P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 17:07:54 +02:00
Code Releases Activity

Built site for AMR@2.1.1.9084: 9141546

Browse Source
This commit is contained in:
github-actions
2024-09-30 20:12:21 +00:00
parent 1f01704397
commit 75d3c3aadc
79 changed files with 463 additions and 642 deletions
Download Patch File Download Diff File Expand all files Collapse all files

30
reference/as.sir.html
View File

@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<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="">2.1.1.9083</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9084</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">
@ -44,13 +44,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
</ul></li>
<li class="nav-item dropdown">
<button class="nav-link dropdown-toggle" type="button" id="dropdown-with-other-pkgs" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-layer-group"></span> With other pkgs</button>
<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs"><li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; dplyr/tidyverse</a></li>
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; data.table</a></li>
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; tidymodels</a></li>
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; base R</a></li>
</ul></li>
<li class="nav-item"><a class="nav-link" href="../articles/AMR_for_Python.html"><span class="fa fab fa-python"></span> AMR for Python</a></li>
<li class="active nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
<li class="nav-item"><a class="nav-link" href="../authors.html"><span class="fa fa-users"></span> Authors</a></li>
</ul><ul class="navbar-nav"><li class="nav-item"><a class="nav-link" href="../news/index.html"><span class="fa far fa-newspaper"></span> Changelog</a></li>
@ -791,16 +785,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-09-30 <span style="color: #949494;">17:18:24</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-09-30 <span style="color: #949494;">17:18:31</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-09-30 <span style="color: #949494;">17:18:31</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-09-30 <span style="color: #949494;">17:18:31</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-09-30 <span style="color: #949494;">17:18:32</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-09-30 <span style="color: #949494;">17:18:24</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-09-30 <span style="color: #949494;">17:18:31</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-09-30 <span style="color: #949494;">17:18:31</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-09-30 <span style="color: #949494;">17:18:31</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-09-30 <span style="color: #949494;">17:18:32</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-09-30 <span style="color: #949494;">20:09:40</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-09-30 <span style="color: #949494;">20:09:48</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-09-30 <span style="color: #949494;">20:09:48</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-09-30 <span style="color: #949494;">20:09:49</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-09-30 <span style="color: #949494;">20:09:49</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-09-30 <span style="color: #949494;">20:09:40</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-09-30 <span style="color: #949494;">20:09:48</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-09-30 <span style="color: #949494;">20:09:48</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-09-30 <span style="color: #949494;">20:09:49</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-09-30 <span style="color: #949494;">20:09:49</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;dbl&gt;, outcome &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>