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(v1.3.0.9001) website update

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dr. M.S. (Matthijs) Berends
2020-08-10 12:46:03 +02:00
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@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</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">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@ -233,34 +233,34 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</div>
<div class="ref-description">
<p>These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in <code>summarise()</code> from the <code>dplyr</code> package and also support grouped variables, please see <em>Examples</em>.</p>
<p>These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code> from the <code>dplyr</code> package and also support grouped variables, please see <em>Examples</em>.</p>
<p><code>count_resistant()</code> should be used to count resistant isolates, <code>count_susceptible()</code> should be used to count susceptible isolates.</p>
</div>
<pre class="usage"><span class='fu'>count_resistant</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<pre class="usage"><span class='fu'>count_resistant</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_susceptible</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_susceptible</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_R</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_R</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_IR</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_IR</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_I</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_I</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_SI</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_SI</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_S</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_S</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_all</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_all</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>n_rsi</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>n_rsi</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
<span class='fu'>count_df</span>(
<span class='no'>data</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
<span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
<span class='kw'>data</span>,
translate_ab = <span class='st'>"name"</span>,
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
combine_SI = <span class='fl'>TRUE</span>,
combine_IR = <span class='fl'>FALSE</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@ -338,22 +338,21 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
-------- -------- ---------- ----------- ---------- -----------
S or I S or I X X X X
R S or I X X X X
&amp;lt;NA&amp;gt; S or I X X - -
&lt;NA&gt; S or I X X - -
S or I R X X X X
R R - X - X
&amp;lt;NA&amp;gt; R - - - -
S or I &amp;lt;NA&amp;gt; X X - -
R &amp;lt;NA&amp;gt; - - - -
&amp;lt;NA&amp;gt; &amp;lt;NA&amp;gt; - - - -
&lt;NA&gt; R - - - -
S or I &lt;NA&gt; X X - -
R &lt;NA&gt; - - - -
&lt;NA&gt; &lt;NA&gt; - - - -
--------------------------------------------------------------------
</pre>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'>count_S</span>() + <span class='fu'>count_I</span>() + <span class='fu'>count_R</span>() <span class='kw'>=</span> <span class='fu'>count_all</span>()
<span class='fu'><a href='proportion.html'>proportion_S</a></span>() + <span class='fu'><a href='proportion.html'>proportion_I</a></span>() + <span class='fu'><a href='proportion.html'>proportion_R</a></span>() <span class='kw'>=</span> <span class='fl'>1</span></pre>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'>count_S</span>() <span class='op'>+</span> <span class='fu'>count_I</span>() <span class='op'>+</span> <span class='fu'>count_R</span>() <span class='op'>=</span> <span class='fu'>count_all</span>()
<span class='fu'><a href='proportion.html'>proportion_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></span>() <span class='op'>=</span> <span class='fl'>1</span></pre>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> count_S() + count_I() + count_R() &amp;gt;= count_all()
proportion_S() + proportion_I() + proportion_R() &amp;gt;= 1
</pre>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> <span class='fu'>count_S</span>() <span class='op'>+</span> <span class='fu'>count_I</span>() <span class='op'>+</span> <span class='fu'>count_R</span>() <span class='op'>&gt;=</span> <span class='fu'>count_all</span>()
<span class='fu'><a href='proportion.html'>proportion_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></span>() <span class='op'>&gt;=</span> <span class='fl'>1</span></pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -367,63 +366,63 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># example_isolates is a data set available in the AMR package.</span>
?<span class='no'>example_isolates</span>
<span class='op'>?</span><span class='kw'>example_isolates</span>
<span class='fu'>count_resistant</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># counts "R"</span>
<span class='fu'>count_susceptible</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># counts "S" and "I"</span>
<span class='fu'>count_all</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) <span class='co'># counts "S", "I" and "R"</span>
<span class='fu'>count_resistant</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># counts "R"</span>
<span class='fu'>count_susceptible</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># counts "S" and "I"</span>
<span class='fu'>count_all</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># counts "S", "I" and "R"</span>
<span class='co'># be more specific</span>
<span class='fu'>count_S</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_SI</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_I</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_IR</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_R</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_S</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'>count_SI</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'>count_I</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'>count_IR</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'>count_R</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='co'># Count all available isolates</span>
<span class='fu'>count_all</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>n_rsi</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_all</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'>n_rsi</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='co'># n_rsi() is an alias of count_all().</span>
<span class='co'># Since it counts all available isolates, you can</span>
<span class='co'># calculate back to count e.g. susceptible isolates.</span>
<span class='co'># These results are the same:</span>
<span class='fu'>count_susceptible</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'><a href='proportion.html'>susceptibility</a></span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>) * <span class='fu'>n_rsi</span>(<span class='no'>example_isolates</span>$<span class='no'>AMX</span>)
<span class='fu'>count_susceptible</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
<span class='fu'><a href='proportion.html'>susceptibility</a></span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='op'>*</span> <span class='fu'>n_rsi</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</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='no'>example_isolates</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='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>CIP</span>),
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>CIP</span>),
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>CIP</span>),
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(R = <span class='fu'>count_R</span>(<span class='kw'>CIP</span>),
I = <span class='fu'>count_I</span>(<span class='kw'>CIP</span>),
S = <span class='fu'>count_S</span>(<span class='kw'>CIP</span>),
n1 = <span class='fu'>count_all</span>(<span class='kw'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
n2 = <span class='fu'>n_rsi</span>(<span class='kw'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
total = <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
<span class='co'># Please mind that `susceptibility()` calculates percentages right away instead.</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='no'>AMC</span>) <span class='co'># 1433</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='no'>AMC</span>) <span class='co'># 1879</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='no'>GEN</span>) <span class='co'># 1399</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='no'>GEN</span>) <span class='co'># 1855</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># 1764</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># 1936</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='kw'>AMC</span>) <span class='co'># 1433</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='kw'>AMC</span>) <span class='co'># 1879</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='kw'>GEN</span>) <span class='co'># 1399</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='kw'>GEN</span>) <span class='co'># 1855</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>count_susceptible</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># 1764</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>count_all</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># 1936</span>
<span class='co'># Get number of S+I vs. R immediately of selected columns</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'>count_df</span>(translate = <span class='fl'>FALSE</span>)
<span class='co'># It also supports grouping variables</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>CIP</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='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>hospital_id</span>, <span class='kw'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%&gt;%</span>
<span class='fu'>count_df</span>(translate = <span class='fl'>FALSE</span>)
}</pre>
</div>
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@ -440,7 +439,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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