re-add atc_ddd and atc_groups

NAMESPACE

@@ -55,6 +55,8 @@ export(as.mic)
 export(as.mo)
 export(as.rsi)
 export(atc_certe)
+export(atc_ddd)
+export(atc_groups)
 export(atc_name)
 export(atc_official)
 export(atc_online_ddd)

NEWS.md

@@ -48,13 +48,13 @@
 #### Changed
 * Added 65 antibiotics to the `antibiotics` data set, from the [Pharmaceuticals Community Register](http://ec.europa.eu/health/documents/community-register/html/atc.htm) of the European Commission
 * Removed columns `atc_group1_nl` and `atc_group2_nl` from the `antibiotics` data set
-* Function `atc_ddd` has been renamed `atc_online_ddd()`
+* Functions `atc_ddd()` and `atc_groups()` have been renamed `atc_online_ddd()` and `atc_online_groups()`. The old function are deprecated and will be removed in a future version.
-* Function `atc_groups` has been renamed `atc_online_groups()`
+* Function `guess_mo()` is now deprecated in favour of `as.mo()` and will be removed in future versions
+* Function `guess_atc()` is now deprecated in favour of `as.atc()` and will be removed in future versions
 * Function `eucast_rules()`:
   * Updated EUCAST Clinical breakpoints to [version 9.0 of 1 January 2019](http://www.eucast.org/clinical_breakpoints/)
   * Fixed a critical bug where some rules that depend on previous applied rules would not be applied adequately
   * Emphasised in manual that penicillin is meant as benzylpenicillin (ATC [J01CE01](https://www.whocc.no/atc_ddd_index/?code=J01CE01))
-* Function `guess_mo()` is now deprecated in favour of `as.mo()` and will be removed in future versions
 * Improvements for `as.mo()`:
   * Fix for vector containing only empty values
   * Finds better results when input is in other languages

R/atc.R

@@ -146,17 +146,12 @@ as.atc <- function(x) {
   x.new
 }
 
-#' @rdname AMR-deprecated
-#' @export
-guess_atc <- as.atc
-
 #' @rdname as.atc
 #' @export
 is.atc <- function(x) {
   identical(class(x), "atc")
 }
 
-
 #' @exportMethod print.atc
 #' @export
 #' @noRd

R/deprecated.R

@@ -54,6 +54,13 @@ guess_mo <- function(...) {
   as.mo(...)
 }
 
+#' @rdname AMR-deprecated
+#' @export
+guess_atc <- function(...) {
+  .Deprecated(new = "as.atc", package = "AMR")
+  as.atc(...)
+}
+
 #' @rdname AMR-deprecated
 #' @export
 ab_property <- function(...) {
@@ -109,3 +116,18 @@ ab_tradenames <- function(...) {
   .Deprecated(new = "atc_tradenames", package = "AMR")
   atc_tradenames(...)
 }
+
+#' @rdname AMR-deprecated
+#' @export
+atc_ddd <- function(...) {
+  .Deprecated(new = "atc_online_ddd", package = "AMR")
+  atc_online_ddd(...)
+}
+
+#' @rdname AMR-deprecated
+#' @export
+atc_groups <- function(...) {
+  .Deprecated(new = "atc_online_groups", package = "AMR")
+  atc_online_groups(...)
+}
+

docs/news/index.html

@@ -253,16 +253,14 @@
 <ul>
 <li>Added 65 antibiotics to the <code>antibiotics</code> data set, from the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register</a> of the European Commission</li>
 <li>Removed columns <code>atc_group1_nl</code> and <code>atc_group2_nl</code> from the <code>antibiotics</code> data set</li>
-<li>Function <code>atc_ddd</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_ddd()</a></code>
+<li>Functions <code><a href="../reference/AMR-deprecated.html">atc_ddd()</a></code> and <code><a href="../reference/AMR-deprecated.html">atc_groups()</a></code> have been renamed <code><a href="../reference/atc_online.html">atc_online_ddd()</a></code> and <code><a href="../reference/atc_online.html">atc_online_groups()</a></code>. The old function are deprecated and will be removed in a future version.</li>
-</li>
+<li>Function <code><a href="../reference/AMR-deprecated.html">guess_mo()</a></code> is now deprecated in favour of <code><a href="../reference/as.mo.html">as.mo()</a></code> and will be removed in future versions</li>
-<li>Function <code>atc_groups</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_groups()</a></code>
+<li>Function <code><a href="../reference/AMR-deprecated.html">guess_atc()</a></code> is now deprecated in favour of <code><a href="../reference/as.atc.html">as.atc()</a></code> and will be removed in future versions</li>
-</li>
 <li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</li>
 <li>Updated EUCAST Clinical breakpoints to <a href="http://www.eucast.org/clinical_breakpoints/">version 9.0 of 1 January 2019</a>
 </li>
 <li>Fixed a critical bug where some rules that depend on previous applied rules would not be applied adequately</li>
 <li>Emphasised in manual that penicillin is meant as benzylpenicillin (ATC <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE01">J01CE01</a>)</li>
-<li>Function <code><a href="../reference/AMR-deprecated.html">guess_mo()</a></code> is now deprecated in favour of <code><a href="../reference/as.mo.html">as.mo()</a></code> and will be removed in future versions</li>
 <li>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:</li>
 <li>Fix for vector containing only empty values</li>
 <li>Finds better results when input is in other languages</li>

docs/reference/AMR-deprecated.html

@@ -6,7 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>Deprecated functions — guess_atc • AMR (for R)</title>
+<title>Deprecated functions — AMR-deprecated • AMR (for R)</title>
 
 <!-- favicons -->
 <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -45,7 +45,7 @@
 
   <link href="../extra.css" rel="stylesheet">
   <script src="../extra.js"></script>
-<meta property="og:title" content="Deprecated functions — guess_atc" />
+<meta property="og:title" content="Deprecated functions — AMR-deprecated" />
 
 <meta property="og:description" content="These functions are so-called 'Deprecated'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one)." />
 
@@ -227,12 +227,12 @@
     
     </div>
 
-    <pre class="usage"><span class='fu'>guess_atc</span>(<span class='no'>x</span>)
+    <pre class="usage"><span class='fu'>ratio</span>(<span class='no'>x</span>, <span class='no'>ratio</span>)
-
-<span class='fu'>ratio</span>(<span class='no'>x</span>, <span class='no'>ratio</span>)
 
 <span class='fu'>guess_mo</span>(<span class='no'>...</span>)
 
+<span class='fu'>guess_atc</span>(<span class='no'>...</span>)
+
 <span class='fu'>ab_property</span>(<span class='no'>...</span>)
 
 <span class='fu'>ab_atc</span>(<span class='no'>...</span>)
@@ -247,7 +247,11 @@
 
 <span class='fu'>ab_umcg</span>(<span class='no'>...</span>)
 
-<span class='fu'>ab_tradenames</span>(<span class='no'>...</span>)</pre>
+<span class='fu'>ab_tradenames</span>(<span class='no'>...</span>)
+
+<span class='fu'>atc_ddd</span>(<span class='no'>...</span>)
+
+<span class='fu'>atc_groups</span>(<span class='no'>...</span>)</pre>
         
     <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
 

docs/reference/index.html

@@ -521,7 +521,7 @@
       </tr><tr>
         
         <td>
-          <p><code><a href="AMR-deprecated.html">guess_atc()</a></code> <code><a href="AMR-deprecated.html">ratio()</a></code> <code><a href="AMR-deprecated.html">guess_mo()</a></code> <code><a href="AMR-deprecated.html">ab_property()</a></code> <code><a href="AMR-deprecated.html">ab_atc()</a></code> <code><a href="AMR-deprecated.html">ab_official()</a></code> <code><a href="AMR-deprecated.html">ab_name()</a></code> <code><a href="AMR-deprecated.html">ab_trivial_nl()</a></code> <code><a href="AMR-deprecated.html">ab_certe()</a></code> <code><a href="AMR-deprecated.html">ab_umcg()</a></code> <code><a href="AMR-deprecated.html">ab_tradenames()</a></code> </p>
+          <p><code><a href="AMR-deprecated.html">ratio()</a></code> <code><a href="AMR-deprecated.html">guess_mo()</a></code> <code><a href="AMR-deprecated.html">guess_atc()</a></code> <code><a href="AMR-deprecated.html">ab_property()</a></code> <code><a href="AMR-deprecated.html">ab_atc()</a></code> <code><a href="AMR-deprecated.html">ab_official()</a></code> <code><a href="AMR-deprecated.html">ab_name()</a></code> <code><a href="AMR-deprecated.html">ab_trivial_nl()</a></code> <code><a href="AMR-deprecated.html">ab_certe()</a></code> <code><a href="AMR-deprecated.html">ab_umcg()</a></code> <code><a href="AMR-deprecated.html">ab_tradenames()</a></code> <code><a href="AMR-deprecated.html">atc_ddd()</a></code> <code><a href="AMR-deprecated.html">atc_groups()</a></code> </p>
         </td>
         <td><p>Deprecated functions</p></td>
       </tr>

man/AMR-deprecated.Rd

@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/atc.R, R/deprecated.R
+% Please edit documentation in R/deprecated.R
-\name{guess_atc}
+\name{AMR-deprecated}
-\alias{guess_atc}
 \alias{AMR-deprecated}
 \alias{ratio}
 \alias{guess_mo}
+\alias{guess_atc}
 \alias{ab_property}
 \alias{ab_atc}
 \alias{ab_official}
@@ -13,14 +13,16 @@
 \alias{ab_certe}
 \alias{ab_umcg}
 \alias{ab_tradenames}
+\alias{atc_ddd}
+\alias{atc_groups}
 \title{Deprecated functions}
 \usage{
-guess_atc(x)
-
 ratio(x, ratio)
 
 guess_mo(...)
 
+guess_atc(...)
+
 ab_property(...)
 
 ab_atc(...)
@@ -36,6 +38,10 @@ ab_certe(...)
 ab_umcg(...)
 
 ab_tradenames(...)
+
+atc_ddd(...)
+
+atc_groups(...)
 }
 \description{
 These functions are so-called '\link{Deprecated}'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one).