(v1.5.0.9009) unit test fixes

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.5.0.9007
-Date: 2021-01-18
+Version: 1.5.0.9009
+Date: 2021-01-22
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NAMESPACE

@@ -22,6 +22,7 @@ S3method("[[<-",isolate_identifier)
 S3method("[[<-",mic)
 S3method("[[<-",mo)
 S3method("[[<-",rsi)
+S3method(all.equal,isolate_identifier)
 S3method(as.data.frame,ab)
 S3method(as.data.frame,mo)
 S3method(as.double,mic)

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.5.0.9007
-## <small>Last updated: 18 January 2021</small>
+# AMR 1.5.0.9009
+## <small>Last updated: 22 January 2021</small>
 
 ### New
 * Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
@@ -32,10 +32,12 @@
 * Updated the data set `microorganisms.codes` (which contains popular LIS and WHONET codes for microorganisms) for some species of *Mycobacterium* that previously incorrectly returned *M. africanum*
 * Added Pretomanid (PMD, J04AK08) to the `antibiotics` data set
 * WHONET code `"PNV"` will now correctly be interpreted as `PHN`, the antibiotic code for phenoxymethylpenicillin ('peni V')
-* Fix for verbose output of `mdro(..., verbose = TRUE)` for German guideline (3MGRN and 4MGRN) and *P. aeruginosa* in Dutch guideline (BRMO)
+* Fix for verbose output of `mdro(..., verbose = TRUE)` for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only *P. aeruginosa*)
+* `is.rsi.eligible()` now returns `FALSE` immediately if the input does not contain 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.
 
 ### Other
 * Big documentation updates
+* Loading the package (i.e., `library(AMR)`) now is ~50 times faster than before
 
 
 # AMR 1.5.0

R/aa_helper_functions.R

@@ -479,10 +479,13 @@ format_class <- function(class, plural) {
   if ("matrix" %in% class) {
     class <- "a matrix"
   }
-  if (any(c("mo", "ab", "rsi", "disk", "mic") %in% class)) {
-    class <- paste0("a class <", class[1L], ">")
+  if ("isolate_identifier" %in% class) {
+    class <- "created with isolate_identifier()"
   }
-  class[class == class.bak] <- paste0("a class <", class[class == class.bak], ">")
+  if (any(c("mo", "ab", "rsi", "disk", "mic") %in% class)) {
+    class <- paste0("of class <", class[1L], ">")
+  }
+  class[class == class.bak] <- paste0("of class <", class[class == class.bak], ">")
   # output
   vector_or(class, quotes = FALSE)
 }
@@ -514,7 +517,7 @@ meet_criteria <- function(object,
   if (!is.null(allow_class)) {
     stop_ifnot(inherits(object, allow_class), "argument `", obj_name,
                "` must be ", format_class(allow_class, plural = isTRUE(has_length > 1)),
-               ", not ", format_class(class(object), plural = isTRUE(has_length > 1)),
+               ", i.e. not be ", format_class(class(object), plural = isTRUE(has_length > 1)),
                call = call_depth)
     # check data.frames for data
     if (inherits(object, "data.frame")) {
@@ -615,6 +618,7 @@ get_current_data <- function(arg_name, call) {
       NULL
     }
   })
+  
   vars_df <- tryCatch(frms[[which(!vapply(FUN.VALUE = logical(1), frms, is.null))]], error = function(e) NULL)
   if (is.data.frame(vars_df)) {
     return(vars_df)

R/ab_class_selectors.R

@@ -173,7 +173,15 @@ ab_selector <- function(ab_class, function_name) {
   }
   
   vars_df <- get_current_data(arg_name = NA, call = -3)
+  
+  # improve speed here so it will only run once when e.g. in one select call
+  if (!identical(pkg_env$ab_selector, unique_call_id())) {
     ab_in_data <- get_column_abx(vars_df, info = FALSE)
+    pkg_env$ab_selector <- unique_call_id()
+    pkg_env$ab_selector_cols <- ab_in_data
+  } else {
+    ab_in_data <- pkg_env$ab_selector_cols
+  }
   
   if (length(ab_in_data) == 0) {
     message_("No antimicrobial agents found.")
@@ -199,8 +207,9 @@ ab_selector <- function(ab_class, function_name) {
     } else {
       agents_formatted <- paste0("column '", font_bold(agents, collapse = NULL), "'")
       agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
-      agents_formatted[agents != agents_names] <- paste0(agents_formatted[agents != agents_names],
-                                                         " (", agents_names[agents != agents_names], ")")
+      need_name <- tolower(agents) != tolower(agents_names)
+      agents_formatted[need_name] <- paste0(agents_formatted[need_name],
+                                            " (", agents_names[need_name], ")")
       message_("Selecting ", ab_group, ": ", paste(agents_formatted, collapse = ", "),
                as_note = FALSE,
                extra_indent = nchar(paste0("Selecting ", ab_group, ": ")))

R/eucast_rules.R

@@ -1049,6 +1049,7 @@ eucast_rules <- function(x,
     warn_lacking_rsi_class <- unique(warn_lacking_rsi_class)
     warning_("Not all columns with antimicrobial results are of class <rsi>. Transform them on beforehand, with e.g.:\n",
              "  ", x_deparsed, " %>% mutate_if(is.rsi.eligible, as.rsi)\n",
+             "  ", x_deparsed, " %>% mutate(across((is.rsi.eligible), as.rsi))\n",
              "  ", x_deparsed, " %>% as.rsi(", ifelse(length(warn_lacking_rsi_class) == 1, 
                                                       warn_lacking_rsi_class,
                                                       paste0(warn_lacking_rsi_class[1], ":", warn_lacking_rsi_class[length(warn_lacking_rsi_class)])), 

R/guess_ab_col.R

@@ -137,25 +137,25 @@ get_column_abx <- function(x,
   } else if (info == TRUE) {
     message_("...", appendLF = FALSE, as_note = FALSE)
   }
-  x_bak <- x
+
   # only check columns that are a valid AB code, ATC code, name, abbreviation or synonym,
   # or already have the <rsi> class (as.rsi) 
   # and that they have no more than 50% invalid values
   vectr_antibiotics <- unique(toupper(unlist(antibiotics[, c("ab", "atc", "name", "abbreviations", "synonyms")])))
   vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
-  x_columns <- vapply(FUN.VALUE = character(1), colnames(x), function(col, df = x_bak) {
+  x_columns <- vapply(FUN.VALUE = character(1), colnames(x), function(col, df = x) {
     if (toupper(col) %in% vectr_antibiotics || 
-        is.rsi(as.data.frame(df, stringsAsFactors = FALSE)[, col, drop = TRUE]) ||
-        is.rsi.eligible(as.data.frame(df, stringsAsFactors = FALSE)[, col, drop = TRUE],
-                        threshold = 0.5)) {
+        is.rsi(x[, col, drop = TRUE]) ||
+        is.rsi.eligible(x[, col, drop = TRUE], threshold = 0.5)
+        ) {
       return(col)
     } else {
       return(NA_character_)
     }
   })
+  
   x_columns <- x_columns[!is.na(x_columns)]
   x <- x[, x_columns, drop = FALSE] # without drop = TRUE, x will become a vector when x_columns is length 1
-  
   df_trans <- data.frame(colnames = colnames(x),
                          abcode = suppressWarnings(as.ab(colnames(x), info = FALSE)),
                          stringsAsFactors = FALSE)
@@ -217,7 +217,6 @@ get_column_abx <- function(x,
     }
   }
   
-  
   if (!is.null(hard_dependencies)) {
     hard_dependencies <- unique(hard_dependencies)
     if (!all(hard_dependencies %in% names(x))) {

R/isolate_identifier.R

@@ -26,9 +26,10 @@
 #' Create Identifier of an Isolate
 #' 
 #' This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.
-#' @inheritSection lifecycle Maturing Lifecycle
+#' @inheritSection lifecycle Experimental Lifecycle
 #' @inheritParams eucast_rules
 #' @param cols_ab a character vector of column names of `x`, or (a combination with) an [antibiotic selector function]([ab_class()]), such as [carbapenems()] and [aminoglycosides()]
+#' @rdname isolate_identifier
 #' @export
 #' @inheritSection AMR Read more on Our Website!
 #' @examples 
@@ -43,7 +44,12 @@
 isolate_identifier <- function(x, col_mo = NULL, cols_ab = NULL) {
   if (is.null(col_mo)) {
     col_mo <- search_type_in_df(x, "mo")
+    if (is.null(col_mo)) {
+      # no column found, then ignore the argument
+      col_mo <- FALSE
     }
+  }
+  
   if (isFALSE(col_mo)) {
     # is FALSE then ignore mo column
     x$col_mo <- ""
@@ -60,14 +66,83 @@ isolate_identifier <- function(x, col_mo = NULL, cols_ab = NULL) {
                         # tryCatch adds 4 calls, so total is -5
                         error = function(e) stop_(e$message, call = -5))
   }
-  if (length(cols_ab) == 0) {
-    warning_("no columns with antimicrobial agents found", call = TRUE)
+  
+  # cope with empty values
+  if (length(cols_ab) == 0 && all(x[, col_mo, drop = TRUE] == "", na.rm = TRUE)) {
+    warning_("in isolate_identifier(): no column with microorganisms and no columns with antimicrobial agents found", call = FALSE)
+  } else if (length(cols_ab) == 0) {
+    warning_("in isolate_identifier(): no columns with antimicrobial agents found", call = FALSE)
   }
   
   out <- x[, c(col_mo, cols_ab), drop = FALSE]
   out <- do.call(paste, c(out, sep = ""))
   out <- gsub("NA", ".", out, fixed = TRUE)
-  set_clean_class(out, new_class = c("isolate_identifier", "character"))
+  out <- set_clean_class(out, new_class = c("isolate_identifier", "character"))
+  attr(out, "ab") <- cols_ab
+  out
+}
+
+#' @method all.equal isolate_identifier
+#' @inheritParams base::all.equal
+#' @param ignore_empty_results a logical to indicate whether empty results must be ignored, so that only values R, S and I will be compared
+#' @rdname isolate_identifier
+#' @export
+all.equal.isolate_identifier <- function(target, current, ignore_empty_results = TRUE, ...) {
+  meet_criteria(target, allow_class = "isolate_identifier")
+  meet_criteria(current, allow_class = "isolate_identifier")
+  meet_criteria(ignore_empty_results, allow_class = "logical", has_length = 1)
+  
+  if (isTRUE(all.equal.character(target, current))) {
+    return(TRUE)
+  }
+  # vectorise over both target and current
+  if (length(target) > 1 && length(current) == 1) {
+    current <- rep(current, length(target))
+  } else if (length(current) > 1 && length(target) == 1) {
+    target <- rep(target, length(current))
+  }
+  stop_if(length(target) != length(current),
+          "length of `target` and `current` must be the same, or one must be 1")
+  
+  get_vector <- function(x) {
+    if (grepl("|", x, fixed = TRUE)) {
+      mo <- gsub("(.*)\\|.*", "\\1", x)
+    } else {
+      mo <- NULL
+    }
+    if (grepl("|", x, fixed = TRUE)) {
+      ab <- gsub(".*\\|(.*)", "\\1", x)
+    } else {
+      ab <- x
+    }
+    ab <- strsplit(ab, "")[[1L]]
+    if (is.null(mo)) {
+      out <- as.character(ab)
+      names(out) <- attributes(x)$ab
+    } else {
+      out <- as.character(c(mo, ab))
+      names(out) <- c("mo", attributes(x)$ab)
+    }
+    out
+  }
+  
+  # run it
+  for (i in seq_len(length(target))) {
+    if (i == 1) {
+      df <- data.frame(object = paste0(c("target[", "current["), i, "]"))
+    }
+    trgt <- get_vector(target[i])
+    crnt <- get_vector(current[i])
+    if (ignore_empty_results == TRUE) {
+      diff <- names(trgt[trgt != crnt & trgt != "." & crnt != "."])  
+    } else {
+      diff <- names(trgt[trgt != crnt])
+    }
+    
+  }
+  
+  stop("THIS FUNCTION IS WORK IN PROGRESS AND NOT AVAILABLE IN THIS BETA VERSION")
+  
 }
 
 #' @method print isolate_identifier

R/rsi.R

@@ -50,7 +50,7 @@
 #'    * Using `dplyr`, R/SI interpretation can be done very easily with either: 
 #'      ```
 #'      your_data %>% mutate_if(is.mic, as.rsi)         # until dplyr 1.0.0
-#'      your_data %>% mutate(across(where(is.mic), as.rsi)) # since dplyr 1.0.0
+#'      your_data %>% mutate(across((is.mic), as.rsi))  # since dplyr 1.0.0
 #'      ```
 #'    * Operators like "<=" will be stripped before interpretation. When using `conserve_capped_values = TRUE`, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (`conserve_capped_values = FALSE`) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
 #'      
@@ -58,7 +58,7 @@
 #'    * Using `dplyr`, R/SI interpretation can be done very easily with either: 
 #'      ```
 #'      your_data %>% mutate_if(is.disk, as.rsi)         # until dplyr 1.0.0
-#'      your_data %>% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
+#'      your_data %>% mutate(across((is.disk), as.rsi))  # since dplyr 1.0.0
 #'      ```
 #' 
 #' 4. For **interpreting a complete data set**, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running `as.rsi(data)`.
@@ -133,7 +133,7 @@
 #' if (require("dplyr")) {
 #'   df %>% mutate_if(is.mic, as.rsi)
 #'   df %>% mutate_if(function(x) is.mic(x) | is.disk(x), as.rsi)
-#'   df %>% mutate(across(where(is.mic), as.rsi))
+#'   df %>% mutate(across((is.mic), as.rsi))
 #'   df %>% mutate_at(vars(AMP:TOB), as.rsi)
 #'   df %>% mutate(across(AMP:TOB, as.rsi))
 #'  
@@ -179,7 +179,7 @@
 #'     
 #'   # note: from dplyr 1.0.0 on, this will be: 
 #'   # example_isolates %>%
-#'   #   mutate(across(where(is.rsi.eligible), as.rsi))
+#'   #   mutate(across((is.rsi.eligible), as.rsi))
 #' }
 #' }
 as.rsi <- function(x, ...) {
@@ -202,14 +202,19 @@ is.rsi.eligible <- function(x, threshold = 0.05) {
             "numeric",
             "integer",
             "mo",
+            "ab",
             "Date",
-            "POSIXct",
+            "POSIXt",
             "rsi",
             "raw",
-            "hms")
+            "hms",
+            "mic",
+            "disk")
           %in% class(x))) {
     # no transformation needed
-    FALSE
+    return(FALSE)
+  } else if (!any(c("R", "S", "I") %in% x, na.rm = TRUE)) {
+    return(FALSE)
   } else {
     x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
     if (length(x) == 0) {

R/rsi_calc.R

@@ -148,7 +148,9 @@ rsi_calc <- function(...,
   
   if (print_warning == TRUE) {
     if (message_not_thrown_before("rsi_calc")) {
-      warning_("Increase speed by transforming to class <rsi> on beforehand: your_data %>% mutate_if(is.rsi.eligible, as.rsi)",
+      warning_("Increase speed by transforming to class <rsi> on beforehand:\n",
+               "  your_data %>% mutate_if(is.rsi.eligible, as.rsi)\n",
+               "  your_data %>% mutate(across((is.rsi.eligible), as.rsi))",
                call = FALSE)
       remember_thrown_message("rsi_calc")
     }

R/zzz.R

@@ -28,35 +28,6 @@ pkg_env <- new.env(hash = FALSE)
 pkg_env$mo_failed <- character(0)
 
 .onLoad <- function(libname, pkgname) {
-  
-  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"))
-  
-  assign(x = "INTRINSIC_R",
-         value = create_intr_resistance(),
-         envir = asNamespace("AMR"))
-  
-  assign(x = "LANGUAGES_SUPPORTED",
-         value = sort(c("en", unique(translations_file$lang))),
-         envir = asNamespace("AMR"))
-  
-  assign(x = "MO_CONS",
-         value = create_species_cons_cops("CoNS"),
-         envir = asNamespace("AMR"))
-  
-  assign(x = "MO_COPS",
-         value = create_species_cons_cops("CoPS"),
-         envir = asNamespace("AMR"))
-
   # Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
   # without the need to depend on other packages. This was suggested by the 
   # developers of the vctrs package: 
@@ -102,89 +73,5 @@ pkg_env$mo_failed <- character(0)
                                   font_bold("options(AMR_silentstart = TRUE)"), "]"))
 }
 
-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])
-}
 
-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", "caeli", "capitis", "caprae", 
-                                           "carnosus", "chromogenes", "cohnii", "condimenti",
-                                           "debuckii", "devriesei", "edaphicus", "epidermidis",
-                                           "equorum", "felis", "fleurettii", "gallinarum",
-                                           "haemolyticus", "hominis", "jettensis", "kloosii",
-                                           "lentus", "lugdunensis", "massiliensis", "microti",
-                                           "muscae", "nepalensis", "pasteuri", "petrasii",
-                                           "pettenkoferi", "piscifermentans", "pseudoxylosus",
-                                           "rostri", "saccharolyticus", "saprophyticus",
-                                           "sciuri", "simulans", "stepanovicii", "succinus",
-                                           "vitulinus", "warneri", "xylosus")
-                   | (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
-             "mo", drop = TRUE]
-  } else if (type == "CoPS") {
-    MO_staph[which(MO_staph$species %in% c("coagulase-positive",
-                                           "simiae", "agnetis",
-                                           "delphini", "lutrae",
-                                           "hyicus", "intermedius",
-                                           "pseudintermedius", "pseudointermedius",
-                                           "schweitzeri", "argenteus")
-                   | (MO_staph$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
-}
-
-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), ]
-}

cran-comments.md

@@ -1 +1 @@
-* Since version 0.3.0 (2018-08-14), CHECK returns a NOTE for having a data directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package.
+* Ever since one of the first CRAN releases, CHECK returns a NOTE for having a data and R directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package.

data-raw/internals.R

@@ -23,12 +23,108 @@
 # how to conduct AMR analysis: https://msberends.github.io/AMR/        #
 # ==================================================================== #
 
-# Run this file to update the package using: -------------------------------
+# Run this file to update the package using:
 # source("data-raw/internals.R")
-# --------------------------------------------------------------------------
+
+library(dplyr, warn.conflicts = FALSE)
+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", "caeli", "capitis", "caprae", 
+                                           "carnosus", "chromogenes", "cohnii", "condimenti",
+                                           "debuckii", "devriesei", "edaphicus", "epidermidis",
+                                           "equorum", "felis", "fleurettii", "gallinarum",
+                                           "haemolyticus", "hominis", "jettensis", "kloosii",
+                                           "lentus", "lugdunensis", "massiliensis", "microti",
+                                           "muscae", "nepalensis", "pasteuri", "petrasii",
+                                           "pettenkoferi", "piscifermentans", "pseudoxylosus",
+                                           "rostri", "saccharolyticus", "saprophyticus",
+                                           "sciuri", "simulans", "stepanovicii", "succinus",
+                                           "vitulinus", "warneri", "xylosus")
+                   | (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
+             "mo", drop = TRUE]
+  } else if (type == "CoPS") {
+    MO_staph[which(MO_staph$species %in% c("coagulase-positive",
+                                           "simiae", "agnetis",
+                                           "delphini", "lutrae",
+                                           "hyicus", "intermedius",
+                                           "pseudintermedius", "pseudointermedius",
+                                           "schweitzeri", "argenteus")
+                   | (MO_staph$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$loinc, generalise_antibiotic_name)
+  AB_lookup
+}
+
+create_MO_lookup <- function() {
+  MO_lookup <- AMR::microorganisms
+  
+  MO_lookup$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 sets to R/sysdata.rda --------------------------------
 
 # See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
-library(dplyr, warn.conflicts = FALSE)
 eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
                                        skip = 10,
                                        sep = "\t",
@@ -48,7 +144,7 @@ eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
   mutate(reference.rule_group = as.character(reference.rule_group)) %>% 
   select(-sorting_rule)
 
-# Translations ----
+# Translations
 translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
                                        sep = "\t",
                                        stringsAsFactors = FALSE,
@@ -62,23 +158,42 @@ translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
                                        allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
                                        quote = "")
 
-# Old microorganism codes -------------------------------------------------
-
+# 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", unique(translations_file$lang)))
+
+# vectors of CoNS and CoPS, improves speed in as.mo()
+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()
+
 # Export to package as internal data ----
-usethis::use_data(eucast_rules_file, translations_file, microorganisms.translation,
+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,
                   internal = TRUE,
                   overwrite = TRUE,
                   version = 2,
                   compress = "xz")
 
-# Remove from global environment ----
-rm(eucast_rules_file)
-rm(translations_file)
-rm(microorganisms.translation)
+# Export data sets to the repository in different formats -----------------
 
-# Save to raw data to repository ----
 write_md5 <- function(object) {
   conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
   writeLines(digest::digest(object, "md5"), conn)
@@ -93,7 +208,7 @@ changed_md5 <- function(object) {
   }, error = function(e) TRUE)
 }
 usethis::ui_done(paste0("Saving raw data to {usethis::ui_value('/data-raw/')}"))
-devtools::load_all(quiet = TRUE)
+
 # give official names to ABs and MOs
 rsi <- dplyr::mutate(rsi_translation, ab = ab_name(ab), mo = mo_name(mo))
 if (changed_md5(rsi)) {
@@ -169,5 +284,7 @@ if (changed_md5(dosage)) {
   try(openxlsx::write.xlsx(dosage, "data-raw/dosage.xlsx"), silent = TRUE)
 }
 
-rm(write_md5)
-rm(changed_md5)
+# remove leftovers from global env
+current_globalenv <- ls(envir = globalenv())
+rm(list = current_globalenv[!current_globalenv %in% old_globalenv])
+rm(current_globalenv)

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">1.5.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9009</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">1.5.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9009</span>
       </span>
     </div>
 

docs/articles/SPSS.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">1.5.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9009</span>
       </span>
     </div>
 
@@ -193,7 +193,7 @@
       <h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">29 December 2020</h4>
+            <h4 class="date">22 January 2021</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
       <div class="hidden name"><code>SPSS.Rmd</code></div>
@@ -228,7 +228,7 @@
 </li>
 <li>
 <p><strong>R has a huge community.</strong></p>
-<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, more than <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">360,000 R-related questions</a> have already been asked on this platform (which covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
+<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">383,346 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
 </li>
 <li>
 <p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
@@ -243,7 +243,7 @@
 <li>
 <p><strong>R is (nowadays) the preferred analysis software in academic papers.</strong></p>
 <p>At present, R is among the world most powerful statistical languages, and it is generally very popular in science (Bollmann <em>et al.</em>, 2017). For all the above reasons, the number of references to R as an analysis method in academic papers <a href="https://r4stats.com/2014/08/20/r-passes-spss-in-scholarly-use-stata-growing-rapidly/">is rising continuously</a> and has even surpassed SPSS for academic use (Muenchen, 2014).</p>
-<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2020, I don’t see any reason why SPSS would be of any better use than R.</p>
+<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2021, I don’t see any reason why SPSS would be of any better use than R.</p>
 </li>
 </ul>
 <p>To demonstrate the first point:</p>

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9009</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">1.5.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9009</span>
       </span>
     </div>
 

docs/extra.css

@@ -24,14 +24,6 @@
 # how to conduct AMR analysis: https://msberends.github.io/AMR/        #
 # ==================================================================== #
 */
-@media (prefers-color-scheme: dark) {
-  .navbar-default {
-    background-color: #213730; 
-  }
-  .navbar-default .navbar-nav > .active > a, .navbar-default .navbar-nav > .active > a:hover, .navbar-default .navbar-nav > .active > a:focus {
-    background-color: #355951; 
-  }
-}
 
 /* R for Data Science (r4ds) */
 #r4ds a {
@@ -209,16 +201,6 @@ thead ~ tbody {
   /* only when it has a header */
   border-bottom: 2px solid black;
 }
-@media (prefers-color-scheme: dark) {
-  thead {
-    border-top: 2px solid white;
-    border-bottom: 2px solid white;
-  }
-  thead ~ tbody {
-    /* only when it has a header */
-    border-bottom: 2px solid white;
-  }
-}
 thead th {
   text-align: inherit; 
 }

docs/index.html

@@ -43,7 +43,7 @@
       </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">1.5.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9009</span>
       </span>
     </div>
 

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">1.5.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9009</span>
       </span>
     </div>
 
@@ -236,13 +236,13 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1509007" class="section level1">
-<h1 class="page-header" data-toc-text="1.5.0.9007">
-<a href="#amr-1509007" class="anchor"></a>AMR 1.5.0.9007<small> Unreleased </small>
+    <div id="amr-1509009" class="section level1">
+<h1 class="page-header" data-toc-text="1.5.0.9009">
+<a href="#amr-1509009" class="anchor"></a>AMR 1.5.0.9009<small> Unreleased </small>
 </h1>
-<div id="last-updated-18-january-2021" class="section level2">
+<div id="last-updated-22-january-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-18-january-2021" class="anchor"></a><small>Last updated: 18 January 2021</small>
+<a href="#last-updated-22-january-2021" class="anchor"></a><small>Last updated: 22 January 2021</small>
 </h2>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
@@ -285,7 +285,9 @@
 </li>
 <li>Added Pretomanid (PMD, J04AK08) to the <code>antibiotics</code> data set</li>
 <li>WHONET code <code>"PNV"</code> will now correctly be interpreted as <code>PHN</code>, the antibiotic code for phenoxymethylpenicillin (‘peni V’)</li>
-<li>Fix for verbose output of <code><a href="../reference/mdro.html">mdro(..., verbose = TRUE)</a></code> for German guideline (3MGRN and 4MGRN) and <em>P. aeruginosa</em> in Dutch guideline (BRMO)</li>
+<li>Fix for verbose output of <code><a href="../reference/mdro.html">mdro(..., verbose = TRUE)</a></code> for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only <em>P. aeruginosa</em>)</li>
+<li>
+<code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now returns <code>FALSE</code> immediately if the input does not contain 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>
 </ul>
 </div>
 <div id="other" class="section level3">
@@ -293,6 +295,7 @@
 <a href="#other" class="anchor"></a>Other</h3>
 <ul>
 <li>Big documentation updates</li>
+<li>Loading the package (i.e., <code><a href="https://msberends.github.io/AMR/">library(AMR)</a></code>) now is ~50 times faster than before</li>
 </ul>
 </div>
 </div>

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: 2021-01-18T17:45Z
+last_built: 2021-01-22T09:54Z
 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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

docs/reference/antibiotic_class_selectors.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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

docs/reference/as.mo.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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 
@@ -347,13 +347,13 @@
 <li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
 <li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href='as.mic.html'>as.mic()</a></code>, that also gives your columns the new data class <code><a href='as.mic.html'>mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul>
 <li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.mic</span>, <span class='va'>as.rsi</span><span class='op'>)</span>         <span class='co'># until dplyr 1.0.0</span>
-<span class='va'>your_data</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><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.mic</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># since dplyr 1.0.0</span>
+<span class='va'>your_data</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><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>is.mic</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span>  <span class='co'># since dplyr 1.0.0</span>
 </pre></li>
 <li><p>Operators like "&lt;=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and might in this case return "S" or "I".</p></li>
 </ul></li>
 <li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href='as.disk.html'>as.disk()</a></code>, that also gives your columns the new data class <code><a href='as.disk.html'>disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul>
 <li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.disk</span>, <span class='va'>as.rsi</span><span class='op'>)</span>         <span class='co'># until dplyr 1.0.0</span>
-<span class='va'>your_data</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><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.disk</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># since dplyr 1.0.0</span>
+<span class='va'>your_data</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><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>is.disk</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span>  <span class='co'># since dplyr 1.0.0</span>
 </pre></li>
 </ul></li>
 <li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.rsi(data)</code>.</p></li>
@@ -452,7 +452,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
   <span class='va'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.mic</span>, <span class='va'>as.rsi</span><span class='op'>)</span>
   <span class='va'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='as.mic.html'>is.mic</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='op'>|</span> <span class='fu'><a href='as.disk.html'>is.disk</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span>
-  <span class='va'>df</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><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.mic</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span>
+  <span class='va'>df</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><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>is.mic</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span>
   <span class='va'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span><span class='op'>(</span><span class='va'>AMP</span><span class='op'>:</span><span class='va'>TOB</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span>
   <span class='va'>df</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><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='va'>AMP</span><span class='op'>:</span><span class='va'>TOB</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span>
  
@@ -497,7 +497,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
     
   <span class='co'># note: from dplyr 1.0.0 on, this will be: </span>
   <span class='co'># example_isolates %&gt;%</span>
-  <span class='co'>#   mutate(across(where(is.rsi.eligible), as.rsi))</span>
+  <span class='co'>#   mutate(across((is.rsi.eligible), as.rsi))</span>
 <span class='op'>}</span>
 <span class='co'># }</span>
 </pre>

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

docs/reference/filter_ab_class.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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

docs/reference/first_isolate.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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9009</span>
       </span>
     </div>
 
@@ -459,7 +459,7 @@
       </tr><tr>
         
         <td>
-          <p><code><a href="isolate_identifier.html">isolate_identifier()</a></code> </p>
+          <p><code><a href="isolate_identifier.html">isolate_identifier()</a></code> <code><a href="isolate_identifier.html">all.equal(<i>&lt;isolate_identifier&gt;</i>)</a></code> </p>
         </td>
         <td><p>Create Identifier of an Isolate</p></td>
       </tr>

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

docs/reference/isolate_identifier.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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9009</span>
       </span>
     </div>
 
@@ -242,7 +242,10 @@
     <p>This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>isolate_identifier</span><span class='op'>(</span><span class='va'>x</span>, col_mo <span class='op'>=</span> <span class='cn'>NULL</span>, cols_ab <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span></pre>
+    <pre class="usage"><span class='fu'>isolate_identifier</span><span class='op'>(</span><span class='va'>x</span>, col_mo <span class='op'>=</span> <span class='cn'>NULL</span>, cols_ab <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
+
+<span class='co'># S3 method for isolate_identifier</span>
+<span class='fu'><a href='https://rdrr.io/r/base/all.equal.html'>all.equal</a></span><span class='op'>(</span><span class='va'>target</span>, <span class='va'>current</span>, ignore_empty_results <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span></pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -259,14 +262,30 @@
       <th>cols_ab</th>
       <td><p>a character vector of column names of <code>x</code>, or (a combination with) an <a href='[ab_class()]'>antibiotic selector function</a>, such as <code><a href='antibiotic_class_selectors.html'>carbapenems()</a></code> and <code><a href='antibiotic_class_selectors.html'>aminoglycosides()</a></code></p></td>
     </tr>
+    <tr>
+      <th>target</th>
+      <td><p><span style="R">R</span> object.</p></td>
+    </tr>
+    <tr>
+      <th>current</th>
+      <td><p>other <span style="R">R</span> object, to be compared with <code>target</code>.</p></td>
+    </tr>
+    <tr>
+      <th>ignore_empty_results</th>
+      <td><p>a logical to indicate whether empty results must be ignored, so that only values R, S and I will be compared</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>column name of an antibiotic, see section <em>Antibiotics</em> below</p></td>
+    </tr>
     </table>
 
-    <h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing Lifecycle</h2>
+    <h2 class="hasAnchor" id="experimental-lifecycle"><a class="anchor" href="#experimental-lifecycle"></a>Experimental Lifecycle</h2>
 
     
 
-<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
+<p><img src='figures/lifecycle_experimental.svg' style=margin-bottom:5px /> <br />
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>experimental</strong>. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this <code>AMR</code> package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.</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>
 
     

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

docs/reference/key_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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

docs/reference/lifecycle.html

@@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
       </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

docs/reference/rsi_translation.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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </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">1.5.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
       </span>
     </div>
 

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">1.5.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9009</span>
       </span>
     </div>
 

man/as.rsi.Rd

@@ -88,14 +88,14 @@ The \code{\link[=as.rsi]{as.rsi()}} function works in four ways:
 \item For \strong{interpreting minimum inhibitory concentration (MIC) values} according to EUCAST or CLSI. You must clean your MIC values first using \code{\link[=as.mic]{as.mic()}}, that also gives your columns the new data class \code{\link{mic}}. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the \code{mo} argument.
 \itemize{
 \item Using \code{dplyr}, R/SI interpretation can be done very easily with either:\preformatted{your_data \%>\% mutate_if(is.mic, as.rsi)         # until dplyr 1.0.0
-your_data \%>\% mutate(across(where(is.mic), as.rsi)) # since dplyr 1.0.0
+your_data \%>\% mutate(across((is.mic), as.rsi))  # since dplyr 1.0.0
 }
 \item Operators like "<=" will be stripped before interpretation. When using \code{conserve_capped_values = TRUE}, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (\code{conserve_capped_values = FALSE}) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
 }
 \item For \strong{interpreting disk diffusion diameters} according to EUCAST or CLSI. You must clean your disk zones first using \code{\link[=as.disk]{as.disk()}}, that also gives your columns the new data class \code{\link{disk}}. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the \code{mo} argument.
 \itemize{
 \item Using \code{dplyr}, R/SI interpretation can be done very easily with either:\preformatted{your_data \%>\% mutate_if(is.disk, as.rsi)         # until dplyr 1.0.0
-your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
+your_data \%>\% mutate(across((is.disk), as.rsi))  # since dplyr 1.0.0
 }
 }
 \item For \strong{interpreting a complete data set}, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running \code{as.rsi(data)}.
@@ -193,7 +193,7 @@ as.rsi(x = as.disk(18),
 if (require("dplyr")) {
   df \%>\% mutate_if(is.mic, as.rsi)
   df \%>\% mutate_if(function(x) is.mic(x) | is.disk(x), as.rsi)
-  df \%>\% mutate(across(where(is.mic), as.rsi))
+  df \%>\% mutate(across((is.mic), as.rsi))
   df \%>\% mutate_at(vars(AMP:TOB), as.rsi)
   df \%>\% mutate(across(AMP:TOB, as.rsi))
  
@@ -238,7 +238,7 @@ if (require("dplyr")) {
     
   # note: from dplyr 1.0.0 on, this will be: 
   # example_isolates \%>\%
-  #   mutate(across(where(is.rsi.eligible), as.rsi))
+  #   mutate(across((is.rsi.eligible), as.rsi))
 }
 }
 }

man/isolate_identifier.Rd

@@ -2,9 +2,12 @@
 % Please edit documentation in R/isolate_identifier.R
 \name{isolate_identifier}
 \alias{isolate_identifier}
+\alias{all.equal.isolate_identifier}
 \title{Create Identifier of an Isolate}
 \usage{
 isolate_identifier(x, col_mo = NULL, cols_ab = NULL)
+
+\method{all.equal}{isolate_identifier}(target, current, ignore_empty_results = TRUE, ...)
 }
 \arguments{
 \item{x}{data with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
@@ -12,14 +15,22 @@ isolate_identifier(x, col_mo = NULL, cols_ab = NULL)
 \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
 
 \item{cols_ab}{a character vector of column names of \code{x}, or (a combination with) an \href{[ab_class()]}{antibiotic selector function}, such as \code{\link[=carbapenems]{carbapenems()}} and \code{\link[=aminoglycosides]{aminoglycosides()}}}
+
+\item{target}{\R object.}
+
+\item{current}{other \R object, to be compared with \code{target}.}
+
+\item{ignore_empty_results}{a logical to indicate whether empty results must be ignored, so that only values R, S and I will be compared}
+
+\item{...}{column name of an antibiotic, see section \emph{Antibiotics} below}
 }
 \description{
 This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.
 }
-\section{Maturing Lifecycle}{
+\section{Experimental Lifecycle}{
 
-\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
-The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
+\if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
+The \link[=lifecycle]{lifecycle} of this function is \strong{experimental}. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this \code{AMR} package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
 }
 
 \section{Read more on Our Website!}{

pkgdown/extra.css

@@ -24,14 +24,6 @@
 # how to conduct AMR analysis: https://msberends.github.io/AMR/        #
 # ==================================================================== #
 */
-@media (prefers-color-scheme: dark) {
-  .navbar-default {
-    background-color: #213730; 
-  }
-  .navbar-default .navbar-nav > .active > a, .navbar-default .navbar-nav > .active > a:hover, .navbar-default .navbar-nav > .active > a:focus {
-    background-color: #355951; 
-  }
-}
 
 /* R for Data Science (r4ds) */
 #r4ds a {
@@ -209,16 +201,6 @@ thead ~ tbody {
   /* only when it has a header */
   border-bottom: 2px solid black;
 }
-@media (prefers-color-scheme: dark) {
-  thead {
-    border-top: 2px solid white;
-    border-bottom: 2px solid white;
-  }
-  thead ~ tbody {
-    /* only when it has a header */
-    border-bottom: 2px solid white;
-  }
-}
 thead th {
   text-align: inherit; 
 }

tests/testthat/test-data.R

@@ -63,7 +63,7 @@ test_that("data sets are valid", {
 test_that("creation of data sets is valid", {
   skip_on_cran()
   
-  df <- create_MO_lookup()
+  df <- AMR:::MO_lookup
   expect_lt(nrow(df[which(df$prevalence == 1), ]), nrow(df[which(df$prevalence == 2), ]))
   expect_lt(nrow(df[which(df$prevalence == 2), ]), nrow(df[which(df$prevalence == 3), ]))
   expect_true(all(c("mo", "fullname",
@@ -71,11 +71,10 @@ test_that("creation of data sets is valid", {
                     "rank", "ref", "species_id", "source", "prevalence", "snomed",
                     "kingdom_index", "fullname_lower", "g_species") %in% colnames(df)))
   
-  olddf <- create_MO.old_lookup()
   expect_true(all(c("fullname", "fullname_new", "ref", "prevalence",
-                    "fullname_lower", "g_species") %in% colnames(olddf)))
+                    "fullname_lower", "g_species") %in% colnames(AMR:::MO.old_lookup)))
   
-  expect_s3_class(create_species_cons_cops("CoNS"), "mo")
+  expect_s3_class(AMR:::MO_CONS, "mo")
   
 })
 

tests/testthat/test-isolate_identifier.R

@@ -0,0 +1,44 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis for R                        #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# Developed at the University of Groningen, the Netherlands, in        #
+# collaboration with non-profit organisations Certe Medical            #
+# Diagnostics & Advice, and University Medical Center Groningen.       # 
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR analysis: https://msberends.github.io/AMR/        #
+# ==================================================================== #
+
+context("isolate_identifier.R")
+
+test_that("isolate_identifier works", {
+  x <- suppressMessages(isolate_identifier(example_isolates))
+  expect_s3_class(x, "isolate_identifier")
+  expect_s3_class(x, "character")
+  
+  expect_equal(suppressMessages(
+    unique(nchar(isolate_identifier(example_isolates, cols_ab = carbapenems(), col_mo = FALSE)))),
+    2)
+  
+  expect_warning(isolate_identifier(example_isolates[, 1:3, drop = FALSE])) # without mo and without rsi
+  expect_warning(isolate_identifier(example_isolates[, 1:9, drop = FALSE])) # only without rsi
+  
+  
+  expect_output(print(x))
+  expect_s3_class(unique(c(x, x)), "isolate_identifier")
+  
+})

vignettes/SPSS.Rmd

@@ -49,7 +49,7 @@ As said, SPSS is easier to learn than R. But SPSS, SAS and Stata come with major
   
 * **R has a huge community.**
 
-  Many R users just ask questions on websites like [StackOverflow.com](https://stackoverflow.com), the largest online community for programmers. At the time of writing, more than [360,000 R-related questions](https://stackoverflow.com/questions/tagged/r?sort=votes) have already been asked on this platform (which covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.
+  Many R users just ask questions on websites like [StackOverflow.com](https://stackoverflow.com), the largest online community for programmers. At the time of writing, [`r format(suppressWarnings(read.csv("https://data.stackexchange.com/stackoverflow/csv/1674647", quote = '"'))[[1]], big.mark = ",")` R-related questions](https://stackoverflow.com/questions/tagged/r?sort=votes) have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.
   
 * **R understands any data type, including SPSS/SAS/Stata.**