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(v1.3.0) skip more CRAN tests

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dr. M.S. (Matthijs) Berends
2020-07-31 10:50:08 +02:00
parent c8edcb7439
commit c5f7294381
45 changed files with 66 additions and 65 deletions
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2
docs/reference/ab_from_text.html
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@ -321,7 +321,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='no'>abx</span> <span class='kw'>&lt;-</span> <span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>)
<span class='fu'><a href='ab_property.html'>ab_group</a></span>(<span class='no'>abx</span><span class='kw'>[[</span><span class='fl'>1</span>]])
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>dplyr</span>)) {
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/reexports.html'>tibble</a></span>(<span class='kw'>clinical_text</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"given 400mg cipro and 500 mg amox"</span>,
<span class='st'>"started on doxy iv today"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>abx_codes</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>),

3
docs/reference/antibiotic_class_selectors.html
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@ -281,7 +281,8 @@
<div class='dont-index'><p><code><a href='filter_ab_class.html'>filter_ab_class()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> equivalent.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>

5
docs/reference/filter_ab_class.html
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@ -303,7 +303,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='antibiotic_class_selectors.html'>antibiotic_class_selectors()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code> equivalent.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>dplyr</span>)) {
<pre class="examples"><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># filter on isolates that have any result for any aminoglycoside</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_ab_class</span>(<span class='st'>"aminoglycoside"</span>)
@ -332,9 +333,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
}
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_carbapenems</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'><a href='antibiotic_class_selectors.html'>carbapenems</a></span>(), ~<span class='no'>.</span> <span class='kw'>==</span> <span class='st'>"R"</span>))

3
docs/reference/ggplot_pca.html
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@ -388,7 +388,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># See ?example_isolates.</span>
<span class='co'># See ?pca for more info about Principal Component Analysis (PCA).</span>
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>pca_model</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>species</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>)) <span class='kw'>%&gt;%</span>

4
docs/reference/resistance_predict.html
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@ -411,7 +411,9 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
}
<span class='co'># create nice plots with ggplot2 yourself</span>
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>ggplot2</span>) <span class='kw'>&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>ggplot2</span>)
<span class='no'>data</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>