P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 10:31:53 +02:00
Code Releases Activity

(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-09-18 16:05:53 +02:00
parent 89401ede9f
commit 4e40e42011
138 changed files with 2923 additions and 1472 deletions
Download Patch File Download Diff File Expand all files Collapse all files

17
docs/reference/count.html
View File

@ -51,7 +51,7 @@
<meta property="og:title" content="Count available isolates — count" />
<meta property="og:description" content="These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also support grouped variables, please see Examples.
count_resistant() should be used to count resistant isolates, count_susceptible() should be used to count susceptible isolates." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -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">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9022</span>
</span>
</div>
@ -283,7 +283,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</tr>
<tr>
<th>data</th>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> containing columns with class <code><a href='as.rsi.html'>rsi</a></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> containing columns with class <code><a href='as.rsi.html'>rsi</a></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
</tr>
<tr>
<th>translate_ab</th>
@ -305,7 +305,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>An <code><a href='https://rdrr.io/r/base/integer.html'>integer</a></code></p>
<p>An <a href='https://rdrr.io/r/base/integer.html'>integer</a></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>These functions are meant to count isolates. Use the <code><a href='proportion.html'>resistance()</a></code>/<code><a href='proportion.html'>susceptibility()</a></code> functions to calculate microbial resistance/susceptibility.</p>
@ -356,10 +356,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
</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>
<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> <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>
<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>
@ -430,7 +432,8 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<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>
}
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">