(v0.9.0.9023) EUCAST 2020 guidelines

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.9.0.9022
+Version: 0.9.0.9023
-Date: 2020-02-10
+Date: 2020-02-14
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,7 +1,9 @@
-# AMR 0.9.0.9022
+# AMR 0.9.0.9023
-## <small>Last updated: 10-Feb-2020</small>
+## <small>Last updated: 14-Feb-2020</small>
 
 ### New
+* Support for the newest EUCAST Clinical Breakpoint Tables v.10.0, valid from 2020-01-01 (use `as.rsi()` to transform MICs or disk zones)
+* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
 * Support for LOINC and SNOMED codes
   * Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use a LOINC code for input in any `ab_*` function:
     ```r
@@ -21,7 +23,6 @@
     mo_gramstain(115329001)
     #> [1] "Gram-positive"
     ```
-* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2019 to translate MIC and disk diffusion values to R/SI: https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
 
 ### Changes
 * The `as.mo()` function previously wrote to the package folder to improve calculation speed for previously calculated results. This is no longer the case, to comply with CRAN policies. Consequently, the function `clear_mo_history()` was removed.
@@ -42,6 +43,7 @@
 ### Other
 * Add a `CITATION` file
 * Full support for the upcoming R 4.0
+* Removed unnecessary `AMR::` calls
 
 # AMR 0.9.0
 

R/ab.R

@@ -66,11 +66,14 @@
 #' ab_name("J01FA01")    # "Erythromycin"
 #' ab_name("eryt")       # "Erythromycin"
 as.ab <- function(x, ...) {
+  
+  check_dataset_integrity()
+  
   if (is.ab(x)) {
     return(x)
   }
 
-  if (all(toupper(x) %in% AMR::antibiotics$ab)) {
+  if (all(toupper(x) %in% antibiotics$ab)) {
     # valid AB code, but not yet right class
     return(structure(.Data = toupper(x),
                      class = "ab"))
@@ -117,67 +120,67 @@ as.ab <- function(x, ...) {
     }
 
     # exact AB code
-    found <- AMR::antibiotics[which(AMR::antibiotics$ab == toupper(x[i])), ]$ab
+    found <- antibiotics[which(antibiotics$ab == toupper(x[i])), ]$ab
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
     }
 
     # exact ATC code
-    found <- AMR::antibiotics[which(AMR::antibiotics$atc == toupper(x[i])), ]$ab
+    found <- antibiotics[which(antibiotics$atc == toupper(x[i])), ]$ab
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
     }
 
     # exact CID code
-    found <- AMR::antibiotics[which(AMR::antibiotics$cid == x[i]), ]$ab
+    found <- antibiotics[which(antibiotics$cid == x[i]), ]$ab
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
     }
 
     # exact name
-    found <- AMR::antibiotics[which(toupper(AMR::antibiotics$name) == toupper(x[i])), ]$ab
+    found <- antibiotics[which(toupper(antibiotics$name) == toupper(x[i])), ]$ab
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
     }
     
     # exact LOINC code
-    loinc_found <- unlist(lapply(AMR::antibiotics$loinc,
+    loinc_found <- unlist(lapply(antibiotics$loinc,
                                    function(s) if (x[i] %in% s) {
                                      TRUE
                                    } else {
                                      FALSE
                                    }))
-    found <- AMR::antibiotics$ab[loinc_found == TRUE]
+    found <- antibiotics$ab[loinc_found == TRUE]
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
     }
 
     # exact synonym
-    synonym_found <- unlist(lapply(AMR::antibiotics$synonyms,
+    synonym_found <- unlist(lapply(antibiotics$synonyms,
                                    function(s) if (toupper(x[i]) %in% toupper(s)) {
                                      TRUE
                                    } else {
                                      FALSE
                                    }))
-    found <- AMR::antibiotics$ab[synonym_found == TRUE]
+    found <- antibiotics$ab[synonym_found == TRUE]
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
     }
 
     # exact abbreviation
-    abbr_found <- unlist(lapply(AMR::antibiotics$abbreviations,
+    abbr_found <- unlist(lapply(antibiotics$abbreviations,
                                 function(a) if (toupper(x[i]) %in% toupper(a)) {
                                   TRUE
                                 } else {
                                   FALSE
                                 }))
-    found <- AMR::antibiotics$ab[abbr_found == TRUE]
+    found <- antibiotics$ab[abbr_found == TRUE]
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
@@ -185,7 +188,7 @@ as.ab <- function(x, ...) {
 
     # first >=4 characters of name
     if (nchar(x[i]) >= 4) {
-      found <- AMR::antibiotics[which(toupper(AMR::antibiotics$name) %like% paste0("^", x[i])), ]$ab
+      found <- antibiotics[which(toupper(antibiotics$name) %like% paste0("^", x[i])), ]$ab
       if (length(found) > 0) {
         x_new[i] <- found[1L]
         next
@@ -215,19 +218,19 @@ as.ab <- function(x, ...) {
     x_spelling <- gsub("(.)\\1+", "\\1+", x_spelling)
   
     # try if name starts with it
-    found <- AMR::antibiotics[which(AMR::antibiotics$name %like% paste0("^", x_spelling)), ]$ab
+    found <- antibiotics[which(antibiotics$name %like% paste0("^", x_spelling)), ]$ab
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
     }
     # and try if any synonym starts with it
-    synonym_found <- unlist(lapply(AMR::antibiotics$synonyms,
+    synonym_found <- unlist(lapply(antibiotics$synonyms,
                                    function(s) if (any(s %like% paste0("^", x_spelling))) {
                                      TRUE
                                    } else {
                                      FALSE
                                    }))
-    found <- AMR::antibiotics$ab[synonym_found == TRUE]
+    found <- antibiotics$ab[synonym_found == TRUE]
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
@@ -374,7 +377,7 @@ as.data.frame.ab <- function(x, ...) {
 "[<-.ab" <- function(i, j, ..., value) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
-  class_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
+  class_integrity_check(y, "antimicrobial code", antibiotics$ab)
 }
 #' @exportMethod [[<-.ab
 #' @export
@@ -382,7 +385,7 @@ as.data.frame.ab <- function(x, ...) {
 "[[<-.ab" <- function(i, j, ..., value) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
-  class_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
+  class_integrity_check(y, "antimicrobial code", antibiotics$ab)
 }
 #' @exportMethod c.ab
 #' @export
@@ -390,7 +393,7 @@ as.data.frame.ab <- function(x, ...) {
 c.ab <- function(x, ...) {
   y <- NextMethod()
   attributes(y) <- attributes(x)
-  class_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
+  class_integrity_check(y, "antimicrobial code", antibiotics$ab)
 }
 
 #' @importFrom pillar type_sum

R/ab_property.R

@@ -168,7 +168,7 @@ ab_ddd <- function(x, administration = "oral", units = FALSE, ...) {
 #' @rdname ab_property
 #' @export
 ab_info <- function(x, language = get_locale(), ...) {
-  x <- AMR::as.ab(x, ...)
+  x <- as.ab(x, ...)
   base::list(ab = as.character(x),
              atc = ab_atc(x),
              cid = ab_cid(x),
@@ -189,7 +189,7 @@ ab_property <- function(x, property = "name", language = get_locale(), ...) {
   if (length(property) != 1L) {
     stop("'property' must be of length 1.")
   }
-  if (!property %in% colnames(AMR::antibiotics)) {
+  if (!property %in% colnames(antibiotics)) {
     stop("invalid property: '", property, "' - use a column name of the `antibiotics` data set")
   }
 
@@ -197,14 +197,17 @@ ab_property <- function(x, property = "name", language = get_locale(), ...) {
 }
 
 ab_validate <- function(x, property, ...) {
+  
+  check_dataset_integrity()
+  
   # try to catch an error when inputting an invalid parameter
   # so the 'call.' can be set to FALSE
-  tryCatch(x[1L] %in% AMR::antibiotics[1, property],
+  tryCatch(x[1L] %in% antibiotics[1, property],
            error = function(e) stop(e$message, call. = FALSE))
   x_bak <- x
-  if (!all(x %in% AMR::antibiotics[, property])) {
+  if (!all(x %in% antibiotics[, property])) {
-    x <- data.frame(ab = AMR::as.ab(x, ...), stringsAsFactors = FALSE) %>%
+    x <- data.frame(ab = as.ab(x, ...), stringsAsFactors = FALSE) %>%
-      left_join(AMR::antibiotics, by = "ab") %>%
+      left_join(antibiotics, by = "ab") %>%
       pull(property)
   }
   if (property == "ab") {

R/atc_online.R

@@ -76,12 +76,14 @@ atc_online_property <- function(atc_code,
                                 property,
                                 administration = "O",
                                 url = "https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no") {
+  
+  check_dataset_integrity()
 
   if (!all(c("curl", "rvest", "xml2") %in% rownames(utils::installed.packages()))) {
     stop("Packages 'xml2', 'rvest' and 'curl' are required for this function")
   }
 
-  if (!all(atc_code %in% AMR::antibiotics)) {
+  if (!all(atc_code %in% antibiotics)) {
     atc_code <- as.character(ab_atc(atc_code))
   }
 

R/catalogue_of_life.R

@@ -91,20 +91,23 @@ NULL
 #' microorganisms %>% freq(kingdom)
 #' microorganisms %>% group_by(kingdom) %>% freq(phylum, nmax = NULL)
 catalogue_of_life_version <- function() {
+  
+  check_dataset_integrity()
+  
   # see the `catalogue_of_life` list in R/data.R
   lst <- list(catalogue_of_life =
                 list(version = gsub("{year}", catalogue_of_life$year, catalogue_of_life$version, fixed = TRUE),
                      url = gsub("{year}", catalogue_of_life$year, catalogue_of_life$url_CoL, fixed = TRUE),
-                     n = nrow(filter(AMR::microorganisms, source == "CoL"))),
+                     n = nrow(filter(microorganisms, source == "CoL"))),
               deutsche_sammlung_von_mikroorganismen_und_zellkulturen =
                 list(version = "Prokaryotic Nomenclature Up-to-Date from DSMZ",
                      url = catalogue_of_life$url_DSMZ,
                      yearmonth = catalogue_of_life$yearmonth_DSMZ,
-                     n = nrow(filter(AMR::microorganisms, source == "DSMZ"))),
+                     n = nrow(filter(microorganisms, source == "DSMZ"))),
               total_included =
                 list(
-                  n_total_species = nrow(AMR::microorganisms),
+                  n_total_species = nrow(microorganisms),
-                  n_total_synonyms = nrow(AMR::microorganisms.old)))
+                  n_total_synonyms = nrow(microorganisms.old)))
 
   structure(.Data = lst,
             class = c("catalogue_of_life_version", "list"))

R/deprecated.R

@@ -30,7 +30,7 @@
 #' @rdname AMR-deprecated
 p.symbol <- function(...) {
   .Deprecated("p_symbol()", package = "AMR")
-  AMR::p_symbol(...)
+  p_symbol(...)
 }
 
 #' @rdname AMR-deprecated

R/eucast_rules.R

@@ -202,6 +202,8 @@ eucast_rules <- function(x,
                          verbose = FALSE,
                          ...) {
   
+  check_dataset_integrity()
+  
   if (verbose == TRUE & interactive()) {
     txt <- paste0("WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.",
                   "\n\nThis may overwrite your existing data if you use e.g.:",
@@ -564,7 +566,7 @@ eucast_rules <- function(x,
       strsplit(",") %>%
       unlist() %>%
       trimws() %>%
-      sapply(function(x) if (x %in% AMR::antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE) else x) %>%
+      sapply(function(x) if (x %in% antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE) else x) %>%
       sort() %>%
       paste(collapse = ", ")
     x <- gsub("_", " ", x, fixed = TRUE)
@@ -664,8 +666,8 @@ eucast_rules <- function(x,
       # Print rule  -------------------------------------------------------------
       if (rule_current != rule_previous) {
         # is new rule within group, print its name
-        if (rule_current %in% c(AMR::microorganisms$family,
+        if (rule_current %in% c(microorganisms$family,
-                                AMR::microorganisms$fullname)) {
+                                microorganisms$fullname)) {
           cat(italic(rule_current))
         } else {
           cat(rule_current)
@@ -681,7 +683,7 @@ eucast_rules <- function(x,
     # be sure to comprise all coagulase-negative/-positive Staphylococci when they are mentioned
     if (eucast_rules_df[i, 3] %like% "coagulase-") {
       suppressWarnings(
-        all_staph <- AMR::microorganisms %>%
+        all_staph <- microorganisms %>%
           filter(genus == "Staphylococcus") %>%
           mutate(CNS_CPS = mo_name(mo, Becker = "all"))
       )

R/filter_ab_class.R

@@ -24,7 +24,7 @@
 #' Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.
 #' @inheritSection lifecycle Stable lifecycle
 #' @param x a data set
-#' @param ab_class an antimicrobial class, like `"carbapenems"`, as can be found in [`AMR::antibiotics$group`][antibiotics]
+#' @param ab_class an antimicrobial class, like `"carbapenems"`, as can be found in [`antibiotics$group`][antibiotics]
 #' @param result an antibiotic result: S, I or R (or a combination of more of them)
 #' @param scope the scope to check which variables to check, can be `"any"` (default) or `"all"`
 #' @param ... parameters passed on to `filter_at` from the `dplyr` package
@@ -67,6 +67,9 @@ filter_ab_class <- function(x,
                             result = NULL,
                             scope = "any",
                             ...) {
+  
+  check_dataset_integrity()
+  
   scope <- scope[1L]
   if (is.null(result)) {
     result <- c("S", "I", "R")
@@ -276,7 +279,7 @@ filter_tetracyclines <- function(x,
 #' @importFrom dplyr %>% filter_at vars any_vars select
 ab_class_vars <- function(ab_class) {
   ab_class <- gsub("[^a-z0-9]+", ".*", ab_class)
-  ab_vars <- AMR::antibiotics %>%
+  ab_vars <- antibiotics %>%
     filter(group %like% ab_class) %>% 
     select(ab:name, abbreviations, synonyms) %>%
     unlist() %>%
@@ -289,7 +292,7 @@ ab_class_vars <- function(ab_class) {
   ab_vars <- ab_vars[!ab_vars %in% c(NA, "", "NA") & nchar(ab_vars) > 2]
   if (length(ab_vars) == 0) {
     # try again, searching atc_group1 and atc_group2 columns
-    ab_vars <- AMR::antibiotics %>%
+    ab_vars <- antibiotics %>%
       filter_at(vars(c("atc_group1", "atc_group2")), any_vars(. %like% ab_class)) %>% 
       select(ab:name, abbreviations, synonyms) %>%
       unlist() %>%
@@ -314,7 +317,7 @@ find_ab_group <- function(ab_class) {
                          "macrolide",
                          "tetracycline"),
          paste0(ab_class, "s"),
-         AMR::antibiotics %>%
+         antibiotics %>%
            filter(ab %in% ab_class_vars(ab_class)) %>%
            pull(group) %>%
            unique() %>%

R/freq.R

@@ -58,14 +58,14 @@ freq.mo <- function(x, ...) {
 freq.rsi <- function(x, ...) {
   x_name <- deparse(substitute(x))
   x_name <- gsub(".*[$]", "", x_name)
-  ab <- suppressMessages(suppressWarnings(AMR::as.ab(x_name)))
+  ab <- suppressMessages(suppressWarnings(as.ab(x_name)))
   if (!is.na(ab)) {
     freq.default(x = x, ...,
                  .add_header = list(Drug = paste0(ab_name(ab), " (", ab, ", ", ab_atc(ab), ")"),
                                     group = ab_group(ab),
-                                    `%SI` = AMR::susceptibility(x, minimum = 0, as_percent = TRUE)))
+                                    `%SI` = susceptibility(x, minimum = 0, as_percent = TRUE)))
   } else {
     freq.default(x = x, ...,
-                 .add_header = list(`%SI` = AMR::susceptibility(x, minimum = 0, as_percent = TRUE)))
+                 .add_header = list(`%SI` = susceptibility(x, minimum = 0, as_percent = TRUE)))
   }
 }

R/ggplot_rsi.R

@@ -303,7 +303,7 @@ geom_rsi <- function(position = NULL,
   ggplot2::layer(geom = "bar", stat = "identity", position = position,
                  mapping = ggplot2::aes_string(x = x, y = y, fill = fill),
                  params = list(...), data = function(x) {
-                   AMR::rsi_df(data = x,
+                   rsi_df(data = x,
                                translate_ab = translate_ab,
                                language = language,
                                combine_SI = combine_SI,

R/guess_ab_col.R

@@ -126,7 +126,7 @@ get_column_abx <- function(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 have no more than 50% invalid values
-  vectr_antibiotics <- unique(toupper(unlist(AMR::antibiotics[, c("ab", "atc", "name", "abbreviations", "synonyms")])))
+  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 <- sapply(colnames(x), function(col, df = x_bak) {
     if (toupper(col) %in% vectr_antibiotics | 
@@ -205,7 +205,7 @@ get_column_abx <- function(x,
       # missing a soft dependency may lower the reliability
       missing <- soft_dependencies[!soft_dependencies %in% names(x)]
       missing_txt <- data.frame(missing = missing,
-                                missing_names = AMR::ab_name(missing, tolower = TRUE),
+                                missing_names = ab_name(missing, tolower = TRUE),
                                 stringsAsFactors = FALSE) %>%
         mutate(txt = paste0(bold(missing), " (", missing_names, ")")) %>%
         arrange(missing_names) %>%

R/join_microorganisms.R

@@ -54,7 +54,7 @@ inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   x <- checked$x
   by <- checked$by
   join <- suppressWarnings(
-    dplyr::inner_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
+    dplyr::inner_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
   )
   if (nrow(join) > nrow(x)) {
     warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@@ -69,7 +69,7 @@ left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   x <- checked$x
   by <- checked$by
   join <- suppressWarnings(
-    dplyr::left_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
+    dplyr::left_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
   )
   if (nrow(join) > nrow(x)) {
     warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@@ -84,7 +84,7 @@ right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   x <- checked$x
   by <- checked$by
   join <- suppressWarnings(
-    dplyr::right_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
+    dplyr::right_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
   )
   if (nrow(join) > nrow(x)) {
     warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@@ -99,7 +99,7 @@ full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   x <- checked$x
   by <- checked$by
   join <- suppressWarnings(
-    dplyr::full_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
+    dplyr::full_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
   )
   if (nrow(join) > nrow(x)) {
     warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@@ -114,7 +114,7 @@ semi_join_microorganisms <- function(x, by = NULL, ...) {
   x <- checked$x
   by <- checked$by
   suppressWarnings(
-    dplyr::semi_join(x = x, y = AMR::microorganisms, by = by, ...)
+    dplyr::semi_join(x = x, y = microorganisms, by = by, ...)
   )
 }
 
@@ -125,7 +125,7 @@ anti_join_microorganisms <- function(x, by = NULL, ...) {
   x <- checked$x
   by <- checked$by
   suppressWarnings(
-    dplyr::anti_join(x = x, y = AMR::microorganisms, by = by, ...)
+    dplyr::anti_join(x = x, y = microorganisms, by = by, ...)
   )
 }
 
@@ -149,7 +149,7 @@ joins_check_df <- function(x, by) {
     message('Joining, by = "', by, '"') # message same as dplyr::join functions
   }
   if (is.null(names(by))) {
-    joinby <- colnames(AMR::microorganisms)[1]
+    joinby <- colnames(microorganisms)[1]
     names(joinby) <- by
   } else {
     joinby <- by

R/like.R

@@ -45,15 +45,15 @@
 #'
 #' # also supports multiple patterns, length must be equal to x
 #' a <- c("Test case", "Something different", "Yet another thing")
-#' b <- c("case", "diff", "yet")
+#' b <- c(     "case",           "diff",      "yet")
 #' a %like% b
 #' #> TRUE TRUE TRUE
 #'
 #' # get frequencies of bacteria whose name start with 'Ent' or 'ent'
 #' library(dplyr)
 #' example_isolates %>%
-#'   filter(mo_genus(mo) %like% '^ent') %>%
+#'   filter(mo_name(mo) %like% '^ent') %>%
-#'   freq(mo_fullname(mo))
+#'   freq(mo_genus(mo))
 like <- function(x, pattern, ignore.case = TRUE) {
   if (length(pattern) > 1) {
     if (length(x) != length(pattern)) {

R/mdro.R

@@ -90,6 +90,8 @@ mdro <- function(x,
                  verbose = FALSE,
                  ...) {
   
+  check_dataset_integrity()
+  
   if (verbose == TRUE & interactive()) {
     txt <- paste0("WARNING: In Verbose mode, the mdro() function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.",
                   "\n\nThis may overwrite your existing data if you use e.g.:",
@@ -147,7 +149,7 @@ mdro <- function(x,
   if (is.null(col_mo) & guideline$code == "tb") {
     message(blue("NOTE: No column found as input for `col_mo`,",
                  bold("assuming all records contain", italic("Mycobacterium tuberculosis.\n"))))
-    x$mo <- AMR::as.mo("Mycobacterium tuberculosis")
+    x$mo <- as.mo("Mycobacterium tuberculosis")
     col_mo <- "mo"
   }
   if (is.null(col_mo)) {

R/misc.R

@@ -29,12 +29,23 @@ addin_insert_like <- function() {
   rstudioapi::insertText(" %like% ")
 }
 
-load_AMR_package <- function() {
+check_dataset_integrity <- function() {
-  if (!"package:AMR" %in% base::search()) {
+  if (!all(colnames(microorganisms) %in% c("mo", "fullname", "kingdom", "phylum",
-    require(AMR)
+                                           "class", "order", "family", "genus", 
-    # check onLoad() in R/zzz.R: data tables are created there.
+                                           "species", "subspecies", "rank",
+                                           "col_id", "species_id", "source",
+                                           "ref", "prevalence", "snomed"),
+           na.rm = TRUE) |
+      NROW(microorganisms) != NROW(microorganismsDT) |
+      !all(colnames(antibiotics) %in% c("ab", "atc", "cid", "name", "group", 
+                                        "atc_group1", "atc_group2", "abbreviations",
+                                        "synonyms", "oral_ddd", "oral_units", 
+                                        "iv_ddd", "iv_units", "loinc"),
+           na.rm = TRUE)) {
+    stop("Data set `microorganisms` or data set `antibiotics` is overwritten by your global environment and prevents the AMR package from working correctly. Please rename your object before using this function.", call. = FALSE)
   }
-  base::invisible()
+
+  invisible(TRUE)
 }
 
 #' @importFrom crayon blue bold red
@@ -155,9 +166,6 @@ dataset_UTF8_to_ASCII <- function(df) {
     col <- df[, i]
     if (is.list(col)) {
       col <- lapply(col, function(j) trans(j))
-      # for (j in seq_len(length(col))) {
-      #   col[[j]] <- trans(col[[j]])
-      # }
       df[, i] <- list(col)
     } else {
       if (is.factor(col)) {

R/mo.R

@@ -175,7 +175,7 @@ as.mo <- function(x,
                   reference_df = get_mo_source(), 
                   ...) {
   
-  load_AMR_package()
+  check_dataset_integrity()
   
   # WHONET: xxx = no growth
   x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
@@ -238,7 +238,7 @@ is.mo <- function(x) {
 #' @importFrom data.table data.table as.data.table setkey
 #' @importFrom crayon magenta red blue silver italic
 #' @importFrom cleaner percentage
-# param property a column name of AMR::microorganisms
+# param property a column name of microorganisms
 # param initial_search logical - is FALSE when coming from uncertain tries, which uses exec_as.mo internally too
 # param dyslexia_mode logical - also check for characters that resemble others
 # param debug logical - show different lookup texts while searching
@@ -254,7 +254,7 @@ exec_as.mo <- function(x,
                        debug = FALSE,
                        reference_data_to_use = microorganismsDT) {
   
-  load_AMR_package()
+  check_dataset_integrity()
   
   # WHONET: xxx = no growth
   x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
@@ -365,7 +365,7 @@ exec_as.mo <- function(x,
     suppressWarnings(
       x <- data.frame(x = x, stringsAsFactors = FALSE) %>%
         left_join(reference_df, by = "x") %>%
-        left_join(AMR::microorganisms, by = "mo") %>%
+        left_join(microorganisms, by = "mo") %>%
         pull(property)
     )
     
@@ -393,9 +393,9 @@ exec_as.mo <- function(x,
                                on = "fullname_lower",
                                ..property][[1]]
     
-  } else if (all(toupper(x) %in% AMR::microorganisms.codes$code)) {
+  } else if (all(toupper(x) %in% microorganisms.codes$code)) {
     # commonly used MO codes
-    y <- as.data.table(AMR::microorganisms.codes)[data.table(code = toupper(x)),
+    y <- as.data.table(microorganisms.codes)[data.table(code = toupper(x)),
                                                   on = "code", ]
     
     x <- reference_data_to_use[data.table(mo = y[["mo"]]),
@@ -412,7 +412,7 @@ exec_as.mo <- function(x,
                                ..property][[1]]
     x <- y
     
-  } else if (!all(x %in% AMR::microorganisms[, property])) {
+  } else if (!all(x %in% microorganisms[, property])) {
     
     strip_whitespace <- function(x, dyslexia_mode) {
       # all whitespaces (tab, new lines, etc.) should be one space
@@ -632,8 +632,8 @@ exec_as.mo <- function(x,
       }
       
       # WHONET and other common LIS codes
-      if (any(toupper(c(x_backup[i], x_backup_without_spp[i])) %in% AMR::microorganisms.codes$code)) {
+      if (any(toupper(c(x_backup[i], x_backup_without_spp[i])) %in% microorganisms.codes$code)) {
-        mo_found <- AMR::microorganisms.codes[which(AMR::microorganisms.codes$code %in% toupper(c(x_backup[i], x_backup_without_spp[i]))), "mo"][1L]
+        mo_found <- microorganisms.codes[which(microorganisms.codes$code %in% toupper(c(x_backup[i], x_backup_without_spp[i]))), "mo"][1L]
         if (length(mo_found) > 0) {
           x[i] <- microorganismsDT[mo == mo_found,
                                    ..property][[1]][1L]
@@ -1476,8 +1476,7 @@ exec_as.mo <- function(x,
       msg <- paste0(msg, ": ", paste('"', unique(failures), '"', sep = "", collapse = ", "))
     }
     msg <- paste0(msg,  ". Use mo_failures() to review ", plural[2], ". Edit the `allow_uncertain` parameter if needed (see ?as.mo).")
-    cat("\n")
+    warning(red(paste0("\n", msg)),
-    warning(red(msg),
             call. = FALSE,
             immediate. = TRUE) # thus will always be shown, even if >= warnings
   }
@@ -1491,8 +1490,7 @@ exec_as.mo <- function(x,
     }
     msg <- paste0("Result", plural[1], " of ", nr2char(NROW(uncertainties)), " value", plural[1],
                   " ", plural[3], " guessed with uncertainty. Use mo_uncertainties() to review ", plural[2], ".")
-    cat("\n")
+    warning(red(paste0("\n", msg)),
-    warning(red(msg),
             call. = FALSE,
             immediate. = TRUE) # thus will always be shown, even if >= warnings
   }
@@ -1753,7 +1751,7 @@ as.data.frame.mo <- function(x, ...) {
 "[<-.mo" <- function(i, j, ..., value) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
-  class_integrity_check(y, "microorganism code", c(as.character(AMR::microorganisms$mo), 
+  class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo), 
                                                    as.character(microorganisms.translation$mo_old)))
 }
 #' @exportMethod [[<-.mo
@@ -1762,7 +1760,7 @@ as.data.frame.mo <- function(x, ...) {
 "[[<-.mo" <- function(i, j, ..., value) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
-  class_integrity_check(y, "microorganism code", c(as.character(AMR::microorganisms$mo), 
+  class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo), 
                                                    as.character(microorganisms.translation$mo_old)))
 }
 #' @exportMethod c.mo
@@ -1771,7 +1769,7 @@ as.data.frame.mo <- function(x, ...) {
 c.mo <- function(x, ...) {
   y <- NextMethod()
   attributes(y) <- attributes(x)
-  class_integrity_check(y, "microorganism code", c(as.character(AMR::microorganisms$mo), 
+  class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo), 
                                                    as.character(microorganisms.translation$mo_old)))
 }
 

R/mo_property.R

@@ -145,7 +145,7 @@ mo_fullname <- mo_name
 #' @rdname mo_property
 #' @export
 mo_shortname <- function(x, language = get_locale(), ...) {
-  x.mo <- AMR::as.mo(x, ...)
+  x.mo <- as.mo(x, ...)
   metadata <- get_mo_failures_uncertainties_renamed()
 
   replace_empty <- function(x) {
@@ -223,7 +223,7 @@ mo_type <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_gramstain <- function(x, language = get_locale(), ...) {
-  x.mo <- AMR::as.mo(x, ...)
+  x.mo <- as.mo(x, ...)
   metadata <- get_mo_failures_uncertainties_renamed()
 
   x.phylum <- mo_phylum(x.mo)
@@ -290,17 +290,17 @@ mo_rank <- function(x, ...) {
 #' @rdname mo_property
 #' @export
 mo_taxonomy <- function(x, language = get_locale(),  ...) {
-  x <- AMR::as.mo(x, ...)
+  x <- as.mo(x, ...)
   metadata <- get_mo_failures_uncertainties_renamed()
 
-  result <- base::list(kingdom = AMR::mo_kingdom(x, language = language),
+  result <- base::list(kingdom = mo_kingdom(x, language = language),
-             phylum = AMR::mo_phylum(x, language = language),
+             phylum = mo_phylum(x, language = language),
-             class = AMR::mo_class(x, language = language),
+             class = mo_class(x, language = language),
-             order = AMR::mo_order(x, language = language),
+             order = mo_order(x, language = language),
-             family = AMR::mo_family(x, language = language),
+             family = mo_family(x, language = language),
-             genus = AMR::mo_genus(x, language = language),
+             genus = mo_genus(x, language = language),
-             species = AMR::mo_species(x, language = language),
+             species = mo_species(x, language = language),
-             subspecies = AMR::mo_subspecies(x, language = language))
+             subspecies = mo_subspecies(x, language = language))
 
   load_mo_failures_uncertainties_renamed(metadata)
   result
@@ -309,12 +309,12 @@ mo_taxonomy <- function(x, language = get_locale(),  ...) {
 #' @rdname mo_property
 #' @export
 mo_synonyms <- function(x, ...) {
-  x <- AMR::as.mo(x, ...)
+  x <- as.mo(x, ...)
   metadata <- get_mo_failures_uncertainties_renamed()
 
-  IDs <- AMR::mo_property(x = x, property = "col_id", language = NULL)
+  IDs <- mo_property(x = x, property = "col_id", language = NULL)
   syns <- lapply(IDs, function(col_id) {
-    res <- sort(AMR::microorganisms.old[which(AMR::microorganisms.old$col_id_new == col_id), "fullname"])
+    res <- sort(microorganisms.old[which(microorganisms.old$col_id_new == col_id), "fullname"])
     if (length(res) == 0) {
       NULL
     } else {
@@ -335,7 +335,7 @@ mo_synonyms <- function(x, ...) {
 #' @rdname mo_property
 #' @export
 mo_info <- function(x, language = get_locale(),  ...) {
-  x <- AMR::as.mo(x, ...)
+  x <- as.mo(x, ...)
   metadata <- get_mo_failures_uncertainties_renamed()
 
   info <- lapply(x, function(y)
@@ -360,12 +360,12 @@ mo_info <- function(x, language = get_locale(),  ...) {
 #' @importFrom dplyr %>% left_join select mutate case_when
 #' @export
 mo_url <- function(x, open = FALSE, ...) {
-  mo <- AMR::as.mo(x = x, ... = ...)
+  mo <- as.mo(x = x, ... = ...)
-  mo_names <- AMR::mo_name(mo)
+  mo_names <- mo_name(mo)
   metadata <- get_mo_failures_uncertainties_renamed()
 
   df <- data.frame(mo, stringsAsFactors = FALSE) %>%
-    left_join(select(AMR::microorganisms, mo, source, species_id), by = "mo") %>%
+    left_join(select(microorganisms, mo, source, species_id), by = "mo") %>%
     mutate(url = case_when(source == "CoL" ~
                              paste0(gsub("{year}", catalogue_of_life$year, catalogue_of_life$url_CoL, fixed = TRUE), "details/species/id/", species_id),
                            source == "DSMZ" ~
@@ -394,7 +394,7 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
   if (length(property) != 1L) {
     stop("'property' must be of length 1.")
   }
-  if (!property %in% colnames(AMR::microorganisms)) {
+  if (!property %in% colnames(microorganisms)) {
     stop("invalid property: '", property, "' - use a column name of the `microorganisms` data set")
   }
 
@@ -403,7 +403,7 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
 
 mo_validate <- function(x, property, ...) {
   
-  load_AMR_package()
+  check_dataset_integrity()
 
   dots <- list(...)
   Becker <- dots$Becker
@@ -417,7 +417,7 @@ mo_validate <- function(x, property, ...) {
 
   # try to catch an error when inputting an invalid parameter
   # so the 'call.' can be set to FALSE
-  tryCatch(x[1L] %in% AMR::microorganisms[1, property],
+  tryCatch(x[1L] %in% microorganisms[1, property],
            error = function(e) stop(e$message, call. = FALSE))
   
   if (is.mo(x) 
@@ -426,7 +426,7 @@ mo_validate <- function(x, property, ...) {
     # this will not reset mo_uncertainties and mo_failures
     # because it's already a valid MO
     x <- exec_as.mo(x, property = property, initial_search = FALSE, ...)
-  } else if (!all(x %in% pull(AMR::microorganisms, property))
+  } else if (!all(x %in% pull(microorganisms, property))
              | Becker %in% c(TRUE, "all")
              | Lancefield %in% c(TRUE, "all")) {
     x <- exec_as.mo(x, property = property, ...)

R/mo_source.R

@@ -202,6 +202,9 @@ get_mo_source <- function() {
 }
 
 mo_source_isvalid <- function(x) {
+  
+  check_dataset_integrity()
+  
   if (deparse(substitute(x)) == "get_mo_source()") {
     return(TRUE)
   }
@@ -217,5 +220,5 @@ mo_source_isvalid <- function(x) {
   if (!"mo" %in% colnames(x)) {
     return(FALSE)
   }
-  all(x$mo %in% c("", AMR::microorganisms$mo, microorganisms.translation$mo_old), na.rm = TRUE)
+  all(x$mo %in% c("", microorganisms$mo, microorganisms.translation$mo_old), na.rm = TRUE)
 }

R/rsi.R

@@ -28,10 +28,10 @@
 #' @param mo a microorganism code, generated with [as.mo()]
 #' @param ab an antimicrobial code, generated with [as.ab()]
 #' @inheritParams first_isolate
-#' @param guideline defaults to the latest included EUCAST guideline, run `unique(AMR::rsi_translation$guideline)` for all options
+#' @param guideline defaults to the latest included EUCAST guideline, run `unique(rsi_translation$guideline)` for all options
 #' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples*
 #' @param ... parameters passed on to methods
-#' @details Run `unique(AMR::rsi_translation$guideline)` for a list of all supported guidelines. The repository of this package contains [this machine readable version](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of these guidelines.
+#' @details Run `unique(rsi_translation$guideline)` for a list of all supported guidelines. The repository of this package contains [this machine readable version](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of these guidelines.
 #' 
 #' These guidelines are machine readable, since [](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt).
 #'
@@ -66,11 +66,12 @@
 #' # interpret MIC values
 #' as.rsi(x = as.mic(2),
 #'        mo = as.mo("S. pneumoniae"),
-#'        ab = "AMX",
+#'        ab = "AMP",
 #'        guideline = "EUCAST")
-#' as.rsi(x = as.mic(4),
+#'
-#'        mo = as.mo("S. pneumoniae"),
+#' as.rsi(x = as.disk(18),
-#'        ab = "AMX",
+#'        mo = "Strep pneu",  # `mo` will be coerced with as.mo()
+#'        ab = "ampicillin",  # and `ab` with as.ab()
 #'        guideline = "EUCAST")
 #'
 #' plot(rsi_data)    # for percentages
@@ -188,7 +189,7 @@ as.rsi.disk <- function(x, mo, ab, guideline = "EUCAST", ...) {
 get_guideline <- function(guideline) {
   guideline_param <- toupper(guideline)
   if (guideline_param %in% c("CLSI", "EUCAST")) {
-    guideline_param <- AMR::rsi_translation %>%
+    guideline_param <- rsi_translation %>%
       filter(guideline %like% guideline_param) %>%
       pull(guideline) %>%
       sort() %>%
@@ -196,9 +197,9 @@ get_guideline <- function(guideline) {
       .[1]
   }
   
-  if (!guideline_param %in% AMR::rsi_translation$guideline) {
+  if (!guideline_param %in% rsi_translation$guideline) {
     stop(paste0("invalid guideline: '", guideline,
-                "'.\nValid guidelines are: ", paste0("'", rev(sort(unique(AMR::rsi_translation$guideline))), "'", collapse = ", ")),
+                "'.\nValid guidelines are: ", paste0("'", rev(sort(unique(rsi_translation$guideline))), "'", collapse = ", ")),
          call. = FALSE)
   }
   
@@ -222,6 +223,7 @@ exec_as.rsi <- function(method, x, mo, ab, guideline) {
   mo_order <- as.mo(mo_order(mo))
   mo_becker <- as.mo(mo, Becker = TRUE)
   mo_lancefield <- as.mo(mo, Lancefield = TRUE)
+  mo_other <- as.mo("other")
   
   guideline_coerced <- get_guideline(guideline)
   if (guideline_coerced != guideline) {
@@ -229,7 +231,7 @@ exec_as.rsi <- function(method, x, mo, ab, guideline) {
   }
 
   new_rsi <- rep(NA_character_, length(x))
-  trans <- AMR::rsi_translation %>%
+  trans <- rsi_translation %>%
     filter(guideline == guideline_coerced & method == method_param) %>%
     mutate(lookup = paste(mo, ab))
 
@@ -239,6 +241,7 @@ exec_as.rsi <- function(method, x, mo, ab, guideline) {
   lookup_order <- paste(mo_order, ab)
   lookup_becker <- paste(mo_becker, ab)
   lookup_lancefield <- paste(mo_lancefield, ab)
+  lookup_other <- paste(mo_other, ab)
   
   for (i in seq_len(length(x))) {
     get_record <- trans %>%
@@ -247,7 +250,8 @@ exec_as.rsi <- function(method, x, mo, ab, guideline) {
                            lookup_family[i],
                            lookup_order[i],
                            lookup_becker[i],
-                           lookup_lancefield[i])) %>%
+                           lookup_lancefield[i],
+                           lookup_other[i])) %>%
       # be as specific as possible (i.e. prefer species over genus):
       arrange(desc(nchar(mo))) %>%
       .[1L, ]

R/rsi_calc.R

@@ -179,6 +179,8 @@ rsi_calc_df <- function(type, # "proportion" or "count"
                         combine_IR = FALSE,
                         combine_SI_missing = FALSE) {
   
+  check_dataset_integrity()
+  
   if (!"data.frame" %in% class(data)) {
     stop(paste0("`", type, "_df` must be called on a data.frame"), call. = FALSE)
   }
@@ -252,7 +254,7 @@ rsi_calc_df <- function(type, # "proportion" or "count"
     arrange(antibiotic, interpretation)
   
   if (!translate_ab == FALSE) {
-    res <- res %>% mutate(antibiotic = AMR::ab_property(antibiotic, property = translate_ab, language = language))
+    res <- res %>% mutate(antibiotic = ab_property(antibiotic, property = translate_ab, language = language))
   }
   
   as.data.frame(res, stringsAsFactors = FALSE)

data-raw/internals.R

@@ -73,7 +73,8 @@ rm(microorganisms.translation)
 library(dplyr, warn.conflicts = FALSE, quietly = TRUE)
 usethis::ui_done(paste0("Saving raw data to {usethis::ui_value('/data-raw/')}"))
 devtools::load_all(quiet = TRUE)
-write.table(AMR::rsi_translation,
+# give official names to ABs and MOs
+write.table(rsi_translation %>% mutate(ab = ab_name(ab), mo = mo_name(mo)),
             "data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE)
 write.table(microorganisms %>% mutate_if(~!is.numeric(.), as.character),
             "data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE)

data-raw/read_EUCAST.R

@@ -0,0 +1,206 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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 more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
+library(openxlsx)
+library(dplyr)
+library(cleaner)
+library(AMR)
+
+read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx") { 
+  
+  message("Getting sheet ", sheet)
+  sheet.bak <- sheet
+  
+  raw_data <- read.xlsx(xlsxFile = file,
+                        sheet = sheet,
+                        colNames = FALSE,
+                        skipEmptyRows = FALSE,
+                        skipEmptyCols = FALSE, 
+                        fillMergedCells = TRUE,
+                        na.strings = c("", "-", "NA", "IE", "IP"))
+  
+  # in the info header in the Excel file, EUCAST mentions which genera are targeted
+  if (sheet %like% "anaerob.*Gram.*posi") {
+    sheet <- paste0(c("Actinomyces", "Bifidobacterium", "Clostridioides", 
+                      "Clostridium", "Cutibacterium", "Eggerthella", 
+                      "Eubacterium", "Lactobacillus", "Propionibacterium", 
+                      "Staphylococcus saccharolyticus"), 
+                    collapse = "_")
+  } else if (sheet %like% "anaerob.*Gram.*nega") {
+    sheet <- paste0(c("Bacteroides",
+                      "Bilophila",
+                      "Fusobacterium",
+                      "Mobiluncus",
+                      "Parabacteroides",
+                      "Porphyromonas",
+                      "Prevotella"), 
+                    collapse = "_")
+  } else if (sheet == "Streptococcus A,B,C,G") {
+    sheet <- paste0(microorganisms %>%
+                      filter(genus == "Streptococcus") %>%
+                      mutate(lancefield = mo_name(mo, Lancefield = TRUE)) %>%
+                      filter(lancefield %like% "^Streptococcus group") %>% 
+                      pull(fullname), 
+                    collapse = "_")
+  } else if (sheet %like% "PK.*PD") {
+    sheet <- "UNKNOWN"
+  }
+  mo_sheet <- paste0(as.mo(unlist(strsplit(sheet, "_"))), collapse = "|")
+  
+  set_columns_names <- function(x, cols) {
+    colnames(x) <- cols[1:length(colnames(x))]
+    x
+  }
+  
+  get_mo <- function(x) {
+    for (i in seq_len(length(x))) {
+      y <- trimws(unlist(strsplit(x[i], "(,|and)")))
+      y <- trimws(gsub("[(].*[)]", "", y))
+      y <- suppressWarnings(as.mo(y, allow_uncertain = FALSE))
+      y <- y[!is.na(y) & y != "UNKNOWN"]
+      x[i] <- paste(y, collapse = "|")
+    }
+    x
+  }
+  
+  MICs_with_trailing_superscript <- c(0.0011:0.0019, 11:19, 21:29, 0.51:0.59, 41:49,
+                                      81:89, 0.031:0.039, 0.061:0.069, 0.251:0.259,
+                                      0.1251:0.1259, 161:169, 321:329)
+  
+  has_zone_diameters <- rep(any(unlist(raw_data) %like% "zone diameter"), nrow(raw_data))
+
+  cleaned <- raw_data %>% 
+    as_tibble() %>% 
+    set_columns_names(LETTERS) %>% 
+    transmute(drug = A,
+              MIC_S = B,
+              MIC_R = C,
+              disk_dose = ifelse(has_zone_diameters, E, NA_character_),
+              disk_S = ifelse(has_zone_diameters, `F`, NA_character_),
+              disk_R = ifelse(has_zone_diameters, G, NA_character_)) %>% 
+    filter(!is.na(drug),
+           !(is.na(MIC_S) & is.na(MIC_R) & is.na(disk_S) & is.na(disk_R)),
+           !MIC_S %like% "(MIC|S ≤|note)",
+           drug != MIC_S) %>% 
+    mutate(administration = case_when(drug %like% "[( ]oral" ~ "oral",
+                                      drug %like% "[( ]iv"   ~ "iv",
+                                      TRUE ~ NA_character_),
+           uti = ifelse(drug %like% "(UTI|urinary|urine)", TRUE, FALSE),
+           systemic = ifelse(drug %like% "(systemic|septic)", TRUE, FALSE),
+           mo = ifelse(drug %like% "([.]|spp)", get_mo(drug), mo_sheet)) %>% 
+    # clean disk doses
+    mutate(disk_dose = clean_character(disk_dose, remove = "[^0-9.-]")) %>% 
+    # clean MIC and disk values
+    mutate(MIC_S = gsub(".,.", "", MIC_S), # remove superscript notes with comma, like 0.5^2,3
+           MIC_R = gsub(".,.", "", MIC_R),
+           disk_S = gsub(".,.", "", disk_S),
+           disk_R = gsub(".,.", "", disk_R),
+           MIC_S = clean_double(MIC_S), # make them valid numeric values
+           MIC_R = clean_double(MIC_R),
+           disk_S = clean_integer(disk_S),
+           disk_R = clean_integer(disk_R),
+           # invalid MIC values have a superscript text, delete those
+           MIC_S = ifelse(MIC_S %in% MICs_with_trailing_superscript,
+                          substr(MIC_S, 1, nchar(MIC_S) - 1),
+                          MIC_S),
+           MIC_R = ifelse(MIC_R %in% MICs_with_trailing_superscript,
+                          substr(MIC_R, 1, nchar(MIC_R) - 1),
+                          MIC_R)
+    ) %>% 
+    # clean drug names
+    mutate(drug = gsub(" ?[(, ].*$", "", drug),
+           drug = gsub("[1-9]+$", "", drug),
+           ab = as.ab(drug)) %>% 
+    select(ab, mo, everything(), -drug)
+  
+  # new row for every different MO mentioned
+  for (i in 1:nrow(cleaned)) {
+    mo <- cleaned[i, "mo", drop = TRUE]
+    if (grepl(pattern = "|", mo, fixed = TRUE)) {
+      mo_vect <- unlist(strsplit(mo, "|", fixed = TRUE))
+      cleaned[i, "mo"] <- mo_vect[1]
+      for (j in seq_len(length(mo_vect))) {
+        cleaned <- bind_rows(cleaned, cleaned[i ,])
+        cleaned[nrow(cleaned), "mo"] <- mo_vect[j]
+      }
+    }
+  }
+  
+  cleaned <- cleaned %>% 
+    distinct(ab, mo, administration, uti, systemic, .keep_all = TRUE) %>% 
+    arrange(ab, mo) %>% 
+    mutate_at(c("MIC_S", "MIC_R", "disk_S", "disk_R"), as.double) %>%
+    pivot_longer(c("MIC_S", "MIC_R", "disk_S", "disk_R"), "type") %>% 
+    mutate(method = ifelse(type %like% "MIC", "MIC", "DISK"), 
+           type = gsub("^.*_", "breakpoint_", type)) %>%
+    pivot_wider(names_from = type, values_from = value) %>% 
+    mutate(guideline = "EUCAST 2020",
+           disk_dose = ifelse(method == "DISK", disk_dose, NA_character_),
+           mo = ifelse(mo == "", mo_sheet, mo)) %>% 
+    filter(!(is.na(breakpoint_S) & is.na(breakpoint_R))) %>% 
+    # comply with rsi_translation for now
+    transmute(guideline,
+              method, 
+              site = case_when(uti ~ "UTI",
+                               systemic ~ "Systemic",
+                               TRUE ~ administration),
+              mo, ab, 
+              ref_tbl = sheet.bak, 
+              disk_dose = ifelse(!is.na(disk_dose), paste0(disk_dose, "ug"), NA_character_),
+              breakpoint_S, 
+              breakpoint_R)
+  
+  cleaned
+}
+
+sheets_to_analyse <- c("Enterobacterales",
+                       "Pseudomonas",
+                       "S.maltophilia",
+                       "Acinetobacter",
+                       "Staphylococcus",
+                       "Enterococcus",
+                       "Streptococcus A,B,C,G",
+                       "S.pneumoniae",
+                       "Viridans group streptococci",
+                       "H.influenzae",
+                       "M.catarrhalis",
+                       "N.gonorrhoeae",
+                       "N.meningitidis",
+                       "Anaerobes, Grampositive",
+                       "C.difficile",
+                       "Anaerobes, Gramnegative",
+                       "H.pylori",
+                       "L.monocytogenes",
+                       "P.multocida",
+                       "C.jejuni_C.coli",
+                       "Corynebacterium",
+                       "A.sanguinicola_A.urinae",
+                       "K.kingae",
+                       "Aeromonas",
+                       "B.pseudomallei",
+                       "M.tuberculosis",
+                       "PK PD breakpoints")
+
+new_EUCAST <- read_EUCAST(sheets_to_analyse[1]) # takes the longest time
+for (i in 2:length(sheets_to_analyse)) {
+  new_EUCAST <<- new_EUCAST %>% bind_rows(read_EUCAST(sheets_to_analyse[i]))
+}
+

data-raw/reproduction_of_rsi_translation.R

@@ -3,7 +3,7 @@ library(dplyr)
 # Installed WHONET 2019 software on Windows (http://www.whonet.org/software.html),
 #    opened C:\WHONET\Codes\WHONETCodes.mdb in MS Access
 #    and exported table 'DRGLST1' to MS Excel
-DRGLST1 <- readxl::read_excel("data-raw/DRGLST1.xlsx")
+DRGLST1 <- readxl::read_excel("data-raw/DRGLST1.xlsx", na = c("", "NA", "-"))
 rsi_translation <- DRGLST1 %>%
   # only keep CLSI and EUCAST guidelines:
   filter(GUIDELINES %like% "^(CLSI|EUCST)") %>%
@@ -38,11 +38,17 @@ tbl_disk <- rsi_translation %>%
 rsi_translation <- bind_rows(tbl_mic, tbl_disk) %>%
   rename(disk_dose = dose_disk) %>% 
   mutate(disk_dose = gsub("µ", "u", disk_dose)) %>% 
-  select(-ends_with("_mic"), -ends_with("_disk")) %>%
+  select(-ends_with("_mic"), -ends_with("_disk"))
+
+# add new EUCAST with read_EUCAST.R
+rsi_translation <- rsi_translation %>%
+  bind_rows(new_EUCAST) %>% 
+  mutate(uti = site %like% "(UTI|urinary)") %>% 
   as.data.frame(stringsAsFactors = FALSE) %>%
   # force classes again
   mutate(mo = as.mo(mo),
-         ab = as.ab(ab))
+         ab = as.ab(ab)) %>% 
+  arrange(desc(guideline), ab, mo, method)
 
 # save to package
 usethis::use_data(rsi_translation, overwrite = TRUE)

docs/404.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span>
       </span>
     </div>
 

docs/authors.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span>
       </span>
     </div>
 

docs/index.html

@@ -45,7 +45,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span>
       </span>
     </div>
 
@@ -187,9 +187,9 @@
 
       </header><div class="row">
   <div class="contents col-md-9">
-<div id="amr-for-r" class="section level1">
+<div id="amr-for-r-" class="section level1">
 <div class="page-header"><h1 class="hasAnchor">
-<a href="#amr-for-r" class="anchor"></a><code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px">
+<a href="#amr-for-r-" class="anchor"></a><code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px">
 </h1></div>
 <blockquote>
 <p><em>18 October 2019</em><br><strong>METHODS PAPER PREPRINTED</strong><br>
@@ -265,7 +265,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
 <h4 class="hasAnchor">
 <a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
 <p>This package is available <a href="https://cran.r-project.org/package=AMR">here on the official R network (CRAN)</a>, which has a peer-reviewed submission process. Install this package in R from CRAN by using the command:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"AMR"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"AMR"</span>)</span></code></pre></div>
 <p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
 <p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
 </div>
@@ -273,8 +273,8 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
 <h4 class="hasAnchor">
 <a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
 <p>The latest and unpublished development version can be installed with (<strong>precaution: may be unstable</strong>):</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"devtools"</span>)</a>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a><span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"devtools"</span>)</span>
-<a class="sourceLine" id="cb2-2" data-line-number="2">devtools<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/devtools/man/remote-reexports.html">install_gitlab</a></span>(<span class="st">"msberends/AMR"</span>)</a></code></pre></div>
+<span id="cb2-2"><a href="#cb2-2"></a>devtools<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/devtools/man/remote-reexports.html">install_gitlab</a></span>(<span class="st">"msberends/AMR"</span>)</span></code></pre></div>
 </div>
 </div>
 <div id="get-started" class="section level3">
@@ -298,9 +298,9 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
 <p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
 <p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
 </div>
-<div id="whonet-ears-net" class="section level4">
+<div id="whonet--ears-net" class="section level4">
 <h4 class="hasAnchor">
-<a href="#whonet-ears-net" class="anchor"></a>WHONET / EARS-Net</h4>
+<a href="#whonet--ears-net" class="anchor"></a>WHONET / EARS-Net</h4>
 <p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure as a WHONET export file. Furthermore, this package also contains a <a href="./reference/antibiotics.html">data set antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
 <p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
 </div>

docs/pkgdown.yml

@@ -1,4 +1,4 @@
-pandoc: 2.3.1
+pandoc: 2.7.3
 pkgdown: 1.4.1
 pkgdown_sha: ~
 articles:

docs/reference/as.rsi.html

@@ -85,7 +85,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span>
       </span>
     </div>
 
@@ -273,7 +273,7 @@
     </tr>
     <tr>
       <th>guideline</th>
-      <td><p>defaults to the latest included EUCAST guideline, run <code><a href='https://rdrr.io/r/base/unique.html'>unique(AMR::rsi_translation$guideline)</a></code> for all options</p></td>
+      <td><p>defaults to the latest included EUCAST guideline, run <code><a href='https://rdrr.io/r/base/unique.html'>unique(rsi_translation$guideline)</a></code> for all options</p></td>
     </tr>
     <tr>
       <th>col_mo</th>
@@ -290,7 +290,7 @@
     <p>Ordered factor with new class <code>rsi</code></p>
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p>Run <code><a href='https://rdrr.io/r/base/unique.html'>unique(AMR::rsi_translation$guideline)</a></code> for a list of all supported guidelines. The repository of this package contains <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>this machine readable version</a> of these guidelines.</p>
+    <p>Run <code><a href='https://rdrr.io/r/base/unique.html'>unique(rsi_translation$guideline)</a></code> for a list of all supported guidelines. The repository of this package contains <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>this machine readable version</a> of these guidelines.</p>
 <p>These guidelines are machine readable, since <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'></a>.</p>
 <p>After using <code>as.rsi()</code>, you can use <code><a href='eucast_rules.html'>eucast_rules()</a></code> to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
 <p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p>
@@ -335,11 +335,12 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='co'># interpret MIC values</span>
 <span class='fu'>as.rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>2</span>),
        <span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
-       <span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
+       <span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMP"</span>,
        <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
-<span class='fu'>as.rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>4</span>),
+
-       <span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
+<span class='fu'>as.rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>18</span>),
-       <span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
+       <span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"Strep pneu"</span>,  <span class='co'># `mo` will be coerced with as.mo()</span>
+       <span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"ampicillin"</span>,  <span class='co'># and `ab` with as.ab()</span>
        <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
 
 <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>rsi_data</span>)    <span class='co'># for percentages</span>

docs/reference/filter_ab_class.html

@@ -85,7 +85,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span>
       </span>
     </div>
 
@@ -272,7 +272,7 @@
     </tr>
     <tr>
       <th>ab_class</th>
-      <td><p>an antimicrobial class, like <code>"carbapenems"</code>, as can be found in <code><a href='antibiotics.html'>AMR::antibiotics$group</a></code></p></td>
+      <td><p>an antimicrobial class, like <code>"carbapenems"</code>, as can be found in <code><a href='antibiotics.html'>antibiotics$group</a></code></p></td>
     </tr>
     <tr>
       <th>result</th>

docs/reference/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span>
       </span>
     </div>
 

docs/reference/like.html

@@ -85,7 +85,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9023</span>
       </span>
     </div>
 
@@ -296,15 +296,15 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
 <span class='co'># also supports multiple patterns, length must be equal to x</span>
 <span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Test case"</span>, <span class='st'>"Something different"</span>, <span class='st'>"Yet another thing"</span>)
-<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"case"</span>, <span class='st'>"diff"</span>, <span class='st'>"yet"</span>)
+<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(     <span class='st'>"case"</span>,           <span class='st'>"diff"</span>,      <span class='st'>"yet"</span>)
 <span class='no'>a</span> <span class='kw'>%like%</span> <span class='no'>b</span>
 <span class='co'>#&gt; TRUE TRUE TRUE</span>
 
 <span class='co'># get frequencies of bacteria whose name start with 'Ent' or 'ent'</span>
 <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
 <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span>
+  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='no'>mo</span>) <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='no'>mo</span>))</pre>
+  <span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>))</pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>

man/as.rsi.Rd

@@ -31,7 +31,7 @@ is.rsi.eligible(x, threshold = 0.05)
 
 \item{ab}{an antimicrobial code, generated with \code{\link[=as.ab]{as.ab()}}}
 
-\item{guideline}{defaults to the latest included EUCAST guideline, run \code{unique(AMR::rsi_translation$guideline)} for all options}
+\item{guideline}{defaults to the latest included EUCAST guideline, run \code{unique(rsi_translation$guideline)} for all options}
 
 \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()}}.}
 
@@ -44,7 +44,7 @@ Ordered factor with new class \code{\link{rsi}}
 Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered factor with levels \verb{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning.
 }
 \details{
-Run \code{unique(AMR::rsi_translation$guideline)} for a list of all supported guidelines. The repository of this package contains \href{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{this machine readable version} of these guidelines.
+Run \code{unique(rsi_translation$guideline)} for a list of all supported guidelines. The repository of this package contains \href{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{this machine readable version} of these guidelines.
 
 These guidelines are machine readable, since \href{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{}.
 
@@ -91,11 +91,12 @@ as.rsi("<= 0.002; S") # will return S
 # interpret MIC values
 as.rsi(x = as.mic(2),
        mo = as.mo("S. pneumoniae"),
-       ab = "AMX",
+       ab = "AMP",
        guideline = "EUCAST")
-as.rsi(x = as.mic(4),
+
-       mo = as.mo("S. pneumoniae"),
+as.rsi(x = as.disk(18),
-       ab = "AMX",
+       mo = "Strep pneu",  # `mo` will be coerced with as.mo()
+       ab = "ampicillin",  # and `ab` with as.ab()
        guideline = "EUCAST")
 
 plot(rsi_data)    # for percentages

man/filter_ab_class.Rd

@@ -45,7 +45,7 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
 \arguments{
 \item{x}{a data set}
 
-\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}, as can be found in \code{\link[=antibiotics]{AMR::antibiotics$group}}}
+\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}, as can be found in \code{\link[=antibiotics]{antibiotics$group}}}
 
 \item{result}{an antibiotic result: S, I or R (or a combination of more of them)}
 

man/like.Rd

@@ -55,15 +55,15 @@ b \%like\% a
 
 # also supports multiple patterns, length must be equal to x
 a <- c("Test case", "Something different", "Yet another thing")
-b <- c("case", "diff", "yet")
+b <- c(     "case",           "diff",      "yet")
 a \%like\% b
 #> TRUE TRUE TRUE
 
 # get frequencies of bacteria whose name start with 'Ent' or 'ent'
 library(dplyr)
 example_isolates \%>\%
-  filter(mo_genus(mo) \%like\% '^ent') \%>\%
+  filter(mo_name(mo) \%like\% '^ent') \%>\%
-  freq(mo_fullname(mo))
+  freq(mo_genus(mo))
 }
 \seealso{
 \code{\link[base:grep]{base::grep()}}

tests/testthat/test-data.R

@@ -22,6 +22,9 @@
 context("data.R")
 
 test_that("data sets are valid", {
+  
+  expect_true(check_dataset_integrity()) # in misc.R
+  
   # IDs should always be unique
   expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
   expect_identical(class(microorganisms$mo), "mo")

tests/testthat/test-mo.R

@@ -26,7 +26,7 @@ test_that("as.mo works", {
   skip_on_cran()
  
   library(dplyr)
-  MOs <- AMR::microorganisms %>% filter(!is.na(mo), nchar(mo) > 3)
+  MOs <- microorganisms %>% filter(!is.na(mo), nchar(mo) > 3)
   expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))
   
   expect_identical(

tests/testthat/test-mo_property.R

@@ -63,7 +63,7 @@ test_that("mo_property works", {
   expect_true(mo_url("Escherichia coli") %like% "www.catalogueoflife.org")
 
   # test integrity
-  MOs <- AMR::microorganisms
+  MOs <- microorganisms
   expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
 
   # check languages