(v1.2.0.9029) GitHub actions

.github/workflows/check.yaml

@@ -48,7 +48,7 @@ jobs:
           # - {os: ubuntu-16.04,   r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           - {os: windows-latest, r: 'devel'}
           - {os: macOS-latest,   r: 'devel'}
-          - {os: ubuntu-16.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          # - {os: ubuntu-16.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           # - {os: windows-latest, r: '3.6'}
           # - {os: ubuntu-16.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           # - {os: ubuntu-16.04,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}

.github/workflows/lintr.yaml

@@ -63,5 +63,5 @@ jobs:
         shell: Rscript {0}
 
       - name: Lint
-        run: lintr::lint_package(linters = with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_length_linter = object_length_linter(length = 50L)), exclusions = list("R/aa_helper_functions_dplyr.R"))
+        run: lintr::lint_package(linters = lintr::with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_length_linter = lintr::object_length_linter(length = 50L)), exclusions = list("R/aa_helper_functions_dplyr.R"))
         shell: Rscript {0}

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.2.0.9028
+Version: 1.2.0.9029
 Date: 2020-07-08
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.2.0.9028
+# AMR 1.2.0.9029
 ## <small>Last updated: 08-Jul-2020</small>
 
 ### New

R/globals.R

@@ -34,6 +34,7 @@ globalVariables(c(".",
                   "col_id",
                   "count",
                   "count.x",
+                  "data",
                   "date_lab",
                   "diff.percent",
                   "First name",

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">1.2.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9029</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">1.2.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9029</span>
       </span>
     </div>
 

docs/articles/SPSS.html

@@ -20,7 +20,7 @@
 <script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
 <script src="../extra.js"></script><meta property="og:title" content="How to import data from SPSS / SAS / Stata">
 <meta property="og:description" content="AMR">
-<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg">
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -39,7 +39,7 @@
       </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</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9029</span>
       </span>
     </div>
 
@@ -157,8 +157,8 @@
       </ul>
 <ul class="nav navbar-nav navbar-right">
 <li>
-  <a href="https://gitlab.com/msberends/AMR">
+  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-gitlab"></span>
+    <span class="fab fa fab fa-github"></span>
      
     Source Code
   </a>
@@ -180,15 +180,15 @@
 
       
 
-      </header><div class="row">
+      </header><script src="SPSS_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">28 May 2020</h4>
+            <h4 class="date">08 July 2020</h4>
       
-      <small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
       <div class="hidden name"><code>SPSS.Rmd</code></div>
 
     </div>
@@ -207,7 +207,7 @@
 <ul>
 <li>
 <p><strong>R is highly modular.</strong></p>
-<p>The <a href="https://cran.r-project.org/">official R network (CRAN)</a> features almost 14,000 packages at the time of writing, our <code>AMR</code> package being one of them. All these packages were peer-reviewed before publication. Aside from this official channel, there are also developers who choose not to submit to CRAN, but rather keep it on their own public repository, like GitLab or GitHub. So there may even be a lot more than 14,000 packages out there.</p>
+<p>The <a href="https://cran.r-project.org/">official R network (CRAN)</a> features almost 14,000 packages at the time of writing, our <code>AMR</code> package being one of them. All these packages were peer-reviewed before publication. Aside from this official channel, there are also developers who choose not to submit to CRAN, but rather keep it on their own public repository, like GitHub. So there may even be a lot more than 14,000 packages out there.</p>
 <p>Bottom line is, you can really extend it yourself or ask somebody to do this for you. Take for example our <code>AMR</code> package. Among other things, it adds reliable reference data to R to help you with the data cleaning and analysis. SPSS, SAS and Stata will never know what a valid MIC value is or what the Gram stain of <em>E. coli</em> is. Or that all species of <em>Klebiella</em> are resistant to amoxicillin and that Floxapen<sup>®</sup> is a trade name of flucloxacillin. These facts and properties are often needed to clean existing data, which would be very inconvenient in a software package without reliable reference data. See below for a demonstration.</p>
 </li>
 <li>
@@ -281,10 +281,10 @@
 <a href="#rstudio" class="anchor"></a>RStudio</h3>
 <p>To work with R, probably the best option is to use <a href="https://www.rstudio.com/products/rstudio/">RStudio</a>. It is an open-source and free desktop environment which not only allows you to run R code, but also supports project management, version management, package management and convenient import menus to work with other data sources. You can also install <a href="https://www.rstudio.com/products/rstudio/">RStudio Server</a> on a private or corporate server, which brings nothing less than the complete RStudio software to you as a website (at home or at work).</p>
 <p>To import a data file, just click <em>Import Dataset</em> in the Environment tab:</p>
-<p><img src="https://gitlab.com/msberends/AMR/raw/master/docs/import1.png"></p>
+<p><img src="https://github.com/msberends/AMR/raw/master/docs/import1.png"></p>
 <p>If additional packages are needed, RStudio will ask you if they should be installed on beforehand.</p>
 <p>In the the window that opens, you can define all options (parameters) that should be used for import and you’re ready to go:</p>
-<p><img src="https://gitlab.com/msberends/AMR/raw/master/docs/import2.png"></p>
+<p><img src="https://github.com/msberends/AMR/raw/master/docs/import2.png"></p>
 <p>If you want named variables to be imported as factors so it resembles SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>.</p>
 <p>The difference is this:</p>
 <div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">SPSS_data</span>

docs/articles/SPSS_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

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">1.2.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9029</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">1.2.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9029</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">1.2.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9029</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">1.2.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9029</span>
       </span>
     </div>
 
@@ -229,9 +229,9 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1209028" class="section level1">
+    <div id="amr-1209029" class="section level1">
-<h1 class="page-header" data-toc-text="1.2.0.9028">
+<h1 class="page-header" data-toc-text="1.2.0.9029">
-<a href="#amr-1209028" class="anchor"></a>AMR 1.2.0.9028<small> Unreleased </small>
+<a href="#amr-1209029" class="anchor"></a>AMR 1.2.0.9029<small> Unreleased </small>
 </h1>
 <div id="last-updated-08-jul-2020" class="section level2">
 <h2 class="hasAnchor">

docs/pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   WHONET: WHONET.html
   benchmarks: benchmarks.html
   resistance_predict: resistance_predict.html
-last_built: 2020-07-08T18:41Z
+last_built: 2020-07-08T20:53Z
 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">1.2.0.9028</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9029</span>
       </span>
     </div>