(v0.7.0.9014) unit tests

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.7.0.9013
+Version: 0.7.0.9014
 Date: 2019-06-22
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.7.0.9013
+# AMR 0.7.0.9014
 
 #### New
 * Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:

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="Latest development version">0.7.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9014</span>
       </span>
     </div>
 

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="Latest development version">0.7.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9014</span>
       </span>
     </div>
 
@@ -241,10 +241,8 @@
         <li><a href="MDR.html">How to determine multi-drug resistance (MDR)</a></li>
         <li><a href="SPSS.html">How to import data from SPSS / SAS / Stata</a></li>
         <li><a href="WHONET.html">How to work with WHONET data</a></li>
-        <li><a href="ab_property.html">How to get properties of an antibiotic</a></li>
         <li><a href="benchmarks.html">Benchmarks</a></li>
         <li><a href="freq.html">How to create frequency tables</a></li>
-        <li><a href="mo_property.html">How to get properties of a microorganism</a></li>
         <li><a href="resistance_predict.html">How to predict antimicrobial resistance</a></li>
       </ul>
     </div>

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="Latest development version">0.7.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9014</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">0.7.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9014</span>
       </span>
     </div>
 

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="Latest development version">0.7.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9014</span>
       </span>
     </div>
 
@@ -232,9 +232,9 @@
       
     </div>
 
-    <div id="amr-0709012" class="section level1">
+    <div id="amr-0709014" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0709012" class="anchor"></a>AMR 0.7.0.9012<small> Unreleased </small>
+<a href="#amr-0709014" class="anchor"></a>AMR 0.7.0.9014<small> Unreleased </small>
 </h1>
 <div id="new" class="section level4">
 <h4 class="hasAnchor">
@@ -252,7 +252,7 @@
 <a class="sourceLine" id="cb1-8" title="8"><span class="co"># 4 Ciprofloxacin               R  0.1618169       228</span></a></code></pre></div>
 </li>
 <li>
-<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date. Supported are:</p>
+<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date (that we could find). Supported are:</p>
 <ul>
 <li>AIEC (Adherent-Invasive <em>E. coli</em>)</li>
 <li>ATEC (Atypical Entero-pathogenic <em>E. coli</em>)</li>
@@ -297,10 +297,12 @@
 <li>Removed <code>latest_annual_release</code> from the <code><a href="../reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> function</li>
 <li>Removed antibiotic code <code>PVM1</code> from the <code>antibiotics</code> data set as this was a duplicate of <code>PME</code>
 </li>
-<li>Fixed bug where not all old taxonomic named would not be printed when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
+<li>Fixed bug where not all old taxonomic names would be printed, when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
 </li>
 <li>Manually added <em>Trichomonas vaginalis</em> from the kingdom of Protozoa, which is missing from the Catalogue of Life</li>
 <li>Small improvements to <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> and <code><a href="https://www.rdocumentation.org/packages/graphics/topics/barplot">barplot()</a></code> for MIC and RSI classes</li>
+<li>Allow Catalogue of Life IDs to be coerced by <code><a href="../reference/as.mo.html">as.mo()</a></code>
+</li>
 </ul>
 </div>
 <div id="other" class="section level4">
@@ -1139,7 +1141,7 @@ 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-0709012">0.7.0.9012</a></li>
+        <li><a href="#amr-0709014">0.7.0.9014</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/pkgdown.yml

@@ -7,10 +7,8 @@ articles:
   MDR: MDR.html
   SPSS: SPSS.html
   WHONET: WHONET.html
-  ab_property: ab_property.html
   benchmarks: benchmarks.html
   freq: freq.html
-  mo_property: mo_property.html
   resistance_predict: resistance_predict.html
 urls:
   reference: https://msberends.gitlab.io/AMR/reference

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="Latest development version">0.7.0.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9014</span>
       </span>
     </div>
 

docs/sitemap.xml

@@ -153,18 +153,12 @@
   <url>
     <loc>https://msberends.gitlab.io/AMR/articles/WHONET.html</loc>
   </url>
-  <url>
-    <loc>https://msberends.gitlab.io/AMR/articles/ab_property.html</loc>
-  </url>
   <url>
     <loc>https://msberends.gitlab.io/AMR/articles/benchmarks.html</loc>
   </url>
   <url>
     <loc>https://msberends.gitlab.io/AMR/articles/freq.html</loc>
   </url>
-  <url>
-    <loc>https://msberends.gitlab.io/AMR/articles/mo_property.html</loc>
-  </url>
   <url>
     <loc>https://msberends.gitlab.io/AMR/articles/resistance_predict.html</loc>
   </url>

git_premaster.sh

@@ -66,8 +66,7 @@ echo "• List of changed files •"
 echo "•••••••••••••••••••••••••"
 git status --short
 echo
-
+read -p "Uploading version ${new_version}. Continue (Y/n)? " choice
-read -p "Pushing version ${new_version}. Continue (Y/n)? " choice
 case "$choice" in
   n|N ) exit 1;;
   * ) ;;
@@ -82,6 +81,7 @@ git commit -a -m "(v$new_version) $1" --quiet
 git push --quiet
 echo "Comparison:"
 echo "https://gitlab.com/msberends/AMR/compare/master...premaster?view=inline"
-
+echo "Check for all CRAN tests:"
+echo "rhub::check_for_cran(devtools::build(args = c('--no-build-vignettes')))"
 echo
 echo "Done."

tests/testthat/test-mo.R

@@ -260,9 +260,9 @@ test_that("as.mo works", {
   expect_null(mo_failures())
   expect_true(septic_patients %>% pull(mo) %>% is.mo())
 
-  expect_equal(get_mo_code("test", "mo"), "test")
+  # expect_equal(get_mo_code("test", "mo"), "test")
-  expect_equal(length(get_mo_code("Escherichia", "genus")),
+  # expect_equal(length(get_mo_code("Escherichia", "genus")),
-               nrow(AMR::microorganisms[base::which(AMR::microorganisms[, "genus"] %in% "Escherichia"),]))
+  #              nrow(AMR::microorganisms[base::which(AMR::microorganisms[, "genus"] %in% "Escherichia"),]))
 
   expect_error(translate_allow_uncertain(5))