(v0.7.1.9098) mdro() unit test fix

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.7.1.9097
+Version: 0.7.1.9098
 Date: 2019-10-07
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.7.1.9097
+# AMR 0.7.1.9098
 <small>Last updated: 07-Oct-2019</small>
 
 ### Breaking

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">0.7.1.9097</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</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">0.7.1.9097</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</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">0.7.1.9097</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</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">0.7.1.9097</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</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">0.7.1.9097</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
       </span>
     </div>
 

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">0.7.1.9097</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
       </span>
     </div>
 
@@ -231,9 +231,9 @@
       
     </div>
 
-    <div id="amr-0-7-1-9097" class="section level1">
+    <div id="amr-0-7-1-9098" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-7-1-9097" class="anchor"></a>AMR 0.7.1.9097<small> Unreleased </small>
+<a href="#amr-0-7-1-9098" class="anchor"></a>AMR 0.7.1.9098<small> Unreleased </small>
 </h1>
 <p><small>Last updated: 07-Oct-2019</small></p>
 <div id="breaking" class="section level3">
@@ -1289,7 +1289,7 @@ 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-0-7-1-9097">0.7.1.9097</a></li>
+        <li><a href="#amr-0-7-1-9098">0.7.1.9098</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>
         <li><a href="#amr-0-6-1">0.6.1</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">0.7.1.9097</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
       </span>
     </div>
 

git_merge.sh

@@ -23,7 +23,16 @@ echo "• pushed changes to master"
 git checkout premaster --quiet
 echo "• changed branch back to premaster"
 git status --short
+echo
 
+read -p "Use R-hub to simulate all CRAN checks (y/N)? " choice
+case "$choice" in
+  y|Y|j|J ) ;;
+  * ) exit 1;;
+esac
+Rscript -e "rhub::check(devtools::build(), platform = c('debian-clang-devel', 'debian-gcc-devel', 'fedora-clang-devel', 'fedora-gcc-devel', 'windows-x86_64-devel', 'debian-gcc-patched', 'solaris-x86-patched', 'debian-gcc-release', 'windows-x86_64-release', 'macos-elcapitan-release',
+'windows-x86_64-oldrel'))"
+echo
 
 # and get stashed changes back
 # git stash apply --quiet

git_premaster.sh

@@ -90,10 +90,4 @@ echo "•••••••••"
 echo "• Done •"
 echo "••••••••"
 echo
-read -p "Upload to R-hub builder (y/N)? " choice
+
-case "$choice" in
-  y|Y|j|J ) ;;
-  * ) exit 1;;
-esac
-Rscript -e "rhub::check_for_cran(devtools::build())"
-echo

tests/testthat/test-mdro.R

@@ -45,9 +45,6 @@ test_that("mdro works", {
   expect_equal(brmo(example_isolates, info = FALSE),
                mdro(example_isolates, guideline = "BRMO", info = FALSE))
 
-  # still working on German guidelines
-  expect_error(suppressWarnings(mrgn(example_isolates, info = TRUE)))
-
   # test Dutch P. aeruginosa MDRO
   expect_equal(
     as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),