,9 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
 </li>
 </ul>
 </div>
-<div id="other-1" class="section level4">
+<div id="other-2" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-1" class="anchor"></a>Other</h4>
+<a href="#other-2" class="anchor"></a>Other</h4>
 <ul>
 <li>Fixed a note thrown by CRAN tests</li>
 </ul>
@@ -543,7 +555,7 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Tra
 <li>The <code><a href="../reference/age.html">age()</a></code> function gained a new parameter <code>exact</code> to determine ages with decimals</li>
 <li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code>rsi()</code>
 </li>
-<li>Frequency tables (<code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code>):
+<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
 <ul>
 <li>speed improvement for microbial IDs</li>
 <li>fixed factor level names for R Markdown</li>
@@ -551,12 +563,12 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Tra
 <li>
 <p>support for boxplots:</p>
 <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span><span class="st"> </span></a>
+<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span><span class="st"> </span></a>
 <a class="sourceLine" id="cb9-3" data-line-number="3"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</a>
 <a class="sourceLine" id="cb9-4" data-line-number="4"><span class="co"># grouped boxplots:</span></a>
 <a class="sourceLine" id="cb9-5" data-line-number="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
 <a class="sourceLine" id="cb9-6" data-line-number="6"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb9-7" data-line-number="7"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb9-7" data-line-number="7"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb9-8" data-line-number="8"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</a></code></pre></div>
 </li>
 </ul>
@@ -567,7 +579,7 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUC
 <li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
 </li>
 <li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
-<li>Fix for <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
+<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
 </li>
 <li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
 <li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
@@ -580,9 +592,9 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUC
 <li><p>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</p></li>
 </ul>
 </div>
-<div id="other-2" class="section level4">
+<div id="other-3" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-2" class="anchor"></a>Other</h4>
+<a href="#other-3" class="anchor"></a>Other</h4>
 <ul>
 <li>Support for R 3.6.0 and later by providing support for <a href="https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html">staged install</a>
 </li>
@@ -789,7 +801,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 </li>
 </ul>
 </li>
-<li>Frequency tables (<code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> function):
+<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function):
 <ul>
 <li>
 <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
@@ -797,15 +809,15 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <a class="sourceLine" id="cb19-2" data-line-number="2"><span class="co"># OLD WAY</span></a>
 <a class="sourceLine" id="cb19-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb19-4" data-line-number="4"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb19-5" data-line-number="5"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(genus)</a>
+<a class="sourceLine" id="cb19-5" data-line-number="5"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(genus)</a>
 <a class="sourceLine" id="cb19-6" data-line-number="6"><span class="co"># NEW WAY</span></a>
 <a class="sourceLine" id="cb19-7" data-line-number="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb19-8" data-line-number="8"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
+<a class="sourceLine" id="cb19-8" data-line-number="8"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
 <a class="sourceLine" id="cb19-9" data-line-number="9"></a>
 <a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># Even supports grouping variables:</span></a>
 <a class="sourceLine" id="cb19-11" data-line-number="11">septic_patients <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb19-12" data-line-number="12"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(gender) <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb19-13" data-line-number="13"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
+<a class="sourceLine" id="cb19-13" data-line-number="13"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
 </li>
 <li>Header info is now available as a list, with the <code>header</code> function</li>
 <li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li>
@@ -828,9 +840,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <li>if using different lengths of pattern and x in <code><a href="../reference/like.html">%like%</a></code>, it will now return the call</li>
 </ul>
 </div>
-<div id="other-3" class="section level4">
+<div id="other-4" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-3" class="anchor"></a>Other</h4>
+<a href="#other-4" class="anchor"></a>Other</h4>
 <ul>
 <li>Updated licence text to emphasise GPL 2.0 and that this is an R package.</li>
 </ul>
@@ -892,18 +904,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <li>Using <code>portion_*</code> functions now throws a warning when total available isolate is below parameter <code>minimum</code>
 </li>
 <li>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</li>
-<li>Frequency tables - <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code>:
+<li>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:
 <ul>
 <li>
 <p>Support for grouping variables, test with:</p>
 <div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
 <a class="sourceLine" id="cb21-2" data-line-number="2"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb21-3" data-line-number="3"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(gender)</a></code></pre></div>
+<a class="sourceLine" id="cb21-3" data-line-number="3"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(gender)</a></code></pre></div>
 </li>
 <li>
 <p>Support for (un)selecting columns:</p>
 <div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
-<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
+<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="st">  </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
 <a class="sourceLine" id="cb22-3" data-line-number="3"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
 </li>
 <li>Check for <code><a href="https://rdrr.io/pkg/hms/man/Deprecated.html">hms::is.hms</a></code>
@@ -953,9 +965,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <li><p>Percentages will now will rounded more logically (e.g. in <code>freq</code> function)</p></li>
 </ul>
 </div>
-<div id="other-4" class="section level4">
+<div id="other-5" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-4" class="anchor"></a>Other</h4>
+<a href="#other-5" class="anchor"></a>Other</h4>
 <ul>
 <li>New dependency on package <code>crayon</code>, to support formatted text in the console</li>
 <li>Dependency <code>tidyr</code> is now mandatory (went to <code>Import</code> field) since <code>portion_df</code> and <code>count_df</code> rely on it</li>
@@ -1082,17 +1094,17 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <li>
 <p>Support for types (classes) list and matrix for <code>freq</code></p>
 <div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/with.html">with</a></span>(septic_patients, <span class="kw"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
-<a class="sourceLine" id="cb29-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
+<a class="sourceLine" id="cb29-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
 <p>For lists, subsetting is possible:</p>
 <div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" data-line-number="1">my_list =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
-<a class="sourceLine" id="cb30-2" data-line-number="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(age)</a>
-<a class="sourceLine" id="cb30-3" data-line-number="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(gender)</a></code></pre></div>
+<a class="sourceLine" id="cb30-2" data-line-number="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age)</a>
+<a class="sourceLine" id="cb30-3" data-line-number="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(gender)</a></code></pre></div>
 </li>
 </ul>
 </div>
-<div id="other-5" class="section level4">
+<div id="other-6" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-5" class="anchor"></a>Other</h4>
+<a href="#other-6" class="anchor"></a>Other</h4>
 <ul>
 <li>More unit tests to ensure better integrity of functions</li>
 </ul>
@@ -1160,13 +1172,13 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <ul>
 <li>A vignette to explain its usage</li>
 <li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
-<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq(table(x, y))</a></code>
+<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(table(x, y))</a></code>
 </li>
 <li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
 </li>
 <li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
 </li>
-<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
+<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
 </li>
 <li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
 <li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
@@ -1219,9 +1231,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <li>Other small fixes</li>
 </ul>
 </div>
-<div id="other-6" class="section level4">
+<div id="other-7" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-6" class="anchor"></a>Other</h4>
+<a href="#other-7" class="anchor"></a>Other</h4>
 <ul>
 <li>Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
 <ul>
@@ -1281,9 +1293,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
 <li>Functions <code>as.rsi</code> and <code>as.mic</code> now add the package name and version as attributes</li>
 </ul>
 </div>
-<div id="other-7" class="section level4">
+<div id="other-8" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-7" class="anchor"></a>Other</h4>
+<a href="#other-8" class="anchor"></a>Other</h4>
 <ul>
 <li>Expanded <code>README.md</code> with more examples</li>
 <li>Added <a href="https://orcid.org">ORCID</a> of authors to DESCRIPTION file</li>
@@ -1320,7 +1332,7 @@ 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-0-8-0-9007">0.8.0.9007</a></li>
+        <li><a href="#amr-0-8-0-9008">0.8.0.9008</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>
--- a/docs/reference/as.mic.html
+++ b/docs/reference/as.mic.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">0.8.0.9008</span>
      </span>
    </div>

@@ -288,9 +288,7 @@

 <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>mic_data</span>)
 <span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='no'>mic_data</span>)
-
-<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>clean</span>)
-<span class='fu'><a href='https://rdrr.io/pkg/clean/man/freq.html'>freq</a></span>(<span class='no'>mic_data</span>)</pre>
+<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>mic_data</span>)</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
    <h2>Contents</h2>
--- a/docs/reference/as.rsi.html
+++ b/docs/reference/as.rsi.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">0.8.0.9008</span>
      </span>
    </div>

@@ -336,9 +336,7 @@

 <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>rsi_data</span>)    <span class='co'># for percentages</span>
 <span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for frequencies</span>
-
-<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>clean</span>)
-<span class='fu'><a href='https://rdrr.io/pkg/clean/man/freq.html'>freq</a></span>(<span class='no'>rsi_data</span>)    <span class='co'># frequency table with informative header</span>
+<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>rsi_data</span>)    <span class='co'># frequency table with informative header</span>

 <span class='co'># using dplyr's mutate</span>
 <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
--- a/docs/reference/catalogue_of_life_version.html
+++ b/docs/reference/catalogue_of_life_version.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">0.8.0.9008</span>
      </span>
    </div>

@@ -264,9 +264,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (

    <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='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>clean</span>)
-<span class='no'>microorganisms</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/pkg/clean/man/freq.html'>freq</a></span>(<span class='no'>kingdom</span>)
-<span class='no'>microorganisms</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>kingdom</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/pkg/clean/man/freq.html'>freq</a></span>(<span class='no'>phylum</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+<span class='no'>microorganisms</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>kingdom</span>)
+<span class='no'>microorganisms</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>kingdom</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>phylum</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
    <h2>Contents</h2>
--- a/docs/reference/eucast_rules.html
+++ b/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">0.8.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9008</span>
      </span>
    </div>

--- a/docs/reference/index.html
+++ b/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">0.8.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9008</span>
      </span>
    </div>

--- a/docs/reference/like.html
+++ b/docs/reference/like.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">0.8.0.9008</span>
      </span>
    </div>

@@ -304,11 +304,10 @@

 <span class='co'># get frequencies of bacteria whose name start with 'Ent' or 'ent'</span>
 <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
-<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>clean</span>)
 <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
  <span class='fu'><a href='join.html'>left_join_microorganisms</a></span>() <span class='kw'>%&gt;%</span>
  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://rdrr.io/pkg/clean/man/freq.html'>freq</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)</pre>
+  <span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
    <h2>Contents</h2>
--- a/docs/reference/mdro.html
+++ b/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">0.8.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9008</span>
      </span>
    </div>

@@ -238,7 +238,7 @@
    </div>

    <pre class="usage"><span class='fu'>mdro</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
+  <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>pct_required_classes</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='no'>...</span>)

 <span class='fu'>brmo</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"BRMO"</span>, <span class='no'>...</span>)

@@ -255,7 +255,7 @@
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>x</th>
-      <td><p>table with antibiotic columns, like e.g. <code>AMX</code> and <code>AMC</code></p></td>
+      <td><p>data with antibiotic columns, like e.g. <code>AMX</code> and <code>AMC</code></p></td>
    </tr>
    <tr>
      <th>guideline</th>
@@ -273,10 +273,18 @@
      <th>verbose</th>
      <td><p>print additional info: missing antibiotic columns per parameter</p></td>
    </tr>
+    <tr>
+      <th>pct_required_classes</th>
+      <td><p>minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for <em>S. aureus</em>. Setting this <code>pct_required_classes</code> argument to <code>0.5</code> (default) means that for every <em>S. aureus</em> isolate at least 8 different classes must be available. Any lower number of available classes will return <code>NA</code> for that isolate.</p></td>
+    </tr>
    <tr>
      <th>...</th>
      <td><p>column name of an antibiotic, see section Antibiotics</p></td>
    </tr>
+    <tr>
+      <th>verbose</th>
+      <td><p>a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.</p></td>
+    </tr>
    </table>

    <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
@@ -294,7 +302,8 @@

    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

-    <p>Currently supported guidelines are (case-insensitive):</p><ul>
+    <p>For the <code>pct_required_classes</code> argument, values above 1 will be divided by 100. This is to support both fractions (<code>0.75</code> or <code>3/4</code>) and percentages (<code>75</code>).
+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>
@@ -399,18 +408,18 @@

 <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='fu'><a href='https://rdrr.io/pkg/cleaner/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='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'>eucast_exceptional_phenotypes</span>(<span class='no'>.</span>),
         <span class='kw'>BRMO</span> <span class='kw'>=</span> <span class='fu'>brmo</span>(<span class='no'>.</span>),
         <span class='kw'>MRGN</span> <span class='kw'>=</span> <span class='fu'>mrgn</span>(<span class='no'>.</span>))

 <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>
+  <span class='fu'><a href='https://rdrr.io/pkg/cleaner/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">
--- a/docs/reference/microorganisms.html
+++ b/docs/reference/microorganisms.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">0.8.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9008</span>
      </span>
    </div>

--- a/docs/reference/mo_property.html
+++ b/docs/reference/mo_property.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">0.8.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9008</span>
      </span>
    </div>

--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -54,7 +54,7 @@
 <meta property="og:description" content="These objects are imported from other packages. Follow the links
 below to see their documentation.

-  cleanfreq
+  cleanerfreq

 " />
 <meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
@@ -90,7 +90,7 @@ below to see their documentation.
      </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">0.8.0.9008</span>
      </span>
    </div>

@@ -242,7 +242,7 @@ below to see their documentation.
    <p>These objects are imported from other packages. Follow the links
 below to see their documentation.</p>
 <dl class='dl-horizontal'>
-  <dt>clean</dt><dd><p><code><a href='https://rdrr.io/pkg/clean/man/freq.html'>freq</a></code></p></dd>
+  <dt>cleaner</dt><dd><p><code><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></code></p></dd>

 </dl>
    </div>
--- a/man/as.mic.Rd
+++ b/man/as.mic.Rd
@@ -47,8 +47,6 @@ as.rsi(x = as.mic(4),

 plot(mic_data)
 barplot(mic_data)
-
-library(clean)
 freq(mic_data)
 }
 \seealso{
--- a/man/as.rsi.Rd
+++ b/man/as.rsi.Rd
@@ -90,8 +90,6 @@ as.rsi(x = as.mic(4),

 plot(rsi_data)    # for percentages
 barplot(rsi_data) # for frequencies
-
-library(clean)
 freq(rsi_data)    # frequency table with informative header

 # using dplyr's mutate
--- a/man/catalogue_of_life_version.Rd
+++ b/man/catalogue_of_life_version.Rd
@@ -30,7 +30,6 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://

 \examples{
 library(dplyr)
-library(clean)
 microorganisms \%>\% freq(kingdom)
 microorganisms \%>\% group_by(kingdom) \%>\% freq(phylum, nmax = NULL)
 }
--- a/man/like.Rd
+++ b/man/like.Rd
@@ -62,7 +62,6 @@ a \%like\% b

 # get frequencies of bacteria whose name start with 'Ent' or 'ent'
 library(dplyr)
-library(clean)
 example_isolates \%>\%
  left_join_microorganisms() \%>\%
  filter(genus \%like\% '^ent') \%>\%
--- a/man/mdro.Rd
+++ b/man/mdro.Rd
@@ -13,7 +13,7 @@ Please see Details for the list of publications used for this function.
 }
 \usage{
 mdro(x, guideline = NULL, col_mo = NULL, info = TRUE,
-  verbose = FALSE, ...)
+  verbose = FALSE, pct_required_classes = 0.5, ...)

 brmo(x, guideline = "BRMO", ...)

@@ -26,7 +26,7 @@ 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{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}

 \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.}

@@ -36,7 +36,11 @@ eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)

 \item{verbose}{print additional info: missing antibiotic columns per parameter}

+\item{pct_required_classes}{minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for \emph{S. aureus}. Setting this \code{pct_required_classes} argument to \code{0.5} (default) means that for every \emph{S. aureus} isolate at least 8 different classes must be available. Any lower number of available classes will return \code{NA} for that isolate.}
+
 \item{...}{column name of an antibiotic, see section Antibiotics}
+
+\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
 }
 \value{
 \itemize{
@@ -50,6 +54,7 @@ eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
 Determine which isolates are multidrug-resistant organisms (MDRO) according to (country-specific) guidelines.
 }
 \details{
+For the \code{pct_required_classes} argument, values above 1 will be divided by 100. This is to support both fractions (\code{0.75} or \code{3/4}) and percentages (\code{75}).
 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})}
@@ -156,13 +161,13 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 \examples{
 library(dplyr)

-example_isolates \%>\% 
-  mdro() \%>\% 
+example_isolates \%>\%
+  mdro() \%>\%
  freq()
  
 \donttest{
 example_isolates \%>\%
-  mutate(EUCAST = mdro(.),
+  mutate(EUCAST = eucast_exceptional_phenotypes(.),
         BRMO = brmo(.),
         MRGN = mrgn(.))
         
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -11,6 +11,6 @@ These objects are imported from other packages. Follow the links
 below to see their documentation.

 \describe{
-  \item{clean}{\code{\link[clean]{freq}}}
+  \item{cleaner}{\code{\link[cleaner]{freq}}}
 }}

--- a/tests/testthat/test-freq.R
+++ b/tests/testthat/test-freq.R
@@ -22,7 +22,7 @@
 context("freq.R")

 test_that("frequency table works", {
-  library(clean)
+  library(cleaner)
  # mo
  expect_true(is.freq(freq(example_isolates$mo)))
  # for this to work, the output of mo_gramstain() is to be expected as follows:
--- a/tests/testthat/test-mdro.R
+++ b/tests/testthat/test-mdro.R
@@ -133,6 +133,7 @@ test_that("mdro works", {
    "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))
+  expect_s3_class(mdro(stau, verbose = TRUE), "data.frame")
  
  ente <- tribble(
    ~mo,            ~GEH, ~STH, ~IPM, ~MEM, ~DOR, ~CIP, ~LVX, ~MFX, ~VAN, ~TEC, ~TGC, ~DAP, ~LNZ, ~AMP, ~QDA, ~DOX, ~MNO,
@@ -142,6 +143,7 @@ test_that("mdro works", {
    "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))
+  expect_s3_class(mdro(ente, verbose = TRUE), "data.frame")
  
  entero <- 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,
@@ -151,6 +153,7 @@ test_that("mdro works", {
    "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))
+  expect_s3_class(mdro(entero, verbose = TRUE), "data.frame")
  
  pseud <- tribble(
    ~mo,             ~GEN, ~TOB, ~AMK, ~NET, ~IPM, ~MEM, ~DOR, ~CAZ, ~FEP, ~CIP, ~LVX, ~TCC, ~TZP, ~ATM, ~FOS, ~COL, ~PLB,
@@ -160,6 +163,7 @@ test_that("mdro works", {
    "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))
+  expect_s3_class(mdro(pseud, verbose = TRUE), "data.frame")
  
  acin <- tribble(
    ~mo,            ~GEN, ~TOB, ~AMK, ~NET, ~IPM, ~MEM, ~DOR, ~CIP, ~LVX, ~TZP, ~TCC, ~CTX, ~CRO, ~CAZ, ~FEP, ~SXT, ~SAM, ~COL, ~PLB, ~TCY, ~DOX, ~MNO,
@@ -169,5 +173,6 @@ test_that("mdro works", {
    "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))
+  expect_s3_class(mdro(acin, verbose = TRUE), "data.frame")
  
 })