(v0.7.1.9035) cephalosporins and unit tests

R/ab.R

@@ -233,7 +233,7 @@ as.ab <- function(x) {
   }
 
   if (length(x_unknown) > 0) {
-    warning("These values could not be coerced to a valid antibiotic ID: ",
+    warning("These values could not be coerced to a valid antimicrobial ID: ",
             paste('"', sort(unique(x_unknown)), '"', sep = "", collapse = ', '),
             ".",
             call. = FALSE)

R/deprecated.R

@@ -29,6 +29,5 @@
 #' @rdname AMR-deprecated
 as.atc <- function(x) {
   .Deprecated("ab_atc", package = "AMR")
-  ab_atc(x)
+  AMR::ab_atc(x)
 }
-

R/eucast_rules.R

@@ -669,7 +669,7 @@ eucast_rules <- function(x,
       suppressWarnings(
         all_staph <- AMR::microorganisms %>%
           filter(genus == "Staphylococcus") %>%
-          mutate(CNS_CPS = mo_fullname(mo, Becker = "all"))
+          mutate(CNS_CPS = mo_name(mo, Becker = "all"))
       )
       if (eucast_rules_df[i, 3] %like% "coagulase-") {
         eucast_rules_df[i, 3] <- paste0("^(",

R/get_locale.R

@@ -21,14 +21,16 @@
 
 #' Translate strings from AMR package
 #'
-#' For language-dependent output of AMR functions, like \code{\link{mo_fullname}} and \code{\link{mo_type}}.
+#' For language-dependent output of AMR functions, like \code{\link{mo_name}},  \code{\link{mo_type}} and \code{\link{ab_name}}.
 #' @details Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv}.
 #'
+#' Currently supported languages can be found if running: \code{unique(AMR:::translations_file$lang)}.
+#'
 #' Please suggest your own translations \href{https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation\%20suggestion}{by creating a new issue on our repository}.
 #'
 #' This file will be read by all functions where a translated output can be desired, like all \code{\link{mo_property}} functions (\code{\link{mo_fullname}}, \code{\link{mo_type}}, etc.).
 #'
-#' The system language will be used at default, if supported, using \code{\link{get_locale}}. The system language can be overwritten with \code{\link{getOption}("AMR_locale")}.
+#' The system language will be used at default, if that language is supported. The system language can be overwritten with \code{\link{getOption}("AMR_locale")}.
 #' @inheritSection AMR Read more on our website!
 #' @rdname translate
 #' @name translate
@@ -39,27 +41,27 @@
 #' # with get_locale()
 #'
 #' # English
-#' mo_fullname("CoNS", language = "en")
+#' mo_name("CoNS", language = "en")
 #' #> "Coagulase-negative Staphylococcus (CoNS)"
 #'
 #' # German
-#' mo_fullname("CoNS", language = "de")
+#' mo_name("CoNS", language = "de")
 #' #> "Koagulase-negative Staphylococcus (KNS)"
 #'
 #' # Dutch
-#' mo_fullname("CoNS", language = "nl")
+#' mo_name("CoNS", language = "nl")
 #' #> "Coagulase-negatieve Staphylococcus (CNS)"
 #'
 #' # Spanish
-#' mo_fullname("CoNS", language = "es")
+#' mo_name("CoNS", language = "es")
 #' #> "Staphylococcus coagulasa negativo (SCN)"
 #'
 #' # Italian
-#' mo_fullname("CoNS", language = "it")
+#' mo_name("CoNS", language = "it")
 #' #> "Staphylococcus negativo coagulasi (CoNS)"
 #'
 #' # Portuguese
-#' mo_fullname("CoNS", language = "pt")
+#' mo_name("CoNS", language = "pt")
 #' #> "Staphylococcus coagulase negativo (CoNS)"
 get_locale <- function() {
   if (getOption("AMR_locale", "en") != "en") {

R/like.R

@@ -28,7 +28,7 @@
 #' @rdname like
 #' @export
 #' @details Using RStudio? This function can also be inserted from the Addins menu and can have its own Keyboard Shortcut like Ctrl+Shift+L or Cmd+Shift+L (see Tools > Modify Keyboard Shortcuts...).
-#' @source Idea from the \href{https://github.com/Rdatatable/data.table/blob/master/R/like.R}{\code{like} function from the \code{data.table} package}, but made it case insensitive at default and let it support multiple patterns.
+#' @source Idea from the \href{https://github.com/Rdatatable/data.table/blob/master/R/like.R}{\code{like} function from the \code{data.table} package}, but made it case insensitive at default and let it support multiple patterns. Also, if the regex fails the first time, it tries again with \code{perl = TRUE}.
 #' @seealso \code{\link[base]{grep}}
 #' @inheritSection AMR Read more on our website!
 #' @examples

R/misc.R

@@ -29,48 +29,6 @@ addin_insert_like <- function() {
   rstudioapi::insertText(" %like% ")
 }
 
-# No export, no Rd
-# works exactly like round(), but rounds `round(44.55, 1)` as 44.6 instead of 44.5
-# and adds decimal zeroes until `digits` is reached when force_zero = TRUE
-round2 <- function(x, digits = 0, force_zero = TRUE) {
-  # https://stackoverflow.com/a/12688836/4575331
-  val <- (trunc((abs(x) * 10 ^ digits) + 0.5) / 10 ^ digits) * sign(x)
-  if (digits > 0 & force_zero == TRUE) {
-    val[val != as.integer(val)] <- paste0(val[val != as.integer(val)],
-                                          strrep("0", max(0, digits - nchar(gsub(".*[.](.*)$", "\\1", val[val != as.integer(val)])))))
-  }
-  val
-}
-
-# Coefficient of variation (CV)
-cv <- function(x, na.rm = TRUE) {
-  stats::sd(x, na.rm = na.rm) / base::abs(base::mean(x, na.rm = na.rm))
-}
-
-# Coefficient of dispersion, or coefficient of quartile variation (CQV).
-# (Bonett et al., 2006: Confidence interval for a coefficient of quartile variation).
-cqv <- function(x, na.rm = TRUE) {
-  fives <- stats::fivenum(x, na.rm = na.rm)
-  (fives[4] - fives[2]) / (fives[4] + fives[2])
-}
-
-# show bytes as kB/MB/GB
-# size_humanreadable(123456) # 121 kB
-# size_humanreadable(12345678) # 11.8 MB
-size_humanreadable <- function(bytes, decimals = 1) {
-  bytes <- bytes %>% as.double()
-  # Adapted from:
-  # http://jeffreysambells.com/2012/10/25/human-readable-filesize-php
-  size <- c('B','kB','MB','GB','TB','PB','EB','ZB','YB')
-  factor <- floor((nchar(bytes) - 1) / 3)
-  # added slight improvement; no decimals for B and kB:
-  decimals <- rep(decimals, length(bytes))
-  decimals[size[factor + 1] %in% c('B', 'kB')] <- 0
-
-  out <- paste(sprintf(paste0("%.", decimals, "f"), bytes / (1024 ^ factor)), size[factor + 1])
-  out
-}
-
 percent_clean <- clean:::percent
 # No export, no Rd
 percent <- function(x, round = 1, force_zero = FALSE, decimal.mark = getOption("OutDec"), big.mark = ",", ...) {

R/mo.R

@@ -477,7 +477,8 @@ exec_as.mo <- function(x,
     # translate to English for supported languages of mo_property
     x <- gsub("(gruppe|groep|grupo|gruppo|groupe)", "group", x, ignore.case = TRUE)
     x <- gsub("(hefe|gist|gisten|levadura|lievito|fermento|levure)[a-z]*", "yeast", x, ignore.case = TRUE)
-    x <- gsub("(schimmels?|mofo|molde|stampo|moisissure)[a-z]*", "fungus", x, ignore.case = TRUE)
+    x <- gsub("(schimmels?|mofo|molde|stampo|moisissure|fungi)[a-z]*", "fungus", x, ignore.case = TRUE)
+    x <- gsub("Fungus[ph|f]rya", "Fungiphrya", x, ignore.case = TRUE)
     # remove non-text in case of "E. coli" except dots and spaces
     x <- gsub("[^.a-zA-Z0-9/ \\-]+", "", x)
     # replace minus by a space
@@ -1216,7 +1217,7 @@ exec_as.mo <- function(x,
             }
             return(found[1L])
           }
-          if (b.x_trimmed %like% "fungus") {
+          if (b.x_trimmed %like% "(fungus|fungi)" & !b.x_trimmed %like% "Fungiphrya") {
             found <- "F_FUNGUS"
             found_result <- found
             found <- microorganismsDT[mo == found, ..property][[1]]

R/mo_property.R

@@ -318,7 +318,7 @@ mo_synonyms <- function(x, ...) {
     }
   })
   if (length(syns) > 1) {
-    names(syns) <- mo_fullname(x)
+    names(syns) <- mo_name(x)
     result <- syns
   } else {
     result <- unlist(syns)
@@ -340,7 +340,7 @@ mo_info <- function(x, language = get_locale(),  ...) {
            url = unname(mo_url(y, open = FALSE)),
            ref = mo_ref(y))))
   if (length(info) > 1) {
-    names(info) <- mo_fullname(x)
+    names(info) <- mo_name(x)
     result <- info
   } else {
     result <- info[[1L]]
@@ -368,7 +368,7 @@ mo_url <- function(x, open = FALSE, ...) {
                              NA_character_))
 
   u <- df$url
-  names(u) <- AMR::mo_fullname(mo)
+  names(u) <- AMR::mo_name(mo)
   if (open == TRUE) {
     if (length(u) > 1) {
       warning("only the first URL will be opened, as `browseURL()` only suports one string.")

R/rsi.R

@@ -25,14 +25,14 @@
 #' @rdname as.rsi
 #' @param x vector of values (for class \code{mic}: an MIC value in mg/L, for class \code{disk}: a disk diffusion radius in millimeters)
 #' @param mo a microorganism code, generated with \code{\link{as.mo}}
-#' @param ab an antibiotic code, generated with \code{\link{as.ab}}
+#' @param ab an antimicrobial code, generated with \code{\link{as.ab}}
 #' @inheritParams first_isolate
 #' @param guideline defaults to the latest included EUCAST guideline, run \code{unique(AMR::rsi_translation$guideline)} for all options
-#' @param threshold maximum fraction of \code{x} that is allowed to fail transformation, see Examples
+#' @param threshold maximum fraction of invalid antimicrobial interpretations of \code{x}, see Examples
 #' @param ... parameters passed on to methods
 #' @details Run \code{unique(AMR::rsi_translation$guideline)} for a list of all supported guidelines.
 #'
-#' After using \code{as.rsi}, you can use \code{\link{eucast_rules}} to (1) apply inferred susceptibility and resistance based on results of other antibiotics and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
+#' After using \code{as.rsi}, you can use \code{\link{eucast_rules}} 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.
 #'
 #' The function \code{is.rsi.eligible} returns \code{TRUE} when a columns contains at most 5\% invalid antimicrobial interpretations (not S and/or I and/or R), and \code{FALSE} otherwise. The threshold of 5\% can be set with the \code{threshold} parameter.
 #' @section Interpretation of S, I and R:
@@ -265,7 +265,7 @@ as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", ...) {
 
   ab_cols <- colnames(x)[sapply(x, function(y) is.mic(y) | is.disk(y))]
   if (length(ab_cols) == 0) {
-    stop("No columns with MIC values or disk zones found in this data set. Use as.mic or as.disk to transform antibiotic columns.", call. = FALSE)
+    stop("No columns with MIC values or disk zones found in this data set. Use as.mic or as.disk to transform antimicrobial columns.", call. = FALSE)
   }
 
   # try to find columns based on type