(v0.7.1.9092) as.ab() improvements

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.7.1.9091
+Version: 0.7.1.9092
-Date: 2019-09-30
+Date: 2019-10-04
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 
@@ -34,17 +34,15 @@ Depends:
     R (>= 3.1.0)
 Imports:
     backports,
-    clean (>= 1.1.0.9000),
+    clean (>= 1.1.0),
     crayon (>= 1.3.0),
     data.table (>= 1.9.0),
     dplyr (>= 0.7.0),
     ggplot2,
-    hms,
     knitr (>= 1.0.0),
     microbenchmark,
     pillar,
     rlang (>= 0.3.1),
-    scales,
     tidyr (>= 0.7.0)
 Suggests:
     covr (>= 3.0.1),

NAMESPACE

@@ -233,7 +233,6 @@ exportMethods(summary.mo)
 exportMethods(summary.rsi)
 importFrom(clean,freq)
 importFrom(clean,freq.default)
-importFrom(clean,percentage)
 importFrom(clean,top_freq)
 importFrom(crayon,bgGreen)
 importFrom(crayon,bgRed)

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 0.7.1.9091
+# AMR 0.7.1.9092
-<small>Last updated: 30-Sep-2019</small>
+<small>Last updated: 04-Oct-2019</small>
 
 ### Breaking
 * Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:
@@ -94,6 +94,7 @@
   * Added support for unknown yeasts and fungi
   * Changed most microorganism IDs to improve readability. For example, the old code `B_ENTRC_FAE` could have been both *E. faecalis* and *E. faecium*. Its new code is `B_ENTRC_FCLS` and *E. faecium* has become `B_ENTRC_FACM`. Also, the Latin character æ (ae) is now preserved at the start of each genus and species abbreviation. For example, the old code for *Aerococcus urinae* was `B_ARCCC_NAE`. This is now `B_AERCC_URIN`.
     **IMPORTANT:** Old microorganism IDs are still supported, but support will be dropped in a future version. Use `as.mo()` on your old codes to transform them to the new format. Using functions from the `mo_*` family (like `mo_name()` and `mo_gramstain()`) on old codes, will throw a warning.
+* More intelligent guessing for `as.ab()`
 * Renamed data set `septic_patients` to `example_isolates`
 * Function `eucast_rules()`:
   * Fixed a bug for *Yersinia pseudotuberculosis*

R/ab.R

@@ -23,6 +23,7 @@
 #'
 #' Use this function to determine the antibiotic code of one or more antibiotics. The data set \code{\link{antibiotics}} will be searched for abbreviations, official names and synonyms (brand names).
 #' @param x character vector to determine to antibiotic ID
+#' @param ... arguments passed on to internal functions
 #' @rdname as.ab
 #' @keywords atc
 #' @inheritSection WHOCC WHOCC
@@ -57,7 +58,7 @@
 #' # they use as.ab() internally:
 #' ab_name("J01FA01")    # "Erythromycin"
 #' ab_name("eryt")       # "Erythromycin"
-as.ab <- function(x) {
+as.ab <- function(x, ...) {
   if (is.ab(x)) {
     return(x)
   }
@@ -69,6 +70,9 @@ as.ab <- function(x) {
   }
 
   x_bak <- x
+  # remove diacritics
+  x <- iconv(x, from = "UTF-8", to = "ASCII//TRANSLIT")
+  x <- gsub('"', "", x, fixed = TRUE)
   # remove suffices
   x_bak_clean <- gsub("_(mic|rsi|dis[ck])$", "", x, ignore.case = TRUE)
   # remove disk concentrations, like LVX_NM -> LVX
@@ -76,9 +80,15 @@ as.ab <- function(x) {
   # remove part between brackets if that's followed by another string
   x_bak_clean <- gsub("(.*)+ [(].*[)]", "\\1", x_bak_clean)
   # keep only a-Z, 0-9, space, slash and dash
-  x_bak_clean <- gsub("[^A-Z0-9 /-]", "", x_bak_clean, ignore.case = TRUE)
+  # x_bak_clean <- gsub("[^A-Z0-9 /-]", "", x_bak_clean, ignore.case = TRUE)
   # keep only max 1 space
   x_bak_clean <- trimws(gsub(" +", " ", x_bak_clean, ignore.case = TRUE))
+  # non-character, space or number should be a slash
+  x_bak_clean <- gsub("[^A-Za-z0-9 ]", "/", x_bak_clean)
+  # spaces around non-characters must be removed: amox + clav -> amox/clav
+  x_bak_clean <- gsub("(.*[a-zA-Z0-9]) ([^a-zA-Z0-9].*)", "\\1\\2", x_bak_clean)
+  x_bak_clean <- gsub("(.*[^a-zA-Z0-9]) ([a-zA-Z0-9].*)", "\\1\\2", x_bak_clean)
+
   x <- unique(x_bak_clean)
   x_new <- rep(NA_character_, length(x))
   x_unknown <- character(0)
@@ -181,6 +191,7 @@ as.ab <- function(x) {
     x_spelling <- gsub("(o\\+n|o\\+ne\\+)$", "o+ne*", x_spelling)
     # replace multiple same characters to single one with '+', like "ll" -> "l+"
     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
     if (length(found) > 0) {
@@ -218,6 +229,43 @@ as.ab <- function(x) {
       }
     }
     
+    if (!isFALSE(list(...)$initial_search)) {
+      # transform back from other languages and try again
+      x_translated <- paste(lapply(strsplit(x[i], "[^a-zA-Z0-9 ]"),
+                                   function(y) {
+                                     for (i in 1:length(y)) {
+                                       y[i] <- ifelse(tolower(y[i]) %in% tolower(translations_file$replacement),
+                                                      translations_file[which(tolower(translations_file$replacement) == tolower(y[i]) &
+                                                                                !isFALSE(translations_file$fixed)), "pattern"],
+                                                      y[i])
+                                     }
+                                     y
+                                   })[[1]],
+                            collapse = "/")
+      x_translated_guess <- suppressWarnings(as.ab(x_translated, initial_search = FALSE))
+      if (!is.na(x_translated_guess)) {
+        x_new[i] <- x_translated_guess
+        next
+      }
+      # now also try to coerce brandname combinations like "Amoxy/clavulanic acid"
+      x_translated <- paste(lapply(strsplit(x_translated, "[^a-zA-Z0-9 ]"),
+                                   function(y) {
+                                     for (i in 1:length(y)) {
+                                       y_name <- suppressWarnings(ab_name(y[i], language = NULL, initial_search = FALSE))
+                                       y[i] <- ifelse(!is.na(y_name),
+                                                      y_name,
+                                                      y[i])
+                                     }
+                                     y
+                                   })[[1]],
+                            collapse = "/")
+      x_translated_guess <- suppressWarnings(as.ab(x_translated, initial_search = FALSE))
+      if (!is.na(x_translated_guess)) {
+        x_new[i] <- x_translated_guess
+        next
+      }
+    }
+    
     # not found
     x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
   }

R/ab_property.R

@@ -188,7 +188,7 @@ ab_validate <- function(x, property, ...) {
            error = function(e) stop(e$message, call. = FALSE))
 
   if (!all(x %in% AMR::antibiotics[, property])) {
-    x <- data.frame(ab = AMR::as.ab(x), stringsAsFactors = FALSE) %>%
+    x <- data.frame(ab = AMR::as.ab(x, ...), stringsAsFactors = FALSE) %>%
       left_join(AMR::antibiotics, by = "ab") %>%
       pull(property)
   }

R/availability.R

@@ -27,7 +27,7 @@
 #' @details The function returns a \code{data.frame} with columns \code{"resistant"} and \code{"visual_resistance"}. The values in that columns are calculated with \code{\link{portion_R}}.
 #' @return \code{data.frame} with column names of \code{tbl} as row names
 #' @inheritSection AMR Read more on our website!
-#' @importFrom clean percentage
+# @importFrom clean percentage
 #' @export
 #' @examples
 #' availability(example_isolates)

R/bug_drug_combinations.R

@@ -33,7 +33,7 @@
 #' @inheritParams base::formatC
 #' @importFrom dplyr %>% rename group_by select mutate filter pull
 #' @importFrom tidyr spread
-#' @importFrom clean freq percentage
+# @importFrom clean freq percentage
 #' @details The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S. 
 #' 
 #' The language of the output can be overwritten with \code{options(AMR_locale)}, please see \link{translate}.

R/first_isolate.R

@@ -75,7 +75,7 @@
 #' @export
 #' @importFrom dplyr arrange_at lag between row_number filter mutate arrange pull ungroup
 #' @importFrom crayon blue bold silver
-#' @importFrom clean percentage
+# @importFrom clean percentage
 #' @return Logical vector
 #' @source Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
 #' @inheritSection AMR Read more on our website!

R/freq.R

@@ -25,7 +25,8 @@ clean::freq
 
 #' @exportMethod freq.mo
 #' @importFrom dplyr n_distinct
-#' @importFrom clean freq.default percentage
+#' @importFrom clean freq.default
+# @importFrom clean percentage
 #' @export
 #' @noRd
 freq.mo <- function(x, ...) {

R/ggplot_rsi.R

@@ -337,7 +337,7 @@ facet_rsi <- function(facet = c("interpretation", "antibiotic"), nrow = NULL) {
 }
 
 #' @rdname ggplot_rsi
-#' @importFrom clean percentage
+# @importFrom clean percentage
 #' @export
 scale_y_percent <- function(breaks = seq(0, 1, 0.1), limits = NULL) {
   stopifnot_installed_package("ggplot2")
@@ -387,7 +387,7 @@ theme_rsi <- function() {
 
 #' @rdname ggplot_rsi
 #' @importFrom dplyr mutate %>% group_by_at
-#' @importFrom clean percentage
+# @importFrom clean percentage
 #' @export
 labels_rsi_count <- function(position = NULL,
                              x = "antibiotic",

R/misc.R

@@ -127,3 +127,45 @@ class_integrity_check <- function(value, type, check_vector) {
   }
   value
 }
+
+
+
+
+# Percentages -------------------------------------------------------------
+# Can all be removed when clean 1.2.0 is on CRAN
+
+getdecimalplaces <- function(x, minimum = 0, maximum = 3) {
+  if (maximum < minimum) {
+    maximum <- minimum
+  }
+  if (minimum > maximum) {
+    minimum <- maximum
+  }
+  max_places <- max(unlist(lapply(strsplit(sub('0+$', '', 
+                                               as.character(x * 100)), ".", fixed = TRUE),
+                                  function(y) ifelse(length(y) == 2, nchar(y[2]), 0))), na.rm = TRUE)
+  max(min(max_places,
+          maximum, na.rm = TRUE),
+      minimum, na.rm = TRUE)
+}
+
+round2 <- function(x, digits = 0, force_zero = TRUE) {
+  # https://stackoverflow.com/a/12688836/4575331
+  val <- (trunc((abs(x) * 10 ^ digits) + 0.5) / 10 ^ digits) * sign(x)
+  if (digits > 0 & force_zero == TRUE) {
+    val[val != as.integer(val)] <- paste0(val[val != as.integer(val)],
+                                          strrep("0", max(0, digits - nchar(gsub(".*[.](.*)$", "\\1", val[val != as.integer(val)])))))
+  }
+  val
+}
+
+percentage <- function(x, digits = NULL, ...) {
+  if (is.null(digits)) {
+    digits <- getdecimalplaces(x, minimum = 0, maximum = 1)
+  }
+  # round right: percentage(0.4455) should return "44.6%", not "44.5%"
+  x <- as.numeric(round2(x, digits = digits + 2))
+  x_formatted <- format(as.double(x) * 100, scientific = FALSE, digits = digits, nsmall = digits, ...)
+  x_formatted[!is.na(x)] <- paste0(x_formatted[!is.na(x)], "%")
+  x_formatted
+}

R/mo.R

@@ -268,7 +268,7 @@ is.mo <- function(x) {
 #' @importFrom dplyr %>% pull left_join n_distinct progress_estimated filter distinct
 #' @importFrom data.table data.table as.data.table setkey
 #' @importFrom crayon magenta red blue silver italic
-#' @importFrom clean percentage
+# @importFrom clean percentage
 # param property a column name of AMR::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

R/portion.R

@@ -26,7 +26,7 @@
 #' \code{portion_R} and \code{portion_IR} can be used to calculate resistance, \code{portion_S} and \code{portion_SI} can be used to calculate susceptibility.\cr
 #' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link{as.rsi}} if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See Examples.
 #' @param minimum the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.
-#' @param as_percent a logical to indicate whether the output must be returned as a hundred fold with \% sign (a character) using\code{\link[clean]{percentage}}. A value of \code{0.123456} will then be returned as \code{"12.3\%"}.
+#' @param as_percent a logical to indicate whether the output must be returned as a hundred fold with \% sign (a character). A value of \code{0.123456} will then be returned as \code{"12.3\%"}.
 #' @param only_all_tested (for combination therapies, i.e. using more than one variable for \code{...}) a logical to indicate that isolates must be tested for all antibiotics, see section \emph{Combination therapy} below
 #' @param data a \code{data.frame} containing columns with class \code{rsi} (see \code{\link{as.rsi}})
 #' @param translate_ab a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations to, using \code{\link{ab_property}}

R/rsi_calc.R

@@ -39,7 +39,7 @@ dots2vars <- function(...) {
 }
 
 #' @importFrom dplyr %>% pull all_vars any_vars filter_all funs mutate_all
-#' @importFrom clean percentage
+# @importFrom clean percentage
 rsi_calc <- function(...,
                      ab_result,
                      minimum = 0,

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">0.7.1.9091</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9092</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">0.7.1.9091</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9092</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">0.7.1.9091</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9092</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">0.7.1.9091</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9092</span>
       </span>
     </div>
 

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">0.7.1.9091</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9092</span>
       </span>
     </div>
 

docs/news/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">0.7.1.9091</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9092</span>
       </span>
     </div>
 
@@ -231,11 +231,11 @@
       
     </div>
 
-    <div id="amr-0-7-1-9091" class="section level1">
+    <div id="amr-0-7-1-9092" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-7-1-9091" class="anchor"></a>AMR 0.7.1.9091<small> Unreleased </small>
+<a href="#amr-0-7-1-9092" class="anchor"></a>AMR 0.7.1.9092<small> Unreleased </small>
 </h1>
-<p><small>Last updated: 30-Sep-2019</small></p>
+<p><small>Last updated: 04-Oct-2019</small></p>
 <div id="breaking" class="section level3">
 <h3 class="hasAnchor">
 <a href="#breaking" class="anchor"></a>Breaking</h3>
@@ -336,6 +336,8 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
 <li>Changed most microorganism IDs to improve readability. For example, the old code <code>B_ENTRC_FAE</code> could have been both <em>E. faecalis</em> and <em>E. faecium</em>. Its new code is <code>B_ENTRC_FCLS</code> and <em>E. faecium</em> has become <code>B_ENTRC_FACM</code>. Also, the Latin character æ (ae) is now preserved at the start of each genus and species abbreviation. For example, the old code for <em>Aerococcus urinae</em> was <code>B_ARCCC_NAE</code>. This is now <code>B_AERCC_URIN</code>. <strong>IMPORTANT:</strong> Old microorganism IDs are still supported, but support will be dropped in a future version. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> on your old codes to transform them to the new format. Using functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) on old codes, will throw a warning.</li>
 </ul>
 </li>
+<li>More intelligent guessing for <code><a href="../reference/as.ab.html">as.ab()</a></code>
+</li>
 <li>Renamed data set <code>septic_patients</code> to <code>example_isolates</code>
 </li>
 <li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
@@ -1288,7 +1290,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
-        <li><a href="#amr-0-7-1-9091">0.7.1.9091</a></li>
+        <li><a href="#amr-0-7-1-9092">0.7.1.9092</a></li>
         <li><a href="#amr-0-7-1">0.7.1</a></li>
         <li><a href="#amr-0-7-0">0.7.0</a></li>
         <li><a href="#amr-0-6-1">0.6.1</a></li>

docs/reference/as.ab.html

@@ -15,21 +15,25 @@
 <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
 <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
+
 <!-- jquery -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
 <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
 
+
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
 
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
 
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-<!-- sticky kit -->
+<!-- headroom.js -->
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
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 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -45,15 +49,15 @@
 
   <link href="../extra.css" rel="stylesheet">
   <script src="../extra.js"></script>
+
 <meta property="og:title" content="Transform to antibiotic ID — as.ab" />
-
 <meta property="og:description" content="Use this function to determine the antibiotic code of one or more antibiotics. The data set antibiotics will be searched for abbreviations, official names and synonyms (brand names)." />
-
 <meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
 <meta name="twitter:card" content="summary" />
 
 
 
+
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@@ -64,6 +68,7 @@
 <![endif]-->
 
 
+
   </head>
 
   <body>
@@ -80,7 +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">0.7.1.9055</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9092</span>
       </span>
     </div>
 
@@ -189,7 +194,6 @@
   </a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://gitlab.com/msberends/AMR">
@@ -207,7 +211,7 @@
 </li>
       </ul>
       
-      <form class="navbar-form navbar-right" role="search">
+      <form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
         <div class="form-group">
           <input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
         </div>
@@ -218,6 +222,7 @@
 </div><!--/.navbar -->
 
       
+
       </header>
 
 <div class="row">
@@ -229,12 +234,10 @@
     </div>
 
     <div class="ref-description">
-    
     <p>Use this function to determine the antibiotic code of one or more antibiotics. The data set <code><a href='antibiotics.html'>antibiotics</a></code> will be searched for abbreviations, official names and synonyms (brand names).</p>
-    
     </div>
 
-    <pre class="usage"><span class='fu'>as.ab</span>(<span class='no'>x</span>)
+    <pre class="usage"><span class='fu'>as.ab</span>(<span class='no'>x</span>, <span class='no'>...</span>)
 
 <span class='fu'>is.ab</span>(<span class='no'>x</span>)</pre>
 
@@ -245,46 +248,46 @@
       <th>x</th>
       <td><p>character vector to determine to antibiotic ID</p></td>
     </tr>
+    <tr>
+      <th>...</th>
+      <td><p>arguments passed on to internal functions</p></td>
+    </tr>
     </table>
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>Character (vector) with class <code>"ab"</code>. Unknown values will return <code>NA</code>.</p>
-    
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p>All entries in the <code><a href='antibiotics.html'>antibiotics</a></code> data set have three different identifiers: a human readable EARS-Net code (column <code>ab</code>, used by ECDC and WHONET), an ATC code (column <code>atc</code>, used by WHO), and a CID code (column <code>cid</code>, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem.</p>
 <p>Use the <code><a href='ab_property.html'>ab_property</a></code> functions to get properties based on the returned antibiotic ID, see Examples.</p>
-    
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 
     
-    <p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
+
+<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
 <p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
 <p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a></p>
-    
     <h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
 
     
-    <p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
+
+<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
 This package contains <strong>all ~450 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
 <p>These have become the gold standard for international drug utilisation monitoring and research.</p>
 <p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
 <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/'>https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
-    
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
 
     
-    <p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
 
+<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='antibiotics.html'>antibiotics</a></code> for the dataframe that is being used to determine ATCs.</p></div>
 
-
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+    <pre class="examples"><span class='co'># These examples all return "ERY", the ID of Erythromycin:</span>
-<span class='co'># These examples all return "ERY", the ID of Erythromycin:</span>
 <span class='fu'>as.ab</span>(<span class='st'>"J01FA01"</span>)
 <span class='fu'>as.ab</span>(<span class='st'>"J 01 FA 01"</span>)
 <span class='fu'>as.ab</span>(<span class='st'>"Erythromycin"</span>)
@@ -299,40 +302,34 @@ This package contains <strong>all ~450 antimicrobial drugs</strong> and their An
 <span class='co'># Use ab_* functions to get a specific properties (see ?ab_property);</span>
 <span class='co'># they use as.ab() internally:</span>
 <span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01FA01"</span>)    <span class='co'># "Erythromycin"</span>
-<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>)       <span class='co'># "Erythromycin"</span>
+<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>)       <span class='co'># "Erythromycin"</span></pre>
-<span class='co'># }</span></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
     <ul class="nav nav-pills nav-stacked">
       <li><a href="#arguments">Arguments</a></li>
-      
       <li><a href="#value">Value</a></li>
-
       <li><a href="#details">Details</a></li>
-
       <li><a href="#source">Source</a></li>
-
       <li><a href="#whocc">WHOCC</a></li>
-
       <li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
-
       <li><a href="#see-also">See also</a></li>
-      
       <li><a href="#examples">Examples</a></li>
     </ul>
 
   </div>
 </div>
 
+
       <footer>
       <div class="copyright">
-  <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
+  <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
 </div>
+
       </footer>
    </div>
 
@@ -355,6 +352,8 @@ This package contains <strong>all ~450 antimicrobial drugs</strong> and their An
 </script>
 
 
+
   </body>
 </html>
 
+

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">0.7.1.9091</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9092</span>
       </span>
     </div>
 

docs/reference/portion.html

@@ -86,7 +86,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
       </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">0.7.1.9091</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9092</span>
       </span>
     </div>
 
@@ -275,7 +275,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
     </tr>
     <tr>
       <th>as_percent</th>
-      <td><p>a logical to indicate whether the output must be returned as a hundred fold with % sign (a character) using<code><a href='https://rdrr.io/pkg/clean/man/percentage.html'>percentage</a></code>. A value of <code>0.123456</code> will then be returned as <code>"12.3%"</code>.</p></td>
+      <td><p>a logical to indicate whether the output must be returned as a hundred fold with % sign (a character). A value of <code>0.123456</code> will then be returned as <code>"12.3%"</code>.</p></td>
     </tr>
     <tr>
       <th>only_all_tested</th>

man/as.ab.Rd

@@ -5,12 +5,14 @@
 \alias{is.ab}
 \title{Transform to antibiotic ID}
 \usage{
-as.ab(x)
+as.ab(x, ...)
 
 is.ab(x)
 }
 \arguments{
 \item{x}{character vector to determine to antibiotic ID}
+
+\item{...}{arguments passed on to internal functions}
 }
 \value{
 Character (vector) with class \code{"ab"}. Unknown values will return \code{NA}.

man/portion.Rd

@@ -44,7 +44,7 @@ rsi_df(data, translate_ab = "name", language = get_locale(),
 
 \item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.}
 
-\item{as_percent}{a logical to indicate whether the output must be returned as a hundred fold with \% sign (a character) using\code{\link[clean]{percentage}}. A value of \code{0.123456} will then be returned as \code{"12.3\%"}.}
+\item{as_percent}{a logical to indicate whether the output must be returned as a hundred fold with \% sign (a character). A value of \code{0.123456} will then be returned as \code{"12.3\%"}.}
 
 \item{only_all_tested}{(for combination therapies, i.e. using more than one variable for \code{...}) a logical to indicate that isolates must be tested for all antibiotics, see section \emph{Combination therapy} below}
 

tests/testthat/test-ab.R

@@ -54,6 +54,9 @@ test_that("as.ab works", {
   expect_equal(suppressWarnings(as.character(as.ab(c("Bacteria", "Bacterial")))),
                c(NA, "TMP"))
   
+  expect_equal(as.character(as.ab("Amoxy + clavulaanzuur")),
+               "AMC")
+
   # assigning and subsetting
   x <- antibiotics$ab
   expect_s3_class(x[1], "ab")

tests/testthat/test-misc.R

@@ -21,6 +21,16 @@
 
 context("misc.R")
 
+test_that("percentages works", {
+  expect_equal(percentage(0.25), "25%")
+  expect_equal(percentage(0.5), "50%")
+  expect_equal(percentage(0.500, digits = 1), "50.0%")
+  expect_equal(percentage(0.1234), "12.3%")
+  # round up 0.5
+  expect_equal(percentage(0.0054), "0.5%")
+  expect_equal(percentage(0.0055), "0.6%")
+})
+
 test_that("functions missing in older R versions work", {
   expect_equal(strrep("A", 5), "AAAAA")
   expect_equal(strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))