(v1.7.0.9002) old MO codes

.github/workflows/check.yaml

@@ -79,7 +79,8 @@ jobs:
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
-
+      R_REPOSITORIES: "https://cran.rstudio.com"
+    
     steps:
       - uses: actions/checkout@v2
 

.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
-Date: 2021-05-26
+Version: 1.7.0.9002
+Date: 2021-06-01
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,15 @@
-# `AMR` 1.7.0
+# `AMR` 1.7.0.9002
+## <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)`)
+
+
+# `AMR` 1.7.0
 
 ### Breaking change
 * All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release.

R/aa_helper_functions.R

@@ -178,9 +178,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
       found <- sort(colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)])[1]
     } else if ("mo" %in% colnames(x) &
                suppressWarnings(
-                 all(x$mo %in% c(NA,
-                                 microorganisms$mo,
-                                 microorganisms.translation$mo_old)))) {
+                 all(x$mo %in% c(NA, microorganisms$mo)))) {
       found <- "mo"
     } else if (any(colnames(x) %like% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$")) {
       found <- sort(colnames(x)[colnames(x) %like% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$"])[1]

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)
-  
-  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)
+  # 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]
   }
   
-  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/first_isolate.R

@@ -472,8 +472,8 @@ first_isolate <- function(x = NULL,
                  as_note = FALSE)
       }
       if (type == "points") {
-        message_("Basing inclusion on all antimicrobial results, using a points threshold of "
-                 , points_threshold,
+        message_("Basing inclusion on all antimicrobial results, using a points threshold of ",
+                 points_threshold,
                  add_fn = font_black,
                  as_note = FALSE)
       }

R/key_antimicrobials.R

@@ -140,7 +140,7 @@ key_antimicrobials <- function(x = NULL,
   meet_criteria(antifungal, allow_class = "character", allow_NULL = TRUE)
   meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
   
-  # force regular [data.frame], not a tibble or data.table
+  # force regular data.frame, not a tibble or data.table
   x <- as.data.frame(x, stringsAsFactors = FALSE)
   cols <- get_column_abx(x, info = FALSE, only_rsi_columns = only_rsi_columns)
   
@@ -237,7 +237,7 @@ all_antimicrobials <- function(x = NULL,
   meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
   meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
   
-  # force regular [data.frame], not a tibble or data.table
+  # force regular data.frame, not a tibble or data.table
   x <- as.data.frame(x, stringsAsFactors = FALSE)
   cols <- get_column_abx(x, only_rsi_columns = only_rsi_columns, info = FALSE, sort = FALSE)
   

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
 #'   ---------------    --------------------------------------
@@ -1817,8 +1817,7 @@ as.data.frame.mo <- function(x, ...) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
   # must only contain valid MOs
-  return_after_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
-                                                          as.character(microorganisms.translation$mo_old)))
+  return_after_integrity_check(y, "microorganism code", as.character(microorganisms$mo))
 }
 #' @method [[<- mo
 #' @export
@@ -1827,8 +1826,7 @@ as.data.frame.mo <- function(x, ...) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
   # must only contain valid MOs
-  return_after_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
-                                                          as.character(microorganisms.translation$mo_old)))
+  return_after_integrity_check(y, "microorganism code", as.character(microorganisms$mo))
 }
 #' @method c mo
 #' @export
@@ -1837,8 +1835,7 @@ c.mo <- function(...) {
   x <- list(...)[[1L]]
   y <- NextMethod()
   attributes(y) <- attributes(x)
-  return_after_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
-                                                          as.character(microorganisms.translation$mo_old)))
+  return_after_integrity_check(y, "microorganism code", as.character(microorganisms$mo))
 }
 
 #' @method unique mo
@@ -2053,24 +2050,52 @@ parse_and_convert <- function(x) {
 }
 
 replace_old_mo_codes <- function(x, property) {
-  if (any(toupper(x) %in% microorganisms.translation$mo_old, na.rm = TRUE)) {
+  ind <- x %like_case% "^[A-Z]_[A-Z_]+$" & !x %in% MO_lookup$mo
+  if (any(ind)) {
     # get the ones that match
-    matched <- match(toupper(x), microorganisms.translation$mo_old)
-    # and their new codes
-    mo_new <- microorganisms.translation$mo_new[matched]
+    affected <- x[ind]
+    affected_unique <- unique(affected)
+    all_direct_matches <- TRUE
+    # find their new codes, once per code
+    solved_unique <- unlist(lapply(strsplit(affected_unique, ""), 
+                                   function(m) {
+                                     kingdom <- paste0("^", m[1])
+                                     name <- m[3:length(m)]
+                                     name[name == "_"] <- " "
+                                     name <- tolower(paste0(name, ".*", collapse = ""))
+                                     name <- gsub(" .*", " ", name, fixed = TRUE)
+                                     name <- paste0("^", name)
+                                     results <- MO_lookup$mo[MO_lookup$kingdom %like_case% kingdom & 
+                                                               MO_lookup$fullname_lower %like_case% name]
+                                     if (length(results) > 1) {
+                                       all_direct_matches <<- FALSE
+                                     }
+                                     results[1L]
+                                   }), use.names = FALSE)
+    solved <- solved_unique[match(affected, affected_unique)]
     # assign on places where a match was found
-    x[which(!is.na(matched))] <- mo_new[which(!is.na(matched))]
-    n_matched <- length(matched[!is.na(matched)])
-    if (property != "mo") {
-      message_(font_blue(paste0("The input contained ", n_matched,
-                                " old MO code", ifelse(n_matched == 1, "", "s"),
-                                " (from a previous AMR package version). Please update your MO codes with `as.mo()`.")))
+    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 {
-      message_(font_blue(paste0(n_matched, " old MO code", ifelse(n_matched == 1, "", "s"), 
-                                " (from a previous AMR package version) ", 
-                                ifelse(n_matched == 1, "was", "were"), 
-                                " updated to ", ifelse(n_matched == 1, "a ", ""), 
-                                "currently used MO code", ifelse(n_matched == 1, "", "s"), ".")))
+      n_unique <- ""
+    }
+    if (property != "mo") {
+      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 {
+      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/mo_source.R

@@ -275,9 +275,9 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
       return(FALSE)
     }
   }
-  if (!all(x$mo %in% c("", microorganisms$mo, microorganisms.translation$mo_old), na.rm = TRUE)) {
+  if (!all(x$mo %in% c("", microorganisms$mo), na.rm = TRUE)) {
     if (stop_on_error == TRUE) {
-      invalid <- x[which(!x$mo %in% c("", microorganisms$mo, microorganisms.translation$mo_old)), , drop = FALSE]
+      invalid <- x[which(!x$mo %in% c("", microorganisms$mo)), , drop = FALSE]
       if (nrow(invalid) > 1) {
         plural <- "s"
       } else {

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

R/zzz.R

@@ -72,4 +72,76 @@ if (utf8_supported && !is_latex) {
       invisible(get_mo_source())
     }
   }, silent = TRUE)
+  
+  
+  # reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
+  assign(x = "AB_lookup", value = create_AB_lookup(), envir = asNamespace("AMR"))
+  assign(x = "MO_lookup", value = create_MO_lookup(), envir = asNamespace("AMR"))
+  assign(x = "MO.old_lookup", value = create_MO.old_lookup(), envir = asNamespace("AMR"))
+  # for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
+  assign(x = "INTRINSIC_R", value = create_intr_resistance(), envir = asNamespace("AMR"))
+}
+
+
+# Helper functions --------------------------------------------------------
+
+create_AB_lookup <- function() {
+  AB_lookup <- AMR::antibiotics
+  AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name)
+  AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name)
+  AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name)
+  AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name)
+  AB_lookup$generalised_all <- unname(lapply(as.list(as.data.frame(t(AB_lookup[, 
+                                                                               c("ab", "atc", "cid", "name",
+                                                                                 colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]),
+                                                                               drop = FALSE]),
+                                                                   stringsAsFactors = FALSE)),
+                                             function(x) {
+                                               x <- generalise_antibiotic_name(unname(unlist(x)))
+                                               x[x != ""]
+                                             }))
+  AB_lookup
+}
+
+create_MO_lookup <- function() {
+  MO_lookup <- AMR::microorganisms
+  
+  MO_lookup$kingdom_index <- NA_real_
+  MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
+  MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
+  MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
+  MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
+  # all the rest
+  MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
+  
+  # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
+  MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus, 
+                                                   MO_lookup$species,
+                                                   MO_lookup$subspecies)))
+  ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
+  MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
+  MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
+  
+  # add a column with only "e coli" like combinations
+  MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)
+  
+  # so arrange data on prevalence first, then kingdom, then full name
+  MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), ]
+}
+
+create_MO.old_lookup <- function() {
+  MO.old_lookup <- AMR::microorganisms.old
+  MO.old_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname))))
+  
+  # add a column with only "e coli"-like combinations
+  MO.old_lookup$g_species <- trimws(gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower))
+  
+  # so arrange data on prevalence first, then full name
+  MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), ]
+}
+
+create_intr_resistance <- function() {
+  # for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
+  paste(AMR::microorganisms[match(AMR::intrinsic_resistant$microorganism, AMR::microorganisms$fullname), "mo", drop = TRUE],
+        AMR::antibiotics[match(AMR::intrinsic_resistant$antibiotic, AMR::antibiotics$name), "ab", drop = TRUE])
 }

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/_internals.R

@@ -31,109 +31,6 @@ devtools::load_all(quiet = TRUE)
 
 old_globalenv <- ls(envir = globalenv())
 
-# Helper functions --------------------------------------------------------
-
-create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
-  # Determination of which staphylococcal species are CoNS/CoPS according to:
-  # - Becker et al. 2014, PMID 25278577
-  # - Becker et al. 2019, PMID 30872103
-  # - Becker et al. 2020, PMID 32056452
-  # this function returns class <mo>
-  MO_staph <- AMR::microorganisms
-  MO_staph <- MO_staph[which(MO_staph$genus == "Staphylococcus"), , drop = FALSE]
-  if (type == "CoNS") {
-    MO_staph[which(MO_staph$species %in% c("coagulase-negative", "argensis", "arlettae",
-                                           "auricularis", "borealis", "caeli", "capitis", "caprae", 
-                                           "carnosus", "casei", "chromogenes", "cohnii", "condimenti",
-                                           "croceilyticus",
-                                           "debuckii", "devriesei", "edaphicus", "epidermidis",
-                                           "equorum", "felis", "fleurettii", "gallinarum",
-                                           "haemolyticus", "hominis", "jettensis", "kloosii",
-                                           "lentus", "lugdunensis", "massiliensis", "microti",
-                                           "muscae", "nepalensis", "pasteuri", "petrasii",
-                                           "pettenkoferi", "piscifermentans", "pragensis", "pseudoxylosus",
-                                           "pulvereri", "rostri", "saccharolyticus", "saprophyticus",
-                                           "sciuri", "simulans", "stepanovicii", "succinus",
-                                           "ureilyticus",
-                                           "vitulinus", "vitulus", "warneri", "xylosus")
-                   | (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
-             "mo", drop = TRUE]
-  } else if (type == "CoPS") {
-    MO_staph[which(MO_staph$species %in% c("coagulase-positive", "coagulans",
-                                           "agnetis", "argenteus",
-                                           "cornubiensis",
-                                           "delphini", "lutrae",
-                                           "hyicus", "intermedius",
-                                           "pseudintermedius", "pseudointermedius",
-                                           "schweitzeri", "simiae")
-                   | (MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
-             "mo", drop = TRUE]
-  }
-}
-
-create_AB_lookup <- function() {
-  AB_lookup <- AMR::antibiotics
-  AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name)
-  AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name)
-  AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name)
-  AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name)
-  AB_lookup$generalised_all <- unname(lapply(as.list(as.data.frame(t(AB_lookup[, 
-                                                                               c("ab", "atc", "cid", "name",
-                                                                                 colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]),
-                                                                               drop = FALSE]),
-                                                                   stringsAsFactors = FALSE)),
-                                             function(x) {
-                                               x <- generalise_antibiotic_name(unname(unlist(x)))
-                                               x[x != ""]
-                                             }))
-  AB_lookup
-}
-
-create_MO_lookup <- function() {
-  MO_lookup <- AMR::microorganisms
-  
-  MO_lookup$kingdom_index <- NA_real_
-  MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
-  MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
-  MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
-  MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
-  # all the rest
-  MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
-  
-  # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
-  MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus, 
-                                                   MO_lookup$species,
-                                                   MO_lookup$subspecies)))
-  ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname)
-  MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
-  MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
-  
-  # add a column with only "e coli" like combinations
-  MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)
-  
-  # so arrange data on prevalence first, then kingdom, then full name
-  MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), ]
-}
-
-create_MO.old_lookup <- function() {
-  MO.old_lookup <- AMR::microorganisms.old
-  MO.old_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname))))
-  
-  # add a column with only "e coli"-like combinations
-  MO.old_lookup$g_species <- trimws(gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower))
-  
-  # so arrange data on prevalence first, then full name
-  MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), ]
-}
-
-create_intr_resistance <- function() {
-  # for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
-  paste(AMR::microorganisms[match(AMR::intrinsic_resistant$microorganism, AMR::microorganisms$fullname), "mo", drop = TRUE],
-        AMR::antibiotics[match(AMR::intrinsic_resistant$antibiotic, AMR::antibiotics$name), "ab", drop = TRUE])
-}
-
-
-
 # Save internal data to R/sysdata.rda -------------------------------------
 
 # See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
@@ -170,24 +67,50 @@ translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
                                        allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
                                        quote = "")
 
-# Old microorganism codes
-microorganisms.translation <- readRDS("data-raw/microorganisms.translation.rds")
-
-# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
-INTRINSIC_R <- create_intr_resistance()
-
 # for checking input in `language` argument in e.g. mo_*() and ab_*() functions
 LANGUAGES_SUPPORTED <- sort(c("en", colnames(translations_file)[nchar(colnames(translations_file)) == 2]))
 
 # vectors of CoNS and CoPS, improves speed in as.mo()
+create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
+  # Determination of which staphylococcal species are CoNS/CoPS according to:
+  # - Becker et al. 2014, PMID 25278577
+  # - Becker et al. 2019, PMID 30872103
+  # - Becker et al. 2020, PMID 32056452
+  # this function returns class <mo>
+  MO_staph <- AMR::microorganisms
+  MO_staph <- MO_staph[which(MO_staph$genus == "Staphylococcus"), , drop = FALSE]
+  if (type == "CoNS") {
+    MO_staph[which(MO_staph$species %in% c("coagulase-negative", "argensis", "arlettae",
+                                           "auricularis", "borealis", "caeli", "capitis", "caprae", 
+                                           "carnosus", "casei", "chromogenes", "cohnii", "condimenti",
+                                           "croceilyticus",
+                                           "debuckii", "devriesei", "edaphicus", "epidermidis",
+                                           "equorum", "felis", "fleurettii", "gallinarum",
+                                           "haemolyticus", "hominis", "jettensis", "kloosii",
+                                           "lentus", "lugdunensis", "massiliensis", "microti",
+                                           "muscae", "nepalensis", "pasteuri", "petrasii",
+                                           "pettenkoferi", "piscifermentans", "pragensis", "pseudoxylosus",
+                                           "pulvereri", "rostri", "saccharolyticus", "saprophyticus",
+                                           "sciuri", "simulans", "stepanovicii", "succinus",
+                                           "ureilyticus",
+                                           "vitulinus", "vitulus", "warneri", "xylosus")
+                   | (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
+             "mo", drop = TRUE]
+  } else if (type == "CoPS") {
+    MO_staph[which(MO_staph$species %in% c("coagulase-positive", "coagulans",
+                                           "agnetis", "argenteus",
+                                           "cornubiensis",
+                                           "delphini", "lutrae",
+                                           "hyicus", "intermedius",
+                                           "pseudintermedius", "pseudointermedius",
+                                           "schweitzeri", "simiae")
+                   | (MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
+             "mo", drop = TRUE]
+  }
+}
 MO_CONS <- create_species_cons_cops("CoNS")
 MO_COPS <- create_species_cons_cops("CoPS")
 
-# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
-AB_lookup <- create_AB_lookup()
-MO_lookup <- create_MO_lookup()
-MO.old_lookup <- create_MO.old_lookup()
-
 # antibiotic groups
 # (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
 globalenv_before_ab <- c(ls(envir = globalenv()), "globalenv_before_ab")
@@ -220,14 +143,10 @@ DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_
 # Export to package as internal data ----
 usethis::use_data(eucast_rules_file, 
                   translations_file,
-                  microorganisms.translation,
-                  INTRINSIC_R,
                   LANGUAGES_SUPPORTED,
                   MO_CONS,
                   MO_COPS,
                   AB_lookup,
-                  MO_lookup,
-                  MO.old_lookup,
                   AMINOGLYCOSIDES,
                   AMINOPENICILLINS,
                   CARBAPENEMS,

data-raw/reproduction_of_microorganisms.R

@@ -872,12 +872,12 @@ View(old_new)
 # set new MO codes as names to existing data sets
 rsi_translation$mo <- mo_name(rsi_translation$mo, language = NULL)
 microorganisms.codes$mo <- mo_name(microorganisms.codes$mo, language = NULL)
-microorganisms.translation <- AMR:::microorganisms.translation %>%
-  bind_rows(tibble(mo_old = AMR:::microorganisms.translation$mo_new, mo_new = mo_old)) %>%
-  filter(!mo_old %in% MOs$mo) %>% 
-  mutate(mo_new = mo_name(mo_new, language = NULL)) %>% 
-  bind_rows(old_new %>% select(mo_old, mo_new)) %>% 
-  distinct(mo_old, .keep_all = TRUE)
+# microorganisms.translation <- AMR:::microorganisms.translation %>%
+#   bind_rows(tibble(mo_old = AMR:::microorganisms.translation$mo_new, mo_new = mo_old)) %>%
+#   filter(!mo_old %in% MOs$mo) %>% 
+#   mutate(mo_new = mo_name(mo_new, language = NULL)) %>% 
+#   bind_rows(old_new %>% select(mo_old, mo_new)) %>% 
+#   distinct(mo_old, .keep_all = TRUE)
 
 # arrange the data sets to save
 MOs <- MOs %>% arrange(fullname)
@@ -911,23 +911,23 @@ devtools::load_all(".")
 rsi_translation$mo <- as.mo(rsi_translation$mo)
 microorganisms.codes$mo <- as.mo(microorganisms.codes$mo)
 class(microorganisms.codes$mo) <- c("mo", "character")
-microorganisms.translation <- microorganisms.translation %>%
-  # (to do: add last package version to column pkg_version)
-  left_join(microorganisms.old[, c("fullname", "fullname_new")], # microorganisms.old is now new and loaded
-            by = c("mo_new" = "fullname")) %>%
-  mutate(name = ifelse(!is.na(fullname_new), fullname_new, mo_new)) %>% 
-  left_join(microorganisms[, c("fullname", "mo")],               # as is microorganisms
-            by = c("name" = "fullname")) %>% 
-  select(mo_old, mo_new = mo) %>% 
-  filter(!is.na(mo_old), !is.na(mo_new))
-class(microorganisms.translation$mo_old) <- "character" # no class <mo> since those aren't valid MO codes
-class(microorganisms.translation$mo_new) <- c("mo", "character")
+# microorganisms.translation <- microorganisms.translation %>%
+#   # (to do: add last package version to column pkg_version)
+#   left_join(microorganisms.old[, c("fullname", "fullname_new")], # microorganisms.old is now new and loaded
+#             by = c("mo_new" = "fullname")) %>%
+#   mutate(name = ifelse(!is.na(fullname_new), fullname_new, mo_new)) %>% 
+#   left_join(microorganisms[, c("fullname", "mo")],               # as is microorganisms
+#             by = c("name" = "fullname")) %>% 
+#   select(mo_old, mo_new = mo) %>% 
+#   filter(!is.na(mo_old), !is.na(mo_new))
+# class(microorganisms.translation$mo_old) <- "character" # no class <mo> since those aren't valid MO codes
+# class(microorganisms.translation$mo_new) <- c("mo", "character")
 # save those to the package
 usethis::use_data(rsi_translation, overwrite = TRUE, version = 2)
 usethis::use_data(microorganisms.codes, overwrite = TRUE, version = 2)
-saveRDS(microorganisms.translation, file = "data-raw/microorganisms.translation.rds", version = 2)
+# saveRDS(microorganisms.translation, file = "data-raw/microorganisms.translation.rds", version = 2)
 # to save microorganisms.translation internally to the package
-source("data-raw/_internals.R")
+# source("data-raw/_internals.R")
 
 # load new data sets again
 devtools::load_all(".")
@@ -935,7 +935,7 @@ devtools::load_all(".")
 # and check: these codes should not be missing (will otherwise throw a unit test error):
 AMR::microorganisms.codes %>% filter(!mo %in% MOs$mo)
 AMR::rsi_translation %>% filter(!mo %in% MOs$mo)
-AMR:::microorganisms.translation %>% filter(!mo_new %in% MOs$mo)
+# AMR:::microorganisms.translation %>% filter(!mo_new %in% MOs$mo)
 
 # update the example_isolates data set
 example_isolates$mo <- as.mo(example_isolates$mo)

data-raw/reproduction_of_microorganisms_update.R

@@ -380,37 +380,37 @@ MOs.old <- microorganisms.old %>%
 # Keep old codes for translation ------------------------------------------
 
 # add removed microbial IDs to the internal translation table so old package versions keep working
-MOs.translation <- microorganisms %>% 
-  filter(!mo %in% MOs$mo) %>%
-  select(mo, fullname) %>%
-  left_join(new_synonyms) %>% 
-  left_join(MOs %>% transmute(fullname_new = fullname, mo2 = as.character(mo))) %>% 
-  select(mo_old = mo, mo_new = mo2) %>% 
-  distinct()
-MOs.translation <- AMR:::microorganisms.translation %>% 
-  left_join(MOs.translation %>% select(mo_new_update = mo_new, mo_new = mo_old)) %>% 
-  mutate(mo_new = as.character(ifelse(!is.na(mo_new_update), mo_new_update, mo_new))) %>% 
-  select(-mo_new_update) %>% 
-  bind_rows(
-    # old IDs used in microorganisms.codes must put in here as well
-    microorganisms.codes %>%
-      filter(!mo %in% MOs$mo) %>%
-      transmute(mo_old = mo, fullname = mo_name(mo)) %>%
-      left_join(MOs.old %>%
-                  select(fullname, fullname_new)) %>%
-      left_join(MOs %>%
-                  select(mo_new = mo, fullname_new = fullname)) %>%
-      transmute(mo_old = as.character(mo_old), mo_new)) %>% 
-  arrange(mo_old) %>% 
-  filter(mo_old != mo_new,
-         !mo_old %in% MOs$mo) %>%
-  left_join(., ., 
-            by = c("mo_new" = "mo_old"), 
-            suffix = c("", ".2")) %>%
-  mutate(mo_new = ifelse(!is.na(mo_new.2), mo_new.2, mo_new)) %>% 
-  distinct(mo_old, mo_new) %>% 
-  # clean up
-  df_remove_nonASCII()
+# MOs.translation <- microorganisms %>% 
+#   filter(!mo %in% MOs$mo) %>%
+#   select(mo, fullname) %>%
+#   left_join(new_synonyms) %>% 
+#   left_join(MOs %>% transmute(fullname_new = fullname, mo2 = as.character(mo))) %>% 
+#   select(mo_old = mo, mo_new = mo2) %>% 
+#   distinct()
+# MOs.translation <- AMR:::microorganisms.translation %>% 
+#   left_join(MOs.translation %>% select(mo_new_update = mo_new, mo_new = mo_old)) %>% 
+#   mutate(mo_new = as.character(ifelse(!is.na(mo_new_update), mo_new_update, mo_new))) %>% 
+#   select(-mo_new_update) %>% 
+#   bind_rows(
+#     # old IDs used in microorganisms.codes must put in here as well
+#     microorganisms.codes %>%
+#       filter(!mo %in% MOs$mo) %>%
+#       transmute(mo_old = mo, fullname = mo_name(mo)) %>%
+#       left_join(MOs.old %>%
+#                   select(fullname, fullname_new)) %>%
+#       left_join(MOs %>%
+#                   select(mo_new = mo, fullname_new = fullname)) %>%
+#       transmute(mo_old = as.character(mo_old), mo_new)) %>% 
+#   arrange(mo_old) %>% 
+#   filter(mo_old != mo_new,
+#          !mo_old %in% MOs$mo) %>%
+#   left_join(., ., 
+#             by = c("mo_new" = "mo_old"), 
+#             suffix = c("", ".2")) %>%
+#   mutate(mo_new = ifelse(!is.na(mo_new.2), mo_new.2, mo_new)) %>% 
+#   distinct(mo_old, mo_new) %>% 
+#   # clean up
+#   df_remove_nonASCII()
 
 message("microorganisms new:     ", sum(!MOs$fullname %in% c(microorganisms$fullname, MOs.old$fullname)))
 message("microorganisms renamed: ", sum(!MOs.old$fullname %in% microorganisms.old$fullname))
@@ -424,12 +424,12 @@ class(MOs.translation$mo_new) <- c("mo", "character")
 
 microorganisms <- MOs
 microorganisms.old <- MOs.old
-microorganisms.translation <- MOs.translation
+# microorganisms.translation <- MOs.translation
 
 # on the server, do:
 usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
 usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2)
-saveRDS(microorganisms.translation, file = "data-raw/microorganisms.translation.rds", version = 2)
+# saveRDS(microorganisms.translation, file = "data-raw/microorganisms.translation.rds", version = 2)
 rm(microorganisms)
 rm(microorganisms.old)
 rm(microorganisms.translation)

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
+1a7fe52f8185c9bb2c470712863d1887

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</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</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</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</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</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</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">26 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 14:31:18 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</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</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</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</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</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</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</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</span>
       </span>
     </div>
 
@@ -236,6 +236,31 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
+    <div id="amr-1709002" class="section level1">
+<h1 class="page-header" data-toc-text="1.7.0.9002">
+<a href="#amr-1709002" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.0.9002</h1>
+<div id="last-updated-1-june-2021" class="section level2">
+<h2 class="hasAnchor">
+<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>
+</div>
+</div>
     <div id="amr-170" class="section level1">
 <h1 class="page-header" data-toc-text="1.7.0">
 <a href="#amr-170" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.0</h1>
@@ -264,9 +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>
@@ -284,13 +309,13 @@
 </ul>
 </li>
 <li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><a href="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
-<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
+<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
 </li>
 </ul>
 </div>
-<div id="changed" class="section level3">
+<div id="changed-1" class="section level3">
 <h3 class="hasAnchor">
-<a href="#changed" class="anchor"></a>Changed</h3>
+<a href="#changed-1" class="anchor"></a>Changed</h3>
 <ul>
 <li>Custom MDRO guidelines (<code><a href="../reference/mdro.html">mdro()</a></code>, <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code>):
 <ul>
@@ -347,9 +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>
@@ -382,7 +407,7 @@
 <span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
 </li>
 <li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
-<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
+<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
 <li>
 <p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
@@ -423,9 +448,9 @@
 </li>
 </ul>
 </div>
-<div id="changed-1" class="section level3">
+<div id="changed-2" class="section level3">
 <h3 class="hasAnchor">
-<a href="#changed-1" class="anchor"></a>Changed</h3>
+<a href="#changed-2" class="anchor"></a>Changed</h3>
 <ul>
 <li>Updated the bacterial taxonomy to 3 March 2021 (using <a href="https://lpsn.dsmz.de">LPSN</a>)
 <ul>
@@ -439,7 +464,7 @@
 <li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
 <li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
 <li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
-<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
+<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
 </ul>
 </li>
 <li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
@@ -456,7 +481,7 @@
 <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
 <li>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> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li>
 <li>Argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</li>
-<li>Functions <code><a href="https://docs.ropensci.org/skimr/reference/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
+<li>Functions <code><a href="https://rdrr.io/r/base/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
 </li>
 <li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
 <li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>
@@ -484,9 +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>
@@ -502,9 +527,9 @@
 <li><p>Functions <code><a href="../reference/random.html">random_mic()</a></code>, <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_rsi()</a></code> for random value generation. The functions <code><a href="../reference/random.html">random_mic()</a></code> and <code><a href="../reference/random.html">random_disk()</a></code> take microorganism names and antibiotic names as input to make generation more realistic.</p></li>
 </ul>
 </div>
-<div id="changed-2" class="section level3">
+<div id="changed-3" class="section level3">
 <h3 class="hasAnchor">
-<a href="#changed-2" class="anchor"></a>Changed</h3>
+<a href="#changed-3" class="anchor"></a>Changed</h3>
 <ul>
 <li><p>New argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to correct for AmpC de-repressed cephalosporin-resistant mutants</p></li>
 <li>
@@ -597,9 +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>
@@ -619,9 +644,9 @@
 <li><p>Support for skimming classes <code>&lt;rsi&gt;</code>, <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code> and <code>&lt;mo&gt;</code> with the <code>skimr</code> package</p></li>
 </ul>
 </div>
-<div id="changed-3" class="section level3">
+<div id="changed-4" class="section level3">
 <h3 class="hasAnchor">
-<a href="#changed-3" class="anchor"></a>Changed</h3>
+<a href="#changed-4" class="anchor"></a>Changed</h3>
 <ul>
 <li><p>Although advertised that this package should work under R 3.0.0, we still had a dependency on R 3.6.0. This is fixed, meaning that our package should now work under R 3.0.0.</p></li>
 <li>
@@ -700,9 +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>
@@ -724,9 +749,9 @@
 <li><p>Added argument <code>conserve_capped_values</code> to <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpreting MIC values - it makes sure that values starting with “&lt;” (but not “&lt;=”) will always return “S” and values starting with “&gt;” (but not “&gt;=”) will always return “R”. The default behaviour of <code><a href="../reference/as.rsi.html">as.rsi()</a></code> has not changed, so you need to specifically do <code><a href="../reference/as.rsi.html">as.rsi(..., conserve_capped_values = TRUE)</a></code>.</p></li>
 </ul>
 </div>
-<div id="changed-4" class="section level3">
+<div id="changed-5" class="section level3">
 <h3 class="hasAnchor">
-<a href="#changed-4" class="anchor"></a>Changed</h3>
+<a href="#changed-5" class="anchor"></a>Changed</h3>
 <ul>
 <li>
 <p>Big speed improvement for using any function on microorganism codes from earlier package versions (prior to <code>AMR</code> v1.2.0), such as <code><a href="../reference/as.mo.html">as.mo()</a></code>, <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>, etc.</p>
@@ -791,7 +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><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>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><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>
@@ -799,9 +824,9 @@
 </li>
 </ul>
 </div>
-<div id="changed-5" class="section level3">
+<div id="changed-6" class="section level3">
 <h3 class="hasAnchor">
-<a href="#changed-5" class="anchor"></a>Changed</h3>
+<a href="#changed-6" class="anchor"></a>Changed</h3>
 <ul>
 <li>Taxonomy:
 <ul>
@@ -845,17 +870,17 @@ 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>
 </ul>
 </div>
-<div id="changed-6" class="section level3">
+<div id="changed-7" class="section level3">
 <h3 class="hasAnchor">
-<a href="#changed-6" class="anchor"></a>Changed</h3>
+<a href="#changed-7" class="anchor"></a>Changed</h3>
 <ul>
 <li>Improvements for the algorithm used by <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions, that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally):
 <ul>
@@ -886,9 +911,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     <div id="amr-101" class="section level1">
 <h1 class="page-header" data-toc-text="1.0.1">
 <a href="#amr-101" class="anchor"></a><small> 2020-02-23 </small><code>AMR</code> 1.0.1</h1>
-<div id="changed-7" class="section level3">
+<div id="changed-8" class="section level3">
 <h3 class="hasAnchor">
-<a href="#changed-7" class="anchor"></a>Changed</h3>
+<a href="#changed-8" class="anchor"></a>Changed</h3>
 <ul>
 <li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
 <li>
@@ -911,9 +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>
@@ -1008,9 +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>
@@ -1123,13 +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><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>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>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>
@@ -1194,9 +1219,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 </div>
-<div id="changed-8" class="section level3">
+<div id="changed-9" class="section level3">
 <h3 class="hasAnchor">
-<a href="#changed-8" class="anchor"></a>Changed</h3>
+<a href="#changed-9" class="anchor"></a>Changed</h3>
 <ul>
 <li>Many algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code> (of which some led to additions to the <code>microorganisms</code> data set). Many thanks to all contributors that helped improving the algorithms.
 <ul>
@@ -1260,9 +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>
@@ -1306,9 +1331,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
 </ul>
 </div>
-<div id="changed-9" class="section level4">
+<div id="changed-10" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed-9" class="anchor"></a>Changed</h4>
+<a href="#changed-10" class="anchor"></a>Changed</h4>
 <ul>
 <li>Column names of output <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> are now lowercase</li>
 <li>Fixed bug in translation of microorganism names</li>
@@ -1344,9 +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>
@@ -1354,9 +1379,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><a href="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <a href="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
 </ul>
 </div>
-<div id="changed-10" class="section level4">
+<div id="changed-11" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed-10" class="anchor"></a>Changed</h4>
+<a href="#changed-11" class="anchor"></a>Changed</h4>
 <ul>
 <li>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
 <li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
@@ -1390,7 +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><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
+<li>Frequency tables (<code>freq()</code>):
 <ul>
 <li><p>speed improvement for microbial IDs</p></li>
 <li><p>fixed factor level names for R Markdown</p></li>
@@ -1400,12 +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"><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">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/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"><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">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/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
 </li>
 </ul>
@@ -1415,7 +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><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
+<li>Fix for <code>freq()</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>
@@ -1440,9 +1465,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     <div id="amr-061" class="section level1">
 <h1 class="page-header" data-toc-text="0.6.1">
 <a href="#amr-061" class="anchor"></a><small> 2019-03-29 </small><code>AMR</code> 0.6.1</h1>
-<div id="changed-11" class="section level4">
+<div id="changed-12" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed-11" class="anchor"></a>Changed</h4>
+<a href="#changed-12" class="anchor"></a>Changed</h4>
 <ul>
 <li>Fixed a critical bug when using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> with <code>verbose = TRUE</code>
 </li>
@@ -1459,9 +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>
@@ -1559,9 +1584,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
 </ul>
 </div>
-<div id="changed-12" class="section level4">
+<div id="changed-13" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed-12" class="anchor"></a>Changed</h4>
+<a href="#changed-13" class="anchor"></a>Changed</h4>
 <ul>
 <li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
 <ul>
@@ -1654,7 +1679,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 </li>
-<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function):
+<li>Frequency tables (<code>freq()</code> function):
 <ul>
 <li>
 <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
@@ -1664,15 +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"><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="fu">freq</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"><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="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="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"><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>
+  <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>
 </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>
@@ -1704,9 +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>
@@ -1717,9 +1742,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Functions <code>mo_authors</code> and <code>mo_year</code> to get specific values about the scientific reference of a taxonomic entry</li>
 </ul>
 </div>
-<div id="changed-13" class="section level4">
+<div id="changed-14" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed-13" class="anchor"></a>Changed</h4>
+<a href="#changed-14" class="anchor"></a>Changed</h4>
 <ul>
 <li><p>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code></p></li>
 <li><p><code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</p></li>
@@ -1754,7 +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><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:</p>
+<p>Frequency tables - <code>freq()</code>:</p>
 <ul>
 <li>
 <p>Support for grouping variables, test with:</p>
@@ -1762,14 +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"><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>
+  <span class="fu">freq</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>
 <div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</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">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
+  <span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
 </li>
 <li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
@@ -1787,7 +1812,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
 <li><p>Fix for <code>mo_property</code> not working properly</p></li>
 <li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
-<li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
+<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
 <li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
 <li>
 <p>AI improvements for <code>as.mo</code>:</p>
@@ -1827,9 +1852,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     <div id="amr-040" class="section level1">
 <h1 class="page-header" data-toc-text="0.4.0">
 <a href="#amr-040" class="anchor"></a><small> 2018-10-01 </small><code>AMR</code> 0.4.0</h1>
-<div id="new-13" class="section level4">
+<div id="new-14" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-13" class="anchor"></a>New</h4>
+<a href="#new-14" class="anchor"></a>New</h4>
 <ul>
 <li><p>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <a href="https://itis.gov" class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</p></li>
 <li>
@@ -1907,9 +1932,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li>
 </ul>
 </div>
-<div id="changed-14" class="section level4">
+<div id="changed-15" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed-14" class="anchor"></a>Changed</h4>
+<a href="#changed-15" class="anchor"></a>Changed</h4>
 <ul>
 <li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
 <li>
@@ -1954,13 +1979,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span><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="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</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="va">my_matrix</span><span class="op">)</span></code></pre></div>
+<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
 <p>For lists, subsetting is possible:</p>
 <div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
-<span class="va">my_list</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="va">my_list</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">gender</span><span class="op">)</span></code></pre></div>
+<span class="va">my_list</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="va">my_list</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>
 </li>
 </ul>
 </div>
@@ -1975,9 +2000,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     <div id="amr-030" class="section level1">
 <h1 class="page-header" data-toc-text="0.3.0">
 <a href="#amr-030" class="anchor"></a><small> 2018-08-14 </small><code>AMR</code> 0.3.0</h1>
-<div id="new-14" class="section level4">
+<div id="new-15" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-14" class="anchor"></a>New</h4>
+<a href="#new-15" class="anchor"></a>New</h4>
 <ul>
 <li>
 <strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
@@ -2033,13 +2058,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <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/cleaner/man/freq.html">freq(table(x, y))</a></code>
+<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</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/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
+<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</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>
@@ -2048,9 +2073,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 </div>
-<div id="changed-15" class="section level4">
+<div id="changed-16" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed-15" class="anchor"></a>Changed</h4>
+<a href="#changed-16" class="anchor"></a>Changed</h4>
 <ul>
 <li>Improvements for forecasting with <code>resistance_predict</code> and added more examples</li>
 <li>More antibiotics added as arguments for EUCAST rules</li>
@@ -2111,9 +2136,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
     <div id="amr-020" class="section level1">
 <h1 class="page-header" data-toc-text="0.2.0">
 <a href="#amr-020" class="anchor"></a><small> 2018-05-03 </small><code>AMR</code> 0.2.0</h1>
-<div id="new-15" class="section level4">
+<div id="new-16" class="section level4">
 <h4 class="hasAnchor">
-<a href="#new-15" class="anchor"></a>New</h4>
+<a href="#new-16" class="anchor"></a>New</h4>
 <ul>
 <li>Full support for Windows, Linux and macOS</li>
 <li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
@@ -2133,9 +2158,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>
 </ul>
 </div>
-<div id="changed-16" class="section level4">
+<div id="changed-17" class="section level4">
 <h4 class="hasAnchor">
-<a href="#changed-16" class="anchor"></a>Changed</h4>
+<a href="#changed-17" class="anchor"></a>Changed</h4>
 <ul>
 <li>Fixed <code>rsi</code> class for vectors that contain only invalid antimicrobial interpretations</li>
 <li>Renamed dataset <code>ablist</code> to <code>antibiotics</code>

docs/pkgdown.yml

@@ -12,7 +12,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-05-26T12:00Z
+last_built: 2021-06-01T14:35Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

docs/reference/AMR-deprecated.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -431,7 +431,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

docs/reference/AMR.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -277,7 +277,7 @@
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="contact-us"><a class="anchor" href="#contact-us"></a>Contact Us</h2>
 
     
@@ -286,7 +286,7 @@
 <p>Matthijs S. Berends <br />
 m.s.berends [at] umcg [dot] nl <br />
 University of Groningen
-Department of Medical Microbiology
+Department of Medical Microbiology and Infection Prevention
 University Medical Center Groningen <br />
 Post Office Box 30001 <br />
 9700 RB Groningen <br />

docs/reference/WHOCC.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -257,7 +257,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'><a href='as.ab.html'>as.ab</a></span><span class='op'>(</span><span class='st'>"meropenem"</span><span class='op'>)</span>

docs/reference/WHONET.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -285,7 +285,7 @@
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

docs/reference/ab_from_text.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -317,7 +317,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># mind the bad spelling of amoxicillin in this line, </span>

docs/reference/ab_property.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -342,7 +342,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><a href='antibiotics.html'>antibiotics</a></p></div>

docs/reference/age.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -287,7 +287,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p>To split ages into groups, use the <code><a href='age_groups.html'>age_groups()</a></code> function.</p></div>

docs/reference/age_groups.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -288,7 +288,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p>To determine ages, based on one or more reference dates, use the <code><a href='age.html'>age()</a></code> function.</p></div>

docs/reference/antibiotic_class_selectors.html

@@ -83,7 +83,7 @@
       </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>
 
@@ -312,7 +312,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>

docs/reference/antibiotics.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -326,7 +326,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a>, <a href='intrinsic_resistant.html'>intrinsic_resistant</a></p></div>

docs/reference/as.ab.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -314,7 +314,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'>

docs/reference/as.disk.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -276,7 +276,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>

docs/reference/as.mic.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -307,7 +307,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>

docs/reference/as.mo.html

@@ -6,7 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>Transform Input to a Microorganism ID — as.mo • AMR (for R)</title>
+<title>Transform Input to a Microorganism Code — as.mo • AMR (for R)</title>
 
 <!-- favicons -->
 <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,8 +48,8 @@
   <link href="../extra.css" rel="stylesheet">
   <script src="../extra.js"></script>
 
-<meta property="og:title" content="Transform Input to a Microorganism ID — as.mo" />
-<meta property="og:description" content="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 &quot;Staphylococcus aureus&quot;), an abbreviated name (such as &quot;S. aureus&quot;), an abbreviation known in the field (such as &quot;MRSA&quot;), or just a genus. See Examples." />
+<meta property="og:title" content="Transform Input to a Microorganism Code — as.mo" />
+<meta property="og:description" content="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 &quot;Staphylococcus aureus&quot;), an abbreviated name (such as &quot;S. aureus&quot;), an abbreviation known in the field (such as &quot;MRSA&quot;), or just a genus. See Examples." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
 
 
@@ -82,7 +82,7 @@
       </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>
 
@@ -233,13 +233,13 @@
 <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>Transform Input to a Microorganism ID</h1>
+    <h1>Transform Input to a Microorganism Code</h1>
     <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo.R'><code>R/mo.R</code></a></small>
     <div class="hidden name"><code>as.mo.Rd</code></div>
     </div>
 
     <div class="ref-description">
-    <p>Use this function to determine a valid microorganism ID (<code>mo</code>). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see <em>Source</em>). The input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (such as <code>"S. aureus"</code>), an abbreviation known in the field (such as <code>"MRSA"</code>), or just a genus. See <em>Examples</em>.</p>
+    <p>Use this function to determine a valid microorganism code (<code>mo</code>). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see <em>Source</em>). The input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (such as <code>"S. aureus"</code>), an abbreviation known in the field (such as <code>"MRSA"</code>), or just a genus. See <em>Examples</em>.</p>
     </div>
 
     <pre class="usage"><span class='fu'>as.mo</span><span class='op'>(</span>
@@ -314,7 +314,7 @@
 <h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>General Info</h3>
 
 
-<p>A microorganism ID from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><pre>  Code               Full name
+<p>A microorganism (MO) code from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><pre>  Code               Full name
   ---------------    --------------------------------------
   B_KLBSL            Klebsiella
   B_KLBSL_PNMN       Klebsiella pneumoniae
@@ -422,7 +422,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a> for the <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> that is being used to determine ID's.</p>

docs/reference/as.rsi.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -363,8 +363,8 @@
 <h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Supported Guidelines</h3>
 
 
-<p>For interpreting MIC values as well as disk diffusion diameters, currently supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".</p>
-<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
+<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020).</p>
+<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2021"</code> or <code>"CLSI 2020"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
 
 <h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>After Interpretation</h3>
 
@@ -374,7 +374,7 @@
 <h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Machine-Readable Interpretation Guidelines</h3>
 
 
-<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 20,486 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
+<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 21,996 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
 
 <h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Other</h3>
 
@@ -395,7 +395,7 @@ A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>,
 A microorganism is categorised as <em>Susceptible, Increased exposure</em> 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.</p></li>
 </ul>
 
-<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility()</a></code> (equal to <code><a href='proportion.html'>proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible()</a></code> (equal to <code><a href='count.html'>count_SI()</a></code>) to count susceptible isolates.</p>
+<p>This AMR package honours this (new) insight. Use <code><a href='proportion.html'>susceptibility()</a></code> (equal to <code><a href='proportion.html'>proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible()</a></code> (equal to <code><a href='count.html'>count_SI()</a></code>) to count susceptible isolates.</p>
     <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
 
     
@@ -412,7 +412,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code>, <code><a href='as.disk.html'>as.disk()</a></code>, <code><a href='as.mo.html'>as.mo()</a></code></p></div>

docs/reference/atc_online.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -324,7 +324,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># \donttest{</span>

docs/reference/availability.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -274,7 +274,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'>availability</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>

docs/reference/bug_drug_combinations.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -272,7 +272,7 @@
     </tr>
     <tr>
       <th>FUN</th>
-      <td><p>the function to call on the <code>mo</code> column to transform the microorganism IDs, defaults to <code><a href='mo_property.html'>mo_shortname()</a></code></p></td>
+      <td><p>the function to call on the <code>mo</code> column to transform the microorganism codes, defaults to <code><a href='mo_property.html'>mo_shortname()</a></code></p></td>
     </tr>
     <tr>
       <th>...</th>
@@ -339,7 +339,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># \donttest{</span>

docs/reference/catalogue_of_life.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -270,7 +270,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p>Data set <a href='microorganisms.html'>microorganisms</a> for the actual data. <br />

docs/reference/catalogue_of_life_version.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -262,7 +262,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>

docs/reference/count.html

@@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
       </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>
 
@@ -332,7 +332,7 @@ A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>,
 A microorganism is categorised as <em>Susceptible, Increased exposure</em> 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.</p></li>
 </ul>
 
-<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility()</a></code> (equal to <code><a href='proportion.html'>proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code>count_susceptible()</code> (equal to <code>count_SI()</code>) to count susceptible isolates.</p>
+<p>This AMR package honours this (new) insight. Use <code><a href='proportion.html'>susceptibility()</a></code> (equal to <code><a href='proportion.html'>proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code>count_susceptible()</code> (equal to <code>count_SI()</code>) to count susceptible isolates.</p>
     <h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination Therapy</h2>
 
     
@@ -368,7 +368,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='proportion.html'>proportion_*</a></code> to calculate microbial resistance and susceptibility.</p></div>

docs/reference/custom_eucast_rules.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -348,7 +348,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,

docs/reference/dosage.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -271,7 +271,7 @@
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

docs/reference/eucast_rules.html

@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
       </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>
 
@@ -381,7 +381,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># \donttest{</span>

docs/reference/example_isolates.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -269,7 +269,7 @@
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

docs/reference/example_isolates_unclean.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -264,7 +264,7 @@
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

docs/reference/first_isolate.html

@@ -83,7 +83,7 @@
       </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>
 
@@ -448,7 +448,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code></p></div>

docs/reference/g.test.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -342,7 +342,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
 
     

docs/reference/get_episode.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -287,7 +287,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='first_isolate.html'>first_isolate()</a></code></p></div>

docs/reference/ggplot_pca.html

@@ -82,7 +82,7 @@
       </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">1.7.0.9000</span>
       </span>
     </div>
 

docs/reference/ggplot_rsi.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -426,7 +426,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># \donttest{</span>

docs/reference/guess_ab_col.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -287,7 +287,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>amox <span class='op'>=</span> <span class='st'>"S"</span>,

docs/reference/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</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</span>
       </span>
     </div>
 
@@ -363,7 +363,7 @@
         <td>
           <p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p>
         </td>
-        <td><p>Transform Input to a Microorganism ID</p></td>
+        <td><p>Transform Input to a Microorganism Code</p></td>
       </tr><tr>
         
         <td>

docs/reference/intrinsic_resistant.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -265,7 +265,7 @@
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># \donttest{</span>

docs/reference/italicise_taxonomy.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -274,7 +274,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of Staphylococcus aureus isolates"</span><span class='op'>)</span>

docs/reference/join.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -293,7 +293,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"K. pneumoniae"</span><span class='op'>)</span><span class='op'>)</span>

docs/reference/key_antimicrobials.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -373,7 +373,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='first_isolate.html'>first_isolate()</a></code></p></div>

docs/reference/kurtosis.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -281,7 +281,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='skewness.html'>skewness()</a></code></p></div>

docs/reference/like.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -296,7 +296,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='https://rdrr.io/r/base/grep.html'>grepl()</a></code></p></div>

docs/reference/mdro.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -417,12 +417,12 @@ A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>,
 A microorganism is categorised as <em>Susceptible, Increased exposure</em> 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.</p></li>
 </ul>
 
-<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility()</a></code> (equal to <code><a href='proportion.html'>proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible()</a></code> (equal to <code><a href='count.html'>count_SI()</a></code>) to count susceptible isolates.</p>
+<p>This AMR package honours this (new) insight. Use <code><a href='proportion.html'>susceptibility()</a></code> (equal to <code><a href='proportion.html'>proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible()</a></code> (equal to <code><a href='count.html'>count_SI()</a></code>) to count susceptible isolates.</p>
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>, guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>

docs/reference/microorganisms.codes.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -268,7 +268,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code> <a href='microorganisms.html'>microorganisms</a></p></div>

docs/reference/microorganisms.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -329,7 +329,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code>, <code><a href='mo_property.html'>mo_property()</a></code>, <a href='microorganisms.codes.html'>microorganisms.codes</a>, <a href='intrinsic_resistant.html'>intrinsic_resistant</a></p></div>

docs/reference/microorganisms.old.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -274,7 +274,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code> <code><a href='mo_property.html'>mo_property()</a></code> <a href='microorganisms.html'>microorganisms</a></p></div>

docs/reference/mo_matching_score.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -290,7 +290,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
 
     <p>Matthijs S. Berends</p>

docs/reference/mo_property.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -408,7 +408,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>

docs/reference/mo_source.html

@@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
       </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>
 
@@ -342,7 +342,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

docs/reference/pca.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -322,7 +322,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>

docs/reference/plot.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -380,7 +380,7 @@
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p>The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.</p>
-<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".</p>
+<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".</p>
 <p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p>
     <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
 
@@ -393,7 +393,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='va'>some_mic_values</span> <span class='op'>&lt;-</span> <span class='fu'><a href='random.html'>random_mic</a></span><span class='op'>(</span>size <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>

docs/reference/proportion.html

@@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
       </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>
 
@@ -382,12 +382,12 @@ A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>,
 A microorganism is categorised as <em>Susceptible, Increased exposure</em> 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.</p></li>
 </ul>
 
-<p>This AMR package honours this new insight. Use <code>susceptibility()</code> (equal to <code>proportion_SI()</code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible()</a></code> (equal to <code><a href='count.html'>count_SI()</a></code>) to count susceptible isolates.</p>
+<p>This AMR package honours this (new) insight. Use <code>susceptibility()</code> (equal to <code>proportion_SI()</code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible()</a></code> (equal to <code><a href='count.html'>count_SI()</a></code>) to count susceptible isolates.</p>
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='count.html'>count()</a></code> to count resistant and susceptible isolates.</p></div>

docs/reference/random.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -291,7 +291,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'>random_mic</span><span class='op'>(</span><span class='fl'>100</span><span class='op'>)</span>

docs/reference/resistance_predict.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -387,12 +387,12 @@ A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>,
 A microorganism is categorised as <em>Susceptible, Increased exposure</em> 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.</p></li>
 </ul>
 
-<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility()</a></code> (equal to <code><a href='proportion.html'>proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible()</a></code> (equal to <code><a href='count.html'>count_SI()</a></code>) to count susceptible isolates.</p>
+<p>This AMR package honours this (new) insight. Use <code><a href='proportion.html'>susceptibility()</a></code> (equal to <code><a href='proportion.html'>proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible()</a></code> (equal to <code><a href='count.html'>count_SI()</a></code>) to count susceptible isolates.</p>
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p>The <code><a href='proportion.html'>proportion()</a></code> functions to calculate resistance</p>

docs/reference/rsi_translation.html

@@ -49,7 +49,7 @@
   <script src="../extra.js"></script>
 
 <meta property="og:title" content="Data Set for R/SI Interpretation — rsi_translation" />
-<meta property="og:description" content="Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2021). Use as.rsi() to transform MICs or disks measurements to R/SI values." />
+<meta property="og:description" content="Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020). Use as.rsi() to transform MICs or disks measurements to R/SI values." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
 
 
@@ -82,7 +82,7 @@
       </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>
 
@@ -239,7 +239,7 @@
     </div>
 
     <div class="ref-description">
-    <p>Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2021). Use <code><a href='as.rsi.html'>as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
+    <p>Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020). Use <code><a href='as.rsi.html'>as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
     </div>
 
     <pre class="usage"><span class='va'>rsi_translation</span></pre>
@@ -247,7 +247,7 @@
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 20,486 observations and 10 variables:</p><ul>
+    <p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 21,996 observations and 10 variables:</p><ul>
 <li><p><code>guideline</code><br /> Name of the guideline</p></li>
 <li><p><code>method</code><br /> Either "DISK" or "MIC"</p></li>
 <li><p><code>site</code><br /> Body site, e.g. "Oral" or "Respiratory"</p></li>
@@ -272,7 +272,7 @@
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><a href='intrinsic_resistant.html'>intrinsic_resistant</a></p></div>

docs/reference/skewness.html

@@ -83,7 +83,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
       </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>
 
@@ -279,7 +279,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='kurtosis.html'>kurtosis()</a></code></p></div>

docs/reference/translate.html

@@ -82,7 +82,7 @@
       </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>
 
@@ -270,7 +270,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
     
 
-<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># The 'language' argument of below functions</span>

docs/survey.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</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</span>
       </span>
     </div>
 

index.md

@@ -98,15 +98,22 @@ This package can be used for:
 
 #### Latest released version
 
-This package is [available here](https://msberends.r-universe.dev) on the [rOpenSci R-universe platform](https://ropensci.org/r-universe/), as CRAN does not allow frequent updates of large packages (though the `AMR` 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.
+This package is [available here](https://msberends.r-universe.dev) on the [rOpenSci R-universe platform](https://ropensci.org/r-universe/), as CRAN does not allow frequent updates of large packages (though the `AMR` 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 `AMR` package that only contains all functions.
 
-Install this package in R by using the command:
+In the meanwhile, you have to add [our R-universe address](https://msberends.r-universe.dev) to your list of repositories ('repos'), by running:
 
 ```r
-install.packages("AMR", repos = "https://msberends.r-universe.dev")
+options(repos = c(getOption("repos"),
+                  msberends = "https://msberends.r-universe.dev"))
 ```
 
-It will be downloaded and installed automatically.
+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>.
 
 **Note:** 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.
 

inst/tinytest/test-data.R

@@ -34,8 +34,6 @@ expect_identical(class(antibiotics$ab), c("ab", "character"))
 # check cross table reference
 expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))
 expect_true(all(example_isolates$mo %in% microorganisms$mo))
-expect_true(all(AMR:::microorganisms.translation$mo_new %in% microorganisms$mo))
-expect_false(any(AMR:::microorganisms.translation$mo_old %in% microorganisms$mo))
 expect_true(all(rsi_translation$mo %in% microorganisms$mo))
 expect_true(all(rsi_translation$ab %in% antibiotics$ab))
 expect_true(all(intrinsic_resistant$microorganism %in% microorganisms$fullname)) # also important for mo_is_intrinsic_resistant()

inst/tinytest/test-mo.R

@@ -48,7 +48,6 @@ expect_equal(as.character(as.mo("Strepto")), "B_STRPT")
 expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
 expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
 expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
-expect_equal(as.character(suppressWarnings(as.mo("B_STRPT_PNE"))), "B_STRPT_PNMN") # old MO code (<=v0.8.0)
 expect_equal(as.character(as.mo(c("mycobacterie", "mycobakterium"))), c("B_MYCBC", "B_MYCBC"))
 
 expect_equal(as.character(as.mo(c("GAS", "GBS", "a MGS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_MILL", "B_STRPT_HAEM"))