(v0.7.0.9015) vignette fix

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.7.0.9014
+Version: 0.7.0.9015
 Date: 2019-06-22
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.7.0.9014
+# AMR 0.7.0.9015
 
 #### 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">0.7.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</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">0.7.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
       </span>
     </div>
 

docs/articles/resistance_predict.html

@@ -40,7 +40,7 @@
       </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">0.7.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
       </span>
     </div>
 
@@ -125,13 +125,6 @@
         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>
@@ -199,7 +192,7 @@
       <h1>How to predict antimicrobial resistance</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">07 June 2019</h4>
+            <h4 class="date">22 June 2019</h4>
       
       
       <div class="hidden name"><code>resistance_predict.Rmd</code></div>
@@ -309,7 +302,7 @@
 <a href="#choosing-the-right-model" class="anchor"></a>Choosing the right model</h3>
 <p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram positives, the spread (i.e. standard error) is enormous:</p>
 <div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb8-2" title="2"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo) <span class="op">==</span><span class="st"> "Gram positive"</span>) <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb8-2" title="2"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo, <span class="dt">language =</span> <span class="ot">NULL</span>) <span class="op">==</span><span class="st"> "Gram-positive"</span>) <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb8-3" title="3"><span class="st">  </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"VAN"</span>, <span class="dt">year_min =</span> <span class="dv">2010</span>, <span class="dt">info =</span> <span class="ot">FALSE</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
 <a class="sourceLine" id="cb8-4" title="4"><span class="st">  </span><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()</a>
 <a class="sourceLine" id="cb8-5" title="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a></code></pre></div>
@@ -354,7 +347,7 @@
 </table>
 <p>For the vancomycin resistance in Gram positive bacteria, a linear model might be more appropriate since no (left half of a) binomial distribution is to be expected based on the observed years:</p>
 <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
-<a class="sourceLine" id="cb9-2" title="2"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo) <span class="op">==</span><span class="st"> "Gram positive"</span>) <span class="op">%&gt;%</span></a>
+<a class="sourceLine" id="cb9-2" title="2"><span class="st">  </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo, <span class="dt">language =</span> <span class="ot">NULL</span>) <span class="op">==</span><span class="st"> "Gram-positive"</span>) <span class="op">%&gt;%</span></a>
 <a class="sourceLine" id="cb9-3" title="3"><span class="st">  </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"VAN"</span>, <span class="dt">year_min =</span> <span class="dv">2010</span>, <span class="dt">info =</span> <span class="ot">FALSE</span>, <span class="dt">model =</span> <span class="st">"linear"</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
 <a class="sourceLine" id="cb9-4" title="4"><span class="st">  </span><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()</a>
 <a class="sourceLine" id="cb9-5" title="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a></code></pre></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">0.7.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</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">0.7.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</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">0.7.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
       </span>
     </div>
 
@@ -232,9 +232,9 @@
       
     </div>
 
-    <div id="amr-0709014" class="section level1">
+    <div id="amr-0709015" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0709014" class="anchor"></a>AMR 0.7.0.9014<small> Unreleased </small>
+<a href="#amr-0709015" class="anchor"></a>AMR 0.7.0.9015<small> Unreleased </small>
 </h1>
 <div id="new" class="section level4">
 <h4 class="hasAnchor">
@@ -1141,7 +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-0709014">0.7.0.9014</a></li>
+        <li><a href="#amr-0709015">0.7.0.9015</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="Latest development version">0.7.0.9014</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
       </span>
     </div>
 

git_premaster.sh

@@ -81,7 +81,16 @@ git commit -a -m "(v$new_version) $1" --quiet
 git push --quiet
 echo "Comparison:"
 echo "https://gitlab.com/msberends/AMR/compare/master...premaster?view=inline"
-echo "Check for all CRAN tests:"
+
-echo "rhub::check_for_cran(devtools::build(args = c('--no-build-vignettes')))"
+echo
+echo "•••••••••"
+echo "• Done •"
+echo "••••••••"
+echo
+read -p "Upload to R-hub builder (y/N)? " choice
+case "$choice" in
+  y|Y|j|J ) ;;
+  * ) exit 1;;
+esac
+Rscript -e "rhub::check_for_cran(devtools::build())"
 echo
-echo "Done."

vignettes/resistance_predict.Rmd

@@ -91,7 +91,7 @@ Resistance is not easily predicted; if we look at vancomycin resistance in Gram
 
 ```{r}
 septic_patients %>%
-  filter(mo_gramstain(mo) == "Gram positive") %>%
+  filter(mo_gramstain(mo, language = NULL) == "Gram-positive") %>%
   resistance_predict(col_ab = "VAN", year_min = 2010, info = FALSE) %>% 
   ggplot_rsi_predict()
 ```
@@ -112,7 +112,7 @@ For the vancomycin resistance in Gram positive bacteria, a linear model might be
 
 ```{r}
 septic_patients %>%
-  filter(mo_gramstain(mo) == "Gram positive") %>%
+  filter(mo_gramstain(mo, language = NULL) == "Gram-positive") %>%
   resistance_predict(col_ab = "VAN", year_min = 2010, info = FALSE, model = "linear") %>% 
   ggplot_rsi_predict()
 ```