(v0.8.0.9032) fix regex error

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.8.0.9031
+Version: 0.8.0.9032
 Date: 2019-11-15
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.8.0.9031
+# AMR 0.8.0.9032
 <small>Last updated: 15-Nov-2019</small>
 
 ### Breaking
@@ -35,7 +35,7 @@
     as.mo(c("Stafylococcus aureus",
             "staphylokok aureuz"))
     #> Warning: 
-    #> Results of two values was guessed with uncertainty. Use mo_uncertainties() to review them.
+    #> Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.
     #> Class 'mo'
     #> [1] B_STPHY_AURS B_STPHY_AURS
     

R/mo.R

@@ -545,7 +545,7 @@ exec_as.mo <- function(x,
       x <- gsub("o+", "o+", x)
       x <- gsub("(.)\\1+", "\\1+", x)
       # allow multiplication of all other consonants
-      x <- gsub("([bdghjlnrw]+)", "\\1+", x)
+      x <- gsub("([bdgjlnrw]+)", "\\1+", x)
       # allow ending in -en or -us
       x <- gsub("e\\+n(?![a-z[])", "(e+n|u+(c|k|q|qu|s|z|x|ks)+)", x, perl = TRUE)
       # if the input is longer than 10 characters, allow any forgotten consonant between all characters, as some might just have forgotten one...
@@ -555,10 +555,11 @@ exec_as.mo <- function(x,
       # allow au and ou after all these regex implementations
       x <- gsub("a+[bcdfghjklmnpqrstvwxyz]?u+[bcdfghjklmnpqrstvwxyz]?", "(a+u+|o+u+)[bcdfghjklmnpqrstvwxyz]?", x, fixed = TRUE)
       x <- gsub("o+[bcdfghjklmnpqrstvwxyz]?u+[bcdfghjklmnpqrstvwxyz]?", "(a+u+|o+u+)[bcdfghjklmnpqrstvwxyz]?", x, fixed = TRUE)
-      # make sure to remove regex overkill (will lead to errors)
-      x <- gsub("++", "+", x, fixed = TRUE)
     }
     x <- strip_whitespace(x, dyslexia_mode)
+    # make sure to remove regex overkill (will lead to errors)
+    x <- gsub("++", "+", x, fixed = TRUE)
+    x <- gsub("?+", "?", x, fixed = TRUE)
     
     x_trimmed <- x
     x_trimmed_species <- paste(x_trimmed, "species")
@@ -571,21 +572,22 @@ exec_as.mo <- function(x,
     # add start en stop regex
     x <- paste0("^", x, "$")
     
+    
     x_withspaces_start_only <- paste0("^", x_withspaces)
     x_withspaces_end_only <- paste0(x_withspaces, "$")
     x_withspaces_start_end <- paste0("^", x_withspaces, "$")
     
     if (isTRUE(debug)) {
-      cat(paste0('x                       "', x, '"\n'))
+      cat(paste0(blue('x'), '                       "', x, '"\n'))
-      cat(paste0('x_species               "', x_species, '"\n'))
+      cat(paste0(blue('x_species'), '               "', x_species, '"\n'))
-      cat(paste0('x_withspaces_start_only "', x_withspaces_start_only, '"\n'))
+      cat(paste0(blue('x_withspaces_start_only'), ' "', x_withspaces_start_only, '"\n'))
-      cat(paste0('x_withspaces_end_only   "', x_withspaces_end_only, '"\n'))
+      cat(paste0(blue('x_withspaces_end_only'), '   "', x_withspaces_end_only, '"\n'))
-      cat(paste0('x_withspaces_start_end  "', x_withspaces_start_end, '"\n'))
+      cat(paste0(blue('x_withspaces_start_end'), '  "', x_withspaces_start_end, '"\n'))
-      cat(paste0('x_backup                "', x_backup, '"\n'))
+      cat(paste0(blue('x_backup'), '                "', x_backup, '"\n'))
-      cat(paste0('x_backup_without_spp    "', x_backup_without_spp, '"\n'))
+      cat(paste0(blue('x_backup_without_spp'), '    "', x_backup_without_spp, '"\n'))
-      cat(paste0('x_trimmed               "', x_trimmed, '"\n'))
+      cat(paste0(blue('x_trimmed'), '               "', x_trimmed, '"\n'))
-      cat(paste0('x_trimmed_species       "', x_trimmed_species, '"\n'))
+      cat(paste0(blue('x_trimmed_species'), '       "', x_trimmed_species, '"\n'))
-      cat(paste0('x_trimmed_without_group "', x_trimmed_without_group, '"\n'))
+      cat(paste0(blue('x_trimmed_without_group'), ' "', x_trimmed_without_group, '"\n'))
     }
     
     progress <- progress_estimated(n = length(x), min_time = 3)
@@ -1590,12 +1592,12 @@ exec_as.mo <- function(x,
   if (NROW(uncertainties) > 0 & initial_search == TRUE) {
     options(mo_uncertainties = as.list(distinct(uncertainties, input, .keep_all = TRUE)))
     
-    plural <- c("", "it")
+    plural <- c("", "it", "was")
     if (NROW(uncertainties) > 1) {
-      plural <- c("s", "them")
+      plural <- c("s", "them", "were")
     }
     msg <- paste0("\nResult", plural[1], " of ", nr2char(NROW(uncertainties)), " value", plural[1],
-                  " was guessed with uncertainty. Use mo_uncertainties() to review ", plural[2], ".")
+                  " ", plural[3], " guessed with uncertainty. Use mo_uncertainties() to review ", plural[2], ".")
     warning(red(msg),
             call. = FALSE,
             immediate. = TRUE) # thus will always be shown, even if >= warnings

R/zzz.R

@@ -49,7 +49,7 @@
 #' @importFrom data.table as.data.table setkey
 #' @importFrom dplyr %>% mutate case_when
 make_DT <- function() {
-  microorganismsDT <- as.data.table(AMR::microorganisms %>% 
+  microorganismsDT <- AMR::microorganisms %>% 
     mutate(kingdom_index = case_when(kingdom == "Bacteria" ~ 1,
                                      kingdom == "Fungi" ~ 2,
                                      kingdom == "Protozoa" ~ 3,
@@ -60,12 +60,16 @@ make_DT <- function() {
            fullname_lower = gsub("[^.a-z0-9/ \\-]+", "",
                                  # use this paste instead of `fullname` to
                                  # work with Viridans Group Streptococci, etc.
-                                                                   tolower(trimws(paste(genus, species, subspecies))))))
+                                 tolower(trimws(ifelse(genus == "",
+                                                       fullname,
+                                                       paste(genus, species, subspecies)))))) %>% 
+    as.data.table()
+  
   # so arrange data on prevalence first, then kingdom, then full name
   setkey(microorganismsDT,
          prevalence,
          kingdom_index,
-         fullname)
+         fullname_lower)
   microorganismsDT
 }
 

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">0.8.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</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">0.8.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</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">0.8.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</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">0.8.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</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">0.8.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</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">0.8.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
       </span>
     </div>
 
@@ -231,9 +231,9 @@
       
     </div>
 
-    <div id="amr-0-8-0-9031" class="section level1">
+    <div id="amr-0-8-0-9032" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-8-0-9031" class="anchor"></a>AMR 0.8.0.9031<small> Unreleased </small>
+<a href="#amr-0-8-0-9032" class="anchor"></a>AMR 0.8.0.9032<small> Unreleased </small>
 </h1>
 <p><small>Last updated: 15-Nov-2019</small></p>
 <div id="breaking" class="section level3">
@@ -286,7 +286,7 @@
 <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,</a>
 <a class="sourceLine" id="cb4-2" data-line-number="2">        <span class="st">"staphylokok aureuz"</span>))</a>
 <a class="sourceLine" id="cb4-3" data-line-number="3"><span class="co">#&gt; Warning: </span></a>
-<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co">#&gt; Results of two values was guessed with uncertainty. Use mo_uncertainties() to review them.</span></a>
+<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co">#&gt; Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.</span></a>
 <a class="sourceLine" id="cb4-5" data-line-number="5"><span class="co">#&gt; Class 'mo'</span></a>
 <a class="sourceLine" id="cb4-6" data-line-number="6"><span class="co">#&gt; [1] B_STPHY_AURS B_STPHY_AURS</span></a>
 <a class="sourceLine" id="cb4-7" data-line-number="7"></a>
@@ -1385,7 +1385,7 @@ 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-0-8-0-9031">0.8.0.9031</a></li>
+        <li><a href="#amr-0-8-0-9032">0.8.0.9032</a></li>
         <li><a href="#amr-0-8-0">0.8.0</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>

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">0.8.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9032</span>
       </span>
     </div>