(v1.7.0.9001) CLSI 2020 guideline

.github/workflows/codecovr.yaml

@@ -53,7 +53,7 @@ jobs:
         uses: actions/cache@v1
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: macOS-latest-r-release-v4
+          key: macOS-latest-r-release-v5-codecovr
 
       - name: Unpack AMR and install R dependencies
         run: |

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.7.0.9000
-Date: 2021-05-30
+Version: 1.7.0.9001
+Date: 2021-06-01
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,6 +1,11 @@
-# `AMR` 1.7.0.9000
-## <small>Last updated: 30 May 2021</small>
+# `AMR` 1.7.0.9001
+## <small>Last updated:  1 June 2021</small>
+
+### New
+* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
+
 ### Changed
+* `bug_drug_combinations()` now supports grouping using the `dplyr` package
 * As requested by CRAN administrators: decreased package size by 3 MB in costs of a ~50 times slower loading time of the package (i.e., `library(AMR)`)
 
 

R/amr.R

@@ -54,14 +54,14 @@
 #' @section Reference Data Publicly Available:
 #' All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this `AMR` package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find [all download links on our website](https://msberends.github.io/AMR/articles/datasets.html), which is automatically updated with every code change.
 #' @section Read more on Our Website!:
-#' On our website <https://msberends.github.io/AMR/> you can find [a comprehensive tutorial](https://msberends.github.io/AMR/articles/AMR.html) about how to conduct AMR data analysis, the [complete documentation of all functions](https://msberends.github.io/AMR/reference/) and [an example analysis using WHONET data](https://msberends.github.io/AMR/articles/WHONET.html). As we would like to better understand the backgrounds and needs of our users, please [participate in our survey](https://msberends.github.io/AMR/survey.html)!
+#' On our website <https://msberends.github.io/AMR/> you can find [a comprehensive tutorial](https://msberends.github.io/AMR/articles/AMR.html) about how to conduct AMR data analysis, the [complete documentation of all functions](https://msberends.github.io/AMR/reference/) and [an example analysis using WHONET data](https://msberends.github.io/AMR/articles/WHONET.html).
 #' @section Contact Us:
 #' For suggestions, comments or questions, please contact us at:
 #'
 #' Matthijs S. Berends \cr
 #' m.s.berends \[at\] umcg \[dot\] nl \cr
 #' University of Groningen
-#' Department of Medical Microbiology
+#' Department of Medical Microbiology and Infection Prevention
 #' University Medical Center Groningen \cr
 #' Post Office Box 30001 \cr
 #' 9700 RB Groningen \cr

R/bug_drug_combinations.R

@@ -31,7 +31,7 @@
 #' @param combine_IR a [logical] to indicate whether values R and I should be summed
 #' @param add_ab_group a [logical] to indicate where the group of the antimicrobials must be included as a first column
 #' @param remove_intrinsic_resistant [logical] to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table
-#' @param FUN the function to call on the `mo` column to transform the microorganism IDs, defaults to [mo_shortname()] 
+#' @param FUN the function to call on the `mo` column to transform the microorganism codes, defaults to [mo_shortname()] 
 #' @param translate_ab a [character] of length 1 containing column names of the [antibiotics] data set
 #' @param ... arguments passed on to `FUN`
 #' @inheritParams rsi_df
@@ -74,42 +74,87 @@ bug_drug_combinations <- function(x,
     stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
   }
   
-  x_class <- class(x)
+  x.bak <- x
   x <- as.data.frame(x, stringsAsFactors = FALSE)
   x[, col_mo] <- FUN(x[, col_mo, drop = TRUE], ...)
-  x <- x[, c(col_mo, names(which(vapply(FUN.VALUE = logical(1), x, is.rsi)))), drop = FALSE]
   
   unique_mo <- sort(unique(x[, col_mo, drop = TRUE]))
   
-  out <- data.frame(mo = character(0),
-                    ab = character(0),
-                    S = integer(0),
-                    I = integer(0),
-                    R = integer(0),
-                    total = integer(0),
-                    stringsAsFactors = FALSE)
+  # select only groups and antibiotics
+  if (inherits(x.bak, "grouped_df")) {
+    data_has_groups <- TRUE
+    groups <- setdiff(names(attributes(x.bak)$groups), ".rows")
+    x <- x[, c(groups, col_mo, colnames(x)[vapply(FUN.VALUE = logical(1), x, is.rsi)]), drop = FALSE]
+  } else {
+    data_has_groups <- FALSE
+    x <- x[, c(col_mo, names(which(vapply(FUN.VALUE = logical(1), x, is.rsi)))), drop = FALSE]
+  }
   
-  for (i in seq_len(length(unique_mo))) {
-    # filter on MO group and only select R/SI columns
-    x_mo_filter <- x[which(x[, col_mo, drop = TRUE] == unique_mo[i]), names(which(vapply(FUN.VALUE = logical(1), x, is.rsi))), drop = FALSE]
-    # turn and merge everything
-    pivot <- lapply(x_mo_filter, function(x) {
-      m <- as.matrix(table(x))
-      data.frame(S = m["S", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE)
-    })
-    merged <- do.call(rbind, pivot)
-    out_group <- data.frame(mo = unique_mo[i],
-                            ab = rownames(merged),
-                            S = merged$S,
-                            I = merged$I,
-                            R = merged$R,
-                            total = merged$S + merged$I + merged$R,
-                            stringsAsFactors = FALSE)
-    out <- rbind(out, out_group, stringsAsFactors = FALSE)
-  }
-  
-  set_clean_class(out,
-                  new_class = c("bug_drug_combinations", x_class))
+  run_it <- function(x) {
+    out <- data.frame(mo = character(0),
+                      ab = character(0),
+                      S = integer(0),
+                      I = integer(0),
+                      R = integer(0),
+                      total = integer(0),
+                      stringsAsFactors = FALSE)
+    if (data_has_groups) {
+      group_values <- unique(x[, which(colnames(x) %in% groups), drop = FALSE])
+      rownames(group_values) <- NULL
+      x <- x[, which(!colnames(x) %in% groups), drop = FALSE]
+    }
+    
+    for (i in seq_len(length(unique_mo))) {
+      # filter on MO group and only select R/SI columns
+      x_mo_filter <- x[which(x[, col_mo, drop = TRUE] == unique_mo[i]), names(which(vapply(FUN.VALUE = logical(1), x, is.rsi))), drop = FALSE]
+      # turn and merge everything
+      pivot <- lapply(x_mo_filter, function(x) {
+        m <- as.matrix(table(x))
+        data.frame(S = m["S", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE)
+      })
+      merged <- do.call(rbind, pivot)
+      out_group <- data.frame(mo = unique_mo[i],
+                              ab = rownames(merged),
+                              S = merged$S,
+                              I = merged$I,
+                              R = merged$R,
+                              total = merged$S + merged$I + merged$R,
+                              stringsAsFactors = FALSE)
+      if (data_has_groups) {
+        if (nrow(group_values) < nrow(out_group)) {
+          # repeat group_values for the number of rows in out_group
+          repeated <- rep(seq_len(nrow(group_values)),
+                          each = nrow(out_group) / nrow(group_values))
+          group_values <- group_values[repeated, , drop = FALSE]
+        }
+        out_group <- cbind(group_values, out_group)
+      }
+      out <- rbind(out, out_group, stringsAsFactors = FALSE)
+    }
+    out
+  }
+  # based on pm_apply_grouped_function
+  apply_group <- function(.data, fn, groups, drop = FALSE, ...) {
+    grouped <- pm_split_into_groups(.data, groups, drop)
+    res <- do.call(rbind, unname(lapply(grouped, fn, ...)))
+    if (any(groups %in% colnames(res))) {
+      class(res) <- c("grouped_data", class(res))
+      res <- pm_set_groups(res, groups[groups %in% colnames(res)])
+    }
+    res
+  }
+  
+  if (data_has_groups) {
+    out <- apply_group(x, "run_it", groups)
+    rownames(out) <- NULL
+    set_clean_class(out,
+                    new_class = c("grouped", "bug_drug_combinations", "data.frame"))
+  } else {
+    out <- run_it(x)
+    rownames(out) <- NULL
+    set_clean_class(out,
+                    new_class = c("bug_drug_combinations", "data.frame"))
+  }
 }
 
 #' @method format bug_drug_combinations
@@ -137,6 +182,21 @@ format.bug_drug_combinations <- function(x,
   meet_criteria(decimal.mark, allow_class = "character", has_length = 1)
   meet_criteria(big.mark, allow_class = "character", has_length = 1)
   
+  if (inherits(x, "grouped")) {
+    # bug_drug_combinations() has been run on groups, so de-group here
+    warning_("formatting the output of `bug_drug_combinations()` does not support grouped variables, they are ignored", call = FALSE)
+    idx <- split(seq_len(nrow(x)), paste0(x$mo, "%%", x$ab))
+    x <- data.frame(mo = gsub("(.*)%%(.*)", "\\1", names(idx)),
+                    ab = gsub("(.*)%%(.*)", "\\2", names(idx)),
+                    S = sapply(idx, function(i) sum(y$S[i], na.rm = TRUE)), 
+                    I = sapply(idx, function(i) sum(y$I[i], na.rm = TRUE)), 
+                    R = sapply(idx, function(i) sum(y$R[i], na.rm = TRUE)),
+                    total = sapply(idx, function(i) sum(y$S[i], na.rm = TRUE) + 
+                                     sum(y$I[i], na.rm = TRUE) +
+                                     sum(y$R[i], na.rm = TRUE)),
+                    stringsAsFactors = FALSE)
+  }
+  
   x <- as.data.frame(x, stringsAsFactors = FALSE)
   x <- subset(x, total >= minimum)
   
@@ -249,7 +309,9 @@ format.bug_drug_combinations <- function(x,
 print.bug_drug_combinations <- function(x, ...) {
   x_class <- class(x)
   print(set_clean_class(x, 
-                        new_class = x_class[x_class != "bug_drug_combinations"]),
+                        new_class = x_class[!x_class %in% c("bug_drug_combinations", "grouped")]),
         ...)
-  message_("Use 'format()' on this result to get a publishable/printable format.", as_note = FALSE)
+  message_("Use 'format()' on this result to get a publishable/printable format.",
+           ifelse(inherits(x, "grouped"), " Note: The grouping variable(s) will be ignored.", ""),
+           as_note = FALSE)
 }

R/data.R

@@ -239,7 +239,7 @@
 
 #' Data Set for R/SI Interpretation
 #'
-#' Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`) and EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`). Use [as.rsi()] to transform MICs or disks measurements to R/SI values.
+#' Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`). Use [as.rsi()] to transform MICs or disks measurements to R/SI values.
 #' @format A [data.frame] with `r format(nrow(rsi_translation), big.mark = ",")` observations and `r ncol(rsi_translation)` variables:
 #' - `guideline`\cr Name of the guideline
 #' - `method`\cr Either `r vector_or(rsi_translation$method)`

R/mo.R

@@ -23,9 +23,9 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-#' Transform Input to a Microorganism ID
+#' Transform Input to a Microorganism Code
 #'
-#' Use this function to determine a valid microorganism ID ([`mo`]). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see *Source*). The input can be almost anything: a full name (like `"Staphylococcus aureus"`), an abbreviated name (such as `"S. aureus"`), an abbreviation known in the field (such as `"MRSA"`), or just a genus. See *Examples*.
+#' Use this function to determine a valid microorganism code ([`mo`]). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see *Source*). The input can be almost anything: a full name (like `"Staphylococcus aureus"`), an abbreviated name (such as `"S. aureus"`), an abbreviation known in the field (such as `"MRSA"`), or just a genus. See *Examples*.
 #' @inheritSection lifecycle Stable Lifecycle
 #' @param x a [character] vector or a [data.frame] with one or two columns
 #' @param Becker a [logical] to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker *et al.* (1,2,3).
@@ -46,7 +46,7 @@
 #' @details
 #' ## General Info
 #'
-#' A microorganism ID from this package (class: [`mo`]) is human readable and typically looks like these examples:
+#' A microorganism (MO) code from this package (class: [`mo`]) is human readable and typically looks like these examples:
 #' ```
 #'   Code               Full name
 #'   ---------------    --------------------------------------
@@ -2050,7 +2050,7 @@ parse_and_convert <- function(x) {
 }
 
 replace_old_mo_codes <- function(x, property) {
-  ind <- x %like% "[A-Z_]" & !x %in% MO_lookup$mo
+  ind <- x %like_case% "^[A-Z]_[A-Z_]+$" & !x %in% MO_lookup$mo
   if (any(ind)) {
     # get the ones that match
     affected <- x[ind]
@@ -2059,31 +2059,43 @@ replace_old_mo_codes <- function(x, property) {
     # find their new codes, once per code
     solved_unique <- unlist(lapply(strsplit(affected_unique, ""), 
                                    function(m) {
-                                     m <- m[3:length(m)]
-                                     m <- m[m != "_"]
-                                     m <- tolower(paste0(m, ".*", collapse = ""))
-                                     out <- MO_lookup$mo[MO_lookup$fullname_lower %like_case% m]
-                                     if (length(out) > 1) {
+                                     kingdom <- paste0("^", m[1])
+                                     name <- m[3:length(m)]
+                                     name[name == "_"] <- " "
+                                     name <- tolower(paste0(name, ".*", collapse = ""))
+                                     name <- gsub(" .*", " ", name, fixed = TRUE)
+                                     name <- paste0("^", name)
+                                     results <- MO_lookup$mo[MO_lookup$kingdom %like_case% kingdom & 
+                                                               MO_lookup$fullname_lower %like_case% name]
+                                     if (length(results) > 1) {
                                        all_direct_matches <<- FALSE
                                      }
-                                     out[1L]
+                                     results[1L]
                                    }), use.names = FALSE)
     solved <- solved_unique[match(affected, affected_unique)]
     # assign on places where a match was found
     x[ind] <- solved
     n_matched <- length(affected[!is.na(affected)])
     n_unique <- length(affected_unique[!is.na(affected_unique)])
+    if (n_unique < n_matched) {
+      n_unique <- paste0(n_unique, " unique, ")
+    } else {
+      n_unique <- ""
+    }
     if (property != "mo") {
-      message_(font_blue(paste0("The input contained ", n_matched,
-                                " old MO code", ifelse(n_matched == 1, "", "s"),
-                                " (", n_unique, " unique, from a previous AMR package version). Please update your MO codes with `as.mo()` to increase speed.")))
+      warning_(paste0("The input contained ", n_matched,
+                      " old MO code", ifelse(n_matched == 1, "", "s"),
+                      " (", n_unique, "from a previous AMR package version). ",
+                      "Please update your MO codes with `as.mo()` to increase speed."),
+               call = FALSE)
     } else {
-      message_(font_blue(paste0(n_matched, " old MO code", ifelse(n_matched == 1, "", "s"), 
-                                " (", n_unique, " unique, from a previous AMR package version) ", 
-                                ifelse(n_matched == 1, "was", "were"), 
-                                ifelse(all_direct_matches, " updated ", font_bold(" guessed ")),
-                                "to ", ifelse(n_matched == 1, "a ", ""), 
-                                "currently used MO code", ifelse(n_matched == 1, "", "s"), ".")))
+      warning_(paste0(n_matched, " old MO code", ifelse(n_matched == 1, "", "s"), 
+                      " (", n_unique, "from a previous AMR package version) ", 
+                      ifelse(n_matched == 1, "was", "were"), 
+                      ifelse(all_direct_matches, " updated ", font_bold(" guessed ")),
+                      "to ", ifelse(n_matched == 1, "a ", ""), 
+                      "currently used MO code", ifelse(n_matched == 1, "", "s"), "."),
+               call = FALSE)
     }
   }
   x

R/rsi.R

@@ -65,9 +65,9 @@
 #' 
 #' ## Supported Guidelines
 #' 
-#' For interpreting MIC values as well as disk diffusion diameters, currently supported guidelines to be used as input for the `guideline` argument are: `r vector_and(AMR::rsi_translation$guideline, quotes = TRUE, reverse = TRUE)`.
+#' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`). 
 #' 
-#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
+#' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(rsi_translation, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(rsi_translation, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
 #' 
 #' ## After Interpretation
 #' 
@@ -92,7 +92,7 @@
 #' - **I = Increased exposure, but still susceptible**\cr
 #'   A microorganism is categorised as *Susceptible, Increased exposure* when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
 #'
-#' This AMR package honours this new insight. Use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates.
+#' This AMR package honours this (new) insight. Use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates.
 #' @return Ordered [factor] with new class `<rsi>`
 #' @aliases rsi
 #' @export

README.md

@@ -23,7 +23,20 @@ This is the development source of the `AMR` package for R. Not a developer? Then
 ### How to get this package
 Please see [our website](https://msberends.github.io/AMR/#get-this-package).
 
-Bottom line: `install.packages("AMR", repos = "https://msberends.r-universe.dev")`
+You have to add [our R-universe address](https://msberends.r-universe.dev) to your list of repositories ('repos'), by running:
+
+```r
+options(repos = c(getOption("repos"),
+                  msberends = "https://msberends.r-universe.dev"))
+```
+
+You can now install or update the `AMR` package in the same way you are used to:
+
+```r
+install.packages("AMR")
+```
+
+It will be downloaded and installed automatically. For RStudio, click on the menu *Tools* > *Install Packages...* and then type in "AMR" and press <kbd>Install</kbd>.
 
 ### Copyright
 

cran-comments.md

@@ -1,3 +1 @@
-* This package has been archived on 22 May 2021 because of errors in the dplyr package, causing the skimr package to fail: <https://github.com/tidyverse/dplyr/issues/5881>. This AMR package contains a fix around this error. Perhaps an idea for future development of CRAN to send an automated email to a maintainer with a warning that a package will be archived in due time?
-
-* This package continuously has a tarball size of over 7 MB and an installation size of over 5 MB, which will return a NOTE on R CMD CHECK. This has been the case in the last releases as well. The package size is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. This was written and explained in a manuscript that was accepted for publication in the Journal of Statistical Software earlier this year. We will add the paper as a vignette after publication in a next version. All data sets were compressed using `compression = "xz"` to make them as small as possible.
+* This package now has a data folder size of ~2.8 MB (this was ~5.6 MB), which will return a NOTE on R CMD CHECK. The package size is needed to provide users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. This was written and explained in a manuscript that was accepted for publication in the Journal of Statistical Software earlier this year. We will add the paper as a vignette after publication in a next version. All data sets were compressed using `compression = "xz"` to make them as small as possible. We try to update as infrequent as possible.

data-raw/_install_deps.R

@@ -26,7 +26,7 @@
 # some old R instances have trouble installing tinytest, so we ship it too
 install.packages("data-raw/tinytest_1.2.4.10.tar.gz")
 install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
-install.packages("covr")
+install.packages("covr", repos = "https://cran.rstudio.com/")
 
 pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(packageDescription("AMR", fields = "Suggests"), ", ?")))
 cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n")

data-raw/reproduction_of_rsi_translation.R

@@ -2,10 +2,9 @@ library(dplyr)
 library(readr)
 library(tidyr)
 
-# Installed WHONET 2019 software on Windows (http://www.whonet.org/software.html),
-#    opened C:\WHONET\Codes\WHONETCodes.mdb in MS Access
-#    and exported table 'DRGLST1' to MS Excel
-DRGLST1 <- readxl::read_excel("data-raw/DRGLST1.xlsx", na = c("", "NA", "-"))
+# Installed WHONET software on Windows (http://www.whonet.org/software.html),
+#    imported C:\WHONET\Codes\DRGLST1.txt
+DRGLST1 <- readr::read_tsv("data-raw/DRGLST1.txt", na = c("", "NA", "-"))
 rsi_trans <- DRGLST1 %>%
   # only keep CLSI and EUCAST guidelines:
   filter(GUIDELINES %like% "^(CLSI|EUCST)")
@@ -13,6 +12,9 @@ if (any(is.na(rsi_trans$BREAKPOINT_TYPE)) | !"Human" %in% rsi_trans$BREAKPOINT_T
   stop("Check column BREAKPOINT_TYPE - something is WRONG!")
 }
 rsi_trans <- rsi_trans %>% 
+  ##### If looking for adding a specific guideline, do it here!
+  # filter(GUIDELINES == "CLSI20") %>% 
+  #####
   filter(BREAKPOINT_TYPE == "Human") %>% 
   mutate(DISK_S = ifelse(as.double(DISK_S) > 50, 50, DISK_S),
          MIC_R = ifelse(as.double(MIC_R) %in% c(1025, 129, 513), as.double(MIC_R) - 1, MIC_R)) %>%
@@ -50,7 +52,7 @@ rsi_trans <- bind_rows(tbl_mic, tbl_disk) %>%
   select(-ends_with("_mic"), -ends_with("_disk"))
 
 # add extra CLSI general guidelines
-clsi_general <- read_tsv("data-raw/DRGLST.txt") %>%
+clsi_general <- readr::read_tsv("data-raw/DRGLST.txt") %>%
   filter(CLSI == "X") %>%
   select(WHON5_CODE, 
          disk_dose = POTENCY, 
@@ -76,13 +78,13 @@ clsi_general <- read_tsv("data-raw/DRGLST.txt") %>%
 
 
 # add new EUCAST with read_EUCAST.R
-# 2020-04-14 did that now for 2019 and 2020
 
+# 2020-04-14 did that now for 2019 and 2020
 rsi_trans <- rsi_trans %>%
   filter(guideline != "EUCAST 2019") %>% 
   bind_rows(new_EUCAST) %>% 
   bind_rows(clsi_general) %>% 
-  mutate(uti = site %like% "(UTI|urinary)") %>% 
+  mutate(uti = site %like% "(UTI|urinary|urine)") %>% 
   as.data.frame(stringsAsFactors = FALSE) %>%
   # force classes again
   mutate(mo = as.mo(mo),

data-raw/rsi.md5

@@ -1 +1 @@
-aa80f169fc2cba97f5eedc1d24ca8c03
+a4388a944969e5961917f72383156d33

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9001</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </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">1.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9001</span>
       </span>
     </div>
 

docs/articles/WHONET.html

@@ -39,7 +39,7 @@
       </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">1.7.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9001</span>
       </span>
     </div>
 
@@ -221,7 +221,7 @@
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
 <p>We will have to transform some variables to simplify and automate the analysis:</p>
 <ul>
-<li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="https://msberends.github.io/AMR/reference/catalogue_of_life">our Catalogue of Life reference data set</a>, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
+<li>Microorganisms should be transformed to our own microorganism codes (called an <code>mo</code>) using <a href="https://msberends.github.io/AMR/reference/catalogue_of_life">our Catalogue of Life reference data set</a>, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
 <li>Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values <code>"S"</code>, <code>"I"</code> or <code>"R"</code>. That is exactly where the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function is for.</li>
 </ul>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">

docs/articles/datasets.html

@@ -39,7 +39,7 @@
       </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">1.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9001</span>
       </span>
     </div>
 
@@ -192,7 +192,7 @@
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Data sets for download / own use</h1>
             
-            <h4 class="date">30 May 2021</h4>
+            <h4 class="date">01 June 2021</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="hidden name"><code>datasets.Rmd</code></div>
@@ -1005,27 +1005,27 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div id="interpretation-from-mic-values-disk-diameters-to-rsi" class="section level2">
 <h2 class="hasAnchor">
 <a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
-<p>A data set with 20,486 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
+<p>A data set with 21,996 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
 <p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
+<p>It was last updated on 1 June 2021 06:44:05 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (34 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (37 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx">Excel file</a> (0.7 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt">plain text file</a> (1.7 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt">plain text file</a> (1.8 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sas">SAS file</a> (3.5 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sas">SAS file</a> (3.8 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">SPSS file</a> (3.8 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">SPSS file</a> (2.4 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta">Stata file</a> (3.3 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta">Stata file</a> (3.5 MB)</li>
 </ul>
 <div id="source-5" class="section level3">
 <h3 class="hasAnchor">
 <a href="#source-5" class="anchor"></a>Source</h3>
-<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2021).</p>
+<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2020) and EUCAST (2011-2021).</p>
 </div>
 <div id="example-content-5" class="section level3">
 <h3 class="hasAnchor">

docs/articles/index.html

@@ -81,7 +81,7 @@
       </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">1.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9001</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </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">1.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9001</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </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">1.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9001</span>
       </span>
     </div>
 
@@ -376,18 +376,22 @@
 <div id="latest-released-version" class="section level4">
 <h4 class="hasAnchor">
 <a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
-<p>This package is <a href="https://msberends.r-universe.dev">available here</a> on the <a href="https://ropensci.org/r-universe/">rOpenSci R-universe platform</a>, as CRAN does not allow frequent updates of large packages (though the <code>AMR</code> package is only 7-9 MB). With CRAN, we apparently cannot update this package frequently enough to implement the latest EUCAST/CLSI guidelines or the latest microbial taxonomy.</p>
-<p>Install this package in R by using the command:</p>
+<p>This package is <a href="https://msberends.r-universe.dev">available here</a> on the <a href="https://ropensci.org/r-universe/">rOpenSci R-universe platform</a>, as CRAN does not allow frequent updates of large packages (though the <code>AMR</code> package is only 7-9 MB). We are working on splitting this package into two: a new data package containing the microbial taxonomy, and the <code>AMR</code> package that only contains all functions.</p>
+<p>In the meanwhile, you have to add <a href="https://msberends.r-universe.dev">our R-universe address</a> to your list of repositories (‘repos’), by running:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span>, repos <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span></code></pre></div>
-<p>It will be downloaded and installed automatically.</p>
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
+                  msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<p>You can now install or update the <code>AMR</code> package in the same way you are used to:</p>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
+<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
 <p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
 </div>
 <div id="latest-development-version" class="section level4">
 <h4 class="hasAnchor">
 <a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
 <p>The latest and unpublished development version can be installed from GitHub using:</p>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span>
 <span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
 <p><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"><img src="https://www.codefactor.io/repository/github/msberends/amr" alt="CodeFactor"><img src="https://codecov.io/gh/msberends/AMR?branch=master" alt="Codecov"></p>

docs/news/index.html

@@ -81,7 +81,7 @@
       </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">1.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9001</span>
       </span>
     </div>
 
@@ -236,17 +236,26 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1709000" class="section level1">
-<h1 class="page-header" data-toc-text="1.7.0.9000">
-<a href="#amr-1709000" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.0.9000</h1>
-<div id="last-updated-30-may-2021" class="section level2">
+    <div id="amr-1709001" class="section level1">
+<h1 class="page-header" data-toc-text="1.7.0.9001">
+<a href="#amr-1709001" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.0.9001</h1>
+<div id="last-updated-1-june-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-30-may-2021" class="anchor"></a><small>Last updated: 30 May 2021</small>
+<a href="#last-updated-1-june-2021" class="anchor"></a><small>Last updated: 1 June 2021</small>
 </h2>
+<div id="new" class="section level3">
+<h3 class="hasAnchor">
+<a href="#new" class="anchor"></a>New</h3>
+<ul>
+<li>Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>)</li>
+</ul>
+</div>
 <div id="changed" class="section level3">
 <h3 class="hasAnchor">
 <a href="#changed" class="anchor"></a>Changed</h3>
 <ul>
+<li>
+<code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now supports grouping using the <code>dplyr</code> package</li>
 <li>As requested by CRAN administrators: decreased package size by 3 MB in costs of a ~50 times slower loading time of the package (i.e., <code><a href="https://msberends.github.io/AMR/">library(AMR)</a></code>)</li>
 </ul>
 </div>
@@ -280,9 +289,9 @@
 </li>
 </ul>
 </div>
-<div id="new" class="section level3">
+<div id="new-1" class="section level3">
 <h3 class="hasAnchor">
-<a href="#new" class="anchor"></a>New</h3>
+<a href="#new-1" class="anchor"></a>New</h3>
 <ul>
 <li>Function <code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> that brings support for custom AMR rules in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
 </li>
@@ -363,9 +372,9 @@
     <div id="amr-160" class="section level1">
 <h1 class="page-header" data-toc-text="1.6.0">
 <a href="#amr-160" class="anchor"></a><small> 2021-03-14 </small><code>AMR</code> 1.6.0</h1>
-<div id="new-1" class="section level3">
+<div id="new-2" class="section level3">
 <h3 class="hasAnchor">
-<a href="#new-1" class="anchor"></a>New</h3>
+<a href="#new-2" class="anchor"></a>New</h3>
 <ul>
 <li>
 <p>Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function and in <code><a href="../reference/as.rsi.html">as.rsi()</a></code> to interpret MIC and disk diffusion values. This is now the default guideline in this package.</p>
@@ -500,9 +509,9 @@
     <div id="amr-150" class="section level1">
 <h1 class="page-header" data-toc-text="1.5.0">
 <a href="#amr-150" class="anchor"></a><small> 2021-01-06 </small><code>AMR</code> 1.5.0</h1>
-<div id="new-2" class="section level3">
+<div id="new-3" class="section level3">
 <h3 class="hasAnchor">
-<a href="#new-2" class="anchor"></a>New</h3>
+<a href="#new-3" class="anchor"></a>New</h3>
 <ul>
 <li>
 <p>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> to determine (patient) episodes which are not necessarily based on microorganisms. The <code><a href="../reference/get_episode.html">get_episode()</a></code> function returns the index number of the episode per group, while the <code><a href="../reference/get_episode.html">is_new_episode()</a></code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode. They also support <code>dplyr</code>s grouping (i.e. using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code>):</p>
@@ -613,9 +622,9 @@
     <div id="amr-140" class="section level1">
 <h1 class="page-header" data-toc-text="1.4.0">
 <a href="#amr-140" class="anchor"></a><small> 2020-10-08 </small><code>AMR</code> 1.4.0</h1>
-<div id="new-3" class="section level3">
+<div id="new-4" class="section level3">
 <h3 class="hasAnchor">
-<a href="#new-3" class="anchor"></a>New</h3>
+<a href="#new-4" class="anchor"></a>New</h3>
 <ul>
 <li><p>Support for ‘EUCAST Expert Rules’ / ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can now correct for more than 180 different antibiotics and the <code><a href="../reference/mdro.html">mdro()</a></code> function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function consequently gained the arguments <code>version_breakpoints</code> (at the moment defaults to v10.0, 2020) and <code>version_expertrules</code> (at the moment defaults to v3.2, 2020). The <code>example_isolates</code> data set now also reflects the change from v3.1 to v3.2. The <code><a href="../reference/mdro.html">mdro()</a></code> function now accepts <code>guideline == "EUCAST3.1"</code> and <code>guideline == "EUCAST3.2"</code>.</p></li>
 <li><p>A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: <a href="https://msberends.github.io/AMR/articles/datasets.html" class="uri">https://msberends.github.io/AMR/articles/datasets.html</a></p></li>
@@ -716,9 +725,9 @@
     <div id="amr-130" class="section level1">
 <h1 class="page-header" data-toc-text="1.3.0">
 <a href="#amr-130" class="anchor"></a><small> 2020-07-31 </small><code>AMR</code> 1.3.0</h1>
-<div id="new-4" class="section level3">
+<div id="new-5" class="section level3">
 <h3 class="hasAnchor">
-<a href="#new-4" class="anchor"></a>New</h3>
+<a href="#new-5" class="anchor"></a>New</h3>
 <ul>
 <li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
 <li>
@@ -807,7 +816,7 @@
 <p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
 <p>Negative effects of this change are:</p>
 <ul>
-<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
+<li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
 <li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</del></li>
 <li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
 <li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
@@ -861,9 +870,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     <div id="amr-110" class="section level1">
 <h1 class="page-header" data-toc-text="1.1.0">
 <a href="#amr-110" class="anchor"></a><small> 2020-04-15 </small><code>AMR</code> 1.1.0</h1>
-<div id="new-5" class="section level3">
+<div id="new-6" class="section level3">
 <h3 class="hasAnchor">
-<a href="#new-5" class="anchor"></a>New</h3>
+<a href="#new-6" class="anchor"></a>New</h3>
 <ul>
 <li>Support for easy principal component analysis for AMR, using the new <code><a href="../reference/pca.html">pca()</a></code> function</li>
 <li>Plotting biplots for principal component analysis using the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function</li>
@@ -927,9 +936,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <h1 class="page-header" data-toc-text="1.0.0">
 <a href="#amr-100" class="anchor"></a><small> 2020-02-17 </small><code>AMR</code> 1.0.0</h1>
 <p>This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.</p>
-<div id="new-6" class="section level3">
+<div id="new-7" class="section level3">
 <h3 class="hasAnchor">
-<a href="#new-6" class="anchor"></a>New</h3>
+<a href="#new-7" class="anchor"></a>New</h3>
 <ul>
 <li>Support for the newest <a href="https://www.eucast.org/clinical_breakpoints/">EUCAST Clinical Breakpoint Tables v.10.0</a>, valid from 1 January 2020. This affects translation of MIC and disk zones using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> and inferred resistance and susceptibility using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</li>
 <li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <a href="https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows for machine reading these guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file <a href="https://github.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R">can be found here</a>.</li>
@@ -1024,9 +1033,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 </div>
-<div id="new-7" class="section level3">
+<div id="new-8" class="section level3">
 <h3 class="hasAnchor">
-<a href="#new-7" class="anchor"></a>New</h3>
+<a href="#new-8" class="anchor"></a>New</h3>
 <ul>
 <li>
 <p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
@@ -1139,13 +1148,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="co">#&gt; invalid microorganism code, NA generated</span></code></pre></div>
 <p>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.</p>
 </li>
-<li><p>Function <code>freq()</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>freq()</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).</p></li>
+<li><p>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).</p></li>
 <li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
 </ul>
 </div>
-<div id="new-8" class="section level3">
+<div id="new-9" class="section level3">
 <h3 class="hasAnchor">
-<a href="#new-8" class="anchor"></a>New</h3>
+<a href="#new-9" class="anchor"></a>New</h3>
 <ul>
 <li>
 <p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
@@ -1276,9 +1285,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     <div id="amr-071" class="section level1">
 <h1 class="page-header" data-toc-text="0.7.1">
 <a href="#amr-071" class="anchor"></a><small> 2019-06-23 </small><code>AMR</code> 0.7.1</h1>
-<div id="new-9" class="section level4">
+<div id="new-10" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-9" class="anchor"></a>New</h4>
+<a href="#new-10" class="anchor"></a>New</h4>
 <ul>
 <li>
 <p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> to immediately show resistance percentages and number of available isolates:</p>
@@ -1360,9 +1369,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     <div id="amr-070" class="section level1">
 <h1 class="page-header" data-toc-text="0.7.0">
 <a href="#amr-070" class="anchor"></a><small> 2019-06-03 </small><code>AMR</code> 0.7.0</h1>
-<div id="new-10" class="section level4">
+<div id="new-11" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-10" class="anchor"></a>New</h4>
+<a href="#new-11" class="anchor"></a>New</h4>
 <ul>
 <li>Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><a href="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><a href="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
 <li>Function <code><a href="../reference/mo_property.html">mo_name()</a></code> as alias of <code><a href="../reference/mo_property.html">mo_fullname()</a></code>
@@ -1406,7 +1415,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument <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><a href="../reference/as.rsi.html">rsi()</a></code>
 </li>
-<li>Frequency tables (<code>freq()</code>):
+<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
 <ul>
 <li><p>speed improvement for microbial IDs</p></li>
 <li><p>fixed factor level names for R Markdown</p></li>
@@ -1416,12 +1425,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span> 
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span>
 <span class="co"># grouped boxplots:</span>
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
   <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
 </li>
 </ul>
@@ -1431,7 +1440,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <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>freq()</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>
@@ -1475,9 +1484,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Contains the complete manual of this package and all of its functions with an explanation of their arguments</li>
 <li>Contains a comprehensive tutorial about how to conduct AMR data analysis, import data from WHONET or SPSS and many more.</li>
 </ul>
-<div id="new-11" class="section level4">
+<div id="new-12" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-11" class="anchor"></a>New</h4>
+<a href="#new-12" class="anchor"></a>New</h4>
 <ul>
 <li><p><strong>BREAKING</strong>: removed deprecated functions, arguments and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</p></li>
 <li>
@@ -1670,7 +1679,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 </li>
-<li>Frequency tables (<code>freq()</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>
@@ -1680,15 +1689,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="co"># OLD WAY</span>
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
-  <span class="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
 <span class="co"># NEW WAY</span>
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
 
 <span class="co"># Even supports grouping variables:</span>
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
 </li>
 <li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
 <li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
@@ -1720,9 +1729,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     <div id="amr-050" class="section level1">
 <h1 class="page-header" data-toc-text="0.5.0">
 <a href="#amr-050" class="anchor"></a><small> 2018-11-30 </small><code>AMR</code> 0.5.0</h1>
-<div id="new-12" class="section level4">
+<div id="new-13" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-12" class="anchor"></a>New</h4>
+<a href="#new-13" class="anchor"></a>New</h4>
 <ul>
 <li>Repository moved to GitLab</li>
 <li>Function <code>count_all</code> to get all available isolates (that like all <code>portion_*</code> and <code>count_*</code> functions also supports <code>summarise</code> and <code>group_by</code>), the old <code>n_rsi</code> is now an alias of <code>count_all</code>
@@ -1770,7 +1779,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
 <li><p>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</p></li>
 <li>
-<p>Frequency tables - <code>freq()</code>:</p>
+<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:</p>
 <ul>
 <li>
 <p>Support for grouping variables, test with:</p>
@@ -1778,14 +1787,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
 </li>
 <li>
 <p>Support for (un)selecting columns:</p>