(v1.6.0.9018) unit tests

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.6.0.9017
+Version: 1.6.0.9018
 Date: 2021-05-04
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# `AMR` 1.6.0.9017
+# `AMR` 1.6.0.9018
 ## <small>Last updated:  4 May 2021</small>
 
 ### New

R/aa_helper_functions.R

@@ -841,6 +841,14 @@ message_not_thrown_before <- function(fn, entire_session = FALSE) {
   is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]], unique_call_id(entire_session))
 }
 
+reset_all_thrown_messages <- function() {
+  # for unit tests, where the environment and highest system call do not change
+  # can be found in tests/testthat/*.R
+  pkg_env_contents <- ls(envir = pkg_env)
+  rm(list = pkg_env_contents[pkg_env_contents %like% "^thrown_msg."],
+     envir = pkg_env)
+}
+
 has_colour <- function() {
   # this is a base R version of crayon::has_color, but disables colours on emacs
   

R/rsi.R

@@ -259,12 +259,22 @@ as.rsi.default <- function(x, ...) {
   }
   
   if (inherits(x, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) {
-    x <- as.character(x) # this is needed to prevent the vctrs pkg to throw an error
+    x.bak <- x
-    x[x == "1"] <- "S"
+    x <- as.character(x) # this is needed to prevent the vctrs pkg from throwing an error
-    x[x == "2"] <- "I"
-    x[x == "3"] <- "R"
     
-  } else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R")) && !all(x %in% c("R", "S", "I", NA))) {
+    # support haven package for importing e.g., from SPSS - it adds the 'labels' attribute
+    lbls <- attributes(x)$labels
+    if (!is.null(lbls) && all(c("R", "S", "I") %in% names(lbls)) && all(c(1:3) %in% lbls)) {
+      x[x.bak == 1] <- names(lbls[lbls == 1])
+      x[x.bak == 2] <- names(lbls[lbls == 2])
+      x[x.bak == 3] <- names(lbls[lbls == 3])
+    } else {
+      x[x.bak == 1] <- "S"
+      x[x.bak == 2] <- "I"
+      x[x.bak == 3] <- "R"  
+    }
+
+  } else if (!all(is.na(x)) && !identical(levels(x), c("R", "S", "I")) && !all(x %in% c("R", "S", "I", NA))) {
 
     if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
       # check if they are actually MICs or disks

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">1.6.0.9017</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</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">1.6.0.9017</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</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">1.6.0.9017</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</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">1.6.0.9017</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </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">1.6.0.9017</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</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">1.6.0.9017</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</span>
       </span>
     </div>
 
@@ -236,9 +236,9 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1609017" class="section level1">
+    <div id="amr-1609018" class="section level1">
-<h1 class="page-header" data-toc-text="1.6.0.9017">
+<h1 class="page-header" data-toc-text="1.6.0.9018">
-<a href="#amr-1609017" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9017</h1>
+<a href="#amr-1609018" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9018</h1>
 <div id="last-updated-4-may-2021" class="section level2">
 <h2 class="hasAnchor">
 <a href="#last-updated-4-may-2021" class="anchor"></a><small>Last updated: 4 May 2021</small>

docs/pkgdown.yml

@@ -12,7 +12,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-05-04T10:36Z
+last_built: 2021-05-04T13:19Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.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">1.6.0.9017</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</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">1.6.0.9017</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</span>
       </span>
     </div>