(v1.2.0.9015) ab_from_text()

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.2.0.9014
+Version: 1.2.0.9015
 Date: 2020-06-25
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NAMESPACE

@@ -66,6 +66,7 @@ export(ab_atc_group2)
 export(ab_cid)
 export(ab_class)
 export(ab_ddd)
+export(ab_from_text)
 export(ab_group)
 export(ab_info)
 export(ab_loinc)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.2.0.9014
+# AMR 1.2.0.9015
 ## <small>Last updated: 25-Jun-2020</small>
 
 ### New
@@ -40,7 +40,7 @@
 * Fixed a bug in `bug_drug_combinations()` for when only one antibiotic was in the input data
 * Changed the summary for class `<mo>`, to highlight the %SI vs. %R
 * Improved error handling, giving more useful info when functions return an error
-* Algorithm improvements to `as.ab()`
+* Algorithm improvements to `as.ab()`, many more misspellings are now translatable
 * Added Monuril as trade name for fosfomycin
 
 # AMR 1.2.0

R/ab_from_text.R

@@ -30,6 +30,7 @@
 #' `df %>% mutate(abx = ab_from_text(clinical_text, collapse = "|"))` 
 #' 
 #' This function is also internally used by [as.ab()], although it then only returns the first hit.
+#' @export
 #' @examples 
 #' # mind the bad spelling of amoxicillin in this line, 
 #' # straight from a true health care record:

_pkgdown.yml

@@ -94,6 +94,7 @@ reference:
     contents:
     - starts_with("as.")
     - "`eucast_rules`"
+    - "`ab_from_text`"
     - "`guess_ab_col`"
     - "`mo_source`"
   - title: "Enhancing your data"

docs/404.html

@@ -81,7 +81,7 @@
       </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">1.2.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </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">1.2.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -81,7 +81,7 @@
       </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">1.2.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </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">1.2.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</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">1.2.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
       </span>
     </div>
 

docs/news/index.html

@@ -81,7 +81,7 @@
       </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">1.2.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
       </span>
     </div>
 
@@ -229,9 +229,9 @@
       <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1209014" class="section level1">
+    <div id="amr-1209015" class="section level1">
-<h1 class="page-header" data-toc-text="1.2.0.9014">
+<h1 class="page-header" data-toc-text="1.2.0.9015">
-<a href="#amr-1209014" class="anchor"></a>AMR 1.2.0.9014<small> Unreleased </small>
+<a href="#amr-1209015" class="anchor"></a>AMR 1.2.0.9015<small> Unreleased </small>
 </h1>
 <div id="last-updated-25-jun-2020" class="section level2">
 <h2 class="hasAnchor">
@@ -285,8 +285,7 @@
 <li>Fixed a bug in <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> for when only one antibiotic was in the input data</li>
 <li>Changed the summary for class <code>&lt;mo&gt;</code>, to highlight the %SI vs. %R</li>
 <li>Improved error handling, giving more useful info when functions return an error</li>
-<li>Algorithm improvements to <code><a href="../reference/as.ab.html">as.ab()</a></code>
+<li>Algorithm improvements to <code><a href="../reference/as.ab.html">as.ab()</a></code>, many more misspellings are now translatable</li>
-</li>
 <li>Added Monuril as trade name for fosfomycin</li>
 </ul>
 </div>

docs/pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   WHONET: WHONET.html
   benchmarks: benchmarks.html
   resistance_predict: resistance_predict.html
-last_built: 2020-06-25T15:34Z
+last_built: 2020-06-25T17:20Z
 urls:
   reference: https://msberends.gitlab.io/AMR/reference
   article: https://msberends.gitlab.io/AMR/articles

docs/reference/index.html

@@ -81,7 +81,7 @@
       </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">1.2.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
       </span>
     </div>
 
@@ -286,6 +286,12 @@
         <td><p>Apply EUCAST rules</p></td>
       </tr><tr>
         
+        <td>
+          <p><code><a href="ab_from_text.html">ab_from_text()</a></code> </p>
+        </td>
+        <td><p>Retrieve antimicrobial drugs from text</p></td>
+      </tr><tr>
+        
         <td>
           <p><code><a href="guess_ab_col.html">guess_ab_col()</a></code> </p>
         </td>