(v1.2.0.9027) move to github

.github/workflows/check.yaml

@@ -28,10 +28,10 @@ on:
     branches:
       - master
 
-name: R-CMD-check
+name: check
 
 jobs:
-  R-CMD-check:
+  check:
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -43,9 +43,9 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest,   r: 'release'}
           - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: windows-latest, r: 'oldrel'}
-          - {os: macOS-latest,   r: 'oldrel'}
-          - {os: ubuntu-16.04,   r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          # - {os: windows-latest, r: 'oldrel'}
+          # - {os: macOS-latest,   r: 'oldrel'}
+          # - {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"}

.github/workflows/codecovr.yaml

@@ -64,5 +64,5 @@ jobs:
         shell: Rscript {0}
 
       - name: Test coverage
-        run: covr::codecov()
+        run: covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/resistance_predict.R", "R/aa_helper_functions_dplyr.R"))
         shell: Rscript {0}

.github/workflows/lintr.yaml

@@ -62,5 +62,5 @@ jobs:
         shell: Rscript {0}
 
       - name: Lint
-        run: lintr::lint_package()
+        run: 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"))
         shell: Rscript {0}

.gitlab-ci.yml

@@ -3,7 +3,7 @@
 # Antimicrobial Resistance (AMR) Analysis                              #
 #                                                                      #
 # SOURCE                                                               #
-# https://github.com/msberends/AMR                                     #
+# https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
 # (c) 2018-2020 Berends MS, Luz CF et al.                              #
@@ -16,27 +16,18 @@
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-# Visit our website for more info: https://msberends.github.io/AMR.    #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
-codecov:
-  require_ci_to_pass: no # allow fail
-  ci:
-    - !appveyor # ignore CI builds by AppVeyor
-
-comment: no
-
-coverage:
-  precision: 1
-  round: up
-  range: "0...100"
-  status:
-    project: no
-    patch: no
-    changes: no
-
-ignore:
-  - "R/atc_online.R"
-  - "R/mo_history.R"
-  - "R/mo_source.R"
-  - "R/resistance_predict.R" # gives a strange error but unit tests work
+# as long as GitLab used - make sure the website will be updated
+pages:
+  stage: website
+  allow_failure: true
+  when: always
+  only:
+    - master
+  script:
+    - mv docs public
+  artifacts:
+    paths:
+      - public

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.2.0.9026
+Version: 1.2.0.9027
 Date: 2020-07-08
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.2.0.9026
+# AMR 1.2.0.9027
 ## <small>Last updated: 08-Jul-2020</small>
 
 ### New
@@ -37,6 +37,9 @@
 * Improved error handling, giving more useful info when functions return an error
 * Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
 
+### Other
+* Project moved to GitHub
+
 # AMR 1.2.0
 
 ### Breaking 

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">1.2.0.9026</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</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">1.2.0.9026</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</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">1.2.0.9026</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</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">1.2.0.9026</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</span>
       </span>
     </div>
 

docs/extra.js

@@ -41,7 +41,7 @@ $( document ).ready(function() {
 
   // redirect to GitLab
   var url_old = window.location.href;
-  var url_new = url_old.replace("github", "gitlab");
+  var url_new = url_old.replace("gitlab", "github");
   if (url_old != url_new) {
     window.location.replace(url_new);
   }

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">1.2.0.9026</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</span>
       </span>
     </div>
 
@@ -235,7 +235,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
 <li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
 <li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
 <li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
-<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (<a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt">link</a>)</li>
+<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (<a href="https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt">link</a>)</li>
 <li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li>
 </ul>
 </div>
@@ -253,9 +253,9 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
 <div id="latest-development-version" class="section level4">
 <h4 class="hasAnchor">
 <a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
-<p>The latest and unpublished development version can be installed with (<strong>precaution: may be unstable</strong>):</p>
+<p>The latest and unpublished development version can be installed from GitHub using:</p>
 <div class="sourceCode" id="cb2"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"remotes"</span>)
-<span class="kw pkg">remotes</span><span class="kw ns">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_gitlab.html">install_gitlab</a></span>(<span class="st">"msberends/AMR"</span>)</pre></div>
+<span class="kw pkg">remotes</span><span class="kw ns">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span>(<span class="st">"msberends/AMR"</span>)</pre></div>
 </div>
 </div>
 <div id="get-started" class="section level3">

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">1.2.0.9026</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</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-1209026" class="section level1">
-<h1 class="page-header" data-toc-text="1.2.0.9026">
-<a href="#amr-1209026" class="anchor"></a>AMR 1.2.0.9026<small> Unreleased </small>
+    <div id="amr-1209027" class="section level1">
+<h1 class="page-header" data-toc-text="1.2.0.9027">
+<a href="#amr-1209027" class="anchor"></a>AMR 1.2.0.9027<small> Unreleased </small>
 </h1>
 <div id="last-updated-08-jul-2020" class="section level2">
 <h2 class="hasAnchor">
@@ -288,6 +288,13 @@
 <li>Any progress bar will now only show in interactive mode (i.e. not in R Markdown)</li>
 </ul>
 </div>
+<div id="other" class="section level3">
+<h3 class="hasAnchor">
+<a href="#other" class="anchor"></a>Other</h3>
+<ul>
+<li>Project moved to GitHub</li>
+</ul>
+</div>
 </div>
 </div>
     <div id="amr-120" class="section level1">
@@ -344,9 +351,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Added abbreviation “cfsc” for Cefoxitin and “cfav” for Ceftazidime/avibactam</li>
 </ul>
 </div>
-<div id="other" class="section level3">
+<div id="other-1" class="section level3">
 <h3 class="hasAnchor">
-<a href="#other" class="anchor"></a>Other</h3>
+<a href="#other-1" class="anchor"></a>Other</h3>
 <ul>
 <li>Removed previously deprecated function <code>p.symbol()</code> - it was replaced with <code><a href="../reference/p_symbol.html">p_symbol()</a></code>
 </li>
@@ -386,9 +393,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Added generic CLSI rules for R/SI interpretation using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for years 2010-2019 (thanks to Anthony Underwood)</li>
 </ul>
 </div>
-<div id="other-1" class="section level3">
+<div id="other-2" class="section level3">
 <h3 class="hasAnchor">
-<a href="#other-1" class="anchor"></a>Other</h3>
+<a href="#other-2" class="anchor"></a>Other</h3>
 <ul>
 <li>Support for the upcoming <code>dplyr</code> version 1.0.0</li>
 <li>More robust assigning for classes <code>rsi</code> and <code>mic</code>
@@ -484,9 +491,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 </div>
-<div id="other-2" class="section level3">
+<div id="other-3" class="section level3">
 <h3 class="hasAnchor">
-<a href="#other-2" class="anchor"></a>Other</h3>
+<a href="#other-3" class="anchor"></a>Other</h3>
 <ul>
 <li>Add a <code>CITATION</code> file</li>
 <li>Full support for the upcoming R 4.0</li>
@@ -584,9 +591,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 </div>
-<div id="other-3" class="section level3">
+<div id="other-4" class="section level3">
 <h3 class="hasAnchor">
-<a href="#other-3" class="anchor"></a>Other</h3>
+<a href="#other-4" class="anchor"></a>Other</h3>
 <ul>
 <li>Rewrote the complete documentation to markdown format, to be able to use the very latest version of the great <a href="https://roxygen2.r-lib.org/index.html">Roxygen2</a>, released in November 2019. This tremously improved the documentation quality, since the rewrite forced us to go over all texts again and make changes where needed.</li>
 <li>Change dependency on <code>clean</code> to <code>cleaner</code>, as this package was renamed accordingly upon CRAN request</li>
@@ -738,9 +745,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 <li>Added more MIC factor levels (<code><a href="../reference/as.mic.html">as.mic()</a></code>)</li>
 </ul>
-<div id="other-4" class="section level4">
+<div id="other-5" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-4" class="anchor"></a>Other</h4>
+<a href="#other-5" class="anchor"></a>Other</h4>
 <ul>
 <li>Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors</li>
 <li>Cleaned the coding style of every single syntax line in this package with the help of the <code>lintr</code> package</li>
@@ -821,9 +828,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 </div>
-<div id="other-5" class="section level4">
+<div id="other-6" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-5" class="anchor"></a>Other</h4>
+<a href="#other-6" class="anchor"></a>Other</h4>
 <ul>
 <li>Fixed a note thrown by CRAN tests</li>
 </ul>
@@ -917,9 +924,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</p></li>
 </ul>
 </div>
-<div id="other-6" class="section level4">
+<div id="other-7" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-6" class="anchor"></a>Other</h4>
+<a href="#other-7" class="anchor"></a>Other</h4>
 <ul>
 <li>Support for R 3.6.0 and later by providing support for <a href="https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html">staged install</a>
 </li>
@@ -1164,9 +1171,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>if using different lengths of pattern and x in <code><a href="../reference/like.html">%like%</a></code>, it will now return the call</li>
 </ul>
 </div>
-<div id="other-7" class="section level4">
+<div id="other-8" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-7" class="anchor"></a>Other</h4>
+<a href="#other-8" class="anchor"></a>Other</h4>
 <ul>
 <li>Updated licence text to emphasise GPL 2.0 and that this is an R package.</li>
 </ul>
@@ -1281,9 +1288,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Percentages will now will rounded more logically (e.g. in <code>freq</code> function)</p></li>
 </ul>
 </div>
-<div id="other-8" class="section level4">
+<div id="other-9" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-8" class="anchor"></a>Other</h4>
+<a href="#other-9" class="anchor"></a>Other</h4>
 <ul>
 <li>New dependency on package <code>crayon</code>, to support formatted text in the console</li>
 <li>Dependency <code>tidyr</code> is now mandatory (went to <code>Import</code> field) since <code>portion_df</code> and <code>count_df</code> rely on it</li>
@@ -1416,9 +1423,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 </div>
-<div id="other-9" class="section level4">
+<div id="other-10" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-9" class="anchor"></a>Other</h4>
+<a href="#other-10" class="anchor"></a>Other</h4>
 <ul>
 <li>More unit tests to ensure better integrity of functions</li>
 </ul>
@@ -1545,9 +1552,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Other small fixes</li>
 </ul>
 </div>
-<div id="other-10" class="section level4">
+<div id="other-11" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-10" class="anchor"></a>Other</h4>
+<a href="#other-11" class="anchor"></a>Other</h4>
 <ul>
 <li>Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
 <ul>
@@ -1607,9 +1614,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Functions <code>as.rsi</code> and <code>as.mic</code> now add the package name and version as attributes</li>
 </ul>
 </div>
-<div id="other-11" class="section level4">
+<div id="other-12" class="section level4">
 <h4 class="hasAnchor">
-<a href="#other-11" class="anchor"></a>Other</h4>
+<a href="#other-12" class="anchor"></a>Other</h4>
 <ul>
 <li>Expanded <code>README.md</code> with more examples</li>
 <li>Added <a href="https://orcid.org">ORCID</a> of authors to DESCRIPTION file</li>

docs/pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   WHONET: WHONET.html
   benchmarks: benchmarks.html
   resistance_predict: resistance_predict.html
-last_built: 2020-07-08T12:47Z
+last_built: 2020-07-08T15:02Z
 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">1.2.0.9026</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</span>
       </span>
     </div>
 

index.md

@@ -50,7 +50,7 @@ This package can be used for:
   * Applying EUCAST expert rules ([manual](./reference/eucast_rules.html))
   * Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code ([manual](./reference/mo_property.html))
   * Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code ([manual](./reference/ab_property.html))
-  * Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI ([link](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt))
+  * Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI ([link](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt))
   * Principal component analysis for AMR ([tutorial](./articles/PCA.html))
 
 ### Get this package
@@ -69,10 +69,10 @@ It will be downloaded and installed automatically. For RStudio, click on the men
 
 #### Latest development version
 
-The latest and unpublished development version can be installed with (**precaution: may be unstable**):
+The latest and unpublished development version can be installed from GitHub using:
 ```r
-install.packages("remotes")
-remotes::install_gitlab("msberends/AMR")
+install.packages("remotes") 
+remotes::install_github("msberends/AMR")
 ```
 
 ### Get started

pkgdown/extra.js

@@ -41,7 +41,7 @@ $( document ).ready(function() {
 
   // redirect to GitLab
   var url_old = window.location.href;
-  var url_new = url_old.replace("github", "gitlab");
+  var url_new = url_old.replace("gitlab", "github");
   if (url_old != url_new) {
     window.location.replace(url_new);
   }