(v0.7.1.9095) get_column_abx() fix

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.7.1.9094
+Version: 0.7.1.9095
 Date: 2019-10-06
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.7.1.9094
+# AMR 0.7.1.9095
 <small>Last updated: 06-Oct-2019</small>
 
 ### Breaking

R/guess_ab_col.R

@@ -129,9 +129,14 @@ get_column_abx <- function(x,
   x <- as.character(df_trans$colnames)
   names(x) <- df_trans$abcode
   
-  # remove the ones that do not already have the rsi class (as.rsi) and that have >50% invalid values
+  # remove the ones that are not a valid AB code, ATC code, name, abbreviation or synonym,
-  x <- sapply(x, function(col = x, df = x_bak) {
+  # and do not already have the rsi class (as.rsi) 
-    ifelse(is.rsi(as.data.frame(df)[, col]) | 
+  # and that have >50% invalid values
+  vectr_antibiotics <- unique(toupper(unlist(AMR::antibiotics[,c("ab", "atc", "name", "abbreviations", "synonyms")])))
+  vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
+   x <- sapply(x, function(col = x, df = x_bak) {
+    ifelse(toupper(col) %in% vectr_antibiotics |
+             is.rsi(as.data.frame(df)[, col]) | 
              is.rsi.eligible(as.data.frame(df)[, col], threshold = 0.5),
            col,
            NA)

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">0.7.1.9094</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</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">0.7.1.9094</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</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">0.7.1.9094</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</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">0.7.1.9094</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</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">0.7.1.9094</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</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">0.7.1.9094</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
       </span>
     </div>
 
@@ -231,9 +231,9 @@
       
     </div>
 
-    <div id="amr-0-7-1-9094" class="section level1">
+    <div id="amr-0-7-1-9095" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-7-1-9094" class="anchor"></a>AMR 0.7.1.9094<small> Unreleased </small>
+<a href="#amr-0-7-1-9095" class="anchor"></a>AMR 0.7.1.9095<small> Unreleased </small>
 </h1>
 <p><small>Last updated: 06-Oct-2019</small></p>
 <div id="breaking" class="section level3">
@@ -1289,7 +1289,7 @@ 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-0-7-1-9094">0.7.1.9094</a></li>
+        <li><a href="#amr-0-7-1-9095">0.7.1.9095</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/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">0.7.1.9094</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
       </span>
     </div>