(v0.7.0.9004) pkgdown update

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.7.0.9003
+Version: 0.7.0.9004
-Date: 2019-06-08
+Date: 2019-06-09
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.7.0.9003
+# AMR 0.7.0.9004
 
 #### New
 * Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*:

_pkgdown.yml

@@ -19,152 +19,160 @@
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
-title: 'AMR (for R)'
+title: "AMR (for R)"
-url: 'https://msberends.gitlab.io/AMR'
+url: "https://msberends.gitlab.io/AMR"
+
 development:
-  mode: release # improves indexing by search engines
+  mode: "release" # improves indexing by search engines
+  version_tooltip: "Latest development version"
+
 news:
   one_page: true
 
 navbar:
-  title: 'AMR (for R)'
+  title: "AMR (for R)"
   left:
-    - text: 'Home'
+    - text: "Home"
-      icon: 'fa-home'
+      icon: "fa-home"
-      href: 'index.html'
+      href: "index.html"
-    - text: 'How to'
+    - text: "How to"
-      icon: 'fa-question-circle'
+      icon: "fa-question-circle"
       menu:
-      - text: 'Conduct AMR analysis'
+      - text: "Conduct AMR analysis"
-        icon: 'fa-directions'
+        icon: "fa-directions"
-        href: 'articles/AMR.html'
+        href: "articles/AMR.html"
-      - text: 'Predict antimicrobial resistance'
+      - text: "Predict antimicrobial resistance"
-        icon: 'fa-dice'
+        icon: "fa-dice"
-        href: 'articles/resistance_predict.html'
+        href: "articles/resistance_predict.html"
-      - text: 'Determine multi-drug resistance (MDR)'
+      - text: "Determine multi-drug resistance (MDR)"
-        icon: 'fa-skull-crossbones'
+        icon: "fa-skull-crossbones"
-        href: 'articles/MDR.html'
+        href: "articles/MDR.html"
-      - text: 'Work with WHONET data'
+      - text: "Work with WHONET data"
-        icon: 'fa-globe-americas'
+        icon: "fa-globe-americas"
-        href: 'articles/WHONET.html'
+        href: "articles/WHONET.html"
-      - text: 'Import data from SPSS/SAS/Stata'
+      - text: "Import data from SPSS/SAS/Stata"
-        icon: 'fa-file-upload'
+        icon: "fa-file-upload"
-        href: 'articles/SPSS.html'
+        href: "articles/SPSS.html"
-      - text: 'Apply EUCAST rules'
+      - text: "Apply EUCAST rules"
-        icon: 'fa-exchange-alt'
+        icon: "fa-exchange-alt"
-        href: 'articles/EUCAST.html'
+        href: "articles/EUCAST.html"
-      - text: 'Get properties of a microorganism'
+      - text: "Get properties of a microorganism"
-        icon: 'fa-bug'
+        icon: "fa-bug"
-        href: 'reference/mo_property.html' # reference instead of article
+        href: "reference/mo_property.html" # reference instead of article
-      - text: 'Get properties of an antibiotic'
+      - text: "Get properties of an antibiotic"
-        icon: 'fa-capsules'
+        icon: "fa-capsules"
-        href: 'reference/ab_property.html' # reference instead of article
+        href: "reference/ab_property.html" # reference instead of article
-      - text: 'Create frequency tables'
+      - text: "Create frequency tables"
-        icon: 'fa-sort-amount-down'
+        icon: "fa-sort-amount-down"
-        href: 'articles/freq.html'
+        href: "articles/freq.html"
-      - text: 'Use the G-test'
+#       - text: "Use the G-test"
-        icon: 'fa-clipboard-check'
+#         icon: "fa-clipboard-check"
-        href: 'reference/g.test.html' # reference instead of article
+#         href: "reference/g.test.html" # reference instead of article
-      - text: 'Other: benchmarks'
+      - text: "Other: benchmarks"
-        icon: 'fa-shipping-fast'
+        icon: "fa-shipping-fast"
-        href: 'articles/benchmarks.html'
+        href: "articles/benchmarks.html"
-    - text: 'Manual'
+    - text: "Manual"
-      icon: 'fa-book-open'
+      icon: "fa-book-open"
-      href: 'reference/'
+      href: "reference/"
-    - text: 'Authors'
+    - text: "Authors"
-      icon: 'fa-users'
+      icon: "fa-users"
-      href: 'authors.html'
+      href: "authors.html"
-    - text: 'Changelog'
+    - text: "Changelog"
-      icon: 'far fa-newspaper'
+      icon: "far fa-newspaper"
-      href: 'news/'
+      href: "news/"
   right:
-    - text: 'Source Code'
+    - text: "Source Code"
-      icon: 'fab fa-gitlab'
+      icon: "fab fa-gitlab"
-      href: 'https://gitlab.com/msberends/AMR'
+      href: "https://gitlab.com/msberends/AMR"
-    - text: 'Licence'
+    - text: "Licence"
-      icon: 'fa-book'
+      icon: "fa-book"
-      href: 'LICENSE-text.html'
+      href: "LICENSE-text.html"
 
 reference:
-  - title: 'Background information'
+  - title: "Background information"
     desc: >
       Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
       for more information about how to work with functions in this package.
     contents:
-    - '`AMR`'
+    - "`AMR`"
-    - '`catalogue_of_life`'
+    - "`catalogue_of_life`"
-    - '`catalogue_of_life_version`'
+    - "`catalogue_of_life_version`"
-    - '`WHOCC`'
+    - "`WHOCC`"
-  - title: 'Cleaning your data'
+  - title: "Cleaning your data"
     desc: >
       Functions for cleaning and optimising your data, to be able to add
       variables later on (like taxonomic properties) or to fix and extend
       antibiotic interpretations by applying [EUCAST rules](http://www.eucast.org/expert_rules_and_intrinsic_resistance/).
     contents:
     - starts_with("as.")
-    - '`mo_source`'
+    - "`mo_source`"
-    - '`eucast_rules`'
+    - "`eucast_rules`"
-    - '`rsi_translation`'
+    - "`rsi_translation`"
-    - '`guess_ab_col`'
+    - "`guess_ab_col`"
-    - '`read.4D`'
+    - "`read.4D`"
-  - title: 'Adding variables to your data'
+  - title: "Adding variables to your data"
     desc: >
       Functions to add new data to existing data, like the determination
       of first isolates, multi-drug resistant microorganisms (MDRO), getting
       properties of microorganisms or antibiotics and determining the age of
       patients or divide ages into age groups.
     contents:
-    - '`first_isolate`'
+    - "`first_isolate`"
-    - '`mdro`'
+    - "`mdro`"
-    - '`key_antibiotics`'
+    - "`key_antibiotics`"
-    - '`mo_property`'
+    - "`mo_property`"
-    - '`ab_property`'
+    - "`ab_property`"
-    - '`age`'
+    - "`age`"
-    - '`age_groups`'
+    - "`age_groups`"
-    - '`p.symbol`'
+    - "`p.symbol`"
-    - '`join`'
+    - "`join`"
-    - '`atc_online_property`'
+    - "`atc_online_property`"
-  - title: 'Analysing your data'
+  - title: "Analysing your data"
     desc: >
       Functions for conducting AMR analysis, like counting isolates, calculating
       resistance or susceptibility, creating frequency tables or make plots.
     contents:
-    - '`availability`'
+    - "`availability`"
-    - '`count`'
+    - "`count`"
-    - '`portion`'
+    - "`portion`"
-    - '`filter_ab_class`'
+    - "`filter_ab_class`"
-    - '`freq`'
+    - "`freq`"
-    - '`g.test`'
+    - "`g.test`"
-    - '`ggplot_rsi`'
+    - "`ggplot_rsi`"
-    - '`kurtosis`'
+    - "`kurtosis`"
-    - '`resistance_predict`'
+    - "`resistance_predict`"
-    - '`skewness`'
+    - "`skewness`"
-  - title: 'Included data sets'
+  - title: "Included data sets"
     desc: >
       References for microorganisms and antibiotics, and even a
       genuine data set with isolates from septic patients.
     contents:
-    - '`antibiotics`'
+    - "`antibiotics`"
-    - '`microorganisms`'
+    - "`microorganisms`"
-    - '`septic_patients`'
+    - "`septic_patients`"
-    - '`WHONET`'
+    - "`WHONET`"
-    - '`microorganisms.codes`'
+    - "`microorganisms.codes`"
-    - '`microorganisms.old`'
+    - "`microorganisms.old`"
   - title: Other functions
     desc: >
       These functions are mostly for internal use, but some of
       them may also be suitable for your analysis. Especially the
       'like' function can be useful: `if (x %like% y) {...}`.
     contents:
-    - '`get_locale`'
+    - "`get_locale`"
-    - '`like`'
+    - "`like`"
-  - title: Deprecated functions
+  - title: Extended functions
+    desc: >
+      These functions are extensions of functions in other packages.
+    contents:
+    - "`extended-functions`"
+  - title:  functions
     desc: >
       These functions are deprecated, meaning that they still
       work but show a warning with every use and will be removed
       in a future version.
     contents:
-    - '`AMR-deprecated`'
+    - "`AMR-deprecated`"
 
 authors:
   Matthijs S. Berends:
@@ -179,11 +187,11 @@ authors:
     href: https://www.rug.nl/staff/b.sinha/
 
 template:
-  assets: pkgdown/logos # use logos in this folder
+  assets: "pkgdown/logos" # use logos in this folder
   params:
     noindex: false
-    bootswatch: flatly
+    bootswatch: "flatly"
     docsearch:
       # using algolia.com
-      api_key: 'f737050abfd4d726c63938e18f8c496e'
+      api_key: "f737050abfd4d726c63938e18f8c496e"
-      index_name: 'amr'
+      index_name: "amr"

docs/LICENSE-text.html

@@ -78,7 +78,7 @@
       </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="Released version">0.7.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9004</span>
       </span>
     </div>
 
@@ -163,13 +163,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/articles/index.html

@@ -78,7 +78,7 @@
       </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="Released version">0.7.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9004</span>
       </span>
     </div>
 
@@ -163,13 +163,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/authors.html

@@ -78,7 +78,7 @@
       </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="Released version">0.7.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9004</span>
       </span>
     </div>
 
@@ -163,13 +163,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

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="Released version">0.7.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9004</span>
       </span>
     </div>
 
@@ -127,13 +127,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>

docs/news/index.html

@@ -78,7 +78,7 @@
       </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="Released version">0.7.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9004</span>
       </span>
     </div>
 
@@ -163,13 +163,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -239,9 +232,9 @@
       
     </div>
 
-    <div id="amr-0709003" class="section level1">
+    <div id="amr-0709004" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0709003" class="anchor"></a>AMR 0.7.0.9003<small> Unreleased </small>
+<a href="#amr-0709004" class="anchor"></a>AMR 0.7.0.9004<small> Unreleased </small>
 </h1>
 <div id="new" class="section level4">
 <h4 class="hasAnchor">
@@ -1108,7 +1101,7 @@ 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-0709003">0.7.0.9003</a></li>
+        <li><a href="#amr-0709004">0.7.0.9004</a></li>
         <li><a href="#amr-070">0.7.0</a></li>
         <li><a href="#amr-061">0.6.1</a></li>
         <li><a href="#amr-060">0.6.0</a></li>

docs/reference/index.html

@@ -78,7 +78,7 @@
       </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="Released version">0.7.0.9003</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9004</span>
       </span>
     </div>
 
@@ -163,13 +163,6 @@
         Create frequency tables
       </a>
     </li>
-    <li>
-      <a href="../reference/g.test.html">
-        <span class="fa fa-clipboard-check"></span>
-         
-        Use the G-test
-      </a>
-    </li>
     <li>
       <a href="../articles/benchmarks.html">
         <span class="fa fa-shipping-fast"></span>
@@ -555,7 +548,21 @@
     </tbody><tbody>
       <tr>
         <th colspan="2">
-          <h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2>
+          <h2 id="section-extended-functions" class="hasAnchor"><a href="#section-extended-functions" class="anchor"></a>Extended functions</h2>
+          <p class="section-desc"><p>These functions are extensions of functions in other packages.</p></p>
+        </th>
+      </tr>
+      <tr>
+        
+        <td>
+          <p><code><a href="extended-functions.html">scale_type.mo()</a></code> <code><a href="extended-functions.html">scale_type.ab()</a></code> </p>
+        </td>
+        <td><p>Extended functions</p></td>
+      </tr>
+    </tbody><tbody>
+      <tr>
+        <th colspan="2">
+          <h2 id="section-functions" class="hasAnchor"><a href="#section-functions" class="anchor"></a>functions</h2>
           <p class="section-desc"><p>These functions are deprecated, meaning that they still work but show a warning with every use and will be removed in a future version.</p></p>
         </th>
       </tr>
@@ -579,7 +586,8 @@
       <li><a href="#section-analysing-your-data">Analysing your data</a></li>
       <li><a href="#section-included-data-sets">Included data sets</a></li>
       <li><a href="#section-other-functions">Other functions</a></li>
-      <li><a href="#section-deprecated-functions">Deprecated functions</a></li>
+      <li><a href="#section-extended-functions">Extended functions</a></li>
+      <li><a href="#section-functions">functions</a></li>
     </ul>
   </div>
 </div>

git_premaster.sh

@@ -52,7 +52,9 @@ echo "••••••••••••••••••••••••
 echo "• Reloading/documenting package •"
 echo "•••••••••••••••••••••••••••••••••"
 Rscript -e "devtools::load_all(quiet = TRUE)"
+echo "Documenting..."
 Rscript -e "suppressMessages(devtools::document())"
+echo "Installing..."
 Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
 echo
 echo "••••••••••••••••••••••••••"