(v0.8.0.9001) guideline text on as.rsi()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.8.0.9000
+Version: 0.8.0.9001
-Date: 2019-10-16
+Date: 2019-10-21
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,9 +1,10 @@
-# AMR 0.8.0.9000
+# AMR 0.8.0.9001
-<small>Last updated: 16-Oct-2019</small>
+<small>Last updated: 21-Oct-2019</small>
 
 ### New
 
 ### Changes
+* When running `as.rsi()` over a data set, it will now print the guideline that will be used
 
 
 # AMR 0.8.0

R/rsi.R

@@ -254,8 +254,28 @@ exec_as.rsi <- function(method, x, mo, ab, guideline) {
             class =  c("rsi", "ordered", "factor"))
 }
 
+get_guideline <- function(guideline) {
+  guideline_param <- toupper(guideline)
+  if (guideline_param %in% c("CLSI", "EUCAST")) {
+    guideline_param <- AMR::rsi_translation %>%
+      filter(guideline %like% guideline_param) %>%
+      pull(guideline) %>%
+      sort() %>%
+      rev() %>%
+      .[1]
+  }
+  
+  if (!guideline_param %in% AMR::rsi_translation$guideline) {
+    stop(paste0("invalid guideline: '", guideline,
+                "'.\nValid guidelines are: ", paste0("'", rev(sort(unique(AMR::rsi_translation$guideline))), "'", collapse = ", ")),
+         call. = FALSE)
+  }
+  
+  guideline_param
+}
+
 #' @rdname as.rsi
-#' @importFrom crayon red blue
+#' @importFrom crayon red blue bold
 #' @export
 as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", ...) {
   x <- x
@@ -274,6 +294,9 @@ as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", ...) {
     stop("`col_mo` must be set.", call. = FALSE)
   }
   
+  guideline <- get_guideline(guideline)
+  message(blue("Interpreting using guideline", bold(guideline)))
+
   # transform all MICs
   ab_cols <- colnames(x)[sapply(x, is.mic)]
   if (length(ab_cols) > 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">0.8.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9001</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">0.8.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9001</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">0.8.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9001</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">0.8.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9001</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">0.8.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9001</span>
       </span>
     </div>
 
@@ -192,6 +192,10 @@
 <a href="#amr-for-r" class="anchor"></a><code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px">
 </h1></div>
 <p><em>(<help title="Too Long, Didn't Read">TLDR</help> - to find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.</em></p>
+<blockquote>
+<p><em>18 October 2019</em><br><strong>METHODS PAPER PREPRINTED</strong><br>
+A methods paper about this package has been preprinted at bioRxiv. Please see <a href="https://doi.org/10.1101/810622">here for the publishers page</a> or <a href="https://www.biorxiv.org/content/early/2019/10/18/810622.full.pdf">click here for the PDF</a>.</p>
+</blockquote>
 <hr>
 <div id="what-is-amr-for-r" class="section level3">
 <h3 class="hasAnchor">

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">0.8.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9001</span>
       </span>
     </div>
 
@@ -231,11 +231,11 @@
       
     </div>
 
-    <div id="amr-0-8-0-9000" class="section level1">
+    <div id="amr-0-8-0-9001" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-8-0-9000" class="anchor"></a>AMR 0.8.0.9000<small> Unreleased </small>
+<a href="#amr-0-8-0-9001" class="anchor"></a>AMR 0.8.0.9001<small> Unreleased </small>
 </h1>
-<p><small>Last updated: 16-Oct-2019</small></p>
+<p><small>Last updated: 21-Oct-2019</small></p>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
 <a href="#new" class="anchor"></a>New</h3>
@@ -243,6 +243,9 @@
 <div id="changes" class="section level3">
 <h3 class="hasAnchor">
 <a href="#changes" class="anchor"></a>Changes</h3>
+<ul>
+<li>When running <code><a href="../reference/as.rsi.html">as.rsi()</a></code> over a data set, it will now print the guideline that will be used</li>
+</ul>
 </div>
 </div>
     <div id="amr-0-8-0" class="section level1">
@@ -1305,7 +1308,7 @@ 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-0-8-0-9000">0.8.0.9000</a></li>
+        <li><a href="#amr-0-8-0-9001">0.8.0.9001</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">0.8.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9001</span>
       </span>
     </div>
 

index.md

@@ -2,6 +2,10 @@
 
 *(<help title="Too Long, Didn't Read">TLDR</help> - to find out how to conduct AMR analysis, please [continue reading here to get started](./articles/AMR.html).*
 
+> *18 October 2019*  
+> **METHODS PAPER PREPRINTED**  
+> A methods paper about this package has been preprinted at bioRxiv. Please see [here for the publishers page](https://doi.org/10.1101/810622) or [click here for the PDF](https://www.biorxiv.org/content/early/2019/10/18/810622.full.pdf).
+
 ----
 
 ### What is `AMR` (for R)?