mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 23:21:56 +02:00
Built site for AMR: 1.8.1.9045@e7af5fc
This commit is contained in:
@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@ -260,7 +260,7 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
|
||||
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#> 1. CIP is "R" and age is higher than 60 -> Elderly Type A</span></span>
|
||||
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co">#> 2. ERY is "R" and age is higher than 60 -> Elderly Type B</span></span>
|
||||
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> 3. Otherwise -> Negative</span></span>
|
||||
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co">#> </span></span>
|
||||
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co">#></span></span>
|
||||
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="co">#> Unmatched rows will return NA.</span></span></code></pre><p></p></div>
|
||||
<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code>mdro()</code> function:</p>
|
||||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>x <span class="ot"><-</span> <span class="fu">mdro</span>(example_isolates,</span>
|
||||
@ -270,10 +270,10 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
|
||||
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> 1070 198 732</span></span></code></pre><p></p></div>
|
||||
<p>Rules can also be combined with other custom rules by using <code><a href="https://rdrr.io/r/base/c.html" class="external-link">c()</a></code>:</p>
|
||||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>x <span class="ot"><-</span> <span class="fu">mdro</span>(example_isolates,</span>
|
||||
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="at">guideline =</span> <span class="fu">c</span>(custom, </span>
|
||||
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="at">guideline =</span> <span class="fu">c</span>(custom,</span>
|
||||
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">custom_mdro_guideline</span>(ERY <span class="sc">==</span> <span class="st">"R"</span> <span class="sc">&</span> age <span class="sc">></span> <span class="dv">50</span> <span class="sc">~</span> <span class="st">"Elderly Type C"</span>)))</span>
|
||||
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">table</span>(x)</span>
|
||||
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> Negative Elderly Type A Elderly Type B Elderly Type C </span></span>
|
||||
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> Negative Elderly Type A Elderly Type B Elderly Type C</span></span>
|
||||
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co">#> 961 198 732 109</span></span></code></pre><p></p></div>
|
||||
<p>The rules set (the <code>custom</code> object in this case) could be exported to a shared file location using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS()</a></code>.</p>
|
||||
</div>
|
||||
@ -310,8 +310,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1978 0 6 </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">out</span> <span class="op"><-</span> <span class="fu">mdro</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="fu">custom_mdro_guideline</span><span class="op">(</span><span class="va">AMX</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="st">"Custom MDRO 1"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="va">VAN</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="st">"Custom MDRO 2"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="fu">custom_mdro_guideline</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">AMX</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="st">"Custom MDRO 1"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="va">VAN</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="st">"Custom MDRO 2"</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> out</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Negative Custom MDRO 1 Custom MDRO 2 </span>
|
||||
@ -322,13 +325,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">mdro</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># no need to define `x` when used inside dplyr verbs:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>MDRO <span class="op">=</span> <span class="fu">mdro</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html" class="external-link">pull</a></span><span class="op">(</span><span class="va">MDRO</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> (16 isolates had no test results)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `mdro()`: NA introduced for isolates where the available percentage of</span>
|
||||
|
Reference in New Issue
Block a user