(v1.3.0) v1.3.0

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.2.0.9040
+Version: 1.3.0
 Date: 2020-07-29
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.2.0.9040
+# AMR 1.3.0
-## <small>Last updated: 29 July 2020</small>
+
 
 ### New
 * Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally

R/rsi.R

@@ -143,6 +143,40 @@ as.rsi <- function(x, ...) {
   UseMethod("as.rsi")
 }
 
+#' @rdname as.rsi
+#' @export
+is.rsi <- function(x) {
+  inherits(x, "rsi")
+}
+
+#' @rdname as.rsi
+#' @export
+is.rsi.eligible <- function(x, threshold = 0.05) {
+  stop_if(NCOL(x) > 1, "`x` must be a one-dimensional vector.")
+  
+  if (any(c("logical",
+            "numeric",
+            "integer",
+            "mo",
+            "Date",
+            "POSIXct",
+            "rsi",
+            "raw",
+            "hms")
+          %in% class(x))) {
+    # no transformation needed
+    FALSE
+  } else {
+    x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
+    if (length(x) == 0) {
+      return(FALSE)
+    }
+    checked <- suppressWarnings(as.rsi(x))
+    outcome <- sum(is.na(checked)) / length(x)
+    outcome <= threshold
+  }
+}
+
 #' @export
 as.rsi.default <- function(x, ...) {
   if (is.rsi(x)) {
@@ -513,40 +547,6 @@ exec_as.rsi <- function(method, x, mo, ab, guideline, uti, conserve_capped_value
             class =  c("rsi", "ordered", "factor"))
 }
 
-#' @rdname as.rsi
-#' @export
-is.rsi <- function(x) {
-  inherits(x, "rsi")
-}
-
-#' @rdname as.rsi
-#' @export
-is.rsi.eligible <- function(x, threshold = 0.05) {
-  stop_if(NCOL(x) > 1, "`x` must be a one-dimensional vector.")
-  
-  if (any(c("logical",
-            "numeric",
-            "integer",
-            "mo",
-            "Date",
-            "POSIXct",
-            "rsi",
-            "raw",
-            "hms")
-          %in% class(x))) {
-    # no transformation needed
-    FALSE
-  } else {
-    x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
-    if (length(x) == 0) {
-      return(FALSE)
-    }
-    checked <- suppressWarnings(as.rsi(x))
-    outcome <- sum(is.na(checked)) / length(x)
-    outcome <= threshold
-  }
-}
-
 #' @method print rsi
 #' @export
 #' @noRd

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</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">1.2.0.9040</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</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">1.2.0.9040</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</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">1.2.0.9040</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</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">1.2.0.9040</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</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">1.2.0.9040</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
       </span>
     </div>
 
@@ -229,14 +229,10 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1209040" class="section level1">
+    <div id="amr-130" class="section level1">
-<h1 class="page-header" data-toc-text="1.2.0.9040">
+<h1 class="page-header" data-toc-text="1.3.0">
-<a href="#amr-1209040" class="anchor"></a>AMR 1.2.0.9040<small> Unreleased </small>
+<a href="#amr-130" class="anchor"></a>AMR 1.3.0<small> Unreleased </small>
 </h1>
-<div id="last-updated-29-july-2020" class="section level2">
-<h2 class="hasAnchor">
-<a href="#last-updated-29-july-2020" class="anchor"></a><small>Last updated: 29 July 2020</small>
-</h2>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
 <a href="#new" class="anchor"></a>New</h3>
@@ -311,7 +307,6 @@
 <li>Moved primary location of this project from GitLab to <a href="https://github.com/msberends/AMR">GitHub</a>, giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.</li>
 </ul>
 </div>
-</div>
 </div>
     <div id="amr-120" class="section level1">
 <h1 class="page-header" data-toc-text="1.2.0">

docs/pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   WHONET: WHONET.html
   benchmarks: benchmarks.html
   resistance_predict: resistance_predict.html
-last_built: 2020-07-29T10:44Z
+last_built: 2020-07-29T11:47Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

docs/reference/as.rsi.html

@@ -82,7 +82,7 @@
       </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">1.2.0.9040</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
       </span>
     </div>
 
@@ -237,6 +237,10 @@
 
     <pre class="usage"><span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='no'>...</span>)
 
+<span class='fu'>is.rsi</span>(<span class='no'>x</span>)
+
+<span class='fu'>is.rsi.eligible</span>(<span class='no'>x</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)
+
 <span class='co'># S3 method for mic</span>
 <span class='fu'>as.rsi</span>(
   <span class='no'>x</span>,
@@ -266,11 +270,7 @@
   <span class='kw'>uti</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>conserve_capped_values</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='no'>...</span>
-)
+)</pre>
-
-<span class='fu'>is.rsi</span>(<span class='no'>x</span>)
-
-<span class='fu'>is.rsi.eligible</span>(<span class='no'>x</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -283,6 +283,10 @@
       <th>...</th>
       <td><p>parameters passed on to methods</p></td>
     </tr>
+    <tr>
+      <th>threshold</th>
+      <td><p>maximum fraction of invalid antimicrobial interpretations of <code>x</code>, please see <em>Examples</em></p></td>
+    </tr>
     <tr>
       <th>mo</th>
       <td><p>any (vector of) text that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code></p></td>
@@ -307,10 +311,6 @@
       <th>col_mo</th>
       <td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo()</a></code>), defaults to the first column of class <code><a href='as.mo.html'>mo</a></code>. Values will be coerced using <code><a href='as.mo.html'>as.mo()</a></code>.</p></td>
     </tr>
-    <tr>
-      <th>threshold</th>
-      <td><p>maximum fraction of invalid antimicrobial interpretations of <code>x</code>, please see <em>Examples</em></p></td>
-    </tr>
     </table>
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

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">1.2.0.9040</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
       </span>
     </div>
 

docs/reference/rsi_translation.html

@@ -82,7 +82,7 @@
       </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">1.2.0.9038</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
       </span>
     </div>
 

docs/survey.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">1.2.0.9040</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
       </span>
     </div>
 

man/as.rsi.Rd

@@ -3,15 +3,19 @@
 \name{as.rsi}
 \alias{as.rsi}
 \alias{rsi}
+\alias{is.rsi}
+\alias{is.rsi.eligible}
 \alias{as.rsi.mic}
 \alias{as.rsi.disk}
 \alias{as.rsi.data.frame}
-\alias{is.rsi}
-\alias{is.rsi.eligible}
 \title{Class 'rsi'}
 \usage{
 as.rsi(x, ...)
 
+is.rsi(x)
+
+is.rsi.eligible(x, threshold = 0.05)
+
 \method{as.rsi}{mic}(
   x,
   mo,
@@ -39,16 +43,14 @@ as.rsi(x, ...)
   conserve_capped_values = FALSE,
   ...
 )
-
-is.rsi(x)
-
-is.rsi.eligible(x, threshold = 0.05)
 }
 \arguments{
 \item{x}{vector of values (for class \code{\link{mic}}: an MIC value in mg/L, for class \code{\link{disk}}: a disk diffusion radius in millimetres)}
 
 \item{...}{parameters passed on to methods}
 
+\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, please see \emph{Examples}}
+
 \item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
 
 \item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}}
@@ -60,8 +62,6 @@ is.rsi.eligible(x, threshold = 0.05)
 \item{conserve_capped_values}{a logical to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"}
 
 \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
-
-\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, please see \emph{Examples}}
 }
 \value{
 Ordered factor with new class \code{\link{rsi}}