(v0.7.1.9072) key_antibiotics() for foreign systems

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.7.1.9071
+Version: 0.7.1.9072
-Date: 2019-09-03
+Date: 2019-09-12
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 0.7.1.9071
+# AMR 0.7.1.9072
-<small>Last updated: 03-Sep-2019</small>
+<small>Last updated: 12-Sep-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`:
@@ -99,6 +99,9 @@
 * Function `availability()` now uses `portion_R()` instead of `portion_IR()`, to comply with EUCAST insights
 * Functions `age()` and `age_groups()` now have a `na.rm` parameter to remove empty values
 * Renamed function `p.symbol()` to `p_symbol()` (the former is now deprecated and will be removed in a future version)
+* Using negative values for `x` in `age_groups()` will now introduce `NA`s and not return an error anymore
+* Fix for determining the system's language
+* Fix for `key_antibiotics()` on foreign systems
 
 #### Other
 * Added Prof Dr Casper Albers as doctoral advisor and Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors

R/age.R

@@ -145,6 +145,10 @@ age_groups <- function(x, split_at = c(12, 25, 55, 75), na.rm = FALSE) {
   if (!is.numeric(x)) {
     stop("`x` and must be numeric, not a ", paste0(class(x), collapse = "/"), ".")
   }
+  if (any(x < 0, na.rm = TRUE)) {
+    x[x < 0] <- NA
+    warning("NAs introduced for ages below 0.")
+  }
   if (is.character(split_at)) {
     split_at <- split_at[1L]
     if (split_at %like% "^(child|kid|junior)") {

R/atc_online.R

@@ -81,7 +81,7 @@ atc_online_property <- function(atc_code,
   }
 
   if (!all(atc_code %in% AMR::antibiotics)) {
-    atc_code <- as.character(as.atc(atc_code))
+    atc_code <- as.character(ab_atc(atc_code))
   }
 
   if (!curl::has_internet()) {

R/key_antibiotics.R

@@ -184,25 +184,28 @@ key_antibiotics <- function(x,
 
   # join to microorganisms data set
   x <- x %>%
+    as.data.frame(stringsAsFactors = FALSE) %>% 
     mutate_at(vars(col_mo), as.mo) %>%
     left_join_microorganisms(by = col_mo) %>%
     mutate(key_ab = NA_character_,
-           gramstain = mo_gramstain(pull(., col_mo)))
+           gramstain = mo_gramstain(pull(., col_mo), language = NULL))
   
   # Gram +
   x <- x %>% mutate(key_ab =
                       if_else(gramstain == "Gram-positive",
-                              apply(X = x[, gram_positive],
+                              tryCatch(apply(X = x[, gram_positive],
                                              MARGIN = 1,
                                              FUN = function(x) paste(x, collapse = "")),
+                                       error = function(e) paste0(rep(".", 12), collapse = "")),
                               key_ab))
   
   # Gram -
   x <- x %>% mutate(key_ab =
                       if_else(gramstain == "Gram-negative",
-                              apply(X = x[, gram_negative],
+                              tryCatch(apply(X = x[, gram_negative],
                                              MARGIN = 1,
                                              FUN = function(x) paste(x, collapse = "")),
+                                       error = function(e) paste0(rep(".", 12), collapse = "")),
                               key_ab))
 
   # format
@@ -212,6 +215,10 @@ key_antibiotics <- function(x,
     gsub('[^SIR]', '.', ., ignore.case = TRUE) %>%
     toupper()
   
+  if (n_distinct(key_abs) == 1) {
+    warning("No distinct key antibiotics determined.", call. = FALSE)
+  }
+
   key_abs
 
 }

R/like.R

@@ -56,8 +56,16 @@
 like <- function(x, pattern) {
   if (length(pattern) > 1) {
     if (length(x) != length(pattern)) {
-      pattern <- pattern[1]
+      if (length(x) == 1) {
-      warning('only the first element of argument `pattern` used for `%like%`', call. = TRUE)
+        x <- rep(x, length(pattern))
+      }
+      # return TRUE for every 'x' that matches any 'pattern', FALSE otherwise
+      res <- sapply(pattern, function(pttrn) x %like% pttrn)
+      res2 <- as.logical(rowSums(res))
+      # get only first item of every hit in pattern
+      res2[duplicated(res)] <- FALSE
+      res2[rowSums(res) == 0] <- NA
+      return(res2)
     } else {
       # x and pattern are of same length, so items with each other
       res <- vector(length = length(pattern))

R/misc.R

@@ -123,61 +123,6 @@ stopifnot_installed_package <- function(package) {
   return(invisible())
 }
 
-# translate strings based on inst/translations.tsv
-#' @importFrom dplyr %>% filter
-translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
-  # if (getOption("AMR_locale", "en") != language) {
-  #   language <- getOption("AMR_locale", "en")
-  # }
-
-  if (is.null(language)) {
-    return(from)
-  }
-  if (language %in% c("en", "")) {
-    return(from)
-  }
-
-  df_trans <- translations_file # internal data file
-
-  if (!language %in% df_trans$lang) {
-    stop("Unsupported language: '", language, "' - use one of: ",
-         paste0("'", sort(unique(df_trans$lang)), "'", collapse = ", "),
-         call. = FALSE)
-  }
-
-  df_trans <- df_trans %>% filter(lang == language)
-  if (only_unknown == TRUE) {
-    df_trans <- df_trans %>% filter(pattern %like% "unknown")
-  }
-
-  # default case sensitive if value if 'ignore.case' is missing:
-  df_trans$ignore.case[is.na(df_trans$ignore.case)] <- FALSE
-  # default not using regular expressions (fixed = TRUE) if 'fixed' is missing:
-  df_trans$fixed[is.na(df_trans$fixed)] <- TRUE
-
-  # check if text to look for is in one of the patterns
-  any_form_in_patterns <- tryCatch(any(from %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")),
-                                   error = function(e) {
-                                     warning("Translation not possible. Please open an issue on GitLab (https://gitlab.com/msberends/AMR/issues) or GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
-                                     return(FALSE)
-                                   })
-  if (NROW(df_trans) == 0 | !any_form_in_patterns) {
-    return(from)
-  }
-
-  for (i in 1:nrow(df_trans)) {
-    from <- gsub(x = from,
-                 pattern = df_trans$pattern[i],
-                 replacement = df_trans$replacement[i],
-                 fixed = df_trans$fixed[i],
-                 ignore.case = df_trans$ignore.case[i])
-  }
-
-  # force UTF-8 for diacritics
-  base::enc2utf8(from)
-
-}
-
 "%or%" <- function(x, y) {
   if (is.null(x) | is.null(y)) {
     if (is.null(x)) {

R/mo.R

@@ -432,13 +432,13 @@ exec_as.mo <- function(x,
     }
     x <- y
     
-  } else if (all(x %in% read_mo_history(uncertainty_level,
+    # } else if (all(x %in% read_mo_history(uncertainty_level,
-                                        force = force_mo_history)$x)) {
+    #                                       force = force_mo_history)$x)) {
-    # previously found code
+    #   # previously found code
-    x <- microorganismsDT[data.table(mo = get_mo_history(x,
+    #   x <- microorganismsDT[data.table(mo = get_mo_history(x,
-                                                         uncertainty_level,
+    #                                                        uncertainty_level,
-                                                         force = force_mo_history)),
+    #                                                        force = force_mo_history)),
-                          on = "mo", ..property][[1]]
+    #                         on = "mo", ..property][[1]]
     
   } else if (all(tolower(x) %in% microorganismsDT$fullname_lower)) {
     # we need special treatment for very prevalent full names, they are likely!
@@ -561,17 +561,17 @@ exec_as.mo <- function(x,
       
       progress$tick()$print()
       
-      if (initial_search == TRUE) {
+      # if (initial_search == TRUE) {
-        found <- microorganismsDT[mo == get_mo_history(x_backup[i],
+      #   found <- microorganismsDT[mo == get_mo_history(x_backup[i],
-                                                       uncertainty_level,
+      #                                                  uncertainty_level,
-                                                       force = force_mo_history),
+      #                                                  force = force_mo_history),
-                                  ..property][[1]]
+      #                             ..property][[1]]
-        # previously found result
+      #   # previously found result
-        if (length(found) > 0) {
+      #   if (length(found) > 0) {
-          x[i] <- found[1L]
+      #     x[i] <- found[1L]
-          next
+      #     next
-        }
+      #   }
-      }
+      # }
       
       found <- microorganismsDT[mo == toupper(x_backup[i]), ..property][[1]]
       # is a valid MO code
@@ -826,6 +826,7 @@ exec_as.mo <- function(x,
             if (initial_search == TRUE) {
               set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
             }
+            next
           } else if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_backup_without_spp[i], ignore.case = FALSE)) {
             # Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
             x[i] <- microorganismsDT[mo == 'B_SLMNL_ENT', ..property][[1]][1L]
@@ -833,12 +834,12 @@ exec_as.mo <- function(x,
               set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
             }
             uncertainties <- rbind(uncertainties,
-                                   data.frame(uncertainty_level = 1,
+                                   format_uncertainty_as_df(uncertainty_level = 1,
                                                             input = x_backup_without_spp[i],
                                                             result_mo = "B_SLMNL_ENT"))
-          }
             next
           }
+        }
         
         # trivial names known to the field:
         if ("meningococcus" %like% x_trimmed[i]) {
@@ -1850,8 +1851,11 @@ mo_renamed <- function() {
 #' @export
 #' @noRd
 print.mo_renamed <- function(x, ...) {
-  items <- getOption("mo_renamed")
+  items <- x #getOption("mo_renamed")
-  base::message(blue(paste("NOTE:", names(items), "was renamed", items, collapse = "\n"), collapse = "\n"))
+  old <- names(x)
+  new <- x
+  
+  cat(blue(paste("NOTE:", italic(names(items)), "was renamed", italic(items), collapse = "\n"), collapse = "\n"))
 }
 
 nr2char <- function(x) {

R/translate.R

@@ -64,7 +64,7 @@
 #' mo_name("CoNS", language = "pt")
 #' #> "Staphylococcus coagulase negativo (CoNS)"
 get_locale <- function() {
-  if (getOption("AMR_locale", "en") != "en") {
+  if (!is.null(getOption("AMR_locale", default = NULL))) {
     return(getOption("AMR_locale"))
   }
 
@@ -73,6 +73,7 @@ get_locale <- function() {
   # Check the locale settings for a start with one of these languages:
   
   # grepl() with ignore.case = FALSE is faster than %like%
+  
   if (grepl("^(English|en_|EN_)", lang, ignore.case = FALSE)) {
     # as first option to optimise speed
     "en"
@@ -93,3 +94,55 @@ get_locale <- function() {
     "en"
   }
 }
+
+# translate strings based on inst/translations.tsv
+#' @importFrom dplyr %>% filter
+translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
+
+  if (is.null(language)) {
+    return(from)
+  }
+  if (language %in% c("en", "", NA)) {
+    return(from)
+  }
+  
+  df_trans <- translations_file # internal data file
+  
+  if (!language %in% df_trans$lang) {
+    stop("Unsupported language: '", language, "' - use one of: ",
+         paste0("'", sort(unique(df_trans$lang)), "'", collapse = ", "),
+         call. = FALSE)
+  }
+  
+  df_trans <- df_trans %>% filter(lang == language)
+  if (only_unknown == TRUE) {
+    df_trans <- df_trans %>% filter(pattern %like% "unknown")
+  }
+  
+  # default case sensitive if value if 'ignore.case' is missing:
+  df_trans$ignore.case[is.na(df_trans$ignore.case)] <- FALSE
+  # default not using regular expressions (fixed = TRUE) if 'fixed' is missing:
+  df_trans$fixed[is.na(df_trans$fixed)] <- TRUE
+  
+  # check if text to look for is in one of the patterns
+  any_form_in_patterns <- tryCatch(any(from %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")),
+                                   error = function(e) {
+                                     warning("Translation not possible. Please open an issue on GitLab (https://gitlab.com/msberends/AMR/issues) or GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
+                                     return(FALSE)
+                                   })
+  if (NROW(df_trans) == 0 | !any_form_in_patterns) {
+    return(from)
+  }
+  
+  for (i in 1:nrow(df_trans)) {
+    from <- gsub(x = from,
+                 pattern = df_trans$pattern[i],
+                 replacement = df_trans$replacement[i],
+                 fixed = df_trans$fixed[i],
+                 ignore.case = df_trans$ignore.case[i])
+  }
+  
+  # force UTF-8 for diacritics
+  base::enc2utf8(from)
+  
+}

data-raw/eucast_rules.tsv

@@ -1,9 +1,9 @@
 # ---------------------------------------------------------------------------------------------------
 # For editing this EUCAST reference file, these values can all be used for target antibiotics:
-# all_betalactams, aminoglycosides, carbapenems, cephalosporins, cephalosporins_without_CAZ, fluoroquinolones, 
+# 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_without_CAZ',
-# glycopeptides, macrolides, minopenicillins, polymyxins, streptogramins, tetracyclines, ureidopenicillins
+# 'fluoroquinolones', 'glycopeptides', 'macrolides', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins'
-# and all separate EARS-Net letter codes like AMC. They can be separated by comma: 'AMC, fluoroquinolones'.
+# and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'.
-# The if_mo_property column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
+# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
 # The like.is.one_of column must contain one of: like, is, one_of ('like' will read the first column as regular expression)
 # The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group can be found in: LiPuma J, Curr Opin Pulm Med. 2005 Nov;11(6):528-33. (PMID 16217180).
 # >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<

data-raw/translations.tsv

@@ -354,7 +354,7 @@ nl	Ticarcillin/beta-lactamase inhibitor	Ticarcilline/enzymremmer
 nl	Ticarcillin/clavulanic acid	Ticarcilline/clavulaanzuur
 nl	Tinidazole	Tinidazol
 nl	Tobramycin	Tobramycine
-nl	Trimethoprim/sulfamethoxazole	Trimethoprim/sulfamethoxazol
+nl	Trimethoprim/sulfamethoxazole	Cotrimoxazol
 nl	Troleandomycin	Troleandomycine
 nl	Trovafloxacin	Trovafloxacine
 nl	Vancomycin	Vancomycine

docs/LICENSE-text.html

@@ -78,7 +78,7 @@
       </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">0.7.1.9071</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -78,7 +78,7 @@
       </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">0.7.1.9071</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
       </span>
     </div>
 

docs/authors.html

@@ -78,7 +78,7 @@
       </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">0.7.1.9071</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
       </span>
     </div>
 

docs/news/index.html

@@ -78,7 +78,7 @@
       </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">0.7.1.9071</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
       </span>
     </div>
 
@@ -225,11 +225,11 @@
       
     </div>
 
-    <div id="amr-0-7-1-9071" class="section level1">
+    <div id="amr-0-7-1-9072" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-7-1-9071" class="anchor"></a>AMR 0.7.1.9071<small> Unreleased </small>
+<a href="#amr-0-7-1-9072" class="anchor"></a>AMR 0.7.1.9072<small> Unreleased </small>
 </h1>
-<p><small>Last updated: 03-Sep-2019</small></p>
+<p><small>Last updated: 12-Sep-2019</small></p>
 <div id="breaking" class="section level3">
 <h3 class="hasAnchor">
 <a href="#breaking" class="anchor"></a>Breaking</h3>
@@ -342,6 +342,9 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
 <li>Function <code><a href="../reference/availability.html">availability()</a></code> now uses <code><a href="../reference/portion.html">portion_R()</a></code> instead of <code><a href="../reference/portion.html">portion_IR()</a></code>, to comply with EUCAST insights</li>
 <li>Functions <code><a href="../reference/age.html">age()</a></code> and <code><a href="../reference/age_groups.html">age_groups()</a></code> now have a <code>na.rm</code> parameter to remove empty values</li>
 <li>Renamed function <code><a href="../reference/AMR-deprecated.html">p.symbol()</a></code> to <code><a href="../reference/p_symbol.html">p_symbol()</a></code> (the former is now deprecated and will be removed in a future version)</li>
+<li>Using negative values for <code>x</code> in <code><a href="../reference/age_groups.html">age_groups()</a></code> will now introduce <code>NA</code>s and not return an error anymore</li>
+<li>Fix for determining the system’s language</li>
+<li>Fix for <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> on foreign systems</li>
 </ul>
 <div id="other" class="section level4">
 <h4 class="hasAnchor">
@@ -1261,7 +1264,7 @@ 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-0-7-1-9071">0.7.1.9071</a></li>
+        <li><a href="#amr-0-7-1-9072">0.7.1.9072</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/AMR-deprecated.html

@@ -80,7 +80,7 @@
       </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">0.7.1.9071</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
       </span>
     </div>
 

docs/reference/age.html

@@ -80,7 +80,7 @@
       </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">0.7.1.9070</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
       </span>
     </div>
 

docs/reference/age_groups.html

@@ -80,7 +80,7 @@
       </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">0.7.1.9070</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
       </span>
     </div>
 

docs/reference/index.html

@@ -78,7 +78,7 @@
       </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">0.7.1.9071</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
       </span>
     </div>
 

docs/reference/p_symbol.html

@@ -80,7 +80,7 @@
       </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">0.7.1.9071</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9072</span>
       </span>
     </div>
 

docs/reference/translate.html

@@ -80,7 +80,7 @@
       </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">0.7.1.9072</span>
       </span>
     </div>
 
@@ -297,7 +297,7 @@
 
       <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">

man/translate.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/get_locale.R
+% Please edit documentation in R/translate.R
 \name{translate}
 \alias{translate}
 \alias{get_locale}

tests/testthat/test-data.R

@@ -30,6 +30,8 @@ test_that("data sets are valid", {
 
   # check cross table reference
   expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))
+  expect_false(any(is.na(microorganisms.codes$code)))
+  expect_false(any(is.na(microorganisms.codes$mo)))
 
   # antibiotic names must always be coercible to their original AB code
   expect_identical(antibiotics$ab, as.ab(antibiotics$name))

tests/testthat/test-key_antibiotics.R

@@ -30,4 +30,7 @@ test_that("keyantibiotics work", {
   expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
   expect_true(key_antibiotics_equal(".SS", "SI.", ignore_I = TRUE))
   expect_false(key_antibiotics_equal(".SS", "SI.", ignore_I = FALSE))
+  
+  library(dplyr)
+  expect_warning(key_antibiotics(example_isolates %>% slice(rep(1, 10))))
 })

tests/testthat/test-like.R

@@ -22,7 +22,7 @@
 context("like.R")
 
 test_that("`like` works", {
-  expect_true(suppressWarnings("test" %like% c("^t", "^s")))
+  expect_true(sum("test" %like% c("^t", "^s")) == 1)
   expect_true("test" %like% "test")
   expect_true("test" %like% "TEST")
   expect_true(as.factor("test") %like% "TEST")